Volume 20,
Number 1,
January 2004
Discovery Note
Original Papers
- Sofia Wichert, Konstantinos Fokianos, Korbinian Strimmer:
Identifying periodically expressed transcripts in microarray time series data.
5-20 BibTeX
- Ying Huang, Yanda Li:
Prediction of protein subcellular locations using fuzzy k-NN method.
21-28 BibTeX
- Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya:
Efficient filtering methods for clustering cDNAs with spliced sequence alignment.
29-39 BibTeX
- Saejoon Kim:
Protein ß-turn prediction using nearest-neighbor method.
40-44 BibTeX
- 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 BibTeX
- Stephan Philippi:
Light-weight integration of molecular biological databases.
51-57 BibTeX
- Jianhua Ruan, Gary D. Stormo, Weixiong Zhang:
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.
58-66 BibTeX
- O. Michael Melko, Arcady R. Mushegian:
Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes.
67-74 BibTeX
- Qiang Tu, Haixu Tang, Dafu Ding:
MedBlast: searching articles related to a biological sequence.
75-77 BibTeX
- Karan Vasudeva, Upinder S. Bhalla:
Adaptive stochastic-deterministic chemical kinetic simulations.
78-84 BibTeX
- Li Zhang, Aidong Zhang, Murali Ramanathan:
VizStruct: exploratory visualization for gene expression profiling.
85-92 BibTeX
- 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 BibTeX
- Song Wang, Stewart Ethier:
A generalized likelihood ratio test to identify differentially expressed genes from microarray data.
100-104 BibTeX
- Monica Benito, Joel Parker, Quan Du, Junyuan Wu, Dong Xiang, Charles M. Perou, James Stephen Marron:
Adjustment of systematic microarray data biases.
105-114 BibTeX
- Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, Adriana Neves dos Reis, José C. M. Mombach:
Essentiality and damage in metabolic networks.
115-119 BibTeX
Applications Notes
- Jung-Hsien Chiang, Hsu-Chun Yu, Huai-Jen Hsu:
GIS: a biomedical text-mining system for gene information discovery.
120-121 BibTeX
- Aaron E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna:
GRIL: genome rearrangement and inversion locator.
122-124 BibTeX
- Nils Blüthgen, Szymon M. Kielbasa, Branka Cajavec, Hanspeter Herzel:
HOMGL - comparing genelists across species and with different accession numbers.
125-126 BibTeX
- Andreas Prlic, Francisco S. Domingues, Peter Lackner, Manfred J. Sippl:
WILMA - automated annotation of protein sequences.
127-128 BibTeX
- David P. Leader:
BugView: a browser for comparing genomes.
129-130 BibTeX
- Liam J. McGuffin, Stefano A. Street, Søren-Aksel Sørensen, David T. Jones:
The Genomic Threading Database.
131-132 BibTeX
- Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, Alain Trubuil:
PARIS: a proteomic analysis and resources indexation system.
133-135 BibTeX
- 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 BibTeX
Volume 20,
Number 2,
January 2004
PAG Meeting Preface
PAG Meeting Original Papers
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Nikoleta Juretic, Thomas E. Bureau, Richard M. Bruskiewich:
Transposable element annotation of the rice genome.
155-160
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Kimmen Sjölander:
Phylogenomic inference of protein molecular function: advances and challenges.
170-179
Electronic Edition (link) BibTeX
PAG Meeting Applications Notes
Original Papers
- Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler:
Prediction of locally stable RNA secondary structures for genome-wide surveys.
186-190
Electronic Edition (link) BibTeX
- Jonathan D. Wren, Harold R. Garner:
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network.
191-198
Electronic Edition (link) BibTeX
- Michal Brylinski, W. Jurkowski, Leszek Konieczny, Irena Roterman:
Limited conformational space for early-stage protein folding simulation.
199-205
Electronic Edition (link) BibTeX
- Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida:
Comparative evaluation of word composition distances for the recognition of SCOP relationships.
206-215
Electronic Edition (link) BibTeX
- Jeffrey T. Chang, Hinrich Schütze, Russ B. Altman:
GAPSCORE: finding gene and protein names one word at a time.
216-225
Electronic Edition (link) BibTeX
- Steffen Klamt, Ernst Dieter Gilles:
Minimal cut sets in biochemical reaction networks.
