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Previous Next 		Contents: Volume 24, Number 13, 1 July 2008   [Index by Author] 
Down ISMB 2008 CONFERENCE PROCEEDINGS 19-23 JULY 2008, TORONTO
     EDITORIALS
     ORIGINAL PAPERS
         SEQUENCE ANALYSIS AND ALIGNMENT
         COMPARATIVE GENOMICS
         EVOLUTION AND PHYLOGENY
         GENE REGULATION AND TRANSCRIPTOMICS
         PROTEIN STRUCTURE AND FUNCTION
         PROTEIN INTERACTIONS AND MOLECULAR NETWORKS
         TEXT MINING
         DATABASES AND ONTOLOGIES
         OTHER BIOINFORMATICS APPLICATIONS AND METHODS
         BIOINFORMATICS OF DISEASE
     AUTHOR INDEX
     OTHER BIOINFORMATICS APPLICATIONS AND METHODS
Down ORIGINAL PAPERS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down APPLICATIONS NOTE
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down ERRATUM
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ISMB 2008 CONFERENCE PROCEEDINGS 19-23 JULY 2008, TORONTO Back

EDITORIALS Back

Alfonso Valencia and Ildefonso Cases
Editorial
Bioinformatics 2008 24: i1; doi:10.1093/bioinformatics/btn204 [Extract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

ISMB 2008 Organization
Bioinformatics 2008 24: i2-i5; doi:10.1093/bioinformatics/btn304 [Extract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS Back

SEQUENCE ANALYSIS AND ALIGNMENT Back

Sören Sonnenburg, Alexander Zien, Petra Philips, and Gunnar Rätsch
POIMs: positional oligomer importance matrices—understanding support vector machine-based signal detectors
Bioinformatics 2008 24: i6-i14; doi:10.1093/bioinformatics/btn170 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Aleksandar Stojmirovic, E. Michael Gertz, Stephen F. Altschul, and Yi-Kuo Yu
The effectiveness of position- and composition-specific gap costs for protein similarity searches
Bioinformatics 2008 24: i15-i23; doi:10.1093/bioinformatics/btn171 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Thomas Abeel, Yvan Saeys, Pierre Rouzé, and Yves Van de Peer
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
Bioinformatics 2008 24: i24-i31; doi:10.1093/bioinformatics/btn172 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Iman Hajirasouliha, Fereydoun Hormozdiari, S. Cenk Sahinalp, and Inanc Birol
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies
Bioinformatics 2008 24: i32-i40; doi:10.1093/bioinformatics/btn173 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, and Michal Linial
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
Bioinformatics 2008 24: i41-i49; doi:10.1093/bioinformatics/btn174 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Yunpen Xu, Xuefeng Zhou, and Weixiong Zhang
MicroRNA prediction with a novel ranking algorithm based on random walks
Bioinformatics 2008 24: i50-i58; doi:10.1093/bioinformatics/btn175 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Seunghak Lee, Elango Cheran, and Michael Brudno
A robust framework for detecting structural variations in a genome
Bioinformatics 2008 24: i59-i67; doi:10.1093/bioinformatics/btn176 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Chuong B. Do, Chuan-Sheng Foo, and Serafim Batzoglou
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
Bioinformatics 2008 24: i68-i76; doi:10.1093/bioinformatics/btn177 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

COMPARATIVE GENOMICS Back

Simon Wong and Mark A. Ragan
MACHOS: Markov clusters of homologous subsequences
Bioinformatics 2008 24: i77-i85; doi:10.1093/bioinformatics/btn144 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Jun Liu, Sanjay Ranka, and Tamer Kahveci
Classification and feature selection algorithms for multi-class CGH data
Bioinformatics 2008 24: i86-i95; doi:10.1093/bioinformatics/btn145 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Chunfang Zheng, Qian Zhu, Zaky Adam, and David Sankoff
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes
Bioinformatics 2008 24: i96-i104; doi:10.1093/bioinformatics/btn146 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Minzhu Xie, Jianxin Wang, and Jianer Chen
A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors
Bioinformatics 2008 24: i105-i113; doi:10.1093/bioinformatics/btn147 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

EVOLUTION AND PHYLOGENY Back

Yu Lin and Bernard M.E. Moret
Estimating true evolutionary distances under the DCJ model
Bioinformatics 2008 24: i114-i122; doi:10.1093/bioinformatics/btn148 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

C. Than, R. Sugino, H. Innan, and L. Nakhleh
Efficient inference of bacterial strain trees from genome-scale multilocus data
Bioinformatics 2008 24: i123-i131; doi:10.1093/bioinformatics/btn149 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Mukul S. Bansal and Oliver Eulenstein
The multiple gene duplication problem revisited
Bioinformatics 2008 24: i132-i138; doi:10.1093/bioinformatics/btn150 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENE REGULATION AND TRANSCRIPTOMICS Back

