Volume 9; Issue 1

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BMC Bioinformatics
Volume 9; Issue 1

BMC Bioinformatics

Volume 9; Issue 1

1

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

Jukka Corander, Pekka Marttinen, Jukka Sirén, Jing Tang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 477 KB

english, 2008

2

QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR

Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Riaño-Pachón, Bernd Mueller-Roeber

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.62 MB

english, 2008

3

BatchPrimer3: A high throughput web application for PCR and sequencing primer design

Frank M You, Naxin Huo, Yong Qiang Gu, Ming-cheng Luo, Yaqin Ma, Dave Hane, Gerard R Lazo, Jan Dvorak, Olin D Anderson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 371 KB

english, 2008

4

ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts

Kwangmin Choi, Sun Kim

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 4.52 MB

english, 2008

5

Evaluation of time profile reconstruction from complex two-color microarray designs

Ana C Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal, Nicolas Pollet

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 309 KB

english, 2008

6

Corpus annotation for mining biomedical events from literature

Jin-Dong Kim, Tomoko Ohta, Jun'ichi Tsujii

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 516 KB

english, 2008

7

Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis

Dominik Lutter, Peter Ugocsai, Margot Grandl, Evelyn Orso, Fabian Theis, Elmar W Lang, Gerd Schmitz

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 560 KB

english, 2008

8

Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition ofk-spaced amino acid pairs

Yong-Zi Chen, Yu-Rong Tang, Zhi-Ya Sheng, Ziding Zhang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 358 KB

english, 2008

9

Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics

Indra Neil Sarkar, Mary G Egan, Gloria Coruzzi, Ernest K Lee, Rob DeSalle

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 250 KB

english, 2008

10

PDTD: a web-accessible protein database for drug target identification

Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, Hualiang Jiang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 756 KB

english, 2008

11

Piecewise multivariate modelling of sequential metabolic profiling data

Mattias Rantalainen, Olivier Cloarec, Timothy MD Ebbels, Torbjörn Lundstedt, Jeremy K Nicholson, Elaine Holmes, Johan Trygg

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 386 KB

english, 2008

12

K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space

Max Bylesjö, Mattias Rantalainen, Jeremy K Nicholson, Elaine Holmes, Johan Trygg

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 275 KB

english, 2008

13

Fuzzy association rules for biological data analysis: A case study on yeast

Francisco J Lopez, Armando Blanco, Fernando Garcia, Carlos Cano, Antonio Marin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 859 KB

english, 2008

14

MScanner: a classifier for retrieving Medline citations

Graham L Poulter, Daniel L Rubin, Russ B Altman, Cathal Seoighe

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 414 KB

english, 2008

15

Evolutionary Pareto-optimization of stably folding peptides

Wolfram Gronwald, Tim Hohm, Daniel Hoffmann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.16 MB

english, 2008

16

SeqAn An efficient, generic C++ library for sequence analysis

Andreas Döring, David Weese, Tobias Rausch, Knut Reinert

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 553 KB

english, 2008

17

SPIKE – a database, visualization and analysis tool of cellular signaling pathways

Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, Ron Shamir

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 929 KB

english, 2008

18

Simple integrative preprocessing preserves what is shared in data sources

Abhishek Tripathi, Arto Klami, Samuel Kaski

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 349 KB

english, 2008

19

ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences

Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao, Toshihiko Ishida

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 723 KB

english, 2008

20

Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides

Jian-Yi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh, Li-Qian Zhou

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 522 KB

english, 2008

21

Effects of dependence in high-dimensional multiple testing problems

Kyung In Kim, Mark A van de Wiel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 371 KB

english, 2008

22

Novel methodology for construction and pruning of quasi-median networks

Sarah C Ayling, Terence A Brown

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.43 MB

english, 2008

23

CWRML: representing crop wild relative conservation and use data in XML

Jonathan D Moore, Shelagh P Kell, Jose M Iriondo, Brian V Ford-Lloyd, Nigel Maxted

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 274 KB

english, 2008

24

A mixture model approach to sample size estimation in two-sample comparative microarray experiments

Tommy S Jørstad, Herman Midelfart, Atle M Bones

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 329 KB

english, 2008

25

Exon level integration of proteomics and microarray data

Danny A Bitton, Michał J Okoniewski, Yvonne Connolly, Crispin J Miller

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.33 MB

english, 2008

26

High-precision high-coverage functional inference from integrated data sources

Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, Charles DeLisi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 657 KB

english, 2008

27

Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes

Guy N Brock, John R Shaffer, Richard E Blakesley, Meredith J Lotz, George C Tseng

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 356 KB

english, 2008

28

A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards

Mano Sivaganesan, Shawn Seifring, Manju Varma, Richard A Haugland, Orin C Shanks

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 377 KB

english, 2008

29

SciDBMaker: new software for computer-aided design of specialized biological databases

Riadh Hammami, Abdelmajid Zouhir, Karim Naghmouchi, Jeannette Ben Hamida, Ismail Fliss

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 952 KB

english, 2008

30

Strategies for measuring evolutionary conservation of RNA secondary structures

Andreas R Gruber, Stephan H Bernhart, Ivo L Hofacker, Stefan Washietl

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.73 MB

english, 2008

31

Assessment of composite motif discovery methods

Kjetil Klepper, Geir K Sandve, Osman Abul, Jostein Johansen, Finn Drablos

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 310 KB

english, 2008

32

A gene pattern mining algorithm using interchangeable gene sets for prokaryotes

Meng Hu, Kwangmin Choi, Wei Su, Sun Kim, Jiong Yang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 322 KB

english, 2008

33

Merging microarray data from separate breast cancer studies provides a robust prognostic test

Lei Xu, Aik Choon Tan, Raimond L Winslow, Donald Geman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 629 KB

english, 2008

34

DOVIS: an implementation for high-throughput virtual screening using AutoDock

Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 220 KB

english, 2008

35

DBMLoc: a Database of proteins with multiple subcellular localizations

Song Zhang, Xuefeng Xia, Jincheng Shen, Yun Zhou, Zhirong Sun

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 452 KB

english, 2008

36

Using quality scores and longer reads improves accuracy of Solexa read mapping

Andrew D Smith, Zhenyu Xuan, Michael Q Zhang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 440 KB

english, 2008

37

Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster

Wensheng Zhang, Sige Zou, Jiuzhou Song

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 309 KB

english, 2008

38

FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification

Paolo Verderio, Sara Pizzamiglio, Fabio Gallo, Simon C Ramsden

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 471 KB

english, 2008

39

catmap:Case-controlAndTDTMeta-AnalysisPackage

Kristin K Nicodemus

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 233 KB

english, 2008

40

Shape based indexing for faster search of RNA family databases

Stefan Janssen, Jens Reeder, Robert Giegerich

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 652 KB

english, 2008

41

Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols

Fabien Campagne

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 638 KB

english, 2008

42

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation

Mark K Titulaer, Dana AN Mustafa, Ivar Siccama, Marco Konijnenburg, Peter C Burgers, Arno C Andeweg, Peter AE Sillevis Smitt, Johan M Kros, Theo M Luider

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 567 KB

english, 2008

43

Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling

Grace S Shieh, Chung-Ming Chen, Ching-Yun Yu, Juiling Huang, Woei-Fuh Wang, Yi-Chen Lo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 328 KB

english, 2008

44

Functional discrimination of membrane proteins using machine learning techniques

M Michael Gromiha, Yukimitsu Yabuki

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 260 KB

english, 2008

45

Mining phenotypes for gene function prediction

Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz, Ulf Leser

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 401 KB

english, 2008

46

How reliably can we predict the reliability of protein structure predictions?

István Miklós, Ádám Novák ', Balázs Dombai, Jotun Hein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1007 KB

english, 2008

47

Goldsurfer2 (Gs2): A comprehensive tool for the analysis and visualization of genome wide association studies

Fredrik Pettersson, Andrew P Morris, Michael R Barnes, Lon R Cardon

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

48

Information transfer in signaling pathways: A study using coupled simulated and experimental data

Jürgen Pahle, Anne K Green, C Jane Dixon, Ursula Kummer

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 415 KB

english, 2008

49

Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models

Harald Binder, Martin Schumacher

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 330 KB

english, 2008

50

Normalization of oligonucleotide arrays based on the least-variant set of genes

Stefano Calza, Davide Valentini, Yudi Pawitan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 11.48 MB

english, 2008

51

Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence

Adriano Barbosa-Silva, Venkata P Satagopam, Reinhard Schneider, J Miguel Ortega

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 484 KB

english, 2008

52

Ranking analysis ofF-statistics for microarray data

Yuan-De Tan, Myriam Fornage, Hongyan Xu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 306 KB

english, 2008

53

Discovering gene annotations in biomedical text databases

Ali Cakmak, Gultekin Ozsoyoglu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 321 KB

english, 2008

54

Empirical Bayes analysis of single nucleotide polymorphisms

Holger Schwender, Katja Ickstadt

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 408 KB

english, 2008

55

Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions

Leah E Mechanic, Brian T Luke, Julie E Goodman, Stephen J Chanock, Curtis C Harris

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 297 KB

english, 2008

56

Conditional clustering of temporal expression profiles

Ling Wang, Monty Montano, Matt Rarick, Paola Sebastiani

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.21 MB

english, 2008

57

Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design

Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Christine Bathelt, Thomas Simonson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 536 KB

english, 2008

58

Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses

René Natowicz, Roberto Incitti, Euler Guimarães Horta, Benoît Charles, Philippe Guinot, Kai Yan, Charles Coutant, Fabrice Andre, Lajos Pusztai, Roman Rouzier

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 502 KB

english, 2008

59

Multiple organism algorithm for finding ultraconserved elements

Scott Christley, Neil F Lobo, Greg Madey

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 421 KB

english, 2008

60

Optimizations for the EcoPod field identification tool

Aswath Manoharan, Jeannie Stamberger, YuanYuan Yu, Andreas Paepcke

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.51 MB

english, 2008

61

H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments

Rainer Merkl, Matthias Zwick

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.02 MB

english, 2008

62

13C labeling experiments at metabolic nonstationary conditions: An exploratory study

Sebastian Aljoscha Wahl, Katharina Nöh, Wolfgang Wiechert

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 730 KB

english, 2008

63

Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

Christopher Lau, Lydia Ng, Carol Thompson, Sayan Pathak, Leonard Kuan, Allan Jones, Mike Hawrylycz

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.12 MB

english, 2008

64

DNAAlignEditor: DNA alignment editor tool

Hector Sanchez-Villeda, Steven Schroeder, Sherry Flint-Garcia, Katherine E Guill, Masanori Yamasaki, Michael D McMullen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 900 KB

english, 2008

65

Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

Yin-Jing Tien, Yun-Shien Lee, Han-Ming Wu, Chun-Houh Chen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.12 MB

english, 2008

66

Empirical Bayes models for multiple probe type microarrays at the probe level

Magnus Åstrand, Petter Mostad, Mats Rudemo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 817 KB

english, 2008

67

BioSAVE: Display of scored annotation within a sequence context

Richard F Pollock, Boris Adryan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 709 KB

english, 2008

68

Improving the prediction of mRNA extremities in the parasitic protozoanLeishmania