226-234
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Hideya Kawaji, Yoichi Takenaka, Hideo Matsuda:
Graph-based clustering for finding distant relationships in a large set of protein sequences.
243-252
Electronic Edition (link) BibTeX
- Ulisses 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
Electronic Edition (link) BibTeX
- Albert Burger, Duncan Davidson, Richard A. Baldock:
Formalization of mouse embryo anatomy.
259-267
Electronic Edition (link) BibTeX
Applications Notes
- 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
Electronic Edition (link) BibTeX
- Nancie Reymond, Hubert Charles, Laurent Duret, Federica Calevro, Guillaume Beslon, Jean-Michel Fayard:
ROSO: optimizing oligonucleotide probes for microarrays.
271-273
Electronic Edition (link) BibTeX
- Daniel Barker:
LVB: parsimony and simulated annealing in the search for phylogenetic trees.
274-275
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Ryan Brodie, Rachel L. Roper, Chris Upton:
JDotter: a Java interface to multiple dotplots generated by dotter.
279-281
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Richard J. Orton, William I. Sellers, Dietlind L. Gerloff:
YETI: Yeast Exploration Tool Integrator.
284-285
Electronic Edition (link) BibTeX
- Lakshmi K. Matukumalli, John J. Grefenstette, Tad S. Sonstegard, Curtis P. Van Tassell:
EST-PAGE - managing and analyzing EST data.
286-288
Electronic Edition (link) BibTeX
- Emmanuel Paradis, Julien Claude, Korbinian Strimmer:
APE: Analyses of Phylogenetics and Evolution in R language.
289-290
Electronic Edition (link) BibTeX
- Antonio Jesús Pérez, Guillermo Thode, Oswaldo Trelles:
AnaGram: protein function assignment.
291-292
Electronic Edition (link) BibTeX
Corrigenda
Volume 20,
Number 3,
February 2004
Original Papers
- Lugang Li, Renchao Jin, Poh-Lin Kok, Honghui Wan:
Pseudo-periodic partitions of biological sequences.
295-306
Electronic Edition (link) BibTeX
- Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry:
affy - analysis of Affymetrix GeneChip data at the probe level.
307-315
Electronic Edition (link) BibTeX
- Thomas R. Kiehl, Robert M. Mattheyses, Melvin K. Simmons:
Hybrid simulation of cellular behavior.
316-322
Electronic Edition (link) BibTeX
- Leslie Cope, Rafael A. Irizarry, Harris A. Jaffee, Zhijin Wu, Terence P. Speed:
A benchmark for Affymetrix GeneChip expression measures.
323-331
Electronic Edition (link) BibTeX
- Yihui Luan, Hongzhe Li:
Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data.
332-339
Electronic Edition (link) BibTeX
- Natasa Przulj, Dennis A. Wigle, Igor Jurisica:
Functional topology in a network of protein interactions.
340-348
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Zoltan 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
Electronic Edition (link) BibTeX
- Jeanne Kowalski, Charles Drake, Ronald H. Schwartz, Jonathan Powell:
Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes.
364-373
Electronic Edition (link) BibTeX
- Ulisses Braga-Neto, Edward R. Dougherty:
Is cross-validation valid for small-sample microarray classification?
374-380
Electronic Edition (link) BibTeX
- Sung Geun Lee, Jung Uk Hur, Yang Seok Kim:
A graph-theoretic modeling on GO space for biological interpretation of gene clusters.
381-388
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jacques van Helden:
Metrics for comparing regulatory sequences on the basis of pattern counts.
399-406
Electronic Edition (link) BibTeX
- Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck, Fredrik Ronquist:
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference.
407-415
Electronic Edition (link) BibTeX
Applications Notes
- Mikael Thollesson:
LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences.
416-418
Electronic Edition (link) BibTeX
- Matthew J. Wood, Jonathan D. Hirst:
Predicting protein secondary structure by cascade-correlation neural networks.
419-420
Electronic Edition (link) BibTeX
- Manoj Bhasin, G. P. S. Raghava:
SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence.
421-423
Electronic Edition (link) BibTeX
- Nir Orlev, Ron Shamir, Yosef Shiloh:
PIVOT: Protein Interacions VisualizatiOn Tool.
