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, Bradley J. 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) BibTeX
- John Parkinson, Alasdair Anthony, James Wasmuth, Ralf Schmid, Ann Hedley, Mark Blaxter:
PartiGene-constructing partial genomes.
1398-1404
Electronic Edition (link) BibTeX
- Deepak Sharma, Biju Issac, G. P. S. Raghava, R. Ramaswamy:
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.
1405-1412
Electronic Edition (link) BibTeX
- Phuong-Van Luc, Paul Tempst:
PINdb: a database of nuclear protein complexes from human and yeast.
1413-1415
Electronic Edition (link) BibTeX
- Jeffrey Yuan, Bruce Bush, Alex Elbrecht, Yuan Liu, Theresa Zhang, Wenqing Zhao, Richard Blevins:
Enhanced homology searching through genome reading frame predetermination.
1416-1427
Electronic Edition (link) BibTeX
- Ivo Van Walle, Ignace Lasters, Lode Wyns:
Align-m-a new algorithm for multiple alignment of highly divergent sequences.
1428-1435
Electronic Edition (link) BibTeX
- James J. Chen, Robert R. Delongchamp, Chen-An Tsai, Huey-miin Hsueh, Frank Sistare, Karol L. Thompson, Varsha G. Desai, James C. Fuscoe:
Analysis of variance components in gene expression data.
1436-1446
Electronic Edition (link) BibTeX
- R. Henrik Nilsson, Karl-Henrik Larsson, Björn M. Ursing:
galaxie-CGI scripts for sequence identification through automated phylogenetic analysis.
1447-1452
Electronic Edition (link) BibTeX
Volume 20,
Number 10,
July 1 2004
Editorials
GCB Conference Papers
- Peter F. Arndt, Terence Hwa:
Regional and time-resolved mutation patterns of the human genome.
1482-1485
Electronic Edition (link) BibTeX
- Panos Dafas, Dan M. Bolser, Jacek Gomoluch, Jong Park, Michael Schroeder:
Using convex hulls to extract interaction interfaces from known structures.
1486-1490
Electronic Edition (link) BibTeX
- André Flöter, Jacques Nicolas, Torsten Schaub, Joachim Selbig:
Threshold extraction in metabolite concentration data.
1491-1494
Electronic Edition (link) BibTeX
- Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits:
Conserved RNA secondary structures in viral genomes: a survey.
1495-1499
Electronic Edition (link) BibTeX
- Rainer König, Roland Eils:
Gene expression analysis on biochemical networks using the Potts spin model.
1500-1505
Electronic Edition (link) BibTeX
- Maciej Swat, Alexander E. Kel, Hanspeter Herzel:
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition.
1506-1511
Electronic Edition (link) BibTeX
- Alexander E. Kel, Yuri Tikunov, Nico Voss, Edgar Wingender:
Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods.
1512-1516
Electronic Edition (link) BibTeX
- Florian Sohler, Daniel Hanisch, Ralf Zimmer:
New methods for joint analysis of biological networks and expression data.
1517-1521
Electronic Edition (link) BibTeX
- Nils Weskamp, Daniel Kuhn, Eyke Hüllermeier, Gerhard Klebe:
Efficient similarity search in protein structure databases by k-clique hashing.
1522-1526
Electronic Edition (link) BibTeX
Original Papers
- Michael C. Wendl, Shiaw-Pyng Yang:
Gap statistics for whole genome shotgun DNA sequencing projects.
1527-1534
Electronic Edition (link) BibTeX
- A. Fazel Famili, Ganming Liu, Ziying Liu:
Evaluation and optimization of clustering in gene expression data analysis.
1535-1545
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Shane T. Jensen, Jun S. Liu:
BioOptimizer: a Bayesian scoring function approach to motif discovery.
1557-1564
Electronic Edition (link) BibTeX
- John P. Dekker, Anthony Fodor, Richard W. Aldrich, Gary Yellen:
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments.
1565-1572
Electronic Edition (link) BibTeX
- Björn Voss, Carsten Meyer, Robert Giegerich:
Evaluating the predictability of conformational switching in RNA.
1573-1582
Electronic Edition (link) BibTeX
- Andrew Jones, Ela Hunt, Jonathan M. Wastling, Angel Pizarro, Christian J. Stoeckert Jr.:
An object model and database for functional genomics.
1583-1590
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Rui Kuang, Christina S. Leslie, An-Suei Yang:
Protein backbone angle prediction with machine learning approaches.
1612-1621
Electronic Edition (link) BibTeX
- Alice C. McHardy, Alexander Goesmann, Alfred Pühler, Folker Meyer:
Development of joint application strategies for two microbial gene finders.
1622-1631
Electronic Edition (link) BibTeX
Discovery Notes
Applications Notes
- Thomas Mailund, Christian N. S. Pedersen:
QDist-quartet distance between evolutionary trees.
1636-1637
Electronic Edition (link) BibTeX
- Leping Li, David M. Umbach, Paul Terry, Jack A. Taylor:
Application of the GA/KNN method to SELDI proteomics data.
1638-1640
Electronic Edition (link) BibTeX
- G. Golfier, M. Tran Dang, L. Dauphinot, E. Graison, J. Rossier, M.-C. Potier:
VARAN: a web server for Variability Analysis of DNA microarray experiments.
1641-1643
Electronic Edition (link) BibTeX
- Simon N. Jarman:
Amplicon: software for designing PCR primers on aligned DNA sequences.
1644-1645
Electronic Edition (link) BibTeX
- Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya:
OBIYagns: a grid-based biochemical simulator with a parameter estimator.
1646-1648
Electronic Edition (link) BibTeX
- John Boyle:
SeqExpress: desktop analysis and visualization tool for gene expression experiments.
1649-1650
Electronic Edition (link) BibTeX
- Wolfgang Huber, Robert Gentleman:
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.
1651-1652
Electronic Edition (link) BibTeX
Volume 20,
Number 11,
July 22 2004
- Luciano da Fontoura Costa, M. S. Barbosa, Edson Tadeu Monteiro Manoel, Johannes Streicher, Gerd B. Müller:
Mathematical characterization of three-dimensional gene expression patterns.
1653-1662
Electronic Edition (link) BibTeX
- Debashis Ghosh:
Mixture models for assessing differential expression in complex tissues using microarray data.
1663-1669
Electronic Edition (link) BibTeX
- Eberhard O. Voit, Jonas S. Almeida:
Decoupling dynamical systems for pathway identification from metabolic profiles.
1670-1681
Electronic Edition (link) BibTeX
- Hiroto Saigo, Jean-Philippe Vert, Nobuhisa Ueda, Tatsuya Akutsu:
Protein homology detection using string alignment kernels.
1682-1689
Electronic Edition (link) BibTeX
- Nabil Belacel, Miroslava Cuperlovic-Culf, Mark Laflamme, Rodney Ouellette:
Fuzzy J-Means and VNS methods for clustering genes from microarray data.
1690-1701
Electronic Edition (link) BibTeX
- Thorsteinn S. Rögnvaldsson, Liwen You:
Why neural networks should not be used for HIV-1 protease cleavage site prediction.