Martin Smith, Mathieu Blanchette, Barbara Papadopoulou

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 881 KB

english, 2008

69

Synonym set extraction from the biomedical literature by lexical pattern discovery

John McCrae, Nigel Collier

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 351 KB

english, 2008

70

A new method for class prediction based on signed-rank algorithms applied to Affymetrix®microarray experiments

Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt, Bernard Klein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 440 KB

english, 2008

71

Computational evaluation of TIS annotation for prokaryotic genomes

Gang-Qing Hu, Xiaobin Zheng, Li-Ning Ju, Huaiqiu Zhu, Zhen-Su She

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 684 KB

english, 2008

72

A simple and fast heuristic for protein structure comparison

David A Pelta, Juan R González, Marcos Moreno Vega

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 504 KB

english, 2008

73

Adaptive diffusion kernel learning from biological networks for protein function prediction

Liang Sun, Shuiwang Ji, Jieping Ye

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 413 KB

english, 2008

74

OpenMS – An open-source software framework for mass spectrometry

Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 731 KB

english, 2008

75

A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods

Richard D Pearson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 473 KB

english, 2008

76

Stability analysis of mixtures of mutagenetic trees

Jasmina Bogojeska, Thomas Lengauer, Jörg Rahnenführer

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.05 MB

english, 2008

77

Fast NJ-like algorithms to deal with incomplete distance matrices

Alexis Criscuolo, Olivier Gascuel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 387 KB

english, 2008

78

Efficient computation of absent words in genomic sequences

Julia Herold, Stefan Kurtz, Robert Giegerich

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 288 KB

english, 2008

79

Chromhome: A rich internet application for accessing comparative chromosome homology maps

Sridevi Nagarajan, Willem Rens, James Stalker, Tony Cox, Malcolm A Ferguson-Smith

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 792 KB

english, 2008

80

MausDB: An open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects

Holger Maier, Christoph Lengger, Bruno Simic, Helmut Fuchs, Valérie Gailus-Durner, Martin Hrabé de Angelis

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.87 MB

english, 2008

81

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

David M Kristensen, R Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y Chen, Viacheslav Y Fofanov, Marek Kimmel, Lydia E Kavraki, Olivier Lichtarge

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.11 MB

english, 2008

82

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick, Mitchell J Brittnacher

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 365 KB

english, 2008

83

Interrogating domain-domain interactions with parsimony based approaches

Katia S Guimarães, Teresa M Przytycka

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.17 MB

english, 2008

84

Predicting cancer involvement of genes from heterogeneous data

Ramon Aragues, Chris Sander, Baldo Oliva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 848 KB

english, 2008

85

LocateP: Genome-scale subcellular-location predictor for bacterial proteins

Miaomiao Zhou, Jos Boekhorst, Christof Francke, Roland J Siezen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 813 KB

english, 2008

86

Snagger: A user-friendly program for incorporating additional information for tagSNP selection

Christopher K Edlund, Won H Lee, Dalin Li, David J Van Den Berg, David V Conti

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 402 KB

english, 2008

87

A perl package and an alignment tool for phylogenetic networks

Gabriel Cardona, Francesc Rosselló, Gabriel Valiente

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 322 KB

english, 2008

88

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

Qi Liu, Yu Yang, Chun Chen, Jiajun Bu, Yin Zhang, Xiuzi Ye

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 561 KB

english, 2008

89

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa Beth Duhaime, Jörg Peplies, Oliver Frank Glöckner

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 890 KB

english, 2008

90

Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs

Michaël Bekaert, Ivaylo P Ivanov, John F Atkins, Pavel V Baranov

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 979 KB

english, 2008

91

Multidimensional scaling for large genomic data sets

Jengnan Tzeng, Henry Horng-Shing Lu, Wen-Hsiung Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 642 KB

english, 2008

92

LTRharvest, an efficient and flexible software forde novodetection of LTR retrotransposons

David Ellinghaus, Stefan Kurtz, Ute Willhoeft

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 352 KB

english, 2008

93

annot8r: GO, EC and KEGG annotation of EST datasets

Ralf Schmid, Mark L Blaxter

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 282 KB

english, 2008

94

Proteochemometric modeling of HIV protease susceptibility

Maris Lapins, Martin Eklund, Ola Spjuth, Peteris Prusis, Jarl ES Wikberg

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 450 KB

english, 2008

95

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

Shibu Yooseph, Weizhong Li, Granger Sutton

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 815 KB

english, 2008

96

Data capture in bioinformatics: requirements and experiences with Pedro

Daniel Jameson, Kevin Garwood, Chris Garwood, Tim Booth, Pinar Alper, Stephen G Oliver, Norman W Paton

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 969 KB

english, 2008

97

MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

Nicolas Sauton, David Lagorce, Bruno O Villoutreix, Maria A Miteva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 359 KB

english, 2008

98

A high-throughput pipeline for designing microarray-based pathogen diagnostic assays

Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Jaques Reifman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 558 KB

english, 2008

99

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

Robin P Smith, William J Buchser, Marcus B Lemmon, Jose R Pardinas, John L Bixby, Vance P Lemmon

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 492 KB

english, 2008

100

Significance analysis of microarray for relative quantitation of LC/MS data in proteomics

Bryan AP Roxas, Qingbo Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 419 KB

english, 2008

101

A novel representation of RNA secondary structure based on element-contact graphs

Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 856 KB

english, 2008

102

Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci

Sang Hong Lee, Julius HJ Van der Werf, Brian P Kinghorn

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 247 KB

english, 2008

103

NestedMICA as an ab initio protein motif discovery tool

Mutlu Doğruel, Thomas A Down, Tim JP Hubbard

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.89 MB

english, 2008

104

Local conservation scores without a priori assumptions on neutral substitution rates

Janis Dingel, Pavol Hanus, Niccolò Leonardi, Joachim Hagenauer, Jürgen Zech, Jakob C Mueller

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 569 KB

english, 2008

105

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

Kelvin Li, Anushka Brownley, Timothy B Stockwell, Karen Beeson, Tina C McIntosh, Dana Busam, Steve Ferriera, Sean Murphy, Samuel Levy

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 518 KB

english, 2008

106

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

Minghui Jiang, James Anderson, Joel Gillespie, Martin Mayne

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 372 KB

english, 2008

107

Natural Language Processing in aid of FlyBase curators

Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel Drysdale, Ted Briscoe

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.10 MB

english, 2008

108

A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays

Huanying Ge, Chao Cheng, Lei M Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.11 MB

english, 2008

109

A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations

Harri T Kiiveri

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 299 KB

english, 2008

110

MPDA: Microarray pooled DNA analyzer

Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice LT Yu, Mitchell B Diccianni, Jer-Yuarn Wu, Yuan-Tsong Chen, Cathy SJ Fann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.62 MB

english, 2008

111

Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research

Yoginder S Dandass, Shane C Burgess, Mark Lawrence, Susan M Bridges

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 249 KB

english, 2008

112

Improving protein function prediction methods with integrated literature data

Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter, Debra S Goldberg

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 746 KB

english, 2008

113

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

Nicola Zamboni, Anne Kümmel, Matthias Heinemann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 616 KB

english, 2008

114

Supervised inference of gene-regulatory networks

Cuong C To, Jiri Vohradsky

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 877 KB

english, 2008

115

A simplified approach to disulfide connectivity prediction from protein sequences

Marc Vincent, Andrea Passerini, Matthieu Labbé, Paolo Frasconi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 287 KB

english, 2008

116

ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use

Piotr Kraj, Ashok Sharma, Nikhil Garge, Robert Podolsky, Richard A McIndoe

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 525 KB

english, 2008

117

Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles

Ruchi Verma, Ajit Tiwari, Sukhwinder Kaur, Grish C Varshney, Gajendra PS Raghava

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 426 KB

english, 2008

118

Missing value imputation improves clustering and interpretation of gene expression microarray data

Johannes Tuikkala, Laura L Elo, Olli S Nevalainen, Tero Aittokallio

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 606 KB

english, 2008

119

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke, Habtom W Ressom

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.05 MB

english, 2008

120

Major copy proportion analysis of tumor samples using SNP arrays

Cheng Li, Rameen Beroukhim, Barbara A Weir, Wendy Winckler, Levi A Garraway, William R Sellers, Matthew Meyerson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 475 KB

english, 2008

121

GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

Wei Yu, Melinda Clyne, Siobhan M Dolan, Ajay Yesupriya, Anja Wulf, Tiebin Liu, Muin J Khoury, Marta Gwinn

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 706 KB

english, 2008

122

VariVis: a visualisation toolkit for variation databases

Timothy D Smith, Richard GH Cotton

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 240 KB

english, 2008

123

Extraction of semantic biomedical relations from text using conditional random fields

Markus Bundschus, Mathaeus Dejori, Martin Stetter, Volker Tresp, Hans-Peter Kriegel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 454 KB

english, 2008

124

Conserved co-expression for candidate disease gene prioritization

Martin Oti, Jeroen van Reeuwijk, Martijn A Huynen, Han G Brunner

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 368 KB

english, 2008

125

Discovering biclusters in gene expression data based on high-dimensional linear geometries

Xiangchao Gan, Alan Wee-Chung Liew, Hong Yan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 892 KB

english, 2008

126

LeARN: a platform for detecting, clustering and annotating non-coding RNAs

Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.30 MB

english, 2008

127

Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization

Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu, Alan Wee-Chung Liew

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 881 KB

english, 2008

128

Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations

Hyunsoo Kim, Haesun Park, Barry L Drake

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 132 KB

english, 2008

129

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

Kazutaka Katoh, Hiroyuki Toh

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 336 KB

english, 2008

130

A new protein linear motif benchmark for multiple sequence alignment software

Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson, Julie D Thompson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.17 MB

english, 2008

131

M-BISON: Microarray-based integration of data sources using networks

Bernie J Daigle, Russ B Altman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.65 MB

english, 2008

132

Binning sequences using very sparse labels within a metagenome

Chon-Kit Kenneth Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.47 MB

english, 2008

133

Normalization for triple-target microarray experiments

Marie-Laure Martin-Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, Frederic Magniette, Jean-Pierre Renou, Jean-Jacques Daudin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 335 KB

english, 2008

134

Gene prediction in metagenomic fragments: A large scale machine learning approach

Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 441 KB

english, 2008

135

An efficient visualization tool for the analysis of protein mutation matrices

Maria Pamela C David, Carlo M Lapid, Vincent Ricardo M Daria

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.10 MB

english, 2008

136

ConStruct: Improved construction of RNA consensus structures

Andreas Wilm, Kornelia Linnenbrink, Gerhard Steger

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 925 KB

english, 2008

137

MeInfoText: associated gene methylation and cancer information from text mining

Yu-Ching Fang, Hsuan-Cheng Huang, Hsueh-Fen Juan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 978 KB

english, 2008

138

Studying the functional conservation of cis-regulatory modules and their transcriptional output

