Volume 19, Number 1, January 2003 Editorial
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journals/bioinformatics/Sander03
Reviews
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journals/bioinformatics/Lio03 Pietro Liò :
Wavelets in bioinformatics and computational biology: state of art and perspectives. 2-9
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journals/bioinformatics/OoiT03 C. H. Ooi ,
Patrick Tan :
Genetic algorithms applied to multi-class prediction for the analysis of gene expression data. 37-44
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journals/bioinformatics/Deutsch03 J. M. Deutsch :
Evolutionary algorithms for finding optimal gene sets in microarray prediction. 45-52
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journals/bioinformatics/PrasadPC03 Volume 19, Number 2, February 2003 Discovery Notes
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journals/bioinformatics/MaZ03 Hongwu Ma ,
An-Ping Zeng :
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. 270-277
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journals/bioinformatics/WangX03 Lusheng Wang ,
Ying Xu :
SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments. 297-298
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journals/bioinformatics/Sanderson03 Michael J. Sanderson :
r8s: inferring absolute rates of molecular evolution, divergence times in the absence of a molecular clock. 301-302
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journals/bioinformatics/Leunissen03 Jack A. M. Leunissen :
Chimera: construction of chimeric sequences for phylogenetic analysis. 303-304
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journals/bioinformatics/Bond03 Charles S. Bond :
TopDraw: a sketchpad for protein structure topology cartoons. 311-321
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journals/bioinformatics/JuPPH03 Volume 19, Number 3, February 2003 Jobim Papers
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journals/bioinformatics/ToyodaK03 Tetsuro Toyoda ,
Akihiko Konagaya :
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. 433-434
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journals/bioinformatics/HokampSWC03 Volume 19, Number 4, March 2003 Original Papers
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journals/bioinformatics/DattaD03 Susmita Datta ,
Somnath Datta :
Comparisons and validation of statistical clustering techniques for microarray gene expression data. 459-466
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journals/bioinformatics/LuanL03 Yihui Luan ,
Hongzhe Li :
Clustering of time-course gene expression data using a mixed-effects model with B-splines. 474-482
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journals/bioinformatics/Metzler03 Dirk Metzler :
Statistical alignment based on fragment insertion and deletion models. 490-499
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journals/bioinformatics/HuckaFSBDKABBCCDGGGGHHHHJKKKNLLMMMNNNSSSSSSTTWW03 Michael Hucka ,
Andrew Finney ,
Herbert M. Sauro ,
H. Bolouri ,
John C. Doyle ,
Hiroaki Kitano ,
Adam P. Arkin ,
Benjamin J. Bornstein ,
D. Bray ,
A. Cornish-Bowden ,
Autumn A. Cuellar ,
Serge Dronov ,
Ernst Dieter Gilles ,
Martin Ginkel ,
Victoria Gor ,
Igor Goryanin ,
W. J. Hedley ,
T. Charles Hodgman ,
J. H. Hofmeyr ,
Peter J. Hunter ,
Nick S. Juty ,
J. L. Kasberger ,
Andreas Kremling ,
Ursula Kummer ,
Nicolas Le Novère ,
Leslie M. Loew ,
D. Lucio ,
Pedro Mendes ,
E. Minch ,
Eric Mjolsness ,
Yoichi Nakayama ,
M. R. Nelson ,
Poul M. F. Nielsen ,
T. Sakurada ,
James C. Schaff ,
Bruce E. Shapiro ,
Thomas Simon Shimizu ,
Hugh D. Spence ,
Jörg Stelling ,
Koichi Takahashi ,
Masaru Tomita ,
J. Wagner ,
J. Wang :
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. 524-531
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journals/bioinformatics/HolmeHJ03
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journals/bioinformatics/Wooding03 Stephen Wooding :
PopHist: inferring population history from the spectrum of allele frequencies. 539-540
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journals/bioinformatics/LopezRKHPHQSKJ03 Volume 19, Number 5, March 2003 Discovery Notes
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journals/bioinformatics/SubramanianMGMPKS03
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journals/bioinformatics/Presting03 Gernot G. Presting :
Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome. 579-586
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journals/bioinformatics/Aris-Brosou03 Stéphane Aris-Brosou :
How Bayes tests of molecular phylogenies compare with frequentist approaches. 618-624
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journals/bioinformatics/PerteaHLASKLWCPTQ03 Geo Pertea ,
Xiaoqiu Huang ,
Feng Liang ,
Valentin Antonescu ,
Razvan Sultana ,
Svetlana Karamycheva ,
Yuandan Lee ,
Joseph White ,
Foo Cheung ,
Babak Parvizi ,
Jennifer Tsai ,
John Quackenbush :
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. 651-652
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journals/bioinformatics/Venet03 David Venet :
MatArray: a Matlab toolbox for microarray data. 659-660
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journals/bioinformatics/ShapiroLMWM03 Volume 19, Number 6, April 2003 Editorial
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journals/bioinformatics/Jamison03
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journals/bioinformatics/SubramanianMS03 Subbaya Subramanian ,
Rakesh K. Mishra ,
Lalji Singh :
Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function. 681-685
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journals/bioinformatics/IliopoulosTAECPPLPPHTYTDBVBMLRSO03 Ioannis Iliopoulos ,
Sophia Tsoka ,
Miguel A. Andrade ,
Anton J. Enright ,
Mark Carroll ,
Patrick Poullet ,
Vassilis J. Promponas ,
Theodore Liakopoulos ,
Giorgos Palaios ,
Claude Pasquier ,
Stavros J. Hamodrakas ,
Javier Tamames ,
Asutosh T. Yagnik ,
Anna Tramontano ,
Damien Devos ,
Christian Blaschke ,
Alfonso Valencia ,
David Brett ,
David Martin ,
Christophe Leroy ,
Isidore Rigoutsos ,
Chris Sander ,
Christos A. Ouzounis :
Evaluation of annotation strategies using an entire genome sequence. 717-726
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journals/bioinformatics/MatthiesenLWB03 Volume 19, Number 7, May 2003 Editorial
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journals/bioinformatics/Valencia03
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journals/bioinformatics/LiFX03 Li Wuju ,
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Momiao Xiong :
SamCluster: An Integrated Scheme for Automatic Discovery of Sample Classes Using Gene Expression Profile. 811-817
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journals/bioinformatics/Bickel03 David R. Bickel :
Robust Cluster Analysis of Microarray Gene Expression Data with the Number of Clusters Determined Biologically. 818-824
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journals/bioinformatics/Edwards03 David Edwards :
Non-linear Normalization and Background Correction in One-channel CDNA Microarray Studies. 825-833
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journals/bioinformatics/GoffardGIGD03 Volume 19, Number 8, May 2003 Sac Papers
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journals/bioinformatics/HeDSCESDKJSS03 Yudong D. He ,
Hongyue Dai ,
Eric E. Schadt ,
Guy Cavet ,
Stephen W. Edwards ,
Sergey B. Stepaniants ,
Sven Duenwald ,
Robert Kleinhanz ,
Allan R. Jones ,
Daniel D. Shoemaker ,
Roland B. Stoughton :
Microarray Standard Data Set and Figures of Merit for Comparing Data Processing Methods and Experiment Designs. 956-965
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journals/bioinformatics/Lee03 Christopher Lee :
Generating Consensus Sequences from Partial Order Multiple Sequence Alignment Graphs. 999-1008
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journals/bioinformatics/SheikSSS03 Volume 19, Number 9, June 2003 Editorial
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journals/bioinformatics/Campbell03 Colin Campbell :
New Analytical Techniques for the Interpretation of Microarray Data. 1045
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journals/bioinformatics/ZhaoP03 Yanli Zhao ,
Wei Pan :
Modified Nonparametric Approaches to Detecting Differentially Expressed Genes in Replicated Microarray Experiments. 1046-1054
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journals/bioinformatics/WitM03 Ernst Wit ,
John McClure :
Statistical Adjustment of Signal Censoring in Gene Expression Experiments. 1055-1060
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journals/bioinformatics/JornstenY03 Rebecka Jörnsten ,
Bin Yu :
Simultaneous Gene Clustering and Subset Selection for Sample Classification Via MDL. 1100-1109
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journals/bioinformatics/HornA03 David Horn ,
Inon Axel :
Novel Clustering Algorithm for Microarray Expression Data in A Truncated SVD Space. 1110-1115
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journals/bioinformatics/LeeL03 Yoonkyung Lee ,
Cheol-Koo Lee :
Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Data. 1132-1139
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journals/bioinformatics/HudekCBS03 Volume 19, Number 10, July 2003 PTC (2000/2001) Papers