1702-1709
Electronic Edition (link) BibTeX
- Jain-Shing Wu, Chungnan Lee, Chien-Chang Wu, Yow-Ling Shiue:
Primer design using genetic algorithm.
1710-1717
Electronic Edition (link) BibTeX
- Audrius Meskauskas, Frank Lehmann-Horn, Karin Jurkat-Rott:
Sight: automating genomic data-mining without programming skills.
1718-1720
Electronic Edition (link) BibTeX
- R. S. Anderssen, Y. Wu, R. Dolferus, I. Saunders:
An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments.
1721-1727
Electronic Edition (link) BibTeX
- Mia Hubert, Sanne Engelen:
Robust PCA and classification in biosciences.
1728-1736
Electronic Edition (link) BibTeX
- Stan Pounds, Cheng Cheng:
Improving false discovery rate estimation.
1737-1745
Electronic Edition (link) BibTeX
- N. Kashtan, S. Itzkovitz, R. Milo, U. Alon:
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
1746-1758
Electronic Edition (link) BibTeX
- Tetsuro Toyoda, Akiyoshi Wada:
Omic space: coordinate-based integration and analysis of genomic phenomic interactions.
1759-1765
Electronic Edition (link) BibTeX
- Fenghai Duan, Heping Zhang:
Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights.
1766-1771
Electronic Edition (link) BibTeX
- Radka Stoyanova, Troy D. Querec, Truman R. Brown, Christos Patriotis:
Normalization of single-channel DNA array data by principal component analysis.
1772-1784
Electronic Edition (link) BibTeX
- Chittibabu Guda, Eoin Fahy, Shankar Subramaniam:
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins.
1785-1794
Electronic Edition (link) BibTeX
- Michael Reich, K. Ohm, Michael Angelo, Pablo Tamayo, Jill P. Mesirov:
GeneCluster 2.0: an advanced toolset for bioarray analysis.
1797-1798
Electronic Edition (link) BibTeX
Applications Notes
- Katsuyuki Yugi, Masaru Tomita:
A general computational model of mitochondrial metabolism in a whole organelle scale.
1795-1796
Electronic Edition (link) BibTeX
- Xinglai Ji, Yuan Yuan, Jesse Li-Ling, Yanda Li, Zhirong Sun:
HMMGEP: clustering gene expression data using hidden Markov models.
1799-1800
Electronic Edition (link) BibTeX
- Chesley M. Leslin, Alexej Abyzov, Valentin A. Ilyin:
Structural exon database, SEDB, mapping exon boundaries on multiple protein structures.
1801-1803
Electronic Edition (link) BibTeX
- Wei Wu, William Stafford Noble:
Genomic data visualization on the Web.
1804-1805
Electronic Edition (link) BibTeX
- Iain Milne, Frank Wright, Glenn Rowe, David F. Marshall, Dirk Husmeier, Gráinne McGuire:
TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.
1806-1807
Electronic Edition (link) BibTeX
- Chang-Xing Ma, Rongling Wu, George Casella:
FunMap: functional mapping of complex traits.
1808-1811
Electronic Edition (link) BibTeX
- Robert Kerkhoven, Frank H. J. van Enckevort, Jos Boekhorst, Douwe Molenaar, Roland J. Siezen:
Visualization for genomics: the Microbial Genome Viewer.
1812-1814
Electronic Edition (link) BibTeX
- Peter M. Haverty, Zhiping Weng:
CisML: an XML-based format for sequence motif detection software.
1815-1817
Electronic Edition (link) BibTeX
- Luquan Wang, Forest Y. Mu:
A Web-based design center for vector-based siRNA and siRNA cassette.
1818-1820
Electronic Edition (link) BibTeX
Volume 20,
Number 12,
August 12 2004
Editorials
Original Papers
- Thijs Beuming, Harel Weinstein:
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.
1822-1835
Electronic Edition (link) BibTeX
- Nadia El-Mabrouk, Damian Labuda:
Haplotypes histories as pathways of recombinations.
1836-1841
Electronic Edition (link) BibTeX
- Eran Halperin, Eleazar Eskin:
Haplotype reconstruction from genotype data using Imperfect Phylogeny.
1842-1849
Electronic Edition (link) BibTeX
- Jon D. McAuliffe, Lior Pachter, Michael I. Jordan:
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.
1850-1860
Electronic Edition (link) BibTeX
- Danny Barash:
Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation.
1861-1869
Electronic Edition (link) BibTeX
- Hongwu Ma, Xue-Ming Zhao, Ying-Jin Yuan, An-Ping Zeng:
Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph.
1870-1876
Electronic Edition (link) BibTeX
- Eduardo D. Sontag, Anatoly Kiyatkin, Boris N. Kholodenko:
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data.
1877-1886
Electronic Edition (link) BibTeX
- Kajsa Ljungberg, Sverker Holmgren, Örjan Carlborg:
Simultaneous search for multiple QTL using the global optimization algorithm DIRECT.
1887-1895
Electronic Edition (link) BibTeX
- Kimberly D. Siegmund, Peter W. Laird, Ite A. Laird-Offringa:
A comparison of cluster analysis methods using DNA methylation data.
1896-1904
Electronic Edition (link) BibTeX
- Yi Qu, Shizhong Xu:
Supervised cluster analysis for microarray data based on multivariate Gaussian mixture.
1905-1913
Electronic Edition (link) BibTeX
- Hong-Chu Chen, Hsiao-Ching Lee, Tsai-Yun Lin, Wen-Hsiung Li, Bor-Sen Chen:
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle.
1914-1927
Electronic Edition (link) BibTeX
- Dirk Steinhauser, Björn H. Junker, Alexander Lüdemann, Joachim Selbig, Joachim Kopka:
Hypothesis-driven approach to predict transcriptional units from gene expression data.
1928-1939
Electronic Edition (link) BibTeX
- Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne:
A case study of high-throughput biological data processing on parallel platforms.
1940-1947
Electronic Edition (link) BibTeX
- Yan Fu, Qiang Yang, Ruixiang Sun, Dequan Li, Rong Zeng, Charles X. Ling, Wen Gao:
Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.
1948-1954
Electronic Edition (link) BibTeX
- Troy D. Querec, Radka Stoyanova, Eric Ross, Christos Patriotis:
A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays.
1955-1961
Electronic Edition (link) BibTeX
Applications Notes
- Urban Liebel, Bjoern Kindler, Rainer Pepperkok:
??Harvester??: a fast meta search engine of human protein resources.
1962-1963
Electronic Edition (link) BibTeX
- Jomuna V. Choudhuri, Chris Schleiermacher, Stefan Kurtz, Robert Giegerich:
GenAlyzer: interactive visualization of sequence similarities between entire genomes.
1964-1965
Electronic Edition (link) BibTeX
- Claudia Voigt, Steffen Möller, Saleh M. Ibrahim, Pablo Serrano-Fernández:
Non-linear conversion between genetic and physical chromosomal distances.
1966-1967
Electronic Edition (link) BibTeX
- Mikita Suyama, David Torrents, Peer Bork:
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
1968-1970
Electronic Edition (link) BibTeX
- Roland Pieler, Fatima Sanchez-Cabo, Hubert Hackl, Gerhard G. Thallinger, Zlatko Trajanoski:
ArrayNorm: comprehensive normalization and analysis of microarray data.