Denis C Bauer, Timothy L Bailey

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 387 KB

english, 2008

139

Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry

Andrej-Nikolai Spiess, Caroline Feig, Christian Ritz

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 344 KB

english, 2008

140

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions

Alexander Churkin, Danny Barash

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.10 MB

english, 2008

141

GENOMEPOP: A program to simulate genomes in populations

Antonio Carvajal-Rodríguez

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 326 KB

english, 2008

142

Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory

Alexander Churbanov, Stephen Winters-Hilt

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 749 KB

english, 2008

143

A copula method for modeling directional dependence of genes

Jong-Min Kim, Yoon-Sung Jung, Engin A Sungur, Kap-Hoon Han, Changyi Park, Insuk Sohn

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 490 KB

english, 2008

144

SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

Lukasz Kurgan, Krzysztof Cios, Ke Chen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 392 KB

english, 2008

145

The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks

Anatolij P Potapov, Björn Goemann, Edgar Wingender

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 372 KB

english, 2008

146

Inferring the role of transcription factors in regulatory networks

Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 705 KB

english, 2008

147

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences

Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo López, Toby J Gibson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 550 KB

english, 2008

148

Function approximation approach to the inference of reduced NGnet models of genetic networks

Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura, Mariko Hatakeyama

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 373 KB

english, 2008

149

CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies

Martin Mann, Sebastian Will, Rolf Backofen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 557 KB

english, 2008

150

Automating dChip: toward reproducible sharing of microarray data analysis

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 601 KB

english, 2008

151

Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites

Jill L Wegrzyn, Thomas M Drudge, Faramarz Valafar, Vivian Hook

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 706 KB

english, 2008

152

Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

Michael Dekhtyar, Amelie Morin, Vehary Sakanyan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 492 KB

english, 2008

153

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

Andrew J Bordner, Andrey A Gorin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 547 KB

english, 2008

154

Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm

Jeremy D DeBarry, Renyi Liu, Jeffrey L Bennetzen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 512 KB

english, 2008

155

A novel series of compositionally biased substitution matrices for comparingPlasmodiumproteins

Kevin Brick, Elisabetta Pizzi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.03 MB

english, 2008

156

Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation

Leonid Zaslavsky, Yiming Bao, Tatiana A Tatusova

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 684 KB

english, 2008

157

Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction

William S Bush, Todd L Edwards, Scott M Dudek, Brett A McKinney, Marylyn D Ritchie

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.60 MB

english, 2008

158

Aspects of coverage in medical DNA sequencing

Michael C Wendl, Richard K Wilson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 377 KB

english, 2008

159

Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

Jonathan G Lees, Robert W Janes

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 261 KB

english, 2008

160

Estimating the size of the solution space of metabolic networks

Alfredo Braunstein, Roberto Mulet, Andrea Pagnani

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.32 MB

english, 2008

161

A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model

Richard Judson, Fathi Elloumi, Woodrow R Setzer, Zhen Li, Imran Shah

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 974 KB

english, 2008

162

Compressing DNA sequence databases with coil

Timothy W J White, Michael D Hendy

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 863 KB

english, 2008

163

MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data

Bryan Chi, Ronald J deLeeuw, Bradley P Coe, Raymond T Ng, Calum MacAulay, Wan L Lam

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.78 MB

english, 2008

164

Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis

Shameek Biswas, John D Storey, Joshua M Akey

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.13 MB

english, 2008

165

Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites

Neil FW Saunders, Ross I Brinkworth, Thomas Huber, Bruce E Kemp, Bostjan Kobe

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 805 KB

english, 2008

166

Using the longest significance run to estimate region-specific p-values in genetic association mapping studies

Ie-Bin Lian, Yi-Hsien Lin, Ying-Chao Lin, Hsin-Chou Yang, Chee-Jang Chang, Cathy SJ Fann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 306 KB

english, 2008

167

A visual analytics approach for understanding biclustering results from microarray data

Rodrigo Santamaría, Roberto Therón, Luis Quintales

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.48 MB

english, 2008

168

Dinucleotide controlled null models for comparative RNA gene prediction

Tanja Gesell, Stefan Washietl

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 535 KB

english, 2008

169

Prediction of enzyme function by combining sequence similarity and protein interactions

Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom, Baldomero Oliva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 958 KB

english, 2008

170

Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data

Huiling Xiong, Dapeng Zhang, Christopher J Martyniuk, Vance L Trudeau, Xuhua Xia

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 649 KB

english, 2008

171

TileQC: A system for tile-based quality control of Solexa data

Peter C Dolan, Dee R Denver

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 4.68 MB

english, 2008

172

Variable selection for largepsmallnregression models with incomplete data: Mapping QTL with epistases

Min Zhang, Dabao Zhang, Martin T Wells

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 734 KB

english, 2008

173

Missing value imputation for microarray gene expression data using histone acetylation information

Qian Xiang, Xianhua Dai, Yangyang Deng, Caisheng He, Jiang Wang, Jihua Feng, Zhiming Dai

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 453 KB

english, 2008

174

New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background

Silvana Penco, Massimo Buscema, Maria Cristina Patrosso, Alessandro Marocchi, Enzo Grossi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 300 KB

english, 2008

175

Protein contact order prediction from primary sequences

Yi Shi, Jianjun Zhou, David Arndt, David S Wishart, Guohui Lin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 385 KB

english, 2008

176

poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening

Raghunandan M Kainkaryam, Peter J Woolf

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 416 KB

english, 2008

177

SODa: An Mn/Fe superoxide dismutase prediction and design server

Jean Marc Kwasigroch, René Wintjens, Dimitri Gilis, Marianne Rooman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 442 KB

english, 2008

178

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Shu-Dong Zhang, Timothy W Gant

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 351 KB

english, 2008

179

Word correlation matrices for protein sequence analysis and remote homology detection

Thomas Lingner, Peter Meinicke

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 343 KB

english, 2008

180

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'

Alexandre Kuhn, Ruth Luthi-Carter, Mauro Delorenzi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 511 KB

english, 2008

181

GMDD: a database of GMO detection methods

Wei Dong, Litao Yang, Kailin Shen, Banghyun Kim, Gijs A Kleter, Hans JP Marvin, Rong Guo, Wanqi Liang, Dabing Zhang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 549 KB

english, 2008

182

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Juan R González, Josep L Carrasco, Lluís Armengol, Sergi Villatoro, Lluís Jover, Yutaka Yasui, Xavier Estivill

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 512 KB

english, 2008

183

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mariño-Ramírez, John L Spouge

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 344 KB

english, 2008

184

GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors

Chiara Parravicini, Graziella Ranghino, Maria P Abbracchio, Piercarlo Fantucci

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 879 KB

english, 2008

185

Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens

Zheng Yin, Xiaobo Zhou, Chris Bakal, Fuhai Li, Youxian Sun, Norbert Perrimon, Stephen TC Wong

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.27 MB

english, 2008

186

StAR: a simple tool for the statistical comparison of ROC curves

Ismael A Vergara, Tomás Norambuena, Evandro Ferrada, Alex W Slater, Francisco Melo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 246 KB

english, 2008

187

An analytic and systematic framework for estimating metabolic flux ratios from13Ctracer experiments

Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 529 KB

english, 2008

188

Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures

Meng P Tan, Erin N Smith, James R Broach, Christodoulos A Floudas

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.73 MB

english, 2008

189

Flexible boosting of accelerated failure time models

Matthias Schmid, Torsten Hothorn

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 376 KB

english, 2008

190

t2prhd: a tool to study the patterns of repeat evolution

Botond Sipos, Kálmán Somogyi, István Andó, Zsolt Pénzes

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 565 KB

english, 2008

191

PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 359 KB

english, 2008

192

TiGER: A database for tissue-specific gene expression and regulation

Xiong Liu, Xueping Yu, Donald J Zack, Heng Zhu, Jiang Qian

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 542 KB

english, 2008

193

SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles

Paul D Yoo, Yung Shwen Ho, Bing Bing Zhou, Albert Y Zomaya

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 640 KB

english, 2008

194

AMYPdb: A database dedicated to amyloid precursor proteins

Sandrine Pawlicki, Antony Le Béchec, Christian Delamarche

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 428 KB

english, 2008

195

A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

Armita Sheari, Mehdi Kargar, Ali Katanforoush, Shahriar Arab, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, Sayed-Amir Marashi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 551 KB

english, 2008

196

Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles

Guangtao Ge, G William Wong

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 503 KB

english, 2008

197

Discovering functional interaction patterns in protein-protein interaction networks

Mehmet E Turanalp, Tolga Can

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.43 MB

english, 2008

198

Semantic role labeling for protein transport predicates

Steven Bethard, Zhiyong Lu, James H Martin, Lawrence Hunter

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 286 KB

english, 2008

199

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, Stephan Waack

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 522 KB

english, 2008

200

Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping

Guohui Lin, Zhipeng Cai, Junfeng Wu, Xiu-Feng Wan, Lizhe Xu, Randy Goebel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 299 KB

english, 2008

201

The XBabelPhish MAGE-ML and XML Translator

Don Maier, Farrell Wymore, Gavin Sherlock, Catherine A Ball

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 922 KB

english, 2008

202

Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification

Manli Zhu, Aleix M Martinez

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.12 MB

english, 2008

203

PURE: A webserver for the prediction of domains in unassigned regions in proteins

Chilamakuri CS Reddy, Khader Shameer, Bernard O Offmann, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

204

The combination approach of SVM and ECOC for powerful identification and classification of transcription factor

Guangyong Zheng, Ziliang Qian, Qing Yang, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 245 KB

english, 2008

205

Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions

Ki-Yeol Kim, Dong Hyuk Ki, Hei-Cheul Jeung, Hyun Cheol Chung, Sun Young Rha

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 606 KB

english, 2008

206

Methods for evaluating gene expression from Affymetrix microarray datasets

Ning Jiang, Lindsey J Leach, Xiaohua Hu, Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J Kearsey, Zewei W Luo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 540 KB

english, 2008

207

Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 427 KB

english, 2008

208

Partial mixture model for tight clustering of gene expression time-course

Yinyin Yuan, Chang-Tsun Li, Roland Wilson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 892 KB

english, 2008

209

Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient

Jianchao Yao, Chunqi Chang, Mari L Salmi, Yeung Sam Hung, Ann Loraine, Stanley J Roux

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 477 KB

english, 2008

210

Stability of gene contributions and identification of outliers in multivariate analysis of microarray data

Florent Baty, Daniel Jaeger, Frank Preiswerk, Martin M Schumacher, Martin H Brutsche

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 576 KB

english, 2008

211

A nonparametric model for quality control of database search results in shotgun proteomics

Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu, Fuchu He

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 540 KB

english, 2008

212

SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis

Jinho Yoo, Youngbok Lee, Yujung Kim, Sun Young Rha, Yangseok Kim

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.11 MB

english, 2008

213

Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease

Rob Jelier, Peter AC 't Hoen, Ellen Sterrenburg, Johan T den Dunnen, Gert-Jan B van Ommen, Jan A Kors, Barend Mons

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.34 MB

english, 2008

214

Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models

Dawei Liu, Debashis Ghosh, Xihong Lin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 295 KB

english, 2008

215

Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins

Michael Hsing, Artem Cherkasov

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 794 KB

english, 2008

216

Relating gene expression data on two-component systems to functional annotations inEscherichia coli

Anne M Denton, Jianfei Wu, Megan K Townsend, Preeti Sule, Birgit M Prüß

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.11 MB

english, 2008

217

Systems biology driven software design for the research enterprise

John Boyle, Christopher Cavnor, Sarah Killcoyne, Ilya Shmulevich

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 532 KB

english, 2008

218

Re-searcher: a system for recurrent detection of homologous protein sequences

Valdemaras Repšys, Mindaugas Margelevičius, Česlovas Venclovas

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.12 MB

english, 2008

219

Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information

Jing Hu, Changhui Yan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 287 KB

english, 2008

220

Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection

Inkyung Jung, Jaehyung Lee, Soo-Young Lee, Dongsup Kim

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.08 MB

english, 2008

221

PseudoGeneQuest – Service for identification of different pseudogene types in the human genome

Csaba Ortutay, Mauno Vihinen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 379 KB

english, 2008

222

Extending pathways based on gene lists using InterPro domain signatures

Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beissbarth

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 272 KB

english, 2008

223

SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data

Ramon Diaz-Uriarte

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 385 KB

english, 2008

224

A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data

Liping Huang, Wenying Zhu, Christopher P Saunders, James N MacLeod, Mai Zhou, Arnold J Stromberg, Arne C Bathke

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 567 KB

english, 2008

225

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks

Ling Yang, Thomas M Vondriska, Zhangang Han, W Robb MacLellan, James N Weiss, Zhilin Qu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 472 KB

english, 2008

226

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments

Jens Allmer, Sebastian Kuhlgert, Michael Hippler

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 653 KB

english, 2008

227

A unified approach to false discovery rate estimation

Korbinian Strimmer

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 438 KB

english, 2008

228

Investigating selection on viruses: a statistical alignment approach

Saskia de Groot, Thomas Mailund, Gerton Lunter, Jotun Hein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 516 KB

english, 2008

229

MAID : An effect size based model for microarray data integration across laboratories and platforms

Ivan Borozan, Limin Chen, Bryan Paeper, Jenny E Heathcote, Aled M Edwards, Michael Katze, Zhaolei Zhang, Ian D McGilvray

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 504 KB

english, 2008

230

Grammar-based distance in progressive multiple sequence alignment

David J Russell, Hasan H Otu, Khalid Sayood

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 384 KB

english, 2008

231

Conditional variable importance for random forests

Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin, Achim Zeileis

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 387 KB

english, 2008

232

GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords

Zhong-Xi Huang, Hui-Yong Tian, Zhen-Fu Hu, Yi-Bo Zhou, Jin Zhao, Kai-Tai Yao

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 692 KB

english, 2008

233

PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies

Brian L Browning

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 225 KB

english, 2008

234

The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem

Andrey M Leontovich, Konstantin Y Tokmachev, Hans C van Houwelingen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 872 KB

english, 2008

235

Computational identification of ubiquitylation sites from protein sequences

Chun-Wei Tung, Shinn-Ying Ho

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.75 MB

english, 2008

236

Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge

Don L Armstrong, Chaim O Jacob, Raphael Zidovetzki

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 269 KB

english, 2008

237

MSDmotif: exploring protein sites and motifs

Adel Golovin, Kim Henrick

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.38 MB

english, 2008

238

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

Michael C Ryan, Barry R Zeeberg, Natasha J Caplen, James A Cleland, Ari B Kahn, Hongfang Liu, John N Weinstein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 361 KB

english, 2008

239

Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies

Li Ma, H Birali Runesha, Daniel Dvorkin, John R Garbe, Yang Da

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 331 KB

english, 2008

240

PatternLab for proteomics: a tool for differential shotgun proteomics

Paulo C Carvalho, Juliana SG Fischer, Emily I Chen, John R Yates, Valmir C Barbosa

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 917 KB

english, 2008

241

Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis

Angela P Presson, Eric M Sobel, Paivi Pajukanta, Christopher Plaisier, Daniel E Weeks, Karolina Åberg, Jeanette C Papp

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 366 KB

english, 2008

242

Directed acyclic graph kernels for structural RNA analysis

Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 371 KB

english, 2008

243

A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

Alexander Statnikov, Lily Wang, Constantin F Aliferis

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 552 KB

english, 2008

244

Prioritization of gene regulatory interactions from large-scale modules in yeast

Ho-Joon Lee, Thomas Manke, Ricardo Bringas, Martin Vingron

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.73 MB

english, 2008

245

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements

Qingwu Yang, Sing-Hoi Sze

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 757 KB

english, 2008

246

GBParsy: A GenBank flatfile parser library with high speed

Tae-Ho Lee, Yeon-Ki Kim, Baek Hie Nahm

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 435 KB

english, 2008

247

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Cuong Than, Derek Ruths, Luay Nakhleh

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

248

LOSITAN: A workbench to detect molecular adaptation based on aFst-outlier method

Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira, Gordon Luikart

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 368 KB

english, 2008

249

Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis

Yuanxin Xi, David M Rocke

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 701 KB

english, 2008

250

A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data

Cong Zhou, Lucas D Bowler, Jianfeng Feng

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 519 KB

english, 2008

251

A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition

Michele Guescini, Davide Sisti, Marco BL Rocchi, Laura Stocchi, Vilberto Stocchi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.24 MB

english, 2008

252

Gene Ontology term overlap as a measure of gene functional similarity

Meeta Mistry, Paul Pavlidis

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.73 MB

english, 2008

253

A Java-based tool for the design of classification microarrays

Da Meng, Shira L Broschat, Douglas R Call

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 355 KB

english, 2008

254

Evaluation of genomic island predictors using a comparative genomics approach

Morgan GI Langille, William WL Hsiao, Fiona SL Brinkman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 507 KB

english, 2008

255

A fast structural multiple alignment method for long RNA sequences

Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 455 KB

english, 2008

256

NullHap – a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles

Robert M Nowak, Rafał Płoski

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 305 KB

english, 2008

257

HAPSIMU: a genetic simulation platform for population-based association studies

Feng Zhang, Jianfeng Liu, Jie Chen, Hong-Wen Deng

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 580 KB

english, 2008

258

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

Olivier Bastien, Eric Maréchal

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 618 KB

english, 2008

259

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage

Hamilton Ganesan, Anna S Rakitianskaia, Colin F Davenport, Burkhard Tümmler, Oleg N Reva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.57 MB

english, 2008

260

Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data

Peter Li, Juan I Castrillo, Giles Velarde, Ingo Wassink, Stian Soiland-Reyes, Stuart Owen, David Withers, Tom Oinn, Matthew R Pocock, Carole A Goble, Stephen G Oliver, Douglas B Kell

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 850 KB

english, 2008

261

Combining transcriptional datasets using the generalized singular value decomposition

Andreas W Schreiber, Neil J Shirley, Rachel A Burton, Geoffrey B Fincher

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 431 KB

english, 2008

262

Determining significance of pairwise co-occurrences of events in bursty sequences

Niina Haiminen, Heikki Mannila, Evimaria Terzi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 698 KB

english, 2008

263

Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands

Wei Dai, Jens M Teodoridis, Janet Graham, Constanze Zeller, Tim HM Huang, Pearlly Yan, J Keith Vass, Robert Brown, Jim Paul

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 594 KB

english, 2008

264

New time-scale criteria for model simplification of bio-reaction systems

Junwon Choi, Kyung-won Yang, Tai-yong Lee, Sang Yup Lee

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 459 KB

english, 2008

265

A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics

Arnab Bhattacharya, Sasha Levy, Adria LeBoeuf, Michelle Gaylord, Leslie Wilson, Ambuj K Singh, Stuart C Feinstein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 343 KB

english, 2008

266

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

Patrick D Schloss, Jo Handelsman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 707 KB

english, 2008

267

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

Mirela Andronescu, Vera Bereg, Holger H Hoos, Anne Condon

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 385 KB

english, 2008

268

SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny ofBlastocystis

Martin Kostka, Magdalena Uzlikova, Ivan Cepicka, Jaroslav Flegr

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 313 KB

english, 2008

269

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool

Zhike Zi, Yanan Zheng, Ann E Rundell, Edda Klipp

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.00 MB

english, 2008

270

Parameter estimation for robust HMM analysis of ChIP-chip data

Peter Humburg, David Bulger, Glenn Stone

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.62 MB

english, 2008

271

An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories

Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota, Yusu Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 864 KB

english, 2008

272

VisualRepbase: an interface for the study of occurrences of transposable element families

Sébastien Tempel, Matthew Jurka, Jerzy Jurka

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 394 KB

english, 2008

273

AccPbFRET: An ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images

János Roszik, János Szöllősi, György Vereb

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.60 MB

english, 2008

274

A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time

Hua Xu, Lanhao Yang, Michael A Freitas

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 773 KB

english, 2008

275

Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments

Stephen W Tanner, Pankaj Agarwal

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 309 KB

english, 2008

276

Enhancing the prediction of protein pairings between interacting families using orthology information

Jose MG Izarzugaza, David Juan, Carles Pons, Florencio Pazos, Alfonso Valencia

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 876 KB

english, 2008

277

Integration of relational and hierarchical network information for protein function prediction

Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, Eric D Kolaczyk

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 441 KB

english, 2008

278

SynBlast: Assisting the analysis of conserved synteny information

Jörg Lehmann, Peter F Stadler, Sonja J Prohaska

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 797 KB

english, 2008

279

Alignment of protein structures in the presence of domain motions

Roberto Mosca, Barbara Brannetti, Thomas R Schneider

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.04 MB

english, 2008

280

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai, László Patthy

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 443 KB

english, 2008

281

Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration

Yulan Liang, Arpad Kelemen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 435 KB

english, 2008

282

NITPICK: peak identification for mass spectrometry data

Bernhard Y Renard, Marc Kirchner, Hanno Steen, Judith AJ Steen, Fred A Hamprecht

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 719 KB

english, 2008

283

FERN – a Java framework for stochastic simulation and evaluation of reaction networks

Florian Erhard, Caroline C Friedel, Ralf Zimmer

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 533 KB

english, 2008

284

Impact of residue accessible surface area on the prediction of protein secondary structures

Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk, Sayed-Amir Marashi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 338 KB

english, 2008

285

TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model

Mallika Veeramalai, Yuzhen Ye, Adam Godzik

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.35 MB

english, 2008

286

Methodology capture: discriminating between the "best" and the rest of community practice

James M Eales, John W Pinney, Robert D Stevens, David L Robertson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.42 MB

english, 2008

287

Universal seeds for cDNA-to-genome comparison

Leming Zhou, Jonathan Stanton, Liliana Florea

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 477 KB

english, 2008

288

TheC1C2: A framework for simultaneous model selection and assessment

Martin Eklund, Ola Spjuth, Jarl ES Wikberg

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 446 KB

english, 2008

289

Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

Stefano Moretti, Danitsja van Leeuwen, Hans Gmuender, Stefano Bonassi, Joost van Delft, Jos Kleinjans, Fioravante Patrone, Domenico Franco Merlo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.63 MB

english, 2008

290

Testing gene set enrichment for subset of genes: Sub-GSE

Xiting Yan, Fengzhu Sun

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 502 KB

english, 2008

291

Virtual screening of GPCRs: Anin silicochemogenomics approach

Laurent Jacob, Brice Hoffmann, Véronique Stoven, Jean-Philippe Vert

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.09 MB

english, 2008

292

Fregene: Simulation of realistic sequence-level data in populations and ascertained samples

Marc Chadeau-Hyam, Clive J Hoggart, Paul F O'Reilly, John C Whittaker, Maria De Iorio, David J Balding

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 598 KB

english, 2008

293

Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions

E Andres Houseman, Brock C Christensen, Ru-Fang Yeh, Carmen J Marsit, Margaret R Karagas, Margaret Wrensch, Heather H Nelson, Joseph Wiemels, Shichun Zheng, John K Wiencke, Karl T Kelsey

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 807 KB

english, 2008

294

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)

Thomas D Otto, Leonardo HF Gomes, Marcelo Alves-Ferreira, Antonio B de Miranda, Wim M Degrave

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1016 KB

english, 2008

295

IgTM: An algorithm to predict transmembrane domains and topology in proteins

Piedachu Peris, Damián López, Marcelino Campos

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 336 KB

english, 2008

296

LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens

Wah Heng Lee, Christopher W Wong, Wan Yee Leong, Lance D Miller, Wing Kin Sung

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 732 KB

english, 2008

297

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

Rekin's Janky, Jacques van Helden

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.14 MB

english, 2008

298

Mixture models for analysis of melting temperature data

Christoffer Nellåker, Fredrik Uhrzander, Joanna Tyrcha, Håkan Karlsson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 334 KB

english, 2008

299

Kismeth: Analyzer of plant methylation states through bisulfite sequencing

Eyal Gruntman, Yijun Qi, R Keith Slotkin, Ted Roeder, Robert A Martienssen, Ravi Sachidanandam

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.83 MB

english, 2008

300

Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast

Uri Keich, Hong Gao, Jeffrey S Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato, Bik K Tye

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 301 KB

english, 2008

301

Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy

Marco AJ Iafolla, Guang Qiang Dong, David R McMillen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 606 KB

english, 2008

302

Large-scale identification of polymorphic microsatellites using anin silicoapproach

Jifeng Tang, Samantha J Baldwin, Jeanne ME Jacobs, C Gerard van der Linden, Roeland E Voorrips, Jack AM Leunissen, Herman van Eck, Ben Vosman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 349 KB

english, 2008

303

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

Eva Lange, Ralf Tautenhahn, Steffen Neumann, Clemens Gröpl

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 525 KB

english, 2008

304

GenomeMatcher: A graphical user interface for DNA sequence comparison

Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, Masataka Tsuda

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 927 KB

english, 2008

305

CBESW: Sequence Alignment on the Playstation 3

Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, Bertil Schmidt

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 836 KB

english, 2008

306

SQUAT: A web tool to mine human, murine and avian SAGE data

Johan Leyritz, Stéphane Schicklin, Sylvain Blachon, Céline Keime, Céline Robardet, Jean-François Boulicaut, Jérémy Besson, Ruggero G Pensa, Olivier Gandrillon

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.32 MB

english, 2008

307

MiMiR – an integrated platform for microarray data sharing, mining and analysis

Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.12 MB

english, 2008

308

A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles

Samiran Ghosh, David F Grant, Dipak K Dey, Dennis W Hill

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 394 KB

english, 2008

309

A Population Proportion approach for ranking differentially expressed genes

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 613 KB

english, 2008

310

MetWAMer: eukaryotic translation initiation site prediction

Michael E Sparks, Volker Brendel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 966 KB

english, 2008

311

A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge

Young-Rae Cho, Lei Shi, Murali Ramanathan, Aidong Zhang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 447 KB

english, 2008

312

caBIG™ VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data

Yitan Zhu, Huai Li, David J Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P Hoffman, Yue Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.20 MB

english, 2008

313

GlycomeDB– integration of open-access carbohydrate structure databases

René Ranzinger, Stephan Herget, Thomas Wetter, Claus-Wilhelm von der Lieth

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.14 MB

english, 2008

314

Improving peptide-MHC class I binding prediction for unbalanced datasets

Ana Paula Sales, Georgia D Tomaras, Thomas B Kepler

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 342 KB

english, 2008

315

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 889 KB

english, 2008

316

"TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis

Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D Koter, Paul D Gershon

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.37 MB

english, 2008

317

Sequence based residue depth prediction using evolutionary information and predicted secondary structure

Hua Zhang, Tuo Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, Lukasz Kurgan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 850 KB

english, 2008

318

miRNAminer: A tool for homologous microRNA gene search

Shay Artzi, Adam Kiezun, Noam Shomron

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 498 KB

english, 2008

319

R/parallel – speeding up bioinformatics analysis with R

Gonzalo Vera, Ritsert C Jansen, Remo L Suppi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 601 KB

english, 2008

320

SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase

Fabrice PA David, Yum L Yip

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 501 KB

english, 2008

321

PredGPI: a GPI-anchor predictor

Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 334 KB

english, 2008

322

HECTAR: A method to predict subcellular targeting in heterokonts

Bernhard Gschloessl, Yann Guermeur, J Mark Cock

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.13 MB

english, 2008

323

Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'

Qi Dai, Tianming Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 640 KB

english, 2008

324

GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach

Li Shen, Jie Liu, Wei Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 636 KB

english, 2008

325

FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects

David Lagorce, Olivier Sperandio, Hervé Galons, Maria A Miteva, Bruno O Villoutreix

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 365 KB

english, 2008

326

Predicting protein linkages in bacteria: Which method is best depends on task

Anis Karimpour-Fard, Sonia M Leach, Ryan T Gill, Lawrence E Hunter

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.79 MB

english, 2008

327

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures

Min Li, Jian-er Chen, Jian-xin Wang, Bin Hu, Gang Chen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 862 KB

english, 2008

328

Presenting and exploring biological pathways with PathVisio

Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, Chris Evelo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.68 MB

english, 2008

329

An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis

Romesh Stanislaus, John M Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen, Jonas S Almeida

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 430 KB

english, 2008

330

I-TASSER server for protein 3D structure prediction

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 637 KB

english, 2008

331

Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction

Stefan Kuhn, Björn Egert, Steffen Neumann, Christoph Steinbeck

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.76 MB

english, 2008

332

Developing and validating predictive decision tree models from mining chemical structural fingerprints and high–throughput screening data in PubChem

Lianyi Han, Yanli Wang, Stephen H Bryant

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 277 KB

english, 2008

333

Abbreviation definition identification based on automatic precision estimates

Sunghwan Sohn, Donald C Comeau, Won Kim, W John Wilbur

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 425 KB

english, 2008

334

MetaMQAP: A meta-server for the quality assessment of protein models

Marcin Pawlowski, Michal J Gajda, Ryszard Matlak, Janusz M Bujnicki

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 5.85 MB

english, 2008

335

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells

Atsushi Niida, Andrew D Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q Zhang, Tetsu Akiyama

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 779 KB

english, 2008

336

iRefIndex: A consolidated protein interaction database with provenance

Sabry Razick, George Magklaras, Ian M Donaldson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 555 KB

english, 2008

337

BibGlimpse: The case for a light-weight reprint manager in distributed literature research

Thomas Tüchler, Golda Velez, Alexandra Graf, David P Kreil

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 389 KB

english, 2008

338

Towards a lightweight generic computational grid framework for biological research

Mark D Halling-Brown, David S Moss, Adrian J Shepherd

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 320 KB

english, 2008

339

Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools

Kevin Bleakley, Marie-Paule Lefranc, Gérard Biau

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 634 KB

english, 2008

340

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

Johan Staaf, Johan Vallon-Christersson, David Lindgren, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg, Markus Ringnér

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.09 MB

english, 2008

341

Predicting the Interactome ofXanthomonas oryzaepathovar oryzae for target selection and DB service

Jeong-Gu Kim, Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Yeong Tae Kim, Young-Jin Park, Hee Jung Cho, Hyunseok Park, Ki-Bong Kim, Kyong-Oh Yoon, Soo-Jun Park, Byoung-Moo Lee, Jong Bhak

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 323 KB

english, 2008

342

Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments

Stefano Parodi, Vito Pistoia, Marco Muselli

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 527 KB

english, 2008

343

Classification of drug molecules considering their IC50values using mixed-integer linear programming based hyper-boxes method

Pelin Armutlu, Muhittin E Ozdemir, Fadime Uney-Yuksektepe, I Halil Kavakli, Metin Turkay

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 461 KB

english, 2008

344

Gene and pathway identification withLppenalized Bayesian logistic regression

Zhenqiu Liu, Ronald B Gartenhaus, Ming Tan, Feng Jiang, Xiaoli Jiao

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 821 KB

english, 2008

345

PhySIC_IST: cleaning source trees to infer more informative supertrees

Celine Scornavacca, Vincent Berry, Vincent Lefort, Emmanuel JP Douzery, Vincent Ranwez

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 934 KB

english, 2008

346

Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach

Firoz Anwar, Syed Murtuza Baker, Taskeed Jabid, Md Mehedi Hasan, Mohammad Shoyaib, Haseena Khan, Ray Walshe

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 289 KB

english, 2008

347

BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments

Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1011 KB

english, 2008

348

Knowledge-guided multi-scale independent component analysis for biomarker identification

Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Wang, Zhen Zhang, Eric Hoffman, Robert Clarke

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 567 KB

english, 2008

349

A method for analyzing censored survival phenotype with gene expression data

Tongtong Wu, Wei Sun, Shinsheng Yuan, Chun-Houh Chen, Ker-Chau Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 325 KB

english, 2008

350

Automatically extracting functionally equivalent proteins from SwissProt

Lisa EM McMillan, Andrew CR Martin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 413 KB

english, 2008

351

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using theDarkHorsealgorithm

Sheila Podell, Terry Gaasterland, Eric E Allen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 699 KB

english, 2008

352

New resampling method for evaluating stability of clusters

Irina M Gana Dresen, Tanja Boes, Johannes Huesing, Markus Neuhaeuser, Karl-Heinz Joeckel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 320 KB

english, 2008

353

XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.09 MB

english, 2008

354

Bayesian modeling of recombination events in bacterial populations

Pekka Marttinen, Adam Baldwin, William P Hanage, Chris Dowson, Eshwar Mahenthiralingam, Jukka Corander