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journals/bioinformatics/Okada03 Takashi Okada :
Characteristic Substructures and Properties in Chemical Carcinogens Studied by the Cascade Model. 1208-1215
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journals/bioinformatics/PoundsM03 Stan Pounds ,
Stephan W. Morris :
Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of P-values. 1236-1242
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journals/bioinformatics/SunX03 Minghe Sun ,
Momiao Xiong :
A Mathematical Programming Approach for Gene Selection and Tissue Classification. 1243-1251
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journals/bioinformatics/Ding03 Chris H. Q. Ding :
Unsupervised Feature Selection Via Two-way Ordering in Gene Expression Analysis. 1259-1266
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journals/bioinformatics/XuL03 Ronghui Xu ,
Xiaochun Li :
A Comparison of Parametric Versus Permutation Methods with Applications to General and Temporal Microarray Gene Expression Data. 1284-1289
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journals/bioinformatics/Allison03 Lloyd Allison :
Longest Biased Interval and Longest Non-negative Sum Interval. 1294-1295
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journals/bioinformatics/ZhangJ03 Volume 19, Number 11, July 2003 Original Papers
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journals/bioinformatics/ChangP03 Pei-chin Chang ,
Konan Peck :
Design and Assessment of A Fast Algorithm for Identifying Specific Probes for Human and Mouse Genes. 1311-1317
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journals/bioinformatics/ScheetzTRKBRBGOBBRSSC03 Todd E. Scheetz ,
Nishank Trivedi ,
Chad A. Roberts ,
Tamara Kucaba ,
Brian Berger ,
Natalie L. Robinson ,
Clayton L. Birkett ,
Allen J. Gavin ,
Brian O'Leary ,
Terry A. Braun ,
Maria F. Bonaldo ,
John P. Robinson ,
Val C. Sheffield ,
Marcelo Bento Soares ,
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ESTprep: Preprocessing CDNA Sequence Reads. 1318-1324
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journals/bioinformatics/Pan03 Wei Pan :
On the Use of Permutation in and the Performance of A Class of Nonparametric Methods to Detect Differential Gene Expression. 1333-1340
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Exact Significance Levels for the Maximum 2 Method of Detecting Recombination. 1368-1370
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Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm. 1391-1396
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journals/bioinformatics/ChiangY03 Jung-Hsien Chiang ,
Hsu-Chun Yu :
MeKE: Discovering the Functions of Gene Products from Biomedical Literature Via Sentence Alignment. 1417-1422
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journals/bioinformatics/MaZ03a Hongwu Ma ,
An-Ping Zeng :
The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks. 1423-1430
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journals/bioinformatics/FischerABMBRHPLREGSFT03 T. B. Fischer ,
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R. Russo ,
D. Huang ,
M. Paczkowski ,
V. Lalchandani ,
C. Ramachandra ,
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J. Shapley ,
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The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfaces. 1453-1454
Volume 19, Number 12, August 2003 Discovery Notes
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journals/bioinformatics/WeinelEO03
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journals/bioinformatics/Rajagopalan03 Dilip Rajagopalan :
A comparison of statistical methods for analysis of high density oligonucleotide array data. 1469-1476
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Serial BLAST searching. 1492-1496
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journals/bioinformatics/Li03 Kuo-Bin Li :
ClustalW-MPI: ClustalW analysis using distributed and parallel computing. 1585-1586
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journals/bioinformatics/MaddenOFBSD03 Volume 19, Number 13, September 2003 Original Papers
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journals/bioinformatics/ParkK03 Keun-Joon Park ,
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Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. 1656-1663
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journals/bioinformatics/GulerER03 Volume 19, Number 14, September 2003 Chia Papers
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Chris Sander: Growth in Bioinformatics. 1