1971-1973
Electronic Edition (link) BibTeX
- Stein Aerts, Peter Van Loo, Yves Moreau, Bart De Moor:
A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes.
1974-1976
Electronic Edition (link) BibTeX
- Carolyn J. Lawrence, Christian M. Zmasek, R. Kelly Dawe, Russell L. Malmberg:
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference.
1977-1979
Electronic Edition (link) BibTeX
- Maksym Korotkiy, Rutger Middelburg, Henk Dekker, Frank van Harmelen, Jan Lankelma:
A tool for gene expression based PubMed search through combining data sources.
1980-1982
Electronic Edition (link) BibTeX
- Roberto H. Higa, Arnaldo J. Montagner, Roberto C. Togawa, Paula R. Kuser, Michel E. B. Yamagishi, Adauto L. Mancini, Georgios Joannis Pappas Jr., Ronald T. Miura, Luiz G. Horita, Goran Neshich:
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure.
1983-1985
Electronic Edition (link) BibTeX
- David H. Ardell:
SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.
1986-1988
Electronic Edition (link) BibTeX
- Roberto H. Higa, Adilton G. Oliveira, Luiz G. Horita, Ronald T. Miura, Marcus K. Inoue, Paula R. Kuser, Adauto L. Mancini, Michel E. B. Yamagishi, Roberto C. Togawa, Goran Neshich:
Defining 3D residue environment in protein structures using SCORPION and FORMIGA.
1989-1991
Electronic Edition (link) BibTeX
Volume 20,
Number 13,
September 1 2004
Original Papers
- Jan Ihmels, Sven Bergmann, Naama Barkai:
Defining transcription modules using large-scale gene expression data.
1993-2003
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- HyungJun Cho, Jae K. Lee:
Bayesian hierarchical error model for analysis of gene expression data.
2016-2025
Electronic Edition (link) BibTeX
- David P. Kreil, Natasha A. Karp, Kathryn S. Lilley:
DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results.
2026-2034
Electronic Edition (link) BibTeX
- Hiroshi Wako, Masaki Kato, Shigeru Endo:
ProMode: a database of normal mode analyses on protein molecules with a full-atom model.
2035-2043
Electronic Edition (link) BibTeX
- Daniel H. Huson, Mike A. Steel:
Phylogenetic trees based on gene content.
2044-2049
Electronic Edition (link) BibTeX
- Andrew B. Horne, T. Charles Hodgman, Hugh D. Spence, Andrew R. Dalby:
Constructing an enzyme-centric view of metabolism.
2050-2055
Electronic Edition (link) BibTeX
- Momiao Xiong, Jinying Zhao, Hao Xiong:
Network-based regulatory pathways analysis.
2056-2066
Electronic Edition (link) BibTeX
- Mark Chaisson, Pavel A. Pevzner, Haixu Tang:
Fragment assembly with short reads.
2067-2074
Electronic Edition (link) BibTeX
- Morris A. Swertz, E. O. de Brock, Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Richard J. S. Baerends, Jan Kok, Oscar P. Kuipers, Ritsert C. Jansen:
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
2075-2083
Electronic Edition (link) BibTeX
- Antonio Jesús Pérez, Carolina Perez-Iratxeta, Peer Bork, Guillermo Thode, Miguel A. Andrade:
Gene annotation from scientific literature using mappings between keyword systems.
2084-2091
Electronic Edition (link) BibTeX
- Monica Chagoyen, M. Erdem Kurul, Pedro A. de Alarcón, José María Carazo, Amarnath Gupta:
Designing and executing scientific workflows with a programmable integrator.
2092-2100
Electronic Edition (link) BibTeX
- Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi:
Efficient selection of unique and popular oligos for large EST databases.
2101-2112
Electronic Edition (link) BibTeX
- Vladimir Makarenkov, François-Joseph Lapointe:
A weighted least-squares approach for inferring phylogenies from incomplete distance matrices.
2113-2121
Electronic Edition (link) BibTeX
- Tamer Kahveci, Vebjorn Ljosa, Ambuj K. Singh:
Speeding up whole-genome alignment by indexing frequency vectors.
2122-2134
Electronic Edition (link) BibTeX
Applications Notes
- Liting Wen, Jin-An Feng:
Repair-FunMap: a functional database of proteins of the DNA repair systems.
2135-2137
Electronic Edition (link) BibTeX
- Jonathan J. Ward, Liam J. McGuffin, Kevin Bryson, Bernard F. Buxton, David T. Jones:
The DISOPRED server for the prediction of protein disorder.
2138-2139
Electronic Edition (link) BibTeX
- Nikola Stojanovic, Ken Dewar:
Identifying multiple alignment regions satisfying simple formulas and patterns.
2140-2142
Electronic Edition (link) BibTeX
- Brett G. Olivier, Jacky L. Snoep:
Web-based kinetic modelling using JWS Online.
2143-2144
Electronic Edition (link) BibTeX
- Adauto L. Mancini, Roberto H. Higa, Adilton G. Oliveira, Fabiana Dominiquini, Paula R. Kuser, Michel E. B. Yamagishi, Roberto C. Togawa, Goran Neshich:
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces.
2145-2147
Electronic Edition (link) BibTeX
- Andrés Moreira, Alejandro Maass:
TIP: protein backtranslation aided by genetic algorithms.
2148-2149
Electronic Edition (link) BibTeX
- Gad Getz, Alina Starovolsky, Eytan Domany:
F2CS: FSSP to CATH and SCOP prediction server.
2150-2152
Electronic Edition (link) BibTeX
- Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, John D. Westbrook:
Ligand Depot: a data warehouse for ligands bound to macromolecules.
2153-2155
Electronic Edition (link) BibTeX
- Ritu Pandey, Raghavendra K. Guru, David W. Mount:
Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data.
2156-2158
Electronic Edition (link) BibTeX
Volume 20,
Number 14,
September 2004
Editorials
Discovery Notes
Letter to the editors
Reply to the letters
Original papers
- Bin Qian, Richard A. Goldstein:
Performance of an iterated T-HMM for homology detection.
2175-2180
Electronic Edition (link) BibTeX
- Takaho A. Endo:
Probabilistic nucleotide assembling method for sequencing by hybridization.
2181-2188
Electronic Edition (link) BibTeX
- Tuan D. Pham, Denis I. Crane, Tuan H. Tran, Tam H. Nguyen:
Extraction of fluorescent cell puncta by adaptive fuzzy segmentation.
2189-2196
Electronic Edition (link) BibTeX
- H. P. Shanahan, Janet M. Thornton:
An examination of the conservation of surface patch polarity for proteins.
2197-2204
Electronic Edition (link) BibTeX
- Guillaume Koum, Augustin Yekel, Bengyella Ndifon, Frédéric Simard:
Design and implementation of a mosquito database through an entomological ontology.
2205-2211
Electronic Edition (link) BibTeX
- Ekaterina Poustelnikova, Andrei Pisarev, Maxim Blagov, Maria Samsonova, John Reinitz:
A database for management of gene expression data in situ.
2212-2221
Electronic Edition (link) BibTeX
- Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler:
Alignment of RNA base pairing probability matrices.