424-425
Electronic Edition (link) BibTeX
- Michele E. Clamp, James A. Cuff, Stephen M. J. Searle, Geoffrey J. Barton:
The Jalview Java alignment editor.
426-427
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Natasha Levenkova, Qingjuan Gu, John J. Rux:
Gene specific siRNA selector.
430-432
Electronic Edition (link) BibTeX
- Michael Spitzer, Georg Fuellen, Paul Cullen, Stefan Lorkowski:
VisCoSe: visualization and comparison of consensus sequences.
433-435
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Volume 20,
Number 4,
March 2004
Discovery Notes
Original Papers
- Elisabetta Manduchi, Gregory R. Grant, H. He, Junmin Liu, Matthew D. Mailman, A. 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.
Electronic Edition (link) BibTeX
- Yue Huang, Ling Zhang:
Rapid and sensitive dot-matrix methods for genome analysis.
Electronic Edition (link) BibTeX
- Christina S. Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston, William Stafford Noble:
Mismatch string kernels for discriminative protein classification.
Electronic Edition (link) BibTeX
- 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.
Electronic Edition (link) BibTeX
- Daehee Hwang, George Stephanopoulos, Christina Chan:
Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function.
Electronic Edition (link) BibTeX
- Tzu-Ming Chu, B. S. Weir, Russell D. Wolfinger:
Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays.
Electronic Edition (link) BibTeX
- Tatiana V. Karpinets, Brent D. Foy, John M. Frazier:
Tailored gene array databases: applications in mechanistic toxicology.
Electronic Edition (link) BibTeX
- Neil D. Lawrence, Marta Milo, Mahesan Niranjan, Penny Rashbass, Stephan Soullier:
Reducing the variability in cDNA microarray image processing by Bayesian inference.
Electronic Edition (link) BibTeX
- Eytan Adar:
SaRAD: a Simple and Robust Abbreviation Dictionary.
Electronic Edition (link) BibTeX
- Olivier Bastien, Jean-Christophe Aude, Sylvaine Roy, Eric Maréchal:
Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics.
Electronic Edition (link) BibTeX
- Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita:
A multi-algorithm, multi-timescale method for cell simulation.
Electronic Edition (link) BibTeX
- 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.
Electronic Edition (link) BibTeX
- 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.
Electronic Edition (link) BibTeX
- Wen Xue, Jin Wang, Zhirong Shen, Huaiqiu Zhu:
Enrichment of transcriptional regulatory sites in non-coding genomic region.
Electronic Edition (link) BibTeX
Applications Notes
- Sven Ekdahl, Erik L. L. Sonnhammer:
ChromoWheel: a new spin on eukaryotic chromosome visualization.
Electronic Edition (link) BibTeX
- Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo:
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
Electronic Edition (link) BibTeX
- Soohyun Lee, Changwon Kang:
CHOISS for selection of single nucleotide polymorphism markers on interval regularity.
Electronic Edition (link) BibTeX
- Giovanni Lavorgna, Luca Sessa, Alessandro Guffanti, Lelio Lassandro, Giorgio Casari:
AntiHunter: searching BLAST output for EST antisense transcripts.
Electronic Edition (link) BibTeX
- Paul Pavlidis, Ilan Wapinski, William Stafford Noble:
Support vector machine classification on the web.
Electronic Edition (link) BibTeX
- Kevin Murphy, Towfique Raj, R. Scott Winters, Peter S. White:
me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements.
Electronic Edition (link) BibTeX
- Marijke J. van Baren, Peter Heutink:
The PCR Suite.
Electronic Edition (link) BibTeX
- Kentaro Tomii, Yutaka Akiyama:
FORTE: a profile-profile comparison tool for protein fold recognition.
Electronic Edition (link) BibTeX
- 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.
Electronic Edition (link) BibTeX
Volume 20,
Number 5,
March 22 2004
Discovery Notes
Original Papers
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Paul H. C. Eilers, Jelle J. Goeman:
Enhancing scatterplots with smoothed densities.
623-628
Electronic Edition (link) BibTeX
- R. Lavigne, W. D. Sun, G. Volckaert:
PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes.
629-635
Electronic Edition (link) BibTeX
- Nameeta 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Alessandro Vullo, Paolo Frasconi:
Disulfide connectivity prediction using recursive neural networks and evolutionary information.
