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ORCIDBioinformatics, Volume 20
Volume 20, Number 1, January 2004
- 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
- Sofia Wichert
, Konstantinos Fokianos, Korbinian Strimmer:
Identifying periodically expressed transcripts in microarray time series data. 5-20 - Ying Huang, Yanda Li:
Prediction of protein subcellular locations using fuzzy k-NN method. 21-28 - Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya:
Efficient filtering methods for clustering cDNAs with spliced sequence alignment. 29-39 - Saejoon Kim:
Protein ß-turn prediction using nearest-neighbor method. 40-44 - Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho:
ClusPro: an automated docking and discrimination method for the prediction of protein complexes. 45-50 - Stephan Philippi:
Light-weight integration of molecular biological databases. 51-57 - Jianhua Ruan, Gary D. Stormo, Weixiong Zhang:
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. 58-66 - O. Michael Melko, Arcady R. Mushegian:
Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes. 67-74 - Qiang Tu, Haixu Tang, Dafu Ding:
MedBlast: searching articles related to a biological sequence. 75-77 - Karan Vasudeva, Upinder S. Bhalla:
Adaptive stochastic-deterministic chemical kinetic simulations. 78-84 - Li Zhang, Aidong Zhang, Murali Ramanathan:
VizStruct: exploratory visualization for gene expression profiling. 85-92 - Jelle J. Goeman, Sara A. van de Geer, Floor de Kort, Hans C. van Houwelingen:
A global test for groups of genes: testing association with a clinical outcome. 93-99 - Song Wang, Stewart Ethier:
A generalized likelihood ratio test to identify differentially expressed genes from microarray data. 100-104 - Mónica Benito, Joel S. Parker, Quan Du, Junyuan Wu, Dong Xiang, Charles M. Perou, James Stephen Marron:
Adjustment of systematic microarray data biases. 105-114 - Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, Adriana Neves dos Reis, José C. M. Mombach:
Essentiality and damage in metabolic networks. 115-119
- Jung-Hsien Chiang, Hsu-Chun Yu, Huai-Jen Hsu:
GIS: a biomedical text-mining system for gene information discovery. 120-121 - Aaron E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna:
GRIL: genome rearrangement and inversion locator. 122-124 - Nils Blüthgen, Szymon M. Kielbasa, Branka Cajavec, Hanspeter Herzel:
HOMGL - comparing genelists across species and with different accession numbers. 125-126 - Andreas Prlic, Francisco S. Domingues, Peter Lackner, Manfred J. Sippl:
WILMA - automated annotation of protein sequences. 127-128 - David P. Leader:
BugView: a browser for comparing genomes. 129-130 - Liam J. McGuffin, Stefano A. Street, Søren-Aksel Sørensen, David T. Jones:
The Genomic Threading Database. 131-132 - Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, Alain Trubuil:
PARIS: a proteomic analysis and resources indexation system. 133-135 - Miklós Cserzo, Frank Eisenhaber, Birgit Eisenhaber, István Simon:
TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. 136-137
Volume 20, Number 2, January 2004
- Richard M. Bruskiewich:
Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competition. 139
- Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, Patrick S. Schnable:
A strategy for assembling the maize (Zea mays L.) genome. 140-147 - Lei Liu, George Gong, Yong Liu, Shreedhar Natarajan, Denis M. Larkin, Annelie Everts-van der Wind, Mark Rebeiz, Jonathan E. Beever:
Multi-species comparative mapping in silico using the COMPASS strategy. 148-154 - Nikoleta Juretic, Thomas E. Bureau, Richard M. Bruskiewich:
Transposable element annotation of the rice genome. 155-160 - Qingsong Zhu, Youping Deng, Phaneendra Vanka, Susan J. Brown, Subbaratnam Muthukrishnan, Karl J. Kramer:
Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome. 161-169 - Kimmen Sjölander:
Phylogenomic inference of protein molecular function: advances and challenges. 170-179
- Brad A. Chapman, John E. Bowers, Stefan R. Schulze, Andrew H. Paterson:
A comparative phylogenetic approach for dating whole genome duplication events. 180-185
- Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler:
Prediction of locally stable RNA secondary structures for genome-wide surveys. 186-190 - Jonathan D. Wren, Harold R. Garner:
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. 191-198 - Michal Brylinski, Wiktor Jurkowski, Leszek Konieczny, Irena Roterman:
Limited conformational space for early-stage protein folding simulation. 199-205 - Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida:
Comparative evaluation of word composition distances for the recognition of SCOP relationships. 206-215 - Jeffrey T. Chang, Hinrich Schütze, Russ B. Altman:
