Volume 11; Issue 1 Suppleme

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BMC Bioinformatics
Volume 11; Issue 1 Suppleme

BMC Bioinformatics

Volume 11; Issue 1 Suppleme

1

APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010

Laxmi Parida, Gene Myers

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 128 KB

english, 2010

2

Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.75 MB

english, 2010

3

PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship

Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida, Dongsup Kim

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 619 KB

english, 2010

4

Fast motif recognition via application of statistical thresholds

Christina Boucher, James King

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 492 KB

english, 2010

5

Short clones or long clones? A simulation study on the use of paired reads in metagenomics

Suparna Mitra, Max Schubach, Daniel H Huson

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.19 MB

english, 2010

6

In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase

Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra, Abhijit Datta

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 136 KB

english, 2010

7

Prediction of novel miRNAs and associated target genes inGlycine max

Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu, Gary Stacey

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.67 MB

english, 2010

8

MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees

Suzanne J Matthews, Tiffani L Williams

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.18 MB

english, 2010

9

Classification of protein sequences by means of irredundant patterns

Matteo Comin, Davide Verzotto

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.12 MB

english, 2010

10

Amino acid classification based spectrum kernel fusion for protein subnuclear localization

Suyu Mei, Wang Fei

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 966 KB

english, 2010

11

Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso

Can Yang, Xiang Wan, Qiang Yang, Hong Xue, Weichuan Yu

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 757 KB

english, 2010

12

AntiBP2: improved version of antibacterial peptide prediction

Sneh Lata, Nitish K Mishra, Gajendra PS Raghava

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 759 KB

english, 2010

13

MTar: a computational microRNA target prediction architecture for human transcriptome

Vinod Chandra, Reshmi Girijadevi, Achuthsankar S Nair, Sreenadhan S Pillai, Radhakrishna M Pillai

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.16 MB

english, 2010

14

Integration of multiple data sources to prioritize candidate genes using discounted rating system

Yongjin Li, Jagdish C Patra

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 660 KB

english, 2010

15

Learning to predict expression efficacy of vectors in recombinant protein production

Wen-Ching Chan, Po-Huang Liang, Yan-Ping Shih, Ueng-Cheng Yang, Wen-chang Lin, Chun-Nan Hsu

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.91 MB

english, 2010

16

SFSSClass: an integrated approach for miRNA based tumor classification

Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q Zhang

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 423 KB

english, 2010

17

An ontology-based search engine for protein-protein interactions

Byungkyu Park, Kyungsook Han

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 715 KB

english, 2010

18

HORI: a web server to compute Higher Order Residue Interactions in protein structures

Pandurangan Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 567 KB

english, 2010

19

A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles

Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 3.43 MB

english, 2010

20

Using genomic signatures for HIV-1 sub-typing

Aridaman Pandit, Somdatta Sinha

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.63 MB

english, 2010

21

Genome rearrangements with duplications

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 784 KB

english, 2010

22

Decoding HMMs using thekbest paths: algorithms and applications

Daniel G Brown, Daniil Golod

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 358 KB

english, 2010

23

Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)

Sumeet Agarwal, Candida Vaz, Alok Bhattacharya, Ashwin Srinivasan

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 498 KB

english, 2010

24

Predicting the protein-protein interactions using primary structures with predicted protein surface

Darby Tien-Hao Chang, Yu-Tang Syu, Po-Chang Lin

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.51 MB

english, 2010

25

Heuristics for the inversion median problem

Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M Swenson, Bernard ME Moret

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.69 MB

english, 2010

26

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism

Hiroto Saigo, Masahiro Hattori, Hisashi Kashima, Koji Tsuda

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 984 KB

english, 2010

27

Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network

Yezhou Huang, Shao Li

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.00 MB

english, 2010

28

A weightedq-gram method for glycan structure classification

Limin Li, Wai-Ki Ching, Takako Yamaguchi, Kiyoko F Aoki-Kinoshita

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 213 KB

english, 2010

29

Efficient protein alignment algorithm for protein search

Zaixin Lu, Zhiyu Zhao, Bin Fu

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 996 KB

english, 2010

30

Functional characterization and topological modularity of molecular interaction networks

Jayesh Pandey, Mehmet Koyutürk, Ananth Grama

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.46 MB

english, 2010

31

Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspective

SPT Krishnan, Sim Sze Liang, Bharadwaj Veeravalli

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.51 MB

english, 2010

32

Hit integration for identifying optimal spaced seeds

Won-Hyoung Chung, Seong-Bae Park

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 579 KB

english, 2010

33

Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways

Adi Mano, Tamir Tuller, Oded Béjà, Ron Y Pinter

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 973 KB

english, 2010

34

A hybrid approach to protein folding problem integrating constraint programming with local search

Abu Dayem Ullah, Kathleen Steinhöfel

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 294 KB

english, 2010

35

Better score function for peptide identification with ETD MS/MS spectra

Xiaowen Liu, Baozhen Shan, Lei Xin, Bin Ma

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 533 KB

english, 2010

36

New decoding algorithms for Hidden Markov Models using distance measures on labellings

Daniel G Brown, Jakub Truszkowski

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 518 KB

english, 2010

37

Analysis of interactions between ribosomal proteins and RNA structural motifs

Giovanni Ciriello, Claudio Gallina, Concettina Guerra

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.36 MB

english, 2010

38

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 279 KB

english, 2010

39

Stability analysis of the GAL regulatory network inSaccharomyces cerevisiaeandKluyveromyces lactis