Moran Yassour, Tommy Kaplan, Ariel Jaimovich, and Nir Friedman
Nucleosome positioning from tiling microarray data
Bioinformatics 2008 24: i139-i146; doi:10.1093/bioinformatics/btn151 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Tien-ho Lin, Naftali Kaminski, and Ziv Bar-Joseph
Alignment and classification of time series gene expression in clinical studies
Bioinformatics 2008 24: i147-i155; doi:10.1093/bioinformatics/btn152 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Ivan G. Costa, Stefan Roepcke, Christoph Hafemeister, and Alexander Schliep
Inferring differentiation pathways from gene expression
Bioinformatics 2008 24: i156-i164; doi:10.1093/bioinformatics/btn153 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Lucas D. Ward and Harmen J. Bussemaker
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
Bioinformatics 2008 24: i165-i171; doi:10.1093/bioinformatics/btn154 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

T.A. Knijnenburg, L.F.A. Wessels, and M.J.T. Reinders
Combinatorial influence of environmental parameters on transcription factor activity
Bioinformatics 2008 24: i172-i181; doi:10.1093/bioinformatics/btn155 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

PROTEIN STRUCTURE AND FUNCTION Back

Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, and Ming Li
Designing succinct structural alphabets
Bioinformatics 2008 24: i182-i189; doi:10.1093/bioinformatics/btn165 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio
Predicting protein thermostability changes from sequence upon multiple mutations
Bioinformatics 2008 24: i190-i195; doi:10.1093/bioinformatics/btn166 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Ivelin Georgiev, Daniel Keedy, Jane S. Richardson, David C. Richardson, and Bruce R. Donald
Algorithm for backrub motions in protein design
Bioinformatics 2008 24: i196-i204; doi:10.1093/bioinformatics/btn169 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Fei Xiong, Gopal Pandurangan, and Chris Bailey-Kellogg
Contact replacement for NMR resonance assignment
Bioinformatics 2008 24: i205-i213; doi:10.1093/bioinformatics/btn167 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Menachem Fromer and Chen Yanover
A computational framework to empower probabilistic protein design
Bioinformatics 2008 24: i214-i222; doi:10.1093/bioinformatics/btn168 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

PROTEIN INTERACTIONS AND MOLECULAR NETWORKS Back

Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, and Tobias Müller
Identifying functional modules in protein–protein interaction networks: an integrated exact approach
Bioinformatics 2008 24: i223-i231; doi:10.1093/bioinformatics/btn161 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, and Minoru Kanehisa
Prediction of drug–target interaction networks from the integration of chemical and genomic spaces
Bioinformatics 2008 24: i232-i240; doi:10.1093/bioinformatics/btn162 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, and S. Cenk Sahinalp
Biomolecular network motif counting and discovery by color coding
Bioinformatics 2008 24: i241-i249; doi:10.1093/bioinformatics/btn163 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, and Ziv Bar-Joseph
Protein complex identification by supervised graph local clustering
Bioinformatics 2008 24: i250-i268; doi:10.1093/bioinformatics/btn164 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

TEXT MINING Back

Thomas J. Lee, Ian Paulsen, and Peter Karp
Annotation-based inference of transporter function
Bioinformatics 2008 24: i259-i267; doi:10.1093/bioinformatics/btn180 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, and Christoph M. Friedrich
Detection of IUPAC and IUPAC-like chemical names
Bioinformatics 2008 24: i268-i276; doi:10.1093/bioinformatics/btn181 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Arzucan Özgür, Thuy Vu, Günes Erkan, and Dragomir R. Radev
Identifying gene-disease associations using centrality on a literature mined gene-interaction network
Bioinformatics 2008 24: i277-i285; doi:10.1093/bioinformatics/btn182 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Chun-Nan Hsu, Yu-Ming Chang, Cheng-Ju Kuo, Yu-Shi Lin, Han-Shen Huang, and I-Fang Chung
Integrating high dimensional bi-directional parsing models for gene mention tagging
Bioinformatics 2008 24: i286-i294; doi:10.1093/bioinformatics/btn183 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES Back

Larisa N. Soldatova, Wayne Aubrey, Ross D. King, and Amanda Clare
The EXACT description of biomedical protocols
Bioinformatics 2008 24: i295-i303; doi:10.1093/bioinformatics/btn156 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Kenneth McLeod and Albert Burger
Towards the use of argumentation in bioinformatics: a gene expression case study
Bioinformatics 2008 24: i304-i312; doi:10.1093/bioinformatics/btn157 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Stefan Schulz, Holger Stenzhorn, and Martin Boeker
The ontology of biological taxa
Bioinformatics 2008 24: i313-i321; doi:10.1093/bioinformatics/btn158 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Frédéric Lemoine, Bernard Labedan, and Christine Froidevaux
GenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics 2008 24: i322-i329; doi:10.1093/bioinformatics/btn159 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