653-659
Electronic Edition (link) BibTeX
- Blythe Durbin, David M. Rocke:
Variance-stabilizing transformations for two-color microarrays.
660-667
Electronic Edition (link) BibTeX
- Jonathan D. Wren:
404 not found: the stability and persistence of URLs published in MEDLINE.
668-672
Electronic Edition (link) BibTeX
- Feng Gao, Chun-Ting Zhang:
Comparison of various algorithms for recognizing short coding sequences of human genes.
673-681
Electronic Edition (link) BibTeX
- David R. Bickel:
Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes.
682-688
Electronic Edition (link) BibTeX
- Michael A. Gilchrist, Laura A. Salter, Andreas Wagner:
A statistical framework for combining and interpreting proteomic datasets.
689-700
Electronic Edition (link) BibTeX
- Akito Taneda:
Adplot: detection and visualization of repetitive patterns in complete genomes.
701-708
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- H. Fujisawa, S. Eguchi, M. Ushijima, S. Miyata, Y. Miki, T. Muto, M. Matsuura:
Genotyping of single nucleotide polymorphism using model-based clustering.
718-726
Electronic Edition (link) BibTeX
- Hao Sun, Ramana V. Davuluri:
Java-based application framework for visualization of gene regulatory region annotations.
727-734
Electronic Edition (link) BibTeX
- Zheng Rong Yang, Kuo-Chen Chou:
Bio-support vector machines for computational proteomics.
735-741
Electronic Edition (link) BibTeX
- Lap Kun Yeung, Lap Keung Szeto, Alan Wee-Chung Liew, Hong Yan:
Dominant spectral component analysis for transcriptional regulations using microarray time-series data.
742-749
Electronic Edition (link) BibTeX
- Tu Minh Phuong, Doheon Lee, Kwang Hyung Lee:
Regression trees for regulatory element identification.
750-757
Electronic Edition (link) BibTeX
- Yinon Shafrir, H. Robert Guy:
STAM: simple Transmembrane Alignment Method.
758-769
Electronic Edition (link) BibTeX
- Ingolf Sommer, Jörg Rahnenführer, Francisco S. Domingues, U. de Lichtenberg, Thomas Lengauer:
Predicting protein structure classes from function predictions.
770-776
Electronic Edition (link) BibTeX
- Keith A. Baggerly, Jeffrey S. Morris, Kevin R. Coombes:
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments.
777-785
Electronic Edition (link) BibTeX
Application Notes
- Jakob C. Mueller, Christophe Andreoli:
Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity.
786-787
Electronic Edition (link) BibTeX
- Gill Bejerano:
Algorithms for variable length Markov chain modeling.
788-789
Electronic Edition (link) BibTeX
- L. Frangeul, Philippe Glaser, C. Rusniok, C. Buchrieser, E. Duchaud, P. Dehoux, Frank Kunst:
CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects.
790-797
Electronic Edition (link) BibTeX
- Joseba Bikandi, Rosario San Millán, Aitor Rementeria, Javier Garaizar:
In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction.
798-799
Electronic Edition (link) BibTeX
- Andre R. O. Cavalcanti, Laura F. Landweber:
Gene Unscrambler for detangling scrambled genes in ciliates.
800-802
Electronic Edition (link) BibTeX
- Martti T. Tammi, Erik Arner, Ellen Kindlund, Björn Andersson:
ReDiT: Repeat Discrepancy Tagger-a shotgun assembly finishing aid.
803-804
Electronic Edition (link) BibTeX
- Gernot Stocker, Dietmar Rieder, Zlatko Trajanoski:
ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.
805-807
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Volume 20,
Number 6,
April 12 2004
Original Papers
- Ruslan Sadreyev, Nick V. Grishin:
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.
818-828
Electronic Edition (link) BibTeX
- Chun Tang, Aidong Zhang, Murali Ramanathan:
ESPD: a pattern detection model underlying gene expression profiles.
829-838
Electronic Edition (link) BibTeX
- Yoseph Barash, Elinor Dehan, Meir Krupsky, Wilbur Franklin, Marc Geraci, Nir Friedman, Naftali Kaminski:
Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays.
839-846
Electronic Edition (link) BibTeX
- R. B. Vilim, R. M. Cunningham, B. Lu, P. Kheradpour, Fred J. Stevens:
Fold-specific substitution matrices for protein classification.
847-853
Electronic Edition (link) BibTeX
- Dung-Tsa Chen, Sue-Hwa Lin, Seng-jaw Soong:
Gene selection for oligonucleotide array: an approach using PM probe level data.
854-862
Electronic Edition (link) BibTeX
- Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama:
Optimizing substitution matrices by separating score distributions.
863-873
Electronic Edition (link) BibTeX
- Jens Nilsson, Thoas Fioretos, Mattias Höglund, Magnus Fontes:
Approximate geodesic distances reveal biologically relevant structures in microarray data.
874-880
Electronic Edition (link) BibTeX
- Florian Frommlet, Andreas Futschik, Malgorzata Bogdan:
On the significance of sequence alignments when using multiple scoring matrices.
881-887
Electronic Edition (link) BibTeX
- Xiaohong Huang, Wei Pan, Soon J. Park, Xinqiang Han, Leslie W. Miller, Jennifer Hall:
Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares.
888-894
Electronic Edition (link) BibTeX
- Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen:
Mapping gene ontology to proteins based on protein-protein interaction data.
895-902
Electronic Edition (link) BibTeX
- Zheng Rong Yang, Kuo-Chen Chou:
Predicting the linkage sites in glycoproteins using bio-basis function neural network.
903-908
Electronic Edition (link) BibTeX
- Qing Zhou, Jun S. Liu:
Modeling within-motif dependence for transcription factor binding site predictions.
909-916
Electronic Edition (link) BibTeX
- Ming Ouyang, William J. Welsh, Panos Georgopoulos:
Gaussian mixture clustering and imputation of microarray data.
917-923
Electronic Edition (link) BibTeX
- Aniruddha Datta, Ashish Choudhary, Michael L. Bittner, Edward R. Dougherty:
External control in Markovian genetic regulatory networks: the imperfect information case.
924-930
Electronic Edition (link) BibTeX
- Martin Dugas, S. Merk, S. Breit, P. Dirschedl:
mdclust-exploratory microarray analysis by multidimensional clustering.
931-936
Electronic Edition (link) BibTeX
- M. Scott, Guoqing Lu, Michael T. Hallett, David Thomas:
The Hera database and its use in the characterization of endoplasmic reticulum proteins.
937-944
Electronic Edition (link) BibTeX
- Morgan N. Price, Eleanor G. Rieffel:
Finding coexpressed genes in counts-based data: an improved measure with validation experiments.
945-952
Electronic Edition (link) BibTeX
- Michael E. Smoot, Stephanie Guerlain, William R. Pearson:
Visualization of near-optimal sequence alignments.
953-958
Electronic Edition (link) BibTeX
- Kyongbum Lee, Daehee Hwang, Tadaaki Yokoyama, George Stephanopoulos, Gregory Stephanopoulos, Martin L. Yarmush:
Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling data.
959-969
Electronic Edition (link) BibTeX
- Xing Han, Wenjun Kang:
Sequence analysis and membrane partitioning energies of -helical antimicrobial peptides.
970-973
Electronic Edition (link) BibTeX
Applications Notes
- Michael L. Tress, Osvaldo Graña, Alfonso Valencia:
SQUARE-determining reliable regions in sequence alignments.
974-975
Electronic Edition (link) BibTeX
- Nelson Young, Zhan Chang, David S. Wishart:
GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.
976-978
Electronic Edition (link) BibTeX
- Peter N. Robinson, Andreas Wollstein, Ulrike Böhme, Brad Beattie:
Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology.
979-981
Electronic Edition (link) BibTeX
- Ross Hall, Linda Stern:
A rapid method for illustrating features in both coding and non-coding regions of a genome.
982-983
Electronic Edition (link) BibTeX
- Kishore R. Sakharkar, Vincent T. K. Chow:
Exploring genome architecture through GOV: a WWW-based gene order visualizer.
984-985
Electronic Edition (link) BibTeX
- Andrew C. R. Martin:
PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt.
986-988
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Volume 20,
Number 7,
May 1 2004
Original Papers
- Rajeev K. Azad, Mark Borodovsky:
Effects of choice of DNA sequence model structure on gene identification accuracy.
993-1005
Electronic Edition (link) BibTeX
- Robert J. Clifford, Michael Edmonson, Cu Nguyen, Kenneth H. Buetow:
Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms.
1006-1014
Electronic Edition (link) BibTeX
- Natalio Krasnogor, David A. Pelta:
Measuring the similarity of protein structures by means of the universal similarity metric.
1015-1021
Electronic Edition (link) BibTeX
- Adele A. Mitchell, Michael E. Zwick, Aravinda Chakravarti, David J. Cutler:
Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns.
1022-1032
Electronic Edition (link) BibTeX
- Jorge Lepre, John Jeremy Rice, Yuhai Tu, Gustavo Stolovitzky:
Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.
1033-1044
Electronic Edition (link) BibTeX
- Zeyar Aung, Kian-Lee Tan:
Rapid 3D protein structure database searching using information retrieval techniques.
1045-1052
Electronic Edition (link) BibTeX
- Kwok Pui Choi, Fanfan Zeng, Louxin Zhang:
Good spaced seeds for homology search.
1053-1059
Electronic Edition (link) BibTeX
- Andrew C. James, Jim G. Veitch, Ali R. Zareh, Timothy Triche:
Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays.
1060-1065
Electronic Edition (link) BibTeX
- Werner G. Krebs, Philip E. Bourne:
Statistically rigorous automated protein annotation.
1066-1073
Electronic Edition (link) BibTeX
- Ramakant Sharma, Jitendra Kumar Maheshwari, Tulika Prakash, Debasis Dash, Samir K. Brahmachari:
Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus.
1074-1080
Electronic Edition (link) BibTeX
- Lida Zhang, Dejun Yuan, Shunwu Yu, Zhugang Li, Youfang Cao, Zhiqi Miao, Hongmei Qian, Kexuan Tang:
Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana.
1081-1086
Electronic Edition (link) BibTeX
- Adrian Arakaki, Yang Zhang, Jeffrey Skolnick:
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.
1087-1096
Electronic Edition (link) BibTeX
- Yohei Minakuchi, Masahiro Ito, Yuji Kohara:
SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis.
1097-1109
Electronic Edition (link) BibTeX
- Ross D. King, Paul H. Wise, Amanda Clare:
Confirmation of data mining based predictions of protein function.
1110-1118
Electronic Edition (link) BibTeX
- Goro Terai, Toshihisa Takagi:
Predicting rules on organization of cis-regulatory elements, taking the order of elements into account.
1119-1128
Electronic Edition (link) BibTeX
- Jesús A. Izaguirre, Rajiv Chaturvedi, Chengbang Huang, Trevor M. Cickovski, J. Coffland, G. Thomas, G. Forgacs, Mark S. Alber, G. Hentschel, Stuart A. Newman, James A. Glazier:
COMPUCELL, a multi-model framework for simulation of morphogenesis.
1129-1137
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Yu-Dong Cai, Kuo-Chen Chou:
Predicting subcellular localization of proteins in a hybridization space.
1151-1156
Electronic Edition (link) BibTeX
- Volker Brendel, Liqun Xing, Wei Zhu:
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
1157-1169
Electronic Edition (link) BibTeX
- Yong Wang, Frederick C. C. Leung:
An evaluation of new criteria for CpG islands in the human genome as gene markers.
1170-1177
Electronic Edition (link) BibTeX
- Guodong Zhou, Jie Zhang, Jian Su, Dan Shen, Chew Lim Tan:
Recognizing names in biomedical texts: a machine learning approach.
1178-1190
Electronic Edition (link) BibTeX
Applications Notes
- Jihoon Kim, Hee-Joon Chung, Chan Hee Park, Woong-Yang Park, Ju Han Kim:
ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics.
1191-1192
Electronic Edition (link) BibTeX
- Justin Ebedes, Amitava Datta:
Multiple sequence alignment in parallel on a workstation cluster.
1193-1195
Electronic Edition (link) BibTeX
- N. H. Shah, Nina V. Fedoroff:
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.
1196-1197
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Nigel I. Kirby, Eugene F. DeRose, Robert E. London, Geoffrey A. Mueller:
NvAssign: protein NMR spectral assignment with NMRView.