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.06 MB

english, 2008

355

SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes

Raj Chari, Bradley P Coe, Craig Wedseltoft, Marie Benetti, Ian M Wilson, Emily A Vucic, Calum MacAulay, Raymond T Ng, Wan L Lam

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.81 MB

english, 2008

356

LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.38 MB

english, 2008

357

Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks

Iaroslav Ispolatov, Sergei Maslov

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 328 KB

english, 2008

358

Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems

Yu-Shuen Tsai, Chin-Teng Lin, George C Tseng, I-Fang Chung, Nikhil Ranjan Pal

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 617 KB

english, 2008

359

Mining protein networks for synthetic genetic interactions

Sri R Paladugu, Shan Zhao, Animesh Ray, Alpan Raval

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 895 KB

english, 2008

360

Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations

Guillaume Launay, Thomas Simonson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.18 MB

english, 2008

361

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access

Jorge Amigo, Antonio Salas, Christopher Phillips, Ángel Carracedo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 542 KB

english, 2008

362

Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure

Christopher Bystroff, Bobbie-Jo Webb-Robertson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 944 KB

english, 2008

363

Predicting biological system objectives de novo from internal state measurements

Erwin P Gianchandani, Matthew A Oberhardt, Anthony P Burgard, Costas D Maranas, Jason A Papin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 623 KB

english, 2008

364

Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments

Ce Zheng, Lukasz Kurgan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 365 KB

english, 2008

365

Probabilistic base calling of Solexa sequencing data

Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 504 KB

english, 2008

366

easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data

Ting-Yu Chang, Yin-Yi Li, Chih-Hung Jen, Tsun-Po Yang, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 884 KB

english, 2008

367

Reranking candidate gene models with cross-species comparison for improved gene prediction

Qian Liu, Koby Crammer, Fernando CN Pereira, David S Roos

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 678 KB

english, 2008

368

Comparative optimism in models involving both classical clinical and gene expression information

Caroline Truntzer, Delphine Maucort-Boulch, Pascal Roy

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 310 KB

english, 2008

369

Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission

Benjamin Roche, Jean-François Guégan, François Bousquet

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 306 KB

english, 2008

370

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

Kieran O'Neill, Alexander Garcia, Anita Schwegmann, Rafael C Jimenez, Dan Jacobson, Henning Hermjakob

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.25 MB

english, 2008

371

AMMOS: Automated Molecular Mechanics Optimization tool forin silicoScreening

Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O Villoutreix, Maria A Miteva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 970 KB

english, 2008

372

CMA – a comprehensive Bioconductor package for supervised classification with high dimensional data

M Slawski, M Daumer, A-L Boulesteix

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 452 KB

english, 2008

373

Generating samples for association studies based on HapMap data

Jing Li, Yixuan Chen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 708 KB

english, 2008

374

PlasmoDraft: a database ofPlasmodium falciparumgene function predictions based on postgenomic data

Laurent Bréhélin, Jean-François Dufayard, Olivier Gascuel

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.52 MB

english, 2008

375

Structural assembly of two-domain proteins by rigid-body docking

Tammy MK Cheng, Tom L Blundell, Juan Fernandez-Recio

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.55 MB

english, 2008

376

Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data

Michael J Gilchrist, Mikkel B Christensen, Richard Harland, Nicolas Pollet, James C Smith, Naoto Ueno, Nancy Papalopulu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 451 KB

english, 2008

377

Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics

Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher, Tim W Nattkemper

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 712 KB

english, 2008

378

Assessment of protein set coherence using functional annotations

Monica Chagoyen, Jose M Carazo, Alberto Pascual-Montano

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 699 KB

english, 2008

379

An incremental approach to automated protein localisation

Marko Tscherepanow, Nickels Jensen, Franz Kummert

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 607 KB

english, 2008

380

Envelope: interactive software for modeling and fitting complex isotope distributions

Michael T Sykes, James R Williamson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 548 KB

english, 2008

381

Identification of hot-spot residues in protein-protein interactions by computational docking

Solène Grosdidier, Juan Fernández-Recio

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 994 KB

english, 2008

382

Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

Salim Bougouffa, Jim Warwicker

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 790 KB

english, 2008

383

A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification

Ning Wei, Erwin Flaschel, Karl Friehs, Tim Wilhelm Nattkemper

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 827 KB

english, 2008

384

A genetic approach for building different alphabets for peptide and protein classification

Loris Nanni, Alessandra Lumini

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 664 KB

english, 2008

385

Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

Jung Soh, Paul MK Gordon, Morgan L Taschuk, Anguo Dong, Andrew C Ah-Seng, Andrei L Turinsky, Christoph W Sensen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.14 MB

english, 2008

386

Feature selection environment for genomic applications

Fabrício Martins Lopes, David Corrêa Martins, Roberto M Cesar

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 891 KB

english, 2008

387

Background correction using dinucleotide affinities improves the performance of GCRMA

Raad Z Gharaibeh, Anthony A Fodor, Cynthia J Gibas

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 454 KB

english, 2008

388

Probe signal correction for differential methylation hybridization experiments

Dustin P Potter, Pearlly Yan, Tim HM Huang, Shili Lin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.40 MB

english, 2008

389

In silicoanalysis of methyltransferase domains involved in biosynthesis of secondary metabolites

Mohd Zeeshan Ansari, Jyoti Sharma, Rajesh S Gokhale, Debasisa Mohanty

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 4.79 MB

english, 2008

390

CompMoby: Comparative MobyDick for detection of cis-regulatory motifs

Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch, Hao Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.67 MB

english, 2008

391

FUNYBASE: a FUNgal phYlogenomic dataBASE

Sylvain Marthey, Gabriela Aguileta, François Rodolphe, Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Angélique Gautier, Marc-Henri Lebrun, Hélène Chiapello

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.72 MB

english, 2008

392

Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles

Hailong Meng, Edward L Murrelle, Guoya Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 465 KB

english, 2008

393

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies

Peter A DiMaggio, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz, Herschel A Rabitz

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1011 KB

english, 2008

394

MetaMine – A tool to detect and analyse gene patterns in their environmental context

Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann, Frank O Glöckner

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.10 MB

english, 2008

395

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

Yuerong Zhu, Yuelin Zhu, Wei Xu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 809 KB

english, 2008

396

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

Sabine Pérès, Laurence Molina, Nicolas Salvetat, Claude Granier, Franck Molina

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 862 KB

english, 2008

397

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

Patrick E Meyer, Frédéric Lafitte, Gianluca Bontempi

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 322 KB

english, 2008

398

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer

Raffaele Giancarlo, Davide Scaturro, Filippo Utro

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.11 MB

english, 2008

399

Information-based methods for predicting gene function from systematic gene knock-downs

Matthew T Weirauch, Christopher K Wong, Alexandra B Byrne, Joshua M Stuart

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 965 KB

english, 2008

400

Neutral network sizes of biological RNA molecules can be computed and are not atypically small

Thomas Jörg, Olivier C Martin, Andreas Wagner

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 438 KB

english, 2008

401

Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats

Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandić, Matko Glunčić, Nils Paar

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.32 MB

english, 2008

402

Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information

Weijun Luo, Kurt D Hankenson, Peter J Woolf

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.40 MB

english, 2008

403

A relation based measure of semantic similarity for Gene Ontology annotations

Brendan Sheehan, Aaron Quigley, Benoit Gaudin, Simon Dobson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 549 KB

english, 2008

404

Gene set analyses for interpreting microarray experiments on prokaryotic organisms

Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik, Ronald C Taylor

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 356 KB

english, 2008

405

Discrimination of outer membrane proteins with improved performance

Changhui Yan, Jing Hu, Yingfeng Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 287 KB

english, 2008

406

MetaFIND: A feature analysis tool for metabolomics data

Kenneth Bryan, Lorraine Brennan, Pádraig Cunningham

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.09 MB

english, 2008

407

Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes

Inna Myslyuk, Tirza Doniger, Yair Horesh, Avraham Hury, Ran Hoffer, Yaara Ziporen, Shulamit Michaeli, Ron Unger

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.76 MB

english, 2008

408

Evaluation of GO-based functional similarity measures usingS. cerevisiaeprotein interaction and expression profile data

Tao Xu, LinFang Du, Yan Zhou

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 779 KB

english, 2008

409

Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling

Thora Pommerencke, Thorsten Steinberg, Hartmut Dickhaus, Pascal Tomakidi, Niels Grabe

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.19 MB

english, 2008

410

RNAalifold: improved consensus structure prediction for RNA alignments

Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber, Peter F Stadler

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 398 KB

english, 2008

411

Standardized high-throughput evaluation of cell-based compound screens

Peter Frommolt, Roman K Thomas

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 292 KB

english, 2008

412

Improved identification of conserved cassette exons using Bayesian networks

Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer, Rolf Backofen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 530 KB

english, 2008

413

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

James K Hane, Richard P Oliver

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 702 KB

english, 2008

414

The Average Mutual Information Profile as a Genomic Signature

Mark Bauer, Sheldon M Schuster, Khalid Sayood

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.50 MB

english, 2008

415

A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data

Luca Corradi, Marco Fato, Ivan Porro, Silvia Scaglione, Livia Torterolo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 557 KB

english, 2008

416

Gene set enrichment analysis for non-monotone association and multiple experimental categories

Rongheng Lin, Shuangshuang Dai, Richard D Irwin, Alexandra N Heinloth, Gary A Boorman, Leping Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 373 KB

english, 2008

417

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, David M Sabatini, Polina Golland, Anne E Carpenter

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 5.31 MB

english, 2008

418

mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

Hwan Young Lee, Injee Song, Eunho Ha, Sung-Bae Cho, Woo Ick Yang, Kyoung-Jin Shin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.28 MB

english, 2008

419

Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne, Jan Komorowski

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 375 KB

english, 2008

420

CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments

Paolo Uva, Emanuele de Rinaldis

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 277 KB

english, 2008

421

Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification

Michael Gormley, Aydin Tozeren

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.76 MB

english, 2008

422

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

Myron Peto, Andrzej Kloczkowski, Vasant Honavar, Robert L Jernigan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 506 KB

english, 2008

423

Identifying differential correlation in gene/pathway combinations

Rosemary Braun, Leslie Cope, Giovanni Parmigiani

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 466 KB

english, 2008

424

Determining gene expression on a single pair of microarrays

Robert W Reid, Anthony A Fodor

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 453 KB

english, 2008

425

A dynamic Bayesian network approach to protein secondary structure prediction

Xin-Qiu Yao, Huaiqiu Zhu, Zhen-Su She

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 581 KB

english, 2008

426

A comparison of four clustering methods for brain expression microarray data

Alexander L Richards, Peter Holmans, Michael C O'Donovan, Michael J Owen, Lesley Jones

