Volume 3; Issue 1

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BMC Bioinformatics
Volume 3; Issue 1

BMC Bioinformatics

Volume 3; Issue 1

1

Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach

Kevin Truong, Mitsuhiko Ikura

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 845 KB

english, 2002

2

RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited – bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure

Janusz M Bujnicki, Leszek Rychlewski

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 874 KB

english, 2002

3

Homology Induction: the use of machine learning to improve sequence similarity searches

Andreas Karwath, Ross D King

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 383 KB

english, 2002

4

CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes

Nikhat Zafar, Raja Mazumder, Donald Seto

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 500 KB

english, 2002

5

NBLAST: a cluster variant of BLAST for NxN comparisons

Michel Dumontier, Christopher WV Hogue

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 206 KB

english, 2002

6

RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

Christian M Zmasek, Sean R Eddy

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 461 KB

english, 2002

7

The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction

Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V Madabusi, Kirsten M Müller, Nupur Pande, Zhidi Shang, Nan Yu, Robin R G

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 136 KB

english, 2002

8

Identifying functional relationships among human genes by systematic analysis of biological literature

Yong-Chuan Tao, Rudolph L Leibel

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 304 KB

english, 2002

9

The limit fold change model: A practical approach for selecting differentially expressed genes from microarray data

David M Mutch, Alvin Berger, Robert Mansourian, Andreas Rytz, Matthew-Alan Roberts

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 460 KB

english, 2002

10

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 434 KB

english, 2002

11

Visualizing the genome: techniques for presenting human genome data and annotations

Ann E Loraine, Gregg A Helt

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 533 KB

english, 2002

12

The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V Madabusi, Kirsten M Müller, Nupur Pande, Zhidi Shang, Nan Yu, Robin R G

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 1.09 MB

english, 2002

13

Kangaroo – A pattern-matching program for biological sequences

Doron Betel, Christopher WV Hogue

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 258 KB

english, 2002

14

The SGS3 protein involved in PTGS finds a family

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 272 KB

english, 2002

15

Microarray results: how accurate are they?

Ravi Kothapalli, Sean J Yoder, Shrikant Mane, Thomas P Loughran

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 632 KB

english, 2002

16

Computational method for reducing variance with Affymetrix microarrays

Stephen Welle, Andrew I Brooks, Charles A Thornton

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 2.22 MB

english, 2002

17

The functional importance of disease-associated mutation

Sean D Mooney, Teri E Klein

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 246 KB

english, 2002

18

Prediction of MHC class I binding peptides, using SVMHC

Pierre Dönnes, Arne Elofsson

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 296 KB

english, 2002

19

Expression profiling of human renal carcinomas with functional taxonomic analysis

Michael A Gieseg, Theresa Cody, Michael Z Man, Steven J Madore, Mark A Rubin, Eric P Kaldjian

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 821 KB

english, 2002

20

Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region

Hao Chen, Burt M Sharp

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 326 KB

english, 2002

21

Efficient Boolean implementation of universal sequence maps (bUSM)

John Schwacke, Jonas S Almeida

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 378 KB

english, 2002

22

Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis

Christoph K Wierling, Matthias Steinfath, Thorsten Elge, Steffen Schulze-Kremer, Pia Aanstad, Matthew Clark, Hans Lehrach, Ralf Herwig

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 988 KB

english, 2002

23

Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis

Yingyao Zhou, Ruben Abagyan

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 439 KB

english, 2002

24

Computational detection of genomiccis-regulatory modules applied to body patterning in the earlyDrosophilaembryo

Nikolaus Rajewsky, Massimo Vergassola, Ulrike Gaul, Eric D Siggia

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 331 KB

english, 2002

25

Making sense of EST sequences by CLOBBing them

John Parkinson, David B Guiliano, Mark Blaxter

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 293 KB

english, 2002

26

SeqHound: biological sequence and structure database as a platform for bioinformatics research

Katerina Michalickova, Gary D Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin, Christopher WV Hogue

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 342 KB

english, 2002

27

Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs

Rehannah HA Borup, Stefano Toppo, Yi-Wen Chen, Tanya M Teslovich, Gerolamo Lanfranchi, Giorgio Valle, Eric P Hoffman

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 550 KB

english, 2002

28

Automated modelling of signal transduction networks

Martin Steffen, Allegra Petti, John Aach, Patrik D'haeseleer, George Church

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 862 KB

english, 2002

29

FunSpec: a web-based cluster interpreter for yeast

Mark D Robinson, Jörg Grigull, Naveed Mohammad, Timothy R Hughes

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 953 KB

english, 2002

30

Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study

Junbai Wang, Jan Delabie, Hans Christian Aasheim, Erlend Smeland, Ola Myklebost

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 868 KB

english, 2002

31

Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases

Catherine H Schein, Numan Özgün, Tadahide Izumi, Werner Braun

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 1.36 MB

english, 2002

32

Quantifying robustness of biochemical network models

Lan Ma, Pablo A Iglesias

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 443 KB

english, 2002

33

Species-specific protein sequence and fold optimizations

Michel Dumontier, Katerina Michalickova, Christopher WV Hogue

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 506 KB

english, 2002

34

Sources of variability and effect of experimental approach on expression profiling data interpretation

Marina Bakay, Yi-Wen Chen, Rehannah Borup, Po Zhao, Kanneboyina Nagaraju, Eric P Hoffman

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 759 KB

english, 2002

35

ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files

Konrad Büssow, Steve Hoffmann, Volker Sievert

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 229 KB

english, 2002

36

Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes

Stéphanie Bocs, Antoine Danchin, Claudine Médigue

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 441 KB

english, 2002

37

Universal sequence map (USM) of arbitrary discrete sequences

Jonas S Almeida, Susana Vinga

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 849 KB

english, 2002

38

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes

Michele Caselle, Ferdinando Di Cunto, Paolo Provero

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 607 KB

english, 2002

39

tacg – agrepfor DNA

Harry J Mangalam

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 245 KB

english, 2002

40

An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification

Alexander E Pozhitkov, Diethard Tautz

Journal:

BMC Bioinformatics

Year:

2002

Language:

english

File:

PDF, 200 KB

english, 2002