2222-2227
Electronic Edition (link) BibTeX
- Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer, Thomas Lengauer:
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures.
2228-2235
Electronic Edition (link) BibTeX
- C. J. Zheng, H. Zhou, B. Xie, L. Y. Han, Chun Wei Yap, Yu Zong Chen:
TRMP: a database of therapeutically relevant multiple pathways.
2236-2241
Electronic Edition (link) BibTeX
- Scott L. Carter, Christian M. Brechbühler, Michael Griffin, Andrew T. Bond:
Gene co-expression network topology provides a framework for molecular characterization of cellular state.
2242-2250
Electronic Edition (link) BibTeX
- Dawn J. Brooks, Jacques R. Fresco, Mona Singh:
A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor.
2251-2257
Electronic Edition (link) BibTeX
- Linyong Mao, Haluk Resat:
Probabilistic representation of gene regulatory networks.
2258-2269
Electronic Edition (link) BibTeX
- Claus Thorn Ekstrøm, Søren Bak, Charlotte Kristensen, Mats Rudemo:
Spot shape modelling and data transformations for microarrays.
2270-2278
Electronic Edition (link) BibTeX
- Edward Susko, Andrew J. Roger:
Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys.
2279-2287
Electronic Edition (link) BibTeX
- James E. Bray, Russell L. Marsden, Stuart C. G. Rison, Alexei Savchenko, Aled M. Edwards, Janet M. Thornton, Christine A. Orengo:
A practical and robust sequence search strategy for structural genomics target selection.
2288-2295
Electronic Edition (link) BibTeX
- Alejandro Heredia-Langner, William R. Cannon, Kenneth D. Jarman, Kristin H. Jarman:
Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data.
2296-2304
Electronic Edition (link) BibTeX
Application notes
- Markus Ringnér, Srinivas Veerla, Samuel Andersson, Johan Staaf, Jari Häkkinen:
ACID: a database for microarray clone information.
2305-2306
Electronic Edition (link) BibTeX
- R. Ciria, Cei Abreu-Goodger, Enrique Morett, Enrique Merino:
GeConT: gene context analysis.
2307-2308
Electronic Edition (link) BibTeX
- Yin-Te Tsai, Yen Pin Huang, Ching Ta Yu, Chin Lung Lu:
MuSiC: a tool for multiple sequence alignment with constraints.
2309-2311
Electronic Edition (link) BibTeX
- Todd J. Dolinsky, P. M. J. Burgers, Kevin Karplus, Nathan A. Baker:
SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome.
2312-2314
Electronic Edition (link) BibTeX
- M. B. Lanktree, L. VanderBeek, F. M. Macciardi, J. L. Kennedy:
PedSplit: pedigree management for stratified analysis.
2315-2316
Electronic Edition (link) BibTeX
- Thomas Huber, Geoffrey Faulkner, Philip Hugenholtz:
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.
2317-2319
Electronic Edition (link) BibTeX
- Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur:
MedPost: a part-of-speech tagger for bioMedical text.
2320-2321
Electronic Edition (link) BibTeX
- George Savva, Jenn Conn, Jo L. Dicks:
Drawing phylogenetic trees in LATEX and Microsoft Word.
2322-2323
Electronic Edition (link) BibTeX
- Anne Arcade, Aymeric Labourdette, Matthieu Falque, Brigitte Mangin, Fabien Chardon, Alain Charcosset, Johann Joets:
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes.
2324-2326
Electronic Edition (link) BibTeX
- Frank Dudbridge, Tim Carver, Gary W. Williams:
Pelican: pedigree editor for linkage computer analysis.
2327-2328
Electronic Edition (link) BibTeX
- Fran Supek, Kristian Vlahovicek:
INCA: synonymous codon usage analysis and clustering by means of self-organizing map.
2329-2330
Electronic Edition (link) BibTeX
- Florian Iragne, Aurélien Barré, Nicolas Goffard, Antoine de Daruvar:
AliasServer: a web server to handle multiple aliases used to refer to proteins.
2331-2332
Electronic Edition (link) BibTeX
Volume 20,
Number 15,
October 2004
Original Papers
- Brian Marsden, Ruben Abagyan:
SAD - a normalized structural alignment database: improving sequence-structure alignments.
2333-2344
Electronic Edition (link) BibTeX
- Ruxandra I. Dima, D. Thirumalai:
Proteins associated with diseases show enhanced sequence correlation between charged residues.
2345-2354
Electronic Edition (link) BibTeX
- Charles Semple, Philip Daniel, Wim Hordijk, Roderic D. M. Page, Mike A. Steel:
Supertree algorithms for ancestral divergence dates and nested taxa.
2355-2360
Electronic Edition (link) BibTeX
- Neil F. W. Saunders, Paul M. G. Curmi, Ricardo Cavicchioli:
An online database for the detection of novel archaeal sequences in human ESTs.
2361-2362
Electronic Edition (link) BibTeX
- Jukka Corander, Patrik Waldmann, Pekka Marttinen, Mikko J. Sillanpää:
BAPS 2: enhanced possibilities for the analysis of genetic population structure.
2363-2369
Electronic Edition (link) BibTeX
- N. Simonis, Shoshana J. Wodak, G. N. Cohen, Jacques van Helden:
Combining pattern discovery and discriminant analysis to predict gene co-regulation.
2370-2379
Electronic Edition (link) BibTeX
- Ricardo Núñez Miguel:
Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families.
2380-2389
Electronic Edition (link) BibTeX
- Yan Zhang, David A. Eberhard, Gretchen D. Frantz, Patrick Dowd, Thomas D. Wu, Yan Zhou, Colin K. Watanabe, Shiuh-Ming Luoh, Paul Polakis, Kenneth J. Hillan, William I. Wood, Zemin Zhang:
GEPIS - quantitative gene expression profiling in normal and cancer tissues.
2390-2398
Electronic Edition (link) BibTeX
- Paul C. Boutros, Allan B. Okey:
PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design.
2399-2400
Electronic Edition (link) BibTeX
- Jonathan M. Keith, Peter Adams, Darryn E. Bryant, Duncan A. E. Cochran, Gita H. Lala, Keith R. Mitchelson:
Algorithms for sequence analysis via mutagenesis.
2401-2410
Electronic Edition (link) BibTeX
- Jyrki P. Kukkonen:
Explicit formulation of different receptor-G-protein interactions and effector regulation.
2411-2420
Electronic Edition (link) BibTeX
- Yuriy Fofanov, Yi Luo, Charles Katili, Jim Wang, Yuri Belosludtsev, Thomas Powdrill, Chetan Belapurkar, Viacheslav Fofanov, Tong-Bin Li, Sergei Chumakov, B. Montgomery Pettitt:
How independent are the appearances of n-mers in different genomes?
2421-2428
Electronic Edition (link) BibTeX
- Tao Li, Chengliang Zhang, Mitsunori Ogihara:
A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression.
2429-2437
Electronic Edition (link) BibTeX
- Jeroen J. Jansen, Huub C. J. Hoefsloot, Hans F. M. Boelens, Jan van der Greef, Age K. Smilde:
Analysis of longitudinal metabolomics data.