Vishwesh V Kulkarni, Venkatesh Kareenhalli, Pushkar Malakar, Lucy Y Pao, Michael G Safonov, Ganesh A Viswanathan

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1005 KB

english, 2010

40

Structure prediction for the helical skeletons detected from the low resolution protein density map

Kamal Al Nasr, Weitao Sun, Jing He

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.45 MB

english, 2010

41

A novel approach for haplotype-based association analysis using family data

Yixuan Chen, Xin Li, Jing Li

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.65 MB

english, 2010

42

A fast indexing approach for protein structure comparison

Lei Zhang, James Bailey, Arun S Konagurthu, Kotagiri Ramamohanarao

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 882 KB

english, 2010

43

Computational prediction of type III secreted proteins from gram-negative bacteria

Yang Yang, Jiayuan Zhao, Robyn L Morgan, Wenbo Ma, Tao Jiang

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 484 KB

english, 2010

44

Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information

Nitish K Mishra, Gajendra PS Raghava

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 398 KB

english, 2010

45

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

MS Vijayabaskar, Saraswathi Vishveshwara

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.53 MB

english, 2010

46

A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data

Pengyi Yang, Bing B Zhou, Zili Zhang, Albert Y Zomaya

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.38 MB

english, 2010

47

Discrete wavelet transform de-noising in eukaryotic gene splicing

Tina P George, Tessamma Thomas

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.44 MB

english, 2010

48

Comparison of PGH2binding site in prostaglandin synthases

Padmapriya Paragi-Vedanthi, Mukesh Doble

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.33 MB

english, 2010

49

Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm

Chih-Hung Hsieh, Darby Tien-Hao Chang, Cheng-Hao Hsueh, Chi-Yeh Wu, Yen-Jen Oyang

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.43 MB

english, 2010

50

Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway ofMycobacterium tuberculosis

Aarti Garg, Rupinder Tewari, Gajendra PS Raghava

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.31 MB

english, 2010

51

Estimating true evolutionary distances under rearrangements, duplications, and losses

Yu Lin, Vaibhav Rajan, Krister M Swenson, Bernard ME Moret

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 983 KB

english, 2010

52

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Kalidas Yeturu, Tapani Utriainen, Graham JL Kemp, Nagasuma Chandra

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 3.54 MB

english, 2010

53

Active learning for human protein-protein interaction prediction

Thahir P Mohamed, Jaime G Carbonell, Madhavi K Ganapathiraju

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.05 MB

english, 2010

54

Active machine learning for transmembrane helix prediction

Hatice U Osmanbeyoglu, Jessica A Wehner, Jaime G Carbonell, Madhavi K Ganapathiraju

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 657 KB

english, 2010

55

Translog, a web browser for studying the expression divergence of homologous genes

Xianjun Dong, Altuna Akalin, Yogita Sharma, Boris Lenhard

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.00 MB

english, 2010

56

Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique

Nitin Bhardwaj, Mark Gerstein, Hui Lu

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 516 KB

english, 2010

57

A parameter-adaptive dynamic programming approach for inferring cophylogenies

Daniel Merkle, Martin Middendorf, Nicolas Wieseke

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 725 KB

english, 2010

58

NeMo: Network Module identification in Cytoscape

Corban G Rivera, Rachit Vakil, Joel S Bader

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.20 MB

english, 2010

59

An integrative modular approach to systematically predict gene-phenotype associations

Michael R Mehan, Juan Nunez-Iglesias, Chao Dai, Michael S Waterman, Xianghong Jasmine Zhou

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.79 MB

english, 2010

60

Bidirectional best hitr-window gene clusters

Melvin Zhang, Hon Wai Leong

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 525 KB

english, 2010

61

Predicting protein functions by relaxation labelling protein interaction network

Pingzhao Hu, Hui Jiang, Andrew Emili

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 504 KB

english, 2010

62

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data

Ravi Gupta, Priyankara Wikramasinghe, Anirban Bhattacharyya, Francisco A Perez, Sharmistha Pal, Ramana V Davuluri

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 904 KB

english, 2010

63

BayesMotif: de novo protein sorting motif discovery from impure datasets

Jianjun Hu, Fan Zhang

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.64 MB

english, 2010

64

Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy

Anil Sorathiya, Andrea Bracciali, Pietro Liò

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.01 MB

english, 2010

65

Molecular dynamics simulation studies andin vitrosite directed mutagenesis of avian beta-defensin Apl_AvBD2

Soja Saghar Soman, Krishnankutty Chandrika Sivakumar, Easwaran Sreekumar

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 5.70 MB

english, 2010

66

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships

Junhee Seok, Amit Kaushal, Ronald W Davis, Wenzhong Xiao

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 636 KB

english, 2010

67

Prediction of protein structural classes for low-homology sequences based on predicted secondary structure

Jian-Yi Yang, Zhen-Ling Peng, Xin Chen

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 908 KB

english, 2010

68

Reverse engineering gene regulatory network from microarray data using linear time-variant model

Mitra Kabir, Nasimul Noman, Hitoshi Iba

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.48 MB

english, 2010