1201-1203
Electronic Edition (link) BibTeX
Volume 20,
Number 8,
May 22 2004
Original Papers
- Ivan Iossifov, Michael Krauthammer, Carol Friedman, Vasileios Hatzivassiloglou, Joel S. Bader, Kevin P. White, Andrey Rzhetsky:
Probabilistic inference of molecular networks from noisy data sources.
1205-1213
Electronic Edition (link) BibTeX
- Weijia Xu, Daniel P. Miranker:
A metric model of amino acid substitution.
1214-1221
Electronic Edition (link) BibTeX
- Mario Medvedovic, Ka Yee Yeung, Roger Eugene Bumgarner:
Bayesian mixture model based clustering of replicated microarray data.
1222-1232
Electronic Edition (link) BibTeX
- Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong, Cheng Li:
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.
1233-1240
Electronic Edition (link) BibTeX
- Ronaldo Fumio Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, Edward R. Dougherty:
Growing genetic regulatory networks from seed genes.
1241-1247
Electronic Edition (link) BibTeX
- Hagay Shmuely, E. Dinitz, I. Dahan, Jerry Eichler, D. Fischer, Boaz Shaanan:
Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins.
1248-1253
Electronic Edition (link) BibTeX
- Viatcheslav R. Akmaev, Clarence J. Wang:
Correction of sequence-based artifacts in serial analysis of gene expression.
1254-1263
Electronic Edition (link) BibTeX
- Stephane Flibotte, Readman Chiu, Chris Fjell, Martin Krzywinski, Jacqueline E. Schein, Heesun Shin, Marco A. Marra:
Automated ordering of fingerprinted clones.
1264-1271
Electronic Edition (link) BibTeX
- R. Keira Curtis, Martin D. Brand:
Analysing microarray data using modular regulation analysis.
1272-1284
Electronic Edition (link) BibTeX
- Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, Tamar Schlick:
RAG: RNA-As-Graphs database-concepts, analysis, features.
1285-1291
Electronic Edition (link) BibTeX
- Yu-Dong Cai, Andrew J. Doig:
Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition.
1292-1300
Electronic Edition (link) BibTeX
- Robert C. Edgar, Kimmen Sjölander:
A comparison of scoring functions for protein sequence profile alignment.
1301-1308
Electronic Edition (link) BibTeX
- Robert C. Edgar, Kimmen Sjölander:
COACH: profile-profile alignment of protein families using hidden Markov models.
1309-1318
Electronic Edition (link) BibTeX
Applications Notes
- Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Mandar Chitre, Hao Zhu, Kishore R. Sakharkar:
Cellware-a multi-algorithmic software for computational systems biology.
1319-1321
Electronic Edition (link) BibTeX
- Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal:
ConSeq: the identification of functionally and structurally important residues in protein sequences.
1322-1324
Electronic Edition (link) BibTeX
- Jing Hua Zhao:
2LD, GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis.
1325-1326
Electronic Edition (link) BibTeX
- Line Olsen, Morten Hansen, Claus Thorn Ekstrøm, Jesper T. Troelsen, Jørgen Olsen:
CVD: the intestinal crypt/villus in situ hybridization database.
1327-1328
Electronic Edition (link) BibTeX
- Kengo Kinoshita, Haruki Nakamura:
eF-site and PDBjViewer: database and viewer for protein functional sites.
1329-1330
Electronic Edition (link) BibTeX
- Flavio Mignone, David S. Horner, Graziano Pesole:
WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments.
1331-1333
Electronic Edition (link) BibTeX
Volume 20,
Number 9,
June 12 2004
Original Papers
- Niranjan Nagarajan, Golan Yona:
Automatic prediction of protein domains from sequence information using a hybrid learning system.
1335-1360
Electronic Edition (link) BibTeX
- Claudia Rangel, John Angus, Zoubin Ghahramani, Maria Lioumi, Elizabeth Sotheran, Alessia Gaiba, David L. Wild, Francesco Falciani:
Modeling T-cell activation using gene expression profiling and state-space models.
1361-1372
Electronic Edition (link) BibTeX
- Claudia Andreini, Ivano Bertini, Antonio Rosato:
A hint to search for metalloproteins in gene banks.
1373-1380
Electronic Edition (link) BibTeX
- Gerhard Kauer, Helmut Blöcker:
Analysis of disturbed images.
1381-1387
Electronic Edition (link) BibTeX
- Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund:
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.
1388-1397
Electronic Edition (link)