OTHER BIOINFORMATICS APPLICATIONS AND METHODS Back

C. Huttenhower and O.G. Troyanskaya
Assessing the functional structure of genomic data
Bioinformatics 2008 24: i330-i338; doi:10.1093/bioinformatics/btn160 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Sean McIlwain, David Page, Edward L. Huttlin, and Michael R. Sussman
Matching isotopic distributions from metabolically labeled samples
Bioinformatics 2008 24: i339-i347; doi:10.1093/bioinformatics/btn190 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, and William Stafford Noble
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification
Bioinformatics 2008 24: i348-i356; doi:10.1093/bioinformatics/btn189 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Pierre Baldi and Ryan W. Benz
BLASTing small molecules—statistics and extreme statistics of chemical similarity scores
Bioinformatics 2008 24: i357-i365; doi:10.1093/bioinformatics/btn187 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Yiqun Cao, Tao Jiang, and Thomas Girke
A maximum common substructure-based algorithm for searching and predicting drug-like compounds
Bioinformatics 2008 24: i366-i374; doi:10.1093/bioinformatics/btn186 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Franck Rapaport, Emmanuel Barillot, and Jean-Philippe Vert
Classification of arrayCGH data using fused SVM
Bioinformatics 2008 24: i375-i382; doi:10.1093/bioinformatics/btn188 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

BIOINFORMATICS OF DISEASE Back

Ashley Vaughan, Sum-Ying Chiu, Gowthaman Ramasamy, Ling Li, Malcolm J. Gardner, Alice S. Tarun, Stefan H.I. Kappe, and Xinxia Peng
Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis
Bioinformatics 2008 24: i383-i389; doi:10.1093/bioinformatics/btn140 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Joshua W.K. Ho, Maurizio Stefani, Cristobal G. dos Remedios, and Michael A. Charleston
Differential variability analysis of gene expression and its application to human diseases
Bioinformatics 2008 24: i390-i398; doi:10.1093/bioinformatics/btn142 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Michal Rosen-Zvi, Andre Altmann, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, and Thomas Lengauer
Selecting anti-HIV therapies based on a variety of genomic and clinical factors
Bioinformatics 2008 24: i399-i406; doi:10.1093/bioinformatics/btn141 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Yuan Wang, Xiaobo Zhou, Honghui Wang, King Li, Lixiu Yao, and Stephen T.C. Wong
Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model
Bioinformatics 2008 24: i407-i413; doi:10.1093/bioinformatics/btn143 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

AUTHOR INDEX Back

Author Index
Bioinformatics 2008 24: i414-i415; doi:10.1093/bioinformatics/btn303 [Extract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

OTHER BIOINFORMATICS APPLICATIONS AND METHODS Back

Nuno Bandeira, Jesper V. Olsen, Matthias Mann, and Pavel A. Pevzner
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
Bioinformatics 2008 24: i416-i423; doi:10.1093/bioinformatics/btn184 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS Back

SEQUENCE ANALYSIS Back

John A. Capra and Mona Singh
Characterization and prediction of residues determining protein functional specificity
Bioinformatics Advance Access published on May 1, 2008
Bioinformatics 2008 24: 1473-1480; doi:10.1093/bioinformatics/btn214 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

PHYLOGENETICS Back

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló, and Gabriel Valiente
A distance metric for a class of tree-sibling phylogenetic networks
Bioinformatics Advance Access published on May 12, 2008
Bioinformatics 2008 24: 1481-1488; doi:10.1093/bioinformatics/btn231 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS Back

Jiangning Song, Hao Tan, Kazuhiro Takemoto, and Tatsuya Akutsu
HSEpred: predict half-sphere exposure from protein sequences
Bioinformatics Advance Access published on May 8, 2008
Bioinformatics 2008 24: 1489-1497; doi:10.1093/bioinformatics/btn222 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