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.01 MB

english, 2008

427

Prediction of specificity-determining residues for small-molecule kinase inhibitors

Daniel R Caffrey, Elizabeth A Lunney, Deborah J Moshinsky

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.15 MB

english, 2008

428

Structural descriptor database: a new tool for sequence-based functional site prediction

Juliana S Bernardes, Jorge H Fernandez, Ana Tereza R Vasconcelos

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 586 KB

english, 2008

429

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

G Barton, J Abbott, N Chiba, DW Huang, Y Huang, M Krznaric, J Mack-Smith, A Saleem, BT Sherman, B Tiwari, C Tomlinson, T Aitman, J Darlington, L Game, MJE Sternberg, SA Butcher

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.51 MB

english, 2008

430

ExonMiner: Web service for analysis of GeneChip Exon array data

Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.54 MB

english, 2008

431

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

Matthew S Hestand, Michiel van Galen, Michel P Villerius, Gert-Jan B van Ommen, Johan T den Dunnen, Peter AC 't Hoen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 797 KB

english, 2008

432

Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes

Josephine F Reyes, Andrew R Francis, Mark M Tanaka

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 616 KB

english, 2008

433

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level

Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit, Meriem El Karoui

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.51 MB

english, 2008

434

Natural computation meta-heuristics for the in silico optimization of microbial strains

Miguel Rocha, Paulo Maia, Rui Mendes, José P Pinto, Eugénio C Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 4.68 MB

english, 2008

435

EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration

Javier Forment, Francisco Gilabert, Antonio Robles, Vicente Conejero, Fernando Nuez, Jose M Blanca

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 629 KB

english, 2008

436

Defining functional distances over Gene Ontology

Angela del Pozo, Florencio Pazos, Alfonso Valencia

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.13 MB

english, 2008

437

Prediction of glycosylation sites using random forests

Stephen E Hamby, Jonathan D Hirst

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.24 MB

english, 2008

438

Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features

Derek Huntley, Y Amy Tang, Tatyana B Nesterova, Sarah Butcher, Neil Brockdorff

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.68 MB

english, 2008

439

Microarray-based gene set analysis: a comparison of current methods

Sarah Song, Michael A Black

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.44 MB

english, 2008

440

ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins

Aarti Garg, Gajendra PS Raghava

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 253 KB

english, 2008

441

Highly sensitive feature detection for high resolution LC/MS

Ralf Tautenhahn, Christoph Böttcher, Steffen Neumann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 612 KB

english, 2008

442

Use of normalization methods for analysis of microarrays containing a high degree of gene effects

Terri T Ni, William J Lemon, Yu Shyr, Tao P Zhong

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 469 KB

english, 2008

443

c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression

Katerina Kechris, Hao Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 288 KB

english, 2008

444

MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids

Jianguo Xia, Trent C Bjorndahl, Peter Tang, David S Wishart

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 441 KB

english, 2008

445

Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method

Joseph W Foley, Fumiaki Katagiri

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.51 MB

english, 2008

446

Position dependent mismatch discrimination on DNA microarrays – experiments and model

Thomas Naiser, Jona Kayser, Timo Mai, Wolfgang Michel, Albrecht Ott

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 800 KB

english, 2008

447

The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction

Jonathan R Manning, Emily R Jefferson, Geoffrey J Barton

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.56 MB

english, 2008

448

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis

Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong, Xuan Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.33 MB

english, 2008

449

Comparison of methods for estimating the nucleotide substitution matrix

Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A Huttley, Manuel E Lladser, Rob Knight

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 415 KB

english, 2008

450

A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips

Marta Blangiardo, Sylvia Richardson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 693 KB

english, 2008

451

Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

Shu-Yi Su, Jonathan White, David J Balding, Lachlan JM Coin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 842 KB

english, 2008

452

ElliPro: a new structure-based tool for the prediction of antibody epitopes

Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette, Bjoern Peters

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.04 MB

english, 2008

453

Improved machine learning method for analysis of gas phase chemistry of peptides

Allison Gehrke, Shaojun Sun, Lukasz Kurgan, Natalie Ahn, Katheryn Resing, Karen Kafadar, Krzysztof Cios

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 496 KB

english, 2008

454

A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions

Martin Bader, Mohamed I Abouelhoda, Enno Ohlebusch

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 353 KB

english, 2008

455

Detection of protein catalytic residues at high precision using local network properties

Patrick Slama, Ioannis Filippis, Michael Lappe

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1020 KB

english, 2008

456

Algorithm of OMA for large-scale orthology inference

Alexander CJ Roth, Gaston H Gonnet, Christophe Dessimoz

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 406 KB

english, 2008

457

Integrated multi-level quality control for proteomic profiling studies using mass spectrometry

David A Cairns, David N Perkins, Anthea J Stanley, Douglas Thompson, Jennifer H Barrett, Peter J Selby, Rosamonde E Banks

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.25 MB

english, 2008

458

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

Chenggang Yu, Nela Zavaljevski, Valmik Desai, Seth Johnson, Fred J Stevens, Jaques Reifman

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 546 KB

english, 2008

459

Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data

Carl R Pelz, Molly Kulesz-Martin, Grover Bagby, Rosalie C Sears

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.90 MB

english, 2008

460

An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.56 MB

english, 2008

461

Systematic identification of yeast cell cycle transcription factors using multiple data sources

Wei-Sheng Wu, Wen-Hsiung Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 509 KB

english, 2008

462

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

David A Nix, Samir J Courdy, Kenneth M Boucher

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.51 MB

english, 2008

463

IDEA: Interactive Display for Evolutionary Analyses

Amy Egan, Anup Mahurkar, Jonathan Crabtree, Jonathan H Badger, Jane M Carlton, Joana C Silva

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.51 MB

english, 2008

464

Multi-label literature classification based on the Gene Ontology graph

Bo Jin, Brian Muller, Chengxiang Zhai, Xinghua Lu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 484 KB

english, 2008

465

SNPFile – A software library and file format for large scale association mapping and population genetics studies

Jesper Nielsen, Thomas Mailund

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 246 KB

english, 2008

466

Compo: composite motif discovery using discrete models

Geir Kjetil Sandve, Osman Abul, Finn Drabløs

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 359 KB

english, 2008

467

Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases

Wei Yu, Anja Wulf, Tiebin Liu, Muin J Khoury, Marta Gwinn

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 367 KB

english, 2008

468

The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results

John C Braisted, Srilatha Kuntumalla, Christine Vogel, Edward M Marcotte, Alan R Rodrigues, Rong Wang, Shih-Ting Huang, Erik S Ferlanti, Alexander I Saeed, Robert D Fleischmann, Scott N Peterson, Remb

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

469

TOBFAC: the database of tobacco transcription factors

Paul J Rushton, Marta T Bokowiec, Thomas W Laudeman, Jennifer F Brannock, Xianfeng Chen, Michael P Timko

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 994 KB

english, 2008

470

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi, David M Gilbert

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.54 MB

english, 2008

471

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

Shashi Bhushan Pandit, Jeffrey Skolnick

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 6.36 MB

english, 2008

472

Extended Newick: it is time for a standard representation of phylogenetic networks

Gabriel Cardona, Francesc Rosselló, Gabriel Valiente

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.10 MB

english, 2008

473

GPAT: Retrieval of genomic annotation from large genomic position datasets

Arnaud Krebs, Mattia Frontini, Làszlò Tora

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 306 KB

english, 2008

474

Optimal neighborhood indexing for protein similarity search

Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.00 MB

english, 2008

475

DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites

Evert-Jan Blom, Sacha AFT van Hijum, Klaas J Hofstede, Remko Silvis, Jos BTM Roerdink, Oscar P Kuipers

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.45 MB

english, 2008

476

SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes

Frédéric Lemoine, Bernard Labedan, Olivier Lespinet

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 932 KB

english, 2008

477

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbert S Omenn, Biaoyang Lin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 763 KB

english, 2008

478

Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis

Yan Xin Huang, Li Yong Bao, Shu Yan Guo, Yan Wang, Chun Guang Zhou, Yu Xin Li

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 570 KB

english, 2008

479

Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes

Cornelia Frömke, Ludwig A Hothorn, Siegfried Kropf

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 307 KB

english, 2008

480

Shape-IT: new rapid and accurate algorithm for haplotype inference

Olivier Delaneau, Cédric Coulonges, Jean-François Zagury

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 396 KB

english, 2008

481

GeNESiS: gene network evolution simulation software

Anton Kratz, Masaru Tomita, Arun Krishnan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 543 KB

english, 2008

482

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

Mi-Youn Brusniak, Bernd Bodenmiller, David Campbell, Kelly Cooke, James Eddes, Andrew Garbutt, Hollis Lau, Simon Letarte, Lukas N Mueller, Vagisha Sharma, Olga Vitek, Ning Zhang, Ruedi Aebersold, Juli

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 4.07 MB

english, 2008

483

PocketMatch: A new algorithm to compare binding sites in protein structures

Kalidas Yeturu, Nagasuma Chandra

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.15 MB

english, 2008

484

AnEnPi: identification and annotation of analogous enzymes

Thomas D Otto, Carolina R Ana Guimarães, Wim M Degrave, Antonio B de Miranda

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 424 KB

english, 2008

485

Examining the significance of fingerprint-based classifiers

Brian T Luke, Jack R Collins

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 326 KB

english, 2008

486

Barcodes for genomes and applications

Fengfeng Zhou, Victor Olman, Ying Xu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.00 MB

english, 2008

487

Prediction of regulatory elements in mammalian genomes using chromatin signatures

Kyoung-Jae Won, Iouri Chepelev, Bing Ren, Wei Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.34 MB

english, 2008

488

GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed

Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J Butte

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 284 KB

english, 2008

489

nGASP – the nematode genome annotation assessment project

Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, the nGASP Consortium, Lincoln D Stein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.81 MB

english, 2008

490

Designing multiple degenerate primers via consecutive pairwise alignments

Hamed Shateri Najafabadi, Noorossadat Torabi, Mahmood Chamankhah

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 711 KB

english, 2008

491

Pathological rate matrices: from primates to pathogens

Harold W Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A Huttley

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 595 KB

english, 2008

492

Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network

Matteo Brilli, Alessio Mengoni, Marco Fondi, Marco Bazzicalupo, Pietro Liò, Renato Fani

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.47 MB

english, 2008

493

GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments

Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan Küntzer, Oliver Kohlbacher, Michael Kaufmann, Hans-Peter Lenhof

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 656 KB

english, 2008

494

Prediction of protein-protein binding site by using core interface residue and support vector machine

Nan Li, Zhonghua Sun, Fan Jiang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 498 KB

english, 2008

495

RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays

Romesh Stanislaus, Mark Carey, Helena F Deus, Kevin Coombes, Bryan T Hennessy, Gordon B Mills, Jonas S Almeida