2438-2446
Electronic Edition (link) BibTeX
- Matthias Scholz, S. Gatzek, A. Sterling, Oliver Fiehn, Joachim Selbig:
Metabolite fingerprinting: detecting biological features by independent component analysis.
2447-2454
Electronic Edition (link) BibTeX
Application notes
- José María Fernández, Alfonso Valencia:
YAdumper: extracting and translating large information volumes from relational databases to structured flat files.
2455-2457
Electronic Edition (link) BibTeX
- Jan K. Rainey, M. Cynthia Goh:
An interactive triple-helical collagen builder.
2458-2459
Electronic Edition (link) BibTeX
- Aleksey A. Porollo, Rafal Adamczak, Jaroslaw Meller:
POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins.
2460-2462
Electronic Edition (link) BibTeX
- Kevin L. Garwood, Chris F. Taylor, Kai J. Runte, Andy Brass, Stephen G. Oliver, Norman W. Paton:
Pedro: a configurable data entry tool for XML.
2463-2465
Electronic Edition (link) BibTeX
- Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong, Jong Park:
HPID: The Human Protein Interaction Database.
2466-2470
Electronic Edition (link) BibTeX
- Owen J. Marshall:
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR.
2471-2472
Electronic Edition (link) BibTeX
- Jiren Wang, Kuo-Bin Li, Wing-Kin Sung:
G-PRIMER: greedy algorithm for selecting minimal primer set.
2473-2475
Electronic Edition (link) BibTeX
- Seán I. O'Donoghue, Joachim E. W. Meyer, Andrea Schafferhans, Karsten Fries:
The SRS 3D module: integrating structures, sequences and features.
2476-2478
Electronic Edition (link) BibTeX
- Eibe Frank, Mark Hall, Leonard E. Trigg, Geoffrey Holmes, Ian H. Witten:
Data mining in bioinformatics using Weka.
2479-2481
Electronic Edition (link) BibTeX
- Daniel Fischer, Jakub Pas, Leszek Rychlewski:
The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries.
2482-2484
Electronic Edition (link) BibTeX
- Guillaume Laval, Laurent Excoffier:
SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history.
2485-2487
Electronic Edition (link) BibTeX
- Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer:
Sfixem - graphical sequence feature display in Java.
2488-2490
Electronic Edition (link) BibTeX
- Alexander G. Williams, Robert W. Williams:
GenomeMixer: a complex genetic cross simulator.
2491-2492
Electronic Edition (link) BibTeX
Volume 20,
Number 16,
November 2004
Review
Discovery notes
Original papers
- Sanju Attoor, Edward R. Dougherty, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent:
Which is better for cDNA-microarray-based classification: ratios or direct intensities.
2513-2520
Electronic Edition (link) BibTeX
- Delong Liu, Clarice R. Weinberg, Shyamal D. Peddada:
A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions.
2521-2528
Electronic Edition (link) BibTeX
- Xiaoqiu Huang, Liang Ye, Hui-Hsien Chou, I-Hsuan Yang, Kun-Mao Chao:
Efficient combination of multiple word models for improved sequence comparison.
2529-2533
Electronic Edition (link) BibTeX
- Jinwook Seo, Marina Bakay, Yi-Wen Chen, Sara Hilmer, Ben Shneiderman, Eric P. Hoffman:
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.
2534-2544
Electronic Edition (link) BibTeX
- Roxana Alexandridis, Shili Lin, Mark Irwin:
Class discovery and classification of tumor samples using mixture modeling of gene expression data - a unified approach.
2545-2552
Electronic Edition (link) BibTeX
- Mahlet G. Tadesse, Marina Vannucci, Pietro Liò:
Identification of DNA regulatory motifs using Bayesian variable selection.
2553-2561
Electronic Edition (link) BibTeX
- Philippe Broët, Alex Lewin, Sylvia Richardson, Cyril Dalmasso, Henri Magdelenat:
A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments.
2562-2571
Electronic Edition (link) BibTeX
- Kuo-Bin Li, Praveen Issac, Arun Krishnan:
Predicting allergenic proteins using wavelet transform.
2572-2578
Electronic Edition (link) BibTeX
- Shobhit Gupta, Dorothea Zink, Bernhard Korn, Martin Vingron, Stefan A. Haas:
Genome wide identification and classification of alternative splicing based on EST data.
2579-2585
Electronic Edition (link) BibTeX
- Chien-Yu Chen, Yen-Jen Oyang, Hsueh-Fen Juan:
Incremental generation of summarized clustering hierarchy for protein family analysis.
2586-2596
Electronic Edition (link) BibTeX
- Martijn J. Schuemie, Marc Weeber, Bob J. A. Schijvenaars, Erik M. van Mulligen, C. Christiaan van der Eijk, Rob Jelier, Barend Mons, Jan A. Kors:
Distribution of information in biomedical abstracts and full-text publications.
2597-2604
Electronic Edition (link) BibTeX
- Feng Luo, Latifur Khan, Farokh B. Bastani, I-Ling Yen, Jizhong Zhou:
A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles.
2605-2617
Electronic Edition (link) BibTeX
- Marcel Smid, Lambert C. J. Dorssers:
GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms.
2618-2625
Electronic Edition (link) BibTeX
- Gert R. G. Lanckriet, Tijl De Bie, Nello Cristianini, Michael I. Jordan, William Stafford Noble:
A statistical framework for genomic data fusion.
2626-2635
Electronic Edition (link) BibTeX
- Claude Pasquier, F. Girardot, K. Jevardat de Fombelle, R. Christen:
THEA: ontology-driven analysis of microarray data.
2636-2643
Electronic Edition (link) BibTeX
- Harm van Bakel, Martijn A. Huynen, Cisca Wijmenga:
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
2644-2655
Electronic Edition (link) BibTeX
- Y.-F. Liu, U.-C. Yang:
SCA db: spinocerebellar ataxia candidate gene database.
2656-2661
Electronic Edition (link) BibTeX
- Koji Kyoda, Kotaro Baba, Shuichi Onami, Hiroaki Kitano:
DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants.
2662-2675
Electronic Edition (link) BibTeX
- Prudence W. H. Wong, Tak Wah Lam, N. Lu, Hing-Fung Ting, Siu-Ming Yiu:
An efficient algorithm for optimizing whole genome alignment with noise.
2676-2684
Electronic Edition (link) BibTeX
- Lori E. Dodd, Edward L. Korn, Lisa M. McShane, G. V. R. Chandramouli, Eric Y. Chuang:
Correcting log ratios for signal saturation in cDNA microarrays.
2685-2693
Electronic Edition (link) BibTeX
- J. G. Liao, Yong Lin, Zachariah E. Selvanayagam, Weichung Joe Shih:
A mixture model for estimating the local false discovery rate in DNA microarray analysis.
2694-2701
Electronic Edition (link) BibTeX
- Arun Krishnan, Francis Tang:
Exhaustive whole-genome tandem repeats search.
2702-2710
Electronic Edition (link) BibTeX
- Liping Ji, Kian-Lee Tan:
Mining gene expression data for positive and negative co-regulated gene clusters.
2711-2718
Electronic Edition (link) BibTeX
- Nicolas Omont, François Képès:
Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication.
