Bioinformatics

Gene Myers

ISMB 2003
Bioinformatics 2003 19: i1-i2; doi:10.1093/bioinformatics/btg1048 [Print PDF][Screen PDF]  

ISMB 2003 Organization
Bioinformatics 2003 19: i3-i6; doi:10.1093/bioinformatics/btg1049 [Print PDF][Screen PDF]  

Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, and Bengt Sennblad

Bayesian gene/species tree reconciliation and orthology analysis using MCMC
Bioinformatics 2003 19: i7-i15; doi:10.1093/bioinformatics/btg1000 [Abstract] [Print PDF][Screen PDF]  

Niko Beerenwinkel, Thomas Lengauer, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, and Joachim Selbig

Methods for optimizing antiviral combination therapies
Bioinformatics 2003 19: i16-i25; doi:10.1093/bioinformatics/btg1001 [Abstract] [Print PDF][Screen PDF]  

Asa Ben-Hur and Douglas Brutlag

Remote homology detection: a motif based approach
Bioinformatics 2003 19: i26-i33; doi:10.1093/bioinformatics/btg1002 [Abstract] [Print PDF][Screen PDF]  

Joseph Bockhorst, Yu Qiu, Jeremy Glasner, Mingzhu Liu, Frederick Blattner, and Mark Craven

Predicting bacterial transcription units using sequence and expression data
Bioinformatics 2003 19: i34-i43; doi:10.1093/bioinformatics/btg1003 [Abstract] [Print PDF][Screen PDF]  

Sebastian Böcker

SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry
Bioinformatics 2003 19: i44-i53; doi:10.1093/bioinformatics/btg1004 [Abstract] [Print PDF][Screen PDF]  

Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, and Serafim Batzoglou

Glocal alignment: finding rearrangements during alignment
Bioinformatics 2003 19: i54-i62; doi:10.1093/bioinformatics/btg1005 [Abstract] [Print PDF][Screen PDF]  

Richard M. Bruskiewich, Alexander B. Cosico, William Eusebio, Arllet M. Portugal, Luralyn M. Ramos, Ma. Teresa Reyes, May Ann B. Sallan, Victor Jun M. Ulat, Xusheng Wang, Kenneth L. McNally, Ruaraidh Sackville Hamilton, and Christopher Graham McLaren

Linking genotype to phenotype: the International Rice Information System (IRIS)
Bioinformatics 2003 19: i63-i65; doi:10.1093/bioinformatics/btg1006 [Abstract] [Print PDF][Screen PDF]  

Liming Cai, Russell L. Malmberg, and Yunzhou Wu

Stochastic modeling of RNA pseudoknotted structures: a grammatical approach
Bioinformatics 2003 19: i66-i73; doi:10.1093/bioinformatics/btg1007 [Abstract] [Print PDF][Screen PDF]  

Peter P. Calabrese, Sugata Chakravarty, and Todd J. Vision

Fast identification and statistical evaluation of segmental homologies in comparative maps
Bioinformatics 2003 19: i74-i80; doi:10.1093/bioinformatics/btg1008 [Abstract] [Print PDF][Screen PDF]  

Orhan Camoglu, Tamer Kahveci, and Ambuj K. Singh

PSI: indexing protein structures for fast similarity search
Bioinformatics 2003 19: i81-i83; doi:10.1093/bioinformatics/btg1009 [Abstract] [Print PDF][Screen PDF]  

Jung Kyoon Choi, Ungsik Yu, Sangsoo Kim, and Ook Joon Yoo

Combining multiple microarray studies and modeling interstudy variation
Bioinformatics 2003 19: i84-i90; doi:10.1093/bioinformatics/btg1010 [Abstract] [Print PDF][Screen PDF]  

Pavel B. Dobrokhotov, Cyril Goutte, Anne-Lise Veuthey, and Eric Gaussier

Combining NLP and probabilistic categorisation for document and term selection for Swiss-Prot medical annotation
Bioinformatics 2003 19: i91-i94; doi:10.1093/bioinformatics/btg1011 [Abstract] [Print PDF][Screen PDF]  

O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson

MASS: multiple structural alignment by secondary structures
Bioinformatics 2003 19: i95-i104; doi:10.1093/bioinformatics/btg1012 [Abstract] [Print PDF][Screen PDF]  

F. Enault, K. Suhre, C. Abergel, O. Poirot, and J.-M. Claverie

Annotation of bacterial genomes using improved phylogenomic profiles
Bioinformatics 2003 19: i105-i107; doi:10.1093/bioinformatics/btg1013 [Abstract] [Print PDF][Screen PDF]  