GAPSCORE: finding gene and protein names one word at a time. 216-225 - Steffen Klamt, Ernst Dieter Gilles:
Minimal cut sets in biochemical reaction networks. 226-234 - Susmita Datta, Glen A. Satten, Dale J. Benos, Jiazeng Xia, Martin J. Heslin, Somnath Datta:
An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments. 235-242 - Hideya Kawaji, Yoichi Takenaka, Hideo Matsuda:
Graph-based clustering for finding distant relationships in a large set of protein sequences. 243-252 - Ulisses M. Braga-Neto, Ronaldo Fumio Hashimoto, Edward R. Dougherty, Danh V. Nguyen, Raymond J. Carroll:
Is cross-validation better than resubstitution for ranking genes? 253-258 - Albert Burger, Duncan Davidson, Richard A. Baldock:
Formalization of mouse embryo anatomy. 259-267
- 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 - Nancie Reymond, Hubert Charles, Laurent Duret, Federica Calevro, Guillaume Beslon, Jean-Michel Fayard:
ROSO: optimizing oligonucleotide probes for microarrays. 271-273 - Daniel Barker:
LVB: parsimony and simulated annealing in the search for phylogenetic trees. 274-275 - Shir-Ly Huang, Li-Cheng Wu, Han-Kuen Liang, Kuan-Ting Pan, Jorng-Tzong Horng, Ming-Tat Ko:
PGTdb: a database providing growth temperatures of prokaryotes. 276-278 - Ryan Brodie, Rachel L. Roper, Chris Upton:
JDotter: a Java interface to multiple dotplots generated by dotter. 279-281 - Jeffrey D. Grant, Luke A. Somers, Yue Zhang, Frank J. Manion, Ghislain Bidaut, Michael F. Ochs:
FGDP: functional genomics data pipeline for automated, multiple microarray data analyses. 282-283 - Richard J. Orton, William I. Sellers, Dietlind L. Gerloff:
YETI: Yeast Exploration Tool Integrator. 284-285 - Lakshmi K. Matukumalli, John J. Grefenstette, Tad S. Sonstegard, Curtis P. Van Tassell:
EST-PAGE - managing and analyzing EST data. 286-288 - Emmanuel Paradis, Julien Claude, Korbinian Strimmer:
APE: Analyses of Phylogenetics and Evolution in R language. 289-290 - Antonio J. Pérez-Pulido, Guillermo Thode, Oswaldo Trelles:
AnaGram: protein function assignment. 291-292
- Torgeir R. Hvidsten, Andriy Kryshtafovych, Henryk Jan Komorowski, Krzysztof Fidelis:
A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. 293
Volume 20, Number 3, February 2004
- Lugang Li, Renchao Jin, Poh-Lin Kok, Honghui Wan:
Pseudo-periodic partitions of biological sequences. 295-306 - Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry:
affy - analysis of Affymetrix GeneChip data at the probe level. 307-315 - Thomas R. Kiehl, Robert M. Mattheyses, Melvin K. Simmons:
Hybrid simulation of cellular behavior. 316-322 - Leslie Cope, Rafael A. Irizarry, Harris A. Jaffee, Zhijin Wu, Terence P. Speed:
A benchmark for Affymetrix GeneChip expression measures. 323-331 - Yihui Luan, Hongzhe Li:
Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data. 332-339 - Natasa Przulj, Dennis A. Wigle, Igor Jurisica:
Functional topology in a network of protein interactions. 340-348 - Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz, Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay:
An ontology for collaborative construction and analysis of cellular pathways. 349-356 - Zoltán Kutalik, Jacqueline Inwald, Steve V. Gordon, R. Glyn Hewinson, Philip D. Butcher, Jason Hinds, Kwang-Hyun Cho, Olaf Wolkenhauer:
Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis. 357-363 - Jeanne Kowalski, Charles G. Drake, Ronald H. Schwartz, Jonathan Powell:
Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes. 364-373 - Ulisses M. Braga-Neto, Edward R. Dougherty:
Is cross-validation valid for small-sample microarray classification? 374-380 - Sung Geun Lee, Junguk Hur, Yang Seok Kim:
A graph-theoretic modeling on GO space for biological interpretation of gene clusters. 381-388 - Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, Harold R. Garner:
Knowledge discovery by automated identification and ranking of implicit relationships. 389-398 - Jacques van Helden:
Metrics for comparing regulatory sequences on the basis of pattern counts. 399-406 - Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck, Fredrik Ronquist:
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. 407-415
- Mikael Thollesson:
LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. 416-418 - Matthew J. Wood, Jonathan D. Hirst:
Predicting protein secondary structure by cascade-correlation neural networks. 419-420 - Manoj Bhasin, G. P. S. Raghava:
SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence. 421-423 - Nir Orlev, Ron Shamir, Yosef Shiloh:
PIVOT: Protein Interacions VisualizatiOn Tool. 424-425 - Michele E. Clamp, James A. Cuff, Stephen M. J. Searle, Geoffrey J. Barton:
The Jalview Java alignment editor. 426-427 - Henrik Hornshøj, Henrik Stengaard, Frank Panitz, Christian Bendixen:
SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments. 428-429 - Natasha Levenkova, Qingjuan Gu, John J. Rux:
Gene specific siRNA selector. 430-432 - Michael Spitzer, Georg Fuellen, Paul Cullen, Stefan Lorkowski:
VisCoSe: visualization and comparison of consensus sequences. 433-435 - Susanna L. Lamers, Scott Beason, Luke Dunlap, Robert Compton, Marco Salemi:
HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data. 436-438 - Tu H. Nguyen, Chunyu Liu, Elliot S. Gershon, Francis J. McMahon:
Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers. 439-443
Volume 20, Number 4, March 2004
- Alexey V. Kochetov, Akinori Sarai:
Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana. 445-447 - Zoltán Gáspári, Csaba P. Ortutay, András Perczel:
A simple fold with variations: the pacifastin inhibitor family. 448-451
- Elisabetta Manduchi, Gregory R. Grant, H. He, Junmin Liu, Matthew D. Mailman, Angel D. Pizarro, Patricia L. Whetzel, Christian J. Stoeckert Jr.:
RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies. 452-459 - Yue Huang, Ling Zhang:
Rapid and sensitive dot-matrix methods for genome analysis. 460-466 - Christina S. Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston, William Stafford Noble:
Mismatch string kernels for discriminative protein classification. 467-476 - Shandar Ahmad, M. Michael Gromiha, Akinori Sarai:
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. 477-486 - Daehee Hwang, George Stephanopoulos, Christina Chan:
Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function. 487-499 - Tzu-Ming Chu, B. S. Weir, Russell D. Wolfinger:
Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays. 500-506 - Tatiana V. Karpinets, Brent D. Foy, John M. Frazier:
Tailored gene array databases: applications in mechanistic toxicology. 507-517 - Neil D. Lawrence, Marta Milo, Mahesan Niranjan, Penny Rashbass, Stephan Soullier:
Reducing the variability in cDNA microarray image processing by Bayesian inference. 518-526 - Eytan Adar:
SaRAD: a Simple and Robust Abbreviation Dictionary. 527-533 - Olivier Bastien, Jean-Christophe Aude, Sylvaine Roy, Eric Maréchal:
Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics. 534-537 - Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita:
A multi-algorithm, multi-timescale method for cell simulation. 538-546 - Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, Roman Eisner:
Predicting subcellular localization of proteins using machine-learned classifiers. 547-556 - Florence Horn, Anthony L. Lau, Fred E. Cohen:
Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors. 557-568 - Wen Xue, Jin Wang, Zhirong Shen, Huaiqiu Zhu:
Enrichment of transcriptional regulatory sites in non-coding genomic region. 569-575
- Sven Ekdahl, Erik L. L. Sonnhammer:
ChromoWheel: a new spin on eukaryotic chromosome visualization. 576-577 - Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo:
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. 578-580 - Soohyun Lee, Changwon Kang:
CHOISS for selection of single nucleotide polymorphism markers on interval regularity. 581-582 - Giovanni Lavorgna, Luca Sessa, Alessandro Guffanti, Lelio Lassandro, Giorgio Casari:
AntiHunter: searching BLAST output for EST antisense transcripts. 583-585 - Paul Pavlidis, Ilan Wapinski, William Stafford Noble:
Support vector machine classification on the web. 586-587 - Kevin Murphy, Towfique Raj, R. Scott Winters, Peter S. White:
me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements. 588-590 - Marijke J. van Baren, Peter Heutink:
The PCR Suite. 591-593 - Kentaro Tomii, Yutaka Akiyama:
FORTE: a profile-profile comparison tool for protein fold recognition. 594-595 - Yukimitsu Yabuki, Yuri Mukai, Mark B. Swindells, Makiko Suwa:
GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures. 596-598
Volume 20, Number 5, March 22 2004
- Yong Zhang, Zhihua Zhang, Lunjiang Ling, Baochen Shi, Runsheng Chen:
Conservation analysis of small RNA genes in Escherichia coli. 599-603
- Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Svetlana Novichkova, Alexander Nikitin, Ilya Mazo:
Extracting human protein interactions from MEDLINE using a full-sentence parser. 604-611 - 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 - Paul H. C. Eilers, Jelle J. Goeman:
Enhancing scatterplots with smoothed densities. 623-628 - Rob Lavigne, W. D. Sun, Guido Volckaert:
PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. 629-635 - Nameeta Y. Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak:
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. 636-643 - Alexey V. Antonov, Igor V. Tetko, Michael T. Mader, Jan Budczies, Hans-Werner Mewes:
Optimization models for cancer classification: extracting gene interaction information from microarray expression data. 644-652 - Alessand