2719-2725
Electronic Edition (link) BibTeX
- Robert Mansourian, David M. Mutch, Nicolas Antille, Jerome Aubert, Paul Fogel, Jean-Marc Le Goff, Julie Moulin, Anton Petrov, Andreas Rytz, Johannes J. Voegel, Matthew-Alan Roberts:
The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data.
2726-2737
Electronic Edition (link) BibTeX
- Yonatan H. Grad, Frederick P. Roth, Marc S. Halfon, George M. Church:
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.
2738-2750
Electronic Edition (link) BibTeX
- Harpreet Kaur, G. P. S. Raghava:
A neural network method for prediction of ?-turn types in proteins using evolutionary information.
2751-2758
Electronic Edition (link) BibTeX
- Zheng Rong Yang:
Mining gene expression data based on template theory.
2759-2766
Electronic Edition (link) BibTeX
- Yimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, Pierre Baldi:
ICBS: a database of interactions between protein chains mediated by ?-sheet formation.
2767-2777
Electronic Edition (link) BibTeX
- Karla V. Ballman, Diane E. Grill, Ann L. Oberg, Terry M. Therneau:
Faster cyclic loess: normalizing RNA arrays via linear models.
2778-2786
Electronic Edition (link) BibTeX
- Manuel Martínez-Bueno, Antonio J. Molina-Henares, Eduardo Pareja, Juan L. Ramos, Raquel Tobes:
BacTregulators: a database of transcriptional regulators in bacteria and archaea.
2787-2791
Electronic Edition (link) BibTeX
- M. Pérez-Enciso, I. Misztal:
Qxpak: a versatile mixed model application for genetical genomics and QTL analyses.
2792-2798
Electronic Edition (link) BibTeX
- Sündüz Keles, Mark J. van der Laan, Chris Vulpe:
Regulatory motif finding by logic regression.
2799-2811
Electronic Edition (link) BibTeX
- Olivier Delgrange, Eric Rivals:
STAR: an algorithm to Search for Tandem Approximate Repeats.
2812-2820
Electronic Edition (link) BibTeX
- Shu-Dong Zhang, Timothy W. Gant:
A statistical framework for the design of microarray experiments and effective detection of differential gene expression.
2821-2828
Electronic Edition (link) BibTeX
Applications notes
- Bruce E. Shapiro, Michael Hucka, Andrew Finney, John Doyle:
MathSBML: a package for manipulating SBML-based biological models.
2829-2831
Electronic Edition (link) BibTeX
- Luiz G. P. Almeida, Roger F. C. Paixão, Rangel C. Souza, Gisele C. da Costa, Frank J. A. Barrientos, M. Trindade dos Santos, Darcy F. de Almeida, Ana Tereza R. Vasconcelos:
A System for Automated Bacterial (genome) Integrated Annotation - SABIA.
2832-2833
Electronic Edition (link) BibTeX
- Robert Friedman, Vikram Ekollu, John R. Rose, Austin L. Hughes:
Dblox: a genome-wide test for ancient segmental duplication.
2834-2835
Electronic Edition (link) BibTeX
- Eisuke Chikayama, Atsushi Kurotani, Yutaka Kuroda, Shigeyuki Yokoyama:
ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences.
2836-2838
Electronic Edition (link) BibTeX
- Terry M. Casstevens, Edward S. Buckler:
GDPC: connecting researchers with multiple integrated data sources.
2839-2840
Electronic Edition (link) BibTeX
- Alexander Lüdemann, Daniel Weicht, Joachim Selbig, Joachim Kopka:
PaVESy: Pathway Visualization and Editing System.
2841-2844
Electronic Edition (link) BibTeX
- Sandra Barth, Markus Fischer, Rolf D. Schmid, Jürgen Pleiss:
The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions.
2845-2847
Electronic Edition (link) BibTeX
- Fulvio Lazzarato, Giuliana Franceschinis, Marco Botta, Francesca Cordero, Raffaele Calogero:
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets.
2848-2850
Electronic Edition (link) BibTeX
- Boris Adryan, Reinhard Schuh:
Gene-Ontology-based clustering of gene expression data.
2851-2852
Electronic Edition (link) BibTeX
- Sachiyo Aburatani, Kousuke Goto, Shigeru Saito, Masaki Fumoto, Akira Imaizumi, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Hiroyuki Toh, Katsuhisa Horimoto:
ASIAN: a website for network inference.
2853-2856
Electronic Edition (link) BibTeX
- Stephen C. Grubb, Gary A. Churchill, Molly A. Bogue:
A collaborative database of inbred mouse strain characteristics.
2857-2859
Electronic Edition (link) BibTeX
- Li Chen, Rose Oughtred, Helen M. Berman, John D. Westbrook:
TargetDB: a target registration database for structural genomics projects.
2860-2862
Electronic Edition (link) BibTeX
- W. H. Lee, V. B. Vega:
Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies.
2863-2864
Electronic Edition (link) BibTeX
- Song Li, Hui-Hsien Chou:
LUCY2: an interactive DNA sequence quality trimming and vector removal tool.
2865-2866
Electronic Edition (link) BibTeX
- Mario A. Fares:
SWAPSC: sliding window analysis procedure to detect selective constraints.
2867-2868
Electronic Edition (link) BibTeX
- Ghislain Bidaut, Michael F. Ochs:
ClutrFree: cluster tree visualization and interpretation.
2869-2871
Electronic Edition (link) BibTeX
- Duhong Chen, Oliver Eulenstein, David Fernández-Baca:
Rainbow: a toolbox for phylogenetic supertree construction and analysis.
2872-2873
Electronic Edition (link) BibTeX
- Robert N. Goldberg, Yadu B. Tewari, Talapady N. Bhat:
Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry.
2874-2877
Electronic Edition (link) BibTeX
- William H. Majoros, Mihaela Pertea, Steven Salzberg:
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
2878-2879
Electronic Edition (link) BibTeX
- Fang Liu, Tor-Kristian Jenssen, Vegard Nygaard, John Sack, Eivind Hovig:
FigSearch: a figure legend indexing and classification system.
2880-2882
Electronic Edition (link) BibTeX
- P. D'Addabbo, Luca Lenzi, Federica Facchin, Raffaella Casadei, Silvia Canaider, Lorenza Vitale, Flavia Frabetti, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli:
GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers.
2883-2885
Electronic Edition (link) BibTeX
- Tulika Prakash, Mamta Khandelwal, Dipayan Dasgupta, Debasis Dash, Samir K. Brahmachari:
CoPS: Comprehensive Peptide Signature Database.
2886-2888
Electronic Edition (link) BibTeX
- Andreas M. Boehm, Florian Grosse-Coosmann, Albert Sickmann:
Command line tool for calculating theoretical MS spectra for given sequences.
2889-2891
Electronic Edition (link) BibTeX
Volume 20,
Number 17,
November 2004
Editorials
Letter To The Editors
Discovery Notes
- Neeraj Pandey, Mythily Ganapathi, Kaushal Kumar, Dipayan Dasgupta, Sushanta Kumar Das Sutar, Debasis Dash:
Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins.