I. Gat-Viks and R. Shamir

Chain functions and scoring functions in genetic networks
Bioinformatics 2003 19: i108-i117; doi:10.1093/bioinformatics/btg1014 [Abstract] [Print PDF][Screen PDF]  

Richard E. Green, Benjamin P. Lewis, R. Tyler Hillman, Marco Blanchette, Liana F. Lareau, Aaron T. Garnett, Donald C. Rio, and Steven E. Brenner

Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes
Bioinformatics 2003 19: i118-i121; doi:10.1093/bioinformatics/btg1015 [Abstract] [Print PDF][Screen PDF]  

E. Halperin, J. Buhler, R. Karp, R. Krauthgamer, and B. Westover

Detecting protein sequence conservation via metric embeddings
Bioinformatics 2003 19: i122-i129; doi:10.1093/bioinformatics/btg1016 [Abstract] [Print PDF][Screen PDF]  

Andreas Heger and Liisa Holm

Sensitive pattern discovery with ‘fuzzy’ alignments of distantly related proteins
Bioinformatics 2003 19: i130-i137; doi:10.1093/bioinformatics/btg1017 [Abstract] [Print PDF][Screen PDF]  

Maureen Heymans and Ambuj K. Singh

Deriving phylogenetic trees from the similarity analysis of metabolic pathways
Bioinformatics 2003 19: i138-i146; doi:10.1093/bioinformatics/btg1018 [Abstract] [Print PDF][Screen PDF]  

I. Holmes

Using guide trees to construct multiple-sequence evolutionary HMMs
Bioinformatics 2003 19: i147-i157; doi:10.1093/bioinformatics/btg1019 [Abstract] [Print PDF][Screen PDF]  

Yuval Inbar, Hadar Benyamini, Ruth Nussinov, and Haim J. Wolfson

Protein structure prediction via combinatorial assembly of sub-structural units
Bioinformatics 2003 19: i158-i168; doi:10.1093/bioinformatics/btg1020 [Abstract] [Print PDF][Screen PDF]  

Ö. Johansson, W. Alkema, W. W. Wasserman, and J. Lagergren

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm
Bioinformatics 2003 19: i169-i176; doi:10.1093/bioinformatics/btg1021 [Abstract] [Print PDF][Screen PDF]  

Byong-Hyon Ju and Kyungsook Han

Complexity management in visualizing protein interaction networks
Bioinformatics 2003 19: i177-i179; doi:10.1093/bioinformatics/btg1022 [Abstract] [Print PDF][Screen PDF]  

J.-D. Kim, T. Ohta, Y. Tateisi, and J. Tsujii

GENIA corpus—a semantically annotated corpus for bio-textmining
Bioinformatics 2003 19: i180-i182; doi:10.1093/bioinformatics/btg1023 [Abstract] [Print PDF][Screen PDF]  

Oliver D. King, Jeffrey C. Lee, Aimée M. Dudley, Daniel M. Janse, George M. Church, and Frederick P. Roth

Predicting phenotype from patterns of annotation
Bioinformatics 2003 19: i183-i189; doi:10.1093/bioinformatics/btg1024 [Abstract] [Print PDF][Screen PDF]  

J.F. Lefebvre, N. El-Mabrouk, E. Tillier, and D. Sankoff

Detection and validation of single gene inversions
Bioinformatics 2003 19: i190-i196; doi:10.1093/bioinformatics/btg1025 [Abstract] [Print PDF][Screen PDF]  

Stanley Letovsky and Simon Kasif

Predicting protein function from protein/protein interaction data: a probabilistic approach
Bioinformatics 2003 19: i197-i204; doi:10.1093/bioinformatics/btg1026 [Abstract] [Print PDF][Screen PDF]  

Pier Luigi Martelli, Piero Fariselli, and Rita Casadio

An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins
Bioinformatics 2003 19: i205-i211; doi:10.1093/bioinformatics/btg1027 [Abstract] [Print PDF][Screen PDF]  

Thomas M. Oinn

Talisman—rapid application development for the grid
Bioinformatics 2003 19: i212-i214; doi:10.1093/bioinformatics/btg1028 [Abstract] [Print PDF][Screen PDF]  

Orla O’Sullivan, Mark Zehnder, Des Higgins, Philipp Bucher, Aurelien Grosdidier, and Cédric Notredame

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
Bioinformatics 2003 19: i215-i221; doi:10.1093/bioinformatics/btg1029 [Abstract] [Print PDF][Screen PDF]  

Naomi Rosen, Vered Chalifa-Caspi, Orit Shmueli, Avital Adato, Michal Lapidot, Julie Stampnitzky, Marilyn Safran, and Doron Lancet

GeneLoc: exon-based integration of human genome maps
Bioinformatics 2003 19: i222-i224; doi:10.1093/bioinformatics/btg1030 [Abstract] [Print PDF][Screen PDF]  

Anthony Rowe, Dimitrios Kalaitzopoulos, Michelle Osmond, Moustafa Ghanem, and Yike Guo

The discovery net system for high throughput bioinformatics
Bioinformatics 2003 19: i225-i231; doi:10.1093/bioinformatics/btg1031 [Abstract] [Print PDF][Screen PDF]  

Yasubumi Sakakibara

Pair hidden Markov models on tree structures
Bioinformatics 2003 19: i232-i240; doi:10.1093/bioinformatics/btg1032 [Abstract] [Print PDF][Screen PDF]  

M. Samsonova, A. Pisarev, and M. Blagov

Processing of natural language queries to a relational database
Bioinformatics 2003 19: i241-i249; doi:10.1093/bioinformatics/btg1033 [Abstract] [Print PDF][Screen PDF]  

Víctor Santander, Miguel Angel Portales, and Francisco Melo

A tool to assist the study of specific features at protein binding sites
Bioinformatics 2003 19: i250-i251; doi:10.1093/bioinformatics/btg1034 [Abstract] [Print PDF][Screen PDF]  

Joanna M. Sasin, Michal A. Kurowski, and Janusz M. Bujnicki

STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification
Bioinformatics 2003 19: i252-i254; doi:10.1093/bioinformatics/btg1035 [Abstract] [Print PDF][Screen PDF]  

Alexander Schliep, Alexander Schönhuth, and Christine Steinhoff

Using hidden Markov models to analyze gene expression time course data
Bioinformatics 2003 19: i255-i263; doi:10.1093/bioinformatics/btg1036 [Abstract] [Print PDF][Screen PDF]  

E. Segal, H. Wang, and D. Koller

Discovering molecular pathways from protein interaction and gene expression data
Bioinformatics 2003 19: i264-i272; doi:10.1093/bioinformatics/btg1037 [Abstract] [Print PDF][Screen PDF]  

E. Segal, R. Yelensky, and D. Koller

Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
Bioinformatics 2003 19: i273-i282; doi:10.1093/bioinformatics/btg1038 [Abstract] [Print PDF][Screen PDF]  

Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, and Richard M. Karp

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments
Bioinformatics 2003 19: i283-i291; doi:10.1093/bioinformatics/btg1039 [Abstract] [Print PDF][Screen PDF]  

Saurabh Sinha, Erik van Nimwegen, and Eric D. Siggia

A probabilistic method to detect regulatory modules
Bioinformatics 2003 19: i292-i301; doi:10.1093/bioinformatics/btg1040 [Abstract] [Print PDF][Screen PDF]  

Robert D. Stevens, Alan J. Robinson, and Carole A. Goble

^myGrid: personalised bioinformatics on the information grid
Bioinformatics 2003 19: i302-i304; doi:10.1093/bioinformatics/btg1041 [Abstract] [Print PDF][Screen PDF]  

Jijun Tang and Bernard M.E. Moret

Scaling up accurate phylogenetic reconstruction from gene-order data
Bioinformatics 2003 19: i305-i312; doi:10.1093/bioinformatics/btg1042 [Abstract] [Print PDF][Screen PDF]  

Tatiana Tatarinova, Vyacheslav Brover, Maxim Troukhan, and Nickolai Alexandrov

Skew in CG content near the transcription start site in Arabidopsis thaliana
Bioinformatics 2003 19: i313-i314; doi:10.1093/bioinformatics/btg1043 [Abstract] [Print PDF][Screen PDF]  

Hui Wang, Earl Hubbell, Jing-shan Hu, Gangwu Mei, Melissa Cline, Gang Lu, Tyson Clark, Michael A. Siani-Rose, Manuel Ares, David C. Kulp, and David Haussler

Gene structure-based splice variant deconvolution using a microarry platform
Bioinformatics 2003 19: i315-i322; doi:10.1093/bioinformatics/btg1044 [Abstract] [Print PDF][Screen PDF]  

Y. Yamanishi, J.-P. Vert, A. Nakaya, and M. Kanehisa

Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis
Bioinformatics 2003 19: i323-i330; doi:10.1093/bioinformatics/btg1045 [Abstract] [Print PDF][Screen PDF]  

Alexander S. Yeh, Lynette Hirschman, and Alexander A. Morgan

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup
Bioinformatics 2003 19: i331-i339; doi:10.1093/bioinformatics/btg1046 [Abstract] [Print PDF][Screen PDF]  

Hong Yu and Eugene Agichtein

Extracting synonymous gene and protein terms from biological literature
Bioinformatics 2003 19: i340-i349; doi:10.1093/bioinformatics/btg1047 [Abstract] [Print PDF][Screen PDF]  

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