Volume 20, Number 1, January 2004 Discovery Note
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journals/bioinformatics/MengZL04 Shao-Wu Meng ,
Zhuo Zhang ,
Jinyan Li :
Twelve C2H2 zinc-finger genes on human chromosome 19 can be each translated into the same type of protein after frameshifts.
1-4
Original Papers
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journals/bioinformatics/HuangL04 Ying Huang ,
Yanda Li :
Prediction of protein subcellular locations using fuzzy k -NN method.
21-28
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journals/bioinformatics/Kim04 Saejoon Kim :
Protein ß-turn prediction using nearest-neighbor method.
40-44
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journals/bioinformatics/Philippi04 Stephan Philippi :
Light-weight integration of molecular biological databases.
51-57
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journals/bioinformatics/WangE04 Song Wang ,
Stewart Ethier :
A generalized likelihood ratio test to identify differentially expressed genes from microarray data.
100-104
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journals/bioinformatics/CserzoEES04
Volume 20, Number 2, January 2004 PAG Meeting Preface
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journals/bioinformatics/Bruskiewich04 Richard M. Bruskiewich :
Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competition.
139
PAG Meeting Original Papers
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journals/bioinformatics/Sjolander04 Kimmen Sjölander :
Phylogenomic inference of protein molecular function: advances and challenges.
170-179
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journals/bioinformatics/WrenG04 Jonathan D. Wren ,
Harold R. Garner :
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network.
191-198
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journals/bioinformatics/CrassABBBCCEEGGGGGHHOKKKLLLLMMMMMMMPRRSSSSSSSTVWWWWZ04 Torsten Crass ,
Iris Antes ,
Rico Basekow ,
Peer Bork ,
Christian Buning ,
Maik Christensen ,
Holger Claussen ,
Christian Ebeling ,
Peter Ernst ,
Valérie Gailus-Durner ,
Karl-Heinz Glatting ,
Rolf Gohla ,
Frank Gößling ,
Korbinian Grote ,
Karsten R. Heidtke ,
Alexander Herrmann ,
Sean O'Keeffe ,
O. Kießlich ,
Sven Kolibal ,
Jan O. Korbel ,
Thomas Lengauer ,
Ines Liebich ,
Mark van der Linden ,
Hannes Luz ,
Kathrin Meissner ,
Christian von Mering ,
Heinz-Theodor Mevissen ,
Hans-Werner Mewes ,
Holger Michael ,
Martin Mokrejs ,
Tobias Müller ,
Heike Pospisil ,
Matthias Rarey ,
Jens G. Reich ,
Ralf Schneider ,
Dietmar Schomburg ,
Steffen Schulze-Kremer ,
Knut Schwarzer ,
Ingolf Sommer ,
Stephan Springstubbe ,
Sándor Suhai ,
Gnanasekaran Thoppae ,
Martin Vingron ,
Jens Warfsmann ,
Thomas Werner ,
Daniel Wetzler ,
Edgar Wingender ,
Ralf Zimmer :
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
268-270
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journals/bioinformatics/Barker04 Daniel Barker :
LVB: parsimony and simulated annealing in the search for phylogenetic trees.
274-275
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journals/bioinformatics/PerezTT04 Corrigenda
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journals/bioinformatics/HvidstenKKF04
Volume 20, Number 3, February 2004 Original Papers
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journals/bioinformatics/LuanL04 Yihui Luan ,
Hongzhe Li :
Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data.
332-339
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journals/bioinformatics/Helden04 Jacques van Helden :
Metrics for comparing regulatory sequences on the basis of pattern counts.
399-406
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journals/bioinformatics/AltekarDHR04 Applications Notes
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journals/bioinformatics/Thollesson04 Mikael Thollesson :
LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences.
416-418
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Volume 20, Number 4, March 2004 Discovery Notes
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journals/bioinformatics/GaspariOP04 Original Papers
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journals/bioinformatics/Adar04 Eytan Adar :
SaRAD: a Simple and Robust Abbreviation Dictionary.
527-533
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journals/bioinformatics/LeeK04 Soohyun Lee ,
Changwon Kang :
CHOISS for selection of single nucleotide polymorphism markers on interval regularity.