2904-2910
Electronic Edition (link) BibTeX
- Eric Bonnet, Jan Wuyts, Pierre Rouzé, Yves Van de Peer:
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
2911-2917
Electronic Edition (link) BibTeX
Original Papers
- Xiaobo Zhou, Xiaodong Wang, Ranadip Pal, Ivan Ivanov, Michael L. Bittner, Edward R. Dougherty:
A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks.
2918-2927
Electronic Edition (link) BibTeX
- Sven Rahmann, Christine Gräfe:
Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions.
2928-2933
Electronic Edition (link) BibTeX
- Iosifina Pournara, Lorenz Wernisch:
Reconstruction of gene networks using Bayesian learning and manipulation experiments.
2934-2942
Electronic Edition (link) BibTeX
- Madhuchhanda Bhattacharjee, Colin C. Pritchard, Peter S. Nelson, Elja Arjas:
Bayesian integrated functional analysis of microarray data.
2943-2953
Electronic Edition (link) BibTeX
- Wenqing He:
A spline function approach for detecting differentially expressed genes in microarray data analysis.
2954-2963
Electronic Edition (link) BibTeX
- Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon:
Transmembrane proteins in the Protein Data Bank: identification and classification.
2964-2972
Electronic Edition (link) BibTeX
- Ji-Ping Z. Wang, Bruce G. Lindsay, James Leebens-Mack, Liying Cui, P. Kerr Wall, Webb C. Miller, Claude W. dePamphilis:
EST clustering error evaluation and correction.
2973-2984
Electronic Edition (link) BibTeX
- Christian Baumgartner, Christian Böhm, Daniela Baumgartner, G. Marini, K. Weinberger, B. Olgemöller, B. Liebl, A. A. Roscher:
Supervised machine learning techniques for the classification of metabolic disorders in newborns.
2985-2996
Electronic Edition (link) BibTeX
- Cynthia Sims Parr, Bongshin Lee, Dana Campbell, Benjamin B. Bederson:
Visualizations for taxonomic and phylogenetic trees.
2997-3004
Electronic Edition (link) BibTeX
- Jörn Lewin, Armin O. Schmitt, Péter Adorján, Thomas Hildmann, Christian Piepenbrock:
Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates.
3005-3012
Electronic Edition (link) BibTeX
- A. D. King, Natasa Przulj, Igor Jurisica:
Protein complex prediction via cost-based clustering.
3013-3020
Electronic Edition (link) BibTeX
- Mark Girolami, Rainer Breitling:
Biologically valid linear factor models of gene expression.
3021-3033
Electronic Edition (link) BibTeX
- Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Scott Soltys, Gongyi Shi, Albert Koong, Quynh-Thu Le:
Sample classification from protein mass spectrometry, by 'peak probability contrasts'.
3034-3044
Electronic Edition (link) BibTeX
- Thomas M. Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Martin Senger, R. Mark Greenwood, Tim Carver, Kevin Glover, Matthew R. Pocock, Anil Wipat, Peter Li:
Taverna: a tool for the composition and enactment of bioinformatics workflows.
3045-3054
Electronic Edition (link) BibTeX
- Pål Sætrom:
Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming.
3055-3063
Electronic Edition (link) BibTeX
- Trees-Juen Chuang, Feng-Chi Chen, Meng-Yuan Chou:
A comparative method for identification of gene structures and alternatively spliced variants.
3064-3079
Electronic Edition (link) BibTeX
- Changyu Hu II, Xiang Li, Jie Liang:
Developing optimal non-linear scoring function for protein design.
3080-3098
Electronic Edition (link) BibTeX
- Yan Liu, Jaime G. Carbonell, Judith Klein-Seetharaman, Vanathi Gopalakrishnan:
Comparison of probabilistic combination methods for protein secondary structure prediction.
3099-3107
Electronic Edition (link) BibTeX
- Albert Hsiao, D. S. Worrall, Jerrold M. Olefsky, Shankar Subramaniam:
Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes.
3108-3127
Electronic Edition (link) BibTeX
- Glen A. Satten, Somnath Datta, Hercules Moura, Adrian R. Woolfitt, Maria da G. Carvalho, George M. Carlone, Barun K. De, Antonis Pavlopoulos, John R. Barr:
Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens.
3128-3136
Electronic Edition (link) BibTeX
- Jun Sese, Yukinori Kurokawa, Morito Monden, Kikuya Kato, Shinichi Morishita:
Constrained clusters of gene expression profiles with pathological features.
3137-3145
Electronic Edition (link) BibTeX
- Yinglei Lai, Baolin Wu, Liang Chen, Hongyu Zhao:
A statistical method for identifying differential gene-gene co-expression patterns.
3146-3155
Electronic Edition (link) BibTeX
- Ben-Yang Liao, Yu-Jung Chang, Jan-Ming Ho, Ming-Jing Hwang:
The UniMarker (UM) method for synteny mapping of large genomes.
3156-3165
Electronic Edition (link) BibTeX
- Jing Wang, Kevin R. Coombes, W. Edward Highsmith, M. J. Keating, Lynne V. Abruzzo:
Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies.
3166-3178
Electronic Edition (link) BibTeX
- Jong-Hun Kim, Juyoung Lee, Bermseok Oh, Kuchan Kimm, InSong Koh:
Prediction of phosphorylation sites using SVMs.
3179-3184
Electronic Edition (link) BibTeX
- Nathalie Pochet, Frank De Smet, Johan A. K. Suykens, Bart De Moor:
Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction.
3185-3195
Electronic Edition (link) BibTeX
- David Baird, Peter Johnstone, Theresa Wilson:
Normalization of microarray data using a spatial mixed model analysis which includes splines.
3196-3205
Electronic Edition (link) BibTeX
- David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones:
BioRAT: extracting biological information from full-length papers.
3206-3213
Electronic Edition (link) BibTeX
- Ralf Bundschuh:
Computational prediction of RNA editing sites.
3214-3220
Electronic Edition (link) BibTeX
- Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, Vassily Hatzimanikatis:
A model-based optimization framework for the inference on gene regulatory networks from DNA array data.
3221-3235
Electronic Edition (link) BibTeX
Applications Notes
- Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, Rolf Apweiler:
UniProt archive.
3236-3237
Electronic Edition (link) BibTeX
- Don Gilbert, Yoshihiro Ugawa, Markus Buchhorn, Tin Wee Tan, Akira Mizushima, Hyun-chul Kim, Kilnam Chon, Seyeon Weon, Juncai Ma, Yoshihiro Ichiyanagi, Der-Ming Liou, Somnuk Keretho, Suhaimi Napis:
Bio-Mirror project for public bio-data distribution.
3238-3240
Electronic Edition (link) BibTeX
- Fredrik Pettersson, Oskar Jonsson, Lon R. Cardon:
GOLDsurfer: three dimensional display of linkage disequilibrium.
3241-3243
Electronic Edition (link) BibTeX
- Jaime R. Robles, Edwin J. C. G. van den Oord:
lga972: a cross-platform application for optimizing LD studies using a genetic algorithm.
3244-3245
Electronic Edition (link) BibTeX
- Alok J. Saldanha:
Java Treeview - extensible visualization of microarray data.
3246-3248
Electronic Edition (link) BibTeX
- Ryan T. McDonald, R. Scott Winters, Mark Mandel, Yang Jin, Peter S. White, Fernando C. N. Pereira:
An entity tagger for recognizing acquired genomic variations in cancer literature.