István A. Bogdán, Jenny Rivers, Robert J. Beynon, and Daniel Coca
High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting
Bioinformatics Advance Access published on May 3, 2008
Bioinformatics 2008 24: 1498-1502; doi:10.1093/bioinformatics/btn216 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Bobbie-Jo M. Webb-Robertson, William R. Cannon, Christopher S. Oehmen, Anuj R. Shah, Vidhya Gurumoorthi, Mary S. Lipton, and Katrina M. Waters
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
Bioinformatics Advance Access published on May 3, 2008
Bioinformatics 2008 24: 1503-1509; doi:10.1093/bioinformatics/btn218 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Mattia Zampieri, Nicola Soranzo, and Claudio Altafini
Discerning static and causal interactions in genome-wide reverse engineering problems
Bioinformatics Advance Access published on May 8, 2008
Bioinformatics 2008 24: 1510-1515; doi:10.1093/bioinformatics/btn220 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Junil Kim, Tae-Geon Kim, Sung Hoon Jung, Jeong-Rae Kim, Taesung Park, Pat Heslop-Harrison, and Kwang-Hyun Cho
Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity
Bioinformatics Advance Access published on May 8, 2008
Bioinformatics 2008 24: 1516-1522; doi:10.1093/bioinformatics/btn229 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Makio Tamura and Patrik D'haeseleer
Microbial genotype–phenotype mapping by class association rule mining
Bioinformatics Advance Access published on May 8, 2008
Bioinformatics 2008 24: 1523-1529; doi:10.1093/bioinformatics/btn210 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTE Back

SEQUENCE ANALYSIS Back

Kay Prüfer, Udo Stenzel, Michael Dannemann, Richard E. Green, Michael Lachmann, and Janet Kelso
PatMaN: rapid alignment of short sequences to large databases
Bioinformatics Advance Access published on May 8, 2008
Bioinformatics 2008 24: 1530-1531; doi:10.1093/bioinformatics/btn223 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Michiel Van Bel, Yvan Saeys, and Yves Van de Peer
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA
Bioinformatics Advance Access published on May 12, 2008
Bioinformatics 2008 24: 1532-1533; doi:10.1093/bioinformatics/btn225 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Igor B. Kuznetsov
ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
Bioinformatics Advance Access published on May 14, 2008
Bioinformatics 2008 24: 1534-1535; doi:10.1093/bioinformatics/btn233 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Anne-Laure Abraham, Eduardo P. C. Rocha, and Joël Pothier
Swelfe: a detector of internal repeats in sequences and structures
Bioinformatics Advance Access published on May 16, 2008
Bioinformatics 2008 24: 1536-1537; doi:10.1093/bioinformatics/btn234 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

PHYLOGENETICS Back

Miklós Csurös
Malin: maximum likelihood analysis of intron evolution in eukaryotes
Bioinformatics Advance Access published on May 12, 2008
Bioinformatics 2008 24: 1538-1539; doi:10.1093/bioinformatics/btn226 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

André Wehe, Mukul S. Bansal, J. Gordon Burleigh, and Oliver Eulenstein
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
Bioinformatics Advance Access published on May 12, 2008
Bioinformatics 2008 24: 1540-1541; doi:10.1093/bioinformatics/btn230 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Scott Hazelhurst, Winston Hide, Zsuzsanna Lipták, Ramon Nogueira, and Richard Starfield
An overview of the wcd EST clustering tool
Bioinformatics Advance Access published on May 14, 2008
Bioinformatics 2008 24: 1542-1546; doi:10.1093/bioinformatics/btn203 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Pan Du, Warren A. Kibbe, and Simon M. Lin
lumi: a pipeline for processing Illumina microarray
Bioinformatics Advance Access published on May 8, 2008
Bioinformatics 2008 24: 1547-1548; doi:10.1093/bioinformatics/btn224 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Christian Ritz and Andrej-Nikolai Spiess
qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis
Bioinformatics Advance Access published on May 14, 2008
Bioinformatics 2008 24: 1549-1551; doi:10.1093/bioinformatics/btn227 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Samuel Neuenschwander, Frédéric Hospital, Frédéric Guillaume, and Jérôme Goudet
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
Bioinformatics Advance Access published on May 1, 2008
Bioinformatics 2008 24: 1552-1553; doi:10.1093/bioinformatics/btn219 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Jason M. Gilmore, Deanna L. Auberry, Julia L. Sharp, Amanda M. White, Kevin K. Anderson, and Don S. Daly
A Bayesian estimator of protein–protein association probabilities
Bioinformatics Advance Access published on May 22, 2008
Bioinformatics 2008 24: 1554-1555; doi:10.1093/bioinformatics/btn238 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp, II, Gordon A. Anderson, and Richard D. Smith
DAnTE: a statistical tool for quantitative analysis of -omics data
Bioinformatics Advance Access published on May 3, 2008
Bioinformatics 2008 24: 1556-1558; doi:10.1093/bioinformatics/btn217 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Curtis Huttenhower, Mark Schroeder, Maria D Chikina, and Olga G. Troyanskaya
The Sleipnir library for computational functional genomics
Bioinformatics Advance Access published on May 21, 2008
Bioinformatics 2008 24: 1559-1561; doi:10.1093/bioinformatics/btn237 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

ERRATUM Back

Lixiao Wang and Uwe H. Sauer
OnD-CRF: prediciting order and disorder in proteins conditional random fields
Bioinformatics 2008 24: 1562; doi:10.1093/bioinformatics/btn261 [Extract] [Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.