581-582
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Volume 20, Number 5, March 22 2004 Discovery Notes
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journals/bioinformatics/ZhangZLSC04 Original Papers
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journals/bioinformatics/ZhangZ04 Ren Zhang ,
Chun-Ting Zhang :
A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I.
612-622
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journals/bioinformatics/Wren04 Jonathan D. Wren :
404 not found: the stability and persistence of URLs published in MEDLINE.
668-672
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journals/bioinformatics/GaoZ04 Feng Gao ,
Chun-Ting Zhang :
Comparison of various algorithms for recognizing short coding sequences of human genes.
673-681
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journals/bioinformatics/Bickel04 David R. Bickel :
Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes.
682-688
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journals/bioinformatics/Taneda04 Akito Taneda :
Adplot: detection and visualization of repetitive patterns in complete genomes.
701-708
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journals/bioinformatics/RomeroK04 Pedro Romero ,
Peter D. Karp :
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases.
709-717
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journals/bioinformatics/SunD04 Hao Sun ,
Ramana V. Davuluri :
Java-based application framework for visualization of gene regulatory region annotations.
727-734
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journals/bioinformatics/BaggerlyMC04 Application Notes
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journals/bioinformatics/Bejerano04 Gill Bejerano :
Algorithms for variable length Markov chain modeling.
788-789
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journals/bioinformatics/WiederkehrBMKSHMICYLCLP04 C. Wiederkehr ,
R. Basavaraj ,
Cyril Sarrauste de Menthière ,
R. Koch ,
U. Schlecht ,
Leandro Hermida ,
Benjamin Masdoua ,
R. Ishii ,
V. Cassen ,
M. Yamamoto ,
Christopher Lane ,
J. Michael Cherry ,
N. Lamb ,
Michael Primig :
Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation.
808-811
Volume 20, Number 6, April 12 2004
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journals/bioinformatics/GroverMBKB04 Original Papers
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journals/bioinformatics/ZhouL04 Qing Zhou ,
Jun S. Liu :
Modeling within-motif dependence for transcription factor binding site predictions.
909-916
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journals/bioinformatics/HanK04 Xing Han ,
Wenjun Kang :
Sequence analysis and membrane partitioning energies of -helical antimicrobial peptides.
970-973
Applications Notes
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journals/bioinformatics/HallS04 Ross Hall ,
Linda Stern :
A rapid method for illustrating features in both coding and non-coding regions of a genome.
982-983
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journals/bioinformatics/Martin04 Andrew C. R. Martin :
PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt.
986-988
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journals/bioinformatics/MajeedARGKBNKCSGH04 Ahmed A. Majeed ,
Niyaz Ahmed ,
K. Rajender Rao ,
S. Ghousunnissa ,
Farhana Kauser ,
Buddhaditta Bose ,
Hampapathalu A. Nagarajaram ,
V. M. Katoch ,
Debby V. Cousins ,
Leonardo A. Sechi ,
Robert H. Gilman ,
Seyed E. Hasnain :
AmpliBASE MTTM : a Mycobacterium tuberculosis diversity knowledgebase.
989-992
Volume 20, Number 7, May 1 2004 Original Papers
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journals/bioinformatics/AungT04 Zeyar Aung ,
Kian-Lee Tan :
Rapid 3D protein structure database searching using information retrieval techniques.
1045-1052
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journals/bioinformatics/TeraiT04 Goro Terai ,
Toshihisa Takagi :
Predicting rules on organization of cis-regulatory elements, taking the order of elements into account.
1119-1128
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journals/bioinformatics/IzaguirreCHCCTFAHNG04 Jesús A. Izaguirre ,
Rajiv Chaturvedi ,
Chengbang Huang ,
Trevor M. Cickovski ,
J. Coffland ,
Gilberto L. Thomas ,
Gabor Forgacs ,
Mark S. Alber ,
G. Hentschel ,
Stuart A. Newman ,
James A. Glazier :
COMPUCELL, a multi-model framework for simulation of morphogenesis.
1129-1137
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journals/bioinformatics/KimBP04 Wan K. Kim ,
Dan M. Bolser ,
Jong H. Park :
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).
1138-1150
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journals/bioinformatics/BrendelXZ04 Volker Brendel ,
Liqun Xing ,
Wei Zhu :
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
1157-1169
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journals/bioinformatics/ZhouZSST04 Applications Notes
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journals/bioinformatics/YuYG04 Han Yu ,
Andrew S. Yoo ,
Iva Greenwald :
Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites.