3249-3251
Electronic Edition (link) BibTeX
- Stacia K. Wyman, Robert K. Jansen, Jeffrey L. Boore:
Automatic annotation of organellar genomes with DOGMA.
3252-3255
Electronic Edition (link) BibTeX
- WangSen Feng, Lusheng Wang, Daming Zhu:
CTRD: a fast applet for computing signed translocation distance between genomes.
3256-3257
Electronic Edition (link) BibTeX
- Ioannis C. Spyropoulos, Theodore Liakopoulos, Pantelis G. Bagos, Stavros J. Hamodrakas:
TMRPres2D: high quality visual representation of transmembrane protein models.
3258-3260
Electronic Edition (link) BibTeX
- Thomas Mailund, Christian N. S. Pedersen:
QuickJoin - fast neighbour-joining tree reconstruction.
3261-3262
Electronic Edition (link) BibTeX
- Tianhua Niu, Zhenjun Hu:
SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays.
3263-3265
Electronic Edition (link) BibTeX
- Eugen C. Buehler, Jeffrey R. Sachs, Kui Shao, Ansuman Bagchi, Lyle H. Ungar:
The CRASSS plug-in for integrating annotation data with hierarchical clustering results.
3266-3269
Electronic Edition (link) BibTeX
- Bo Kyeng Hou, Jin Sik Kim, Ji Hoon Jun, Dong-Yup Lee, Yong Wook Kim, Sujin Chae, Mira Roh, Yong-Ho In, Sang Yup Lee:
BioSilico: an integrated metabolic database system.
3270-3272
Electronic Edition (link) BibTeX
- Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G. Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, Chi-Ying F. Huang:
POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome.
3273-3276
Electronic Edition (link) BibTeX
- Patrick May, Stefan Barthel, Ina Koch:
PTGL - a web-based database application for protein topologies.
3277-3279
Electronic Edition (link) BibTeX
- M. Bahlo, Lei Xing, C. R. Wilkinson:
HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers.
3280-3283
Electronic Edition (link) BibTeX
- Alexey V. Antonov, Igor V. Tetko, Volodymyr V. Prokopenko, Denis Kosykh, Hans-Werner Mewes:
A web portal for classification of expression data using maximal margin linear programming.
3284-3285
Electronic Edition (link) BibTeX
- Jose-Roman Bilbao-Castro, Carlos Oscar Sánchez Sorzano, Inmaculada García, José-Jesús Fernández:
Phan3D: design of biological phantoms in 3D electron microscopy.
3286-3288
Electronic Edition (link) BibTeX
- Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek:
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.
3289-3291
Electronic Edition (link) BibTeX
Volume 20,
Number 18,
December 2004
Discovery Notes
Original Papers
- Huaiqiu Zhu, Gang-Qing Hu, Zheng-Qing Ouyang, Jin Wang, Zhen-Su She:
Accuracy improvement for identifying translation initiation sites in microbial genomes.
3308-3317
Electronic Edition (link) BibTeX
- Joanna H. Shih, Aleksandra M. Michalowska, Kevin Dobbin, Yumei Ye, Ting Hu Qiu, Jeffrey E. Green:
Effects of pooling mRNA in microarray class comparisons.
3318-3325
Electronic Edition (link) BibTeX
- Marco Masseroli, Andrea Stella, Natalia Meani, Myriam Alcalay, Francesco Pinciroli:
MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks.
3326-3335
Electronic Edition (link) BibTeX
- Yong Wang, Frederick C. C. Leung:
DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria.
3336-3345
Electronic Edition (link) BibTeX
- István Albert, Réka Albert:
Conserved network motifs allow protein-protein interaction prediction.
3346-3352
Electronic Edition (link) BibTeX
- Raji Balasubramanian, Thomas LaFramboise, Denise Scholtens, Robert Gentleman:
A graph-theoretic approach to testing associations between disparate sources of functional genomics data.
3353-3362
Electronic Edition (link) BibTeX
- Michael Roberts, Wayne Hayes, Brian R. Hunt, Stephen M. Mount, James A. Yorke:
Reducing storage requirements for biological sequence comparison.
3363-3369
Electronic Edition (link) BibTeX
- Daniel McDonald, Hsinchun Chen, Hua Su, Byron Marshall:
Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser.
3370-3378
Electronic Edition (link) BibTeX
- Mehmet Bilgen, Mehmet Karaca, A. Naci Onus, Ayse Gül Ince:
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences.
3379-3386
Electronic Edition (link) BibTeX
- Vitaly A. Selivanov, Joaquim Puigjaner, Antonio Sillero, Josep J. Centelles, Antonio Ramos-Montoya, Paul W.-N. Lee, Marta Cascante:
An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites.
3387-3397
Electronic Edition (link) BibTeX
- Zheng Rong Yang, Andrew R. Dalby, Jing Qiu:
Mining HIV protease cleavage data using genetic programming with a sum-product function.
3398-3405
Electronic Edition (link) BibTeX
- Lexin Li, Hongzhe Li:
Dimension reduction methods for microarrays with application to censored survival data.
3406-3412
Electronic Edition (link) BibTeX
- Philippe Hupé, Nicolas Stransky, Jean-Paul Thiery, François Radvanyi, Emmanuel Barillot:
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions.
3413-3422
Electronic Edition (link) BibTeX
- Kyounghwa Bae, Bani K. Mallick:
Gene selection using a two-level hierarchical Bayesian model.
3423-3430
Electronic Edition (link) BibTeX
- Peter M. Haverty, Li-Li Hsiao, Steven R. Gullans, Ulla Hansen, Zhiping Weng:
Limited agreement among three global gene expression methods highlights the requirement for non-global validation.
3431-3441
Electronic Edition (link) BibTeX
- Elizabeth Shoop, Paulo Casaes, Getiria Onsongo, Lisa Lesnett, Erla Osk Petursdottir, Edward Kofi Yeboah Donkor, Dennis Tkach, Michael Cosimini:
Data exploration tools for the Gene Ontology database.
3442-3454
Electronic Edition (link) BibTeX
- Tuan D. Pham, Johannes Zuegg:
A probabilistic measure for alignment-free sequence comparison.
3455-3461
Electronic Edition (link) BibTeX
- Jeffrey A. Rosenfeld, Indra Neil Sarkar, Paul J. Planet, David H. Figurski, Robert DeSalle:
ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms.
3462-3465
Electronic Edition (link) BibTeX
- Joyce Phui Yee Siew, Asif M. Khan, Paul T. J. Tan, Judice L. Y. Koh, Seng Hong Seah, Chuay Yeng Koo, Siaw Ching Chai, Arunmozhiarasi Armugam, Vladimir Brusic, Kandiah Jeyaseelan:
Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.
3466-3480
Electronic Edition (link) BibTeX
- Diane J. Rodi, Suneeta Mandava, Lee Makowski:
DIVAA: analysis of amino acid diversity in multiple aligned protein sequences.
3481-3489
Electronic Edition (link) BibTeX
- Kodangattil R. Sreekumar, You-Ping Huang, Mark H. Pausch, Kamalakