BIOINFORMATICS
Genome Assembly/Sequencing id number >>
Section Editor: Adam Kuspa, Baylor College of Medicine, Texas, USA
Contig mapping and analysis - Asim Siddiqui, Steven Jones
Algorithmic challenges in mammalian whole-genome assembly - Serafim Batzoglou
Genome signals and assembly - Marek Kimmel
Microbial sequence assembly - George Weinstock
Statistical signals - Samuel Karlin, Andrew J. Gentles
Comparative analysis for mapping and sequence assembly - Aleksandar Milosavljevic
Errors in sequence assembly and corrections - Martti T. Tammi, Björn Andersson
Repeatfinding - Richard Sucgang
Algorithms for sequence errors - Björn Andersson , Martti T. Tammi
Genome maps and their use in sequence assembly - Paul H. Dear
Polymorphism and sequence assembly - Brinda K. Rana, Douglas W. Smith, Nicholas J. Schork
Gene Finding/Gene Structure id number >>
Section Editor: Steven L. Salzberg, University of Maryland, Maryland, USA
Graphs and metrics - Andreas Dress
Prokaryotic gene identification in silico - Mark Borodovsky, Rajeev Azad
Eukaryotic gene finding - Roderic Guigó
Information theory as a model of genomic sequences - Chengpeng Bi, Peter K. Rogan
Spliced alignment - Xiaoqiu Huang
Pair hidden markov models - Lior Pachter, Marina Alexandersson, Nicolas Bray
Searching for genes and biologically related signals in DNA sequences - Mihaela Pertea
Promoter prediction - Vladimir B. Bajic, Thomas Werner
Gene structure prediction in plant genomes - Volker Brendel
Alternative splicing in humans - John G. Conboy, Inna Dubchak
Operon finding in bacteria - Maria D. Ermolaeva
Eukaryotic regulatory sequences - Mathias Krull, Edgar Wingender
Exonic splicing enhancers and exonic splicing silencers - Stephen M. Mount
Gene finding using multiple related species: a classification approach - Manolis Kellis
Dynamic programming for gene finders - William H. Majoros
Gene structure prediction by genomic sequence alignment - Burkhard Morgenstern
Computational motif discovery - Martin Tompa
Protein Function and Annotation id number >>
Section Editor: L Aravind , National Institutes of Health, Bethesda, USA
In silico approaches to functional analysis of proteins - L. Aravind
Protein domains in eukaryotic signal transduction systems - Kay Hofmann
Contextual inference of protein function - Aswin Sai Narain Seshasayee, M. Madan Babu
Protein repeats - Carolina Perez-Iratxeta, Miguel A. Andrade
Large-scale protein annotation - Sarah K. Kummerfeld
Measuring evolutionary constraints as protein properties reflecting underlying mechanisms - Andrew F. Neuwald, Jun S. Liu
Sequence complexity of proteins and its significance in annotation - Birgit Eisenhaber, Frank Eisenhaber
Large-scale, classification-driven, rule-based functional annotation of proteins - C. R. Vinayaka, Cathy H. Wu, Darren A. Natale
Signal peptides and protein localization prediction - Henrik Nielsen
IMPALA/RPS-BLAST/PSI-BLAST in protein sequence analysis - Yuri I. Wolf
Transmembrane topology prediction - Lukas Käll, Erik Sonnhammer
Comparative Analysis and Phylogeny id number >>
Section Editor: Harris Lewin, Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, USA
Phylogenetic profiling - Matteo Pellegrini, Sorel T. Fitz-Gibbon, Todd O. Yeates, David Eisenberg
The domains of life and their evolutionary implications - C. R. Woese
Evolution of regulatory pathways - Amelie Veron, Erich Bornberg-Bauer
Reconstructing vertebrate phylogenetic trees - Sudhir Kumar, Alan Filipski
Phylogenomics for studies of microbial evolution - Hans-Henrik Fuxelius, Siv G. E. Andersson
Phylogenetic analysis of BLAST results - Fiona S. L. Brinkman
Phylogenomic approaches to bacterial phylogeny - Vincent Daubin
Mapping mutations on phylogenies - Rasmus Nielsen
Chromosome phylogeny - Guillaume Bourque
Connecting genes by comparative genomics - Itai Yanai
Computational Methods for High Throughput Genetic Analysis id number >>
Section Editor: John Quackenbush, Harvard School of Public Health, Massachusetts, USA
Mass spectrometry and computational proteomics - Vineet Bafna, Knut Reinert
Integrating statistical approaches in experimental design and data analysis - Ernst Wit, Raya Khanin
Algorithms for gene expression analysis - Alvis Brazma, Aedín C. Culhane
Experimental design - Kevin K. Dobbin, Richard M. Simon
Mass spectrometric data mining for protein sequences - Christian Cole, Patrick J. Lester, Simon J. Hubbard
Differential expression with the bioconductor project - Anja von Heydebreck, Wolfgang Huber, Robert Gentleman
Statistical methods for gene expression analysis - Shibing Deng, Tzu-Ming Chu, Young K. Truong, Russ D. Wolfinger
Data standardisation and the HUPO proteomics standards initiative - Rolf Apweiler
Extracting networks from expression data - Eleftherios T. Papoutsakis, Vassily Hatzimanikatis
A comparsion of existing tools for ontological analysis of gene expression data - Purvesh Khatri, Sorin Draghici
CGH data analysis - Adam A Margolin, Barbara L Weber, Joel Greshock
Low-level analysis of oligonucleotide expression arrays - Cheng Li, Wing Hung Wong, Xuemin Fang
Relevance networks - Atul J. Butte
Error models for microarray intensities - Anja von Heydebreck, Martin Vingron, Wolfgang Huber
Comparative Methods for Structural Analysis and Prediction id number >>
Section Editor: William Ramsay Taylor, National Institute for Medical Research, London, UK
Analysis and prediction of membrane protein structure - Tina A. Eyre, Linda Partridge, Janet M. Thornton
Protein structure analysis and prediction - William R. Taylor
Ab-initio structure prediction - David Baker
Score functions for structure prediction - Richard A. Goldstein
Protein domains - Jaap Heringa
Complexity in biological structures and systems - Arthur M. Lesk
Modeling by homology - Kenji Mizuguchi
The Protein Data Bank (PDB) and the Worldwide PDB http://www.wwpdb.org - Helen Berman, Haruki Nakamura, Kim Henrick
Threading for protein-fold recognition - Kuang Lin
CASP - Krzysztof Fidelis
Molecular simulations in structure prediction - Franca Fraternali, Jens Kleinjung
Protein structure comparison - Liisa Holm
Secondary structure prediction - Ching Wai Tan, David T. Jones
DNA/protein modeling - Richard Lavery
Modeling tertiary structure of RNA - Benoît Masquida, Eric Westhof
Structuring and Integrating Data id number >>
Section Editor: Russ B. Altman, Stanford University, USA
Introduction to ontologies in biomedicine: from powertools to assistants - Russ B. Altman
The Gene Ontology project - Midori A. Harris, Jane Lomax, Amelia Ireland, Jennifer I. Clark
Ontologies for information retrieval - William Richard Hersh
Unified Medical Language System and associated vocabularies - Christopher G. Chute
Ontologies for natural language processing - Yves A. Lussier
Ontologies for the life sciences - Steffen Schulze-Kremer, Barry Smith
TAMBIS: transparent access to multiple bioinformatics services - Robert Stevens, Norman W. Paton, Sean Bechhofer, Gary Ng, Martin Peim, Patricia Baker, Carole Goble, Andy Brass
Bioinformatics pathway representations, databases, and algorithms - Peter D. Karp
Automatic concept identification in biomedical literature - William H. Majoros
Merging and comparing ontologies - Natalya F. Noy
Ontologies for three-dimensional molecular structure - John Westbrook, Helen M. Berman
Proteomics data representation and management - Norman W. Paton, Andrew Jones, Stephen G. Oliver
Description logics: OWL and DAML + OIL - Phillip Lord, Robert D. Stevens, Carole A. Goble, Ian Horrocks
Frame-based systems: Protégé - Iwei Yeh
Modern Programming Paradigms in Biology id number >>
Section Editor: Peter Clote, Boston College, Massachusetts, USA
Integrated bioinformatics software at NCBI - Fabrizio Ferre
Detecting protein homology using NCBI tools - Wayne T. Matten, Scott D. McGinnis
Hidden Markov models and neural networks - Stefan C. Kremer, Pierre Baldi
Threading algorithms - Jadwiga Bienkowska, Rick Lathrop
Bioconductor: software and development strategies for statistical genomics - Robert Gentleman, Vincent Carey
Ensembl and UniProt (Swiss-Prot) - David Jackson, Reinhard Schneider
RNA secondary structure prediction - David H. Mathews, Michael Zuker
Acedb genome database - Richard Durbin, Edward Griffiths
The MATLAB bioinformatics toolbox - Robert Henson, Lucio Cetto
Design of KEGG and GO - Minoru Kanehisa
Simulation of biochemical networks - Andrzej M. Kierzek
Using the Python programming language for bioinformatics - Michel F. Sanner
Gibbs sampling and bioinformatics - Xiaole Shirley Liu
Perl in bioinformatics - Michael Gribskov, R. Hannes Niedner, T. Murlidharan Nair
Applications of RNA minimum free energy computations - Peter Clote
Cluster architecture - Chris Dagdigian
Relational databases in bioinformatics - Hans-Peter Kriegel, Peer Kröger, Stefan Schönauer
Support vector machine software - William Stafford Noble
A brief Perl tutorial for bioinformatics - Michael J. Moorhouse
Brief Python tutorial for bioinformatics - Michael Poidinger