1198-1200
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journals/bioinformatics/KirbyDLM04
Volume 20, Number 8, May 22 2004 Original Papers
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journals/bioinformatics/CaiD04 Yu-Dong Cai ,
Andrew J. Doig :
Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition.
1292-1300
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journals/bioinformatics/Zhao04 Jing Hua Zhao :
2LD, GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis.
1325-1326
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journals/bioinformatics/MignoneHP04
Volume 20, Number 9, June 12 2004 Original Papers
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journals/bioinformatics/NilssonLU04
Volume 20, Number 10, July 1 2004 Editorials
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journals/bioinformatics/GrassoL04 Catherine Grasso ,
Christopher Lee :
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems.
1546-1556
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journals/bioinformatics/JiXS04 Yongmei Ji ,
Xing Xu ,
Gary D. Stormo :
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.
1603-1611
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journals/bioinformatics/Jarman04 Simon N. Jarman :
Amplicon: software for designing PCR primers on aligned DNA sequences.
1644-1645
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journals/bioinformatics/Boyle04 John Boyle :
SeqExpress: desktop analysis and visualization tool for gene expression experiments.
1649-1650
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journals/bioinformatics/HuberG04
Volume 20, Number 11, July 22 2004
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Mixture models for assessing differential expression in complex tissues using microarray data.
1663-1669
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journals/bioinformatics/DuanZ04 Fenghai Duan ,
Heping Zhang :
Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights.
1766-1771
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journals/bioinformatics/ReichOATM04 Applications Notes
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journals/bioinformatics/WangM04
Volume 20, Number 12, August 12 2004 Editorials
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journals/bioinformatics/BatemanV04 Original Papers
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journals/bioinformatics/BeumingW04 Thijs Beuming ,
Harel Weinstein :
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.
1822-1835
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journals/bioinformatics/Barash04 Danny Barash :
Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation.
1861-1869
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journals/bioinformatics/QuX04 Yi Qu ,
Shizhong Xu :
Supervised cluster analysis for microarray data based on multivariate Gaussian mixture.
1905-1913
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journals/bioinformatics/Ardell04 David H. Ardell :
SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.
1986-1988
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journals/bioinformatics/HigaOHMIKMYTN04
Volume 20, Number 13, September 1 2004 Original Papers
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journals/bioinformatics/XirasagarGMTSCYYSXW04 Sandhya Xirasagar ,
Scott F. Gustafson ,
B. Alex Merrick ,
Kenneth B. Tomer ,
Stanley Stasiewicz ,
Denny D. Chan ,
Kenneth J. Yost III ,
John R. Yates III ,
Susan Sumner ,
Nianqing Xiao ,
Michael D. Waters :
CEBS object model for systems biology data, SysBio-OM.
2004-2015
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journals/bioinformatics/KahveciLS04 Applications Notes
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journals/bioinformatics/WenF04 Liting Wen ,
Jin-An Feng :
Repair-FunMap: a functional database of proteins of the DNA repair systems.
2135-2137
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journals/bioinformatics/PandeyGM04
Volume 20, Number 14, September 2004 Editorials
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journals/bioinformatics/Pevzner04 Pavel A. Pevzner :
Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians.
2159-2161
Discovery Notes
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journals/bioinformatics/KantardjieffR04 Letter to the editors
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journals/bioinformatics/HuberK04 Thomas Huber ,
Bostjan Kobe :
Comment on 'Protein isoelectric point as a predictor for increased crystallization screening efficiency'.
2169-2170
Reply to the letters
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journals/bioinformatics/KantardjieffJR04 Katherine A. Kantardjieff ,
Mortaza Jamshidian ,
Bernhard Rupp :
Distributions of pI versus pH provide prior information for the design of crystallization screening experiments: response to comment on 'Protein isoelectric point as a predictor for increased crystallization screening efficiency'.
2171-2174
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journals/bioinformatics/Endo04 Takaho A. Endo :
Probabilistic nucleotide assembling method for sequencing by hybridization.
2181-2188
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journals/bioinformatics/SuskoR04 Edward Susko ,
Andrew J. Roger :
Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys.
2279-2287
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journals/bioinformatics/Heredia-LangnerCJJ04 