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 885 KB

english, 2008

496

The meaning of alignment: lessons from structural diversity

Walter Pirovano, K Anton Feenstra, Jaap Heringa

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.53 MB

english, 2008

497

SimHap GUI: An intuitive graphical user interface for genetic association analysis

Kim W Carter, Pamela A McCaskie, Lyle J Palmer

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 486 KB

english, 2008

498

SPRINT: A new parallel framework for R

Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M Sloan, Florian Scharinger, Arthur Trew, Peter Ghazal

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 280 KB

english, 2008

499

A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data

Chang Sik Kim, Cheol Soo Bae, Hong Joon Tcha

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.50 MB

english, 2008

500

Gene function prediction using labeled and unlabeled data

Xing-Ming Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 371 KB

english, 2008

501

Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures

Chih-Hung Jen, Tsun-Po Yang, Chien-Yi Tung, Shu-Han Su, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 591 KB

english, 2008

502

Identification of biomarkers for genotypingAspergilliusing non-linear methods for clustering and classification

Irene Kouskoumvekaki, Zhiyong Yang, Svava Ó Jónsdóttir, Lisbeth Olsson, Gianni Panagiotou

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 713 KB

english, 2008

503

Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

Jean-François Taly, Antoine Marin, Jean-François Gibrat

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 3.14 MB

english, 2008

504

Inferring gene expression dynamics via functional regression analysis

Hans-Georg Müller, Jeng-Min Chiou, Xiaoyan Leng

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 644 KB

english, 2008

505

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities

Usman Roshan, Satish Chikkagoudar, Dennis R Livesay

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 341 KB

english, 2008

506

VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens

Aarti Garg, Dinesh Gupta

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 727 KB

english, 2008

507

Meta-analysis of breast cancer microarray studies in conjunction with conservedcis-elements suggest patterns for coordinate regulation

David D Smith, Pål Sætrom, Ola Snøve, Cathryn Lundberg, Guillermo E Rivas, Carlotta Glackin, Garrett P Larson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 491 KB

english, 2008

508

CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions

Woochang Hwang, Young-Rae Cho, Aidong Zhang, Murali Ramanathan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 368 KB

english, 2008

509

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)

Pere Puigbò, Ignacio G Bravo, Santiago Garcia-Vallvé

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 271 KB

english, 2008

510

Validation of protein models by a neural network approach

Paolo Mereghetti, Maria Luisa Ganadu, Elena Papaleo, Piercarlo Fantucci, Luca De Gioia

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 327 KB

english, 2008

511

VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays

Hans A Kestler, André Müller, Johann M Kraus, Malte Buchholz, Thomas M Gress, Hongfang Liu, David W Kane, Barry R Zeeberg, John N Weinstein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.29 MB

english, 2008

512

The strength of co-authorship in gene name disambiguation

Richárd Farkas

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 269 KB

english, 2008

513

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information

Michelle N Knowlton, Tongbin Li, Yongliang Ren, Brent R Bill, Lynda BM Ellis, Stephen C Ekker

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.09 MB

english, 2008

514

GraphCrunch: A tool for large network analyses

Tijana Milenković, Jason Lai, Nataša Pržulj

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 615 KB

english, 2008

515

PEPOP: Computational design of immunogenic peptides

Violaine Moreau, Cécile Fleury, Dominique Piquer, Christophe Nguyen, Nicolas Novali, Sylvie Villard, Daniel Laune, Claude Granier, Franck Molina

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.78 MB

english, 2008

516

Subfamily specific conservation profiles for proteins based on n-gram patterns

John K Vries, Xiong Liu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 487 KB

english, 2008

517

SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 414 KB

english, 2008

518

Towards an automatic classification of protein structural domains based on structural similarity

Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-Francois Gibrat, Byungkook Lee, Peter J Munson

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.36 MB

english, 2008

519

Rank-based edge reconstruction for scale-free genetic regulatory networks

Guanrao Chen, Peter Larsen, Eyad Almasri, Yang Dai

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 563 KB

english, 2008

520

Response projected clustering for direct association with physiological and clinical response data

Sung-Gon Yi, Taesung Park, Jae K Lee

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 874 KB

english, 2008

521

AWclust: point-and-click software for non-parametric population structure analysis

Xiaoyi Gao, Joshua D Starmer

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 449 KB

english, 2008

522

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner, Helen L Johnson, Philip V Ogren, K Bretonnel Cohen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 543 KB

english, 2008

523

Ori-Finder: A web-based system for findingoriCs in unannotated bacterial genomes

Feng Gao, Chun-Ting Zhang

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 779 KB

english, 2008

524

A novel method for high accuracy sumoylation site prediction from protein sequences

Jialin Xu, Yun He, Boqin Qiang, Jiangang Yuan, Xiaozhong Peng, Xian-Ming Pan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 616 KB

english, 2008

525

ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization

Wen-Lin Huang, Chun-Wei Tung, Shih-Wen Ho, Shiow-Fen Hwang, Shinn-Ying Ho

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 641 KB

english, 2008

526

Visualizing and clustering high throughput sub-cellular localization imaging

Nicholas A Hamilton, Rohan D Teasdale

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 844 KB

english, 2008

527

A comparison of common programming languages used in bioinformatics

Mathieu Fourment, Michael R Gillings

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 273 KB

english, 2008

528

The VirusBanker database uses a Java program to allow flexible searching throughBunyaviridaesequences

Mathieu Fourment, Mark J Gibbs

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 696 KB

english, 2008

529

OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

Laura I Furlong, Holger Dach, Martin Hofmann-Apitius, Ferran Sanz

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 961 KB

english, 2008

530

Statistical issues in the analysis of Illumina data

Mark J Dunning, Nuno L Barbosa-Morais, Andy G Lynch, Simon Tavaré, Matthew E Ritchie

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.78 MB

english, 2008

531

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology

Frédéric Chalmel, Michael Primig

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.07 MB

english, 2008

532

Building pathway clusters from Random Forests classification using class votes

Herbert Pang, Hongyu Zhao

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 775 KB

english, 2008

533

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Jos H Beijnen, Marcel JT Reinders, Lodewyk FA Wessels

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 378 KB

english, 2008

534

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

Ana C Casimiro, Susana Vinga, Ana T Freitas, Arlindo L Oliveira

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 510 KB

english, 2008

535

SCOWLP classification: Structural comparison and analysis of protein binding regions

Joan Teyra, Maciej Paszkowski-Rogacz, Gerd Anders, M Teresa Pisabarro

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 945 KB

english, 2008

536

Modularization of biochemical networks based on classification of Petri net t-invariants

Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 859 KB

english, 2008

537

Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset

Cédric Auliac, Vincent Frouin, Xavier Gidrol, Florence d'Alché-Buc

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.20 MB

english, 2008

538

Microarray data mining using landmark gene-guided clustering

Pankaj Chopra, Jaewoo Kang, Jiong Yang, HyungJun Cho, Heenam Stanley Kim, Min-Goo Lee

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.03 MB

english, 2008

539

Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons

Sacha AFT van Hijum, Richard JS Baerends, Aldert L Zomer, Harma A Karsens, Victoria Martin-Requena, Oswaldo Trelles, Jan Kok, Oscar P Kuipers

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 753 KB

english, 2008

540

Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction

Ching-Wai Tan, David T Jones

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 478 KB

english, 2008

541

Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence

Anke Batsch, Andrea Noetel, Christian Fork, Anita Urban, Daliborka Lazic, Tina Lucas, Julia Pietsch, Andreas Lazar, Edgar Schömig, Dirk Gründemann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 361 KB

english, 2008

542

High-throughput bioinformatics with the Cyrille2 pipeline system

Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Joost CW de Groot, Roeland CHJ van Ham

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 572 KB

english, 2008

543

Using a logical model to predict the growth of yeast

KE Whelan, RD King

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 574 KB

english, 2008

544

Statistical methodology for the analysis of dye-switch microarray experiments

Tristan Mary-Huard, Julie Aubert, Nadera Mansouri-Attia, Olivier Sandra, Jean-Jacques Daudin

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 402 KB

english, 2008

545

A perspective for biomedical data integration: Design of databases for flow cytometry

John Drakos, Marina Karakantza, Nicholas C Zoumbos, John Lakoumentas, George C Nikiforidis, George C Sakellaropoulos

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 982 KB

english, 2008

546

Protein structure search and local structure characterization

Shih-Yen Ku, Yuh-Jyh Hu

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.40 MB

english, 2008

547

Automatic detection of exonic splicing enhancers (ESEs) using SVMs

Britta Mersch, Alexander Gepperth, Sándor Suhai, Agnes Hotz-Wagenblatt

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 743 KB

english, 2008

548

Clustering cancer gene expression data: a comparative study

Marcilio CP de Souto, Ivan G Costa, Daniel SA de Araujo, Teresa B Ludermir, Alexander Schliep

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.08 MB

english, 2008

549

Clustering exact matches of pairwise sequence alignments by weighted linear regression

Alvaro J González, Li Liao

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 625 KB

english, 2008

550

Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data

Sudhakar Jonnalagadda, Rajagopalan Srinivasan

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.20 MB

english, 2008

551

Inferring modules of functionally interacting proteins using the Bond Energy Algorithm

Ryosuke LA Watanabe, Enrique Morett, Edgar E Vallejo

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 418 KB

english, 2008

552

Assessing probe-specific dye and slide biases in two-color microarray data

Ruixiao Lu, Geun-Cheol Lee, Michael Shultz, Chris Dardick, Kihong Jung, Jirapa Phetsom, Yi Jia, Robert H Rice, Zelanna Goldberg, Patrick S Schnable, Pamela Ronald, David M Rocke

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.08 MB

english, 2008

553

Combining classifiers for improved classification of proteins from sequence or structure

Iain Melvin, Jason Weston, Christina S Leslie, William S Noble

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 289 KB

english, 2008

554

Prediction of TF target sites based on atomistic models of protein-DNA complexes

Vladimir Espinosa Angarica, Abel González Pérez, Ana T Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 703 KB

english, 2008

555

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

Florian Meereis, Michael Kaufmann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 256 KB

english, 2008

556

ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family

Alberto I Roca, Albert E Almada, Aaron C Abajian

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

557

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder, Steve Horvath

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.73 MB

english, 2008

558

Evaluation of two methods for computational HLA haplotypes inference using a real dataset

Bruno F Bettencourt, Margarida R Santos, Raquel N Fialho, Ana R Couto, Maria J Peixoto, João P Pinheiro, Hélder Spínola, Marian G Mora, Cristina Santos, António Brehm, Jácome Bruges-Armas

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 307 KB

english, 2008

559

CoCoNUT: an efficient system for the comparison and analysis of genomes

Abouelhoda, Mohamed I, Kurtz, Stefan, Ohlebusch, Enno

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.12 MB

english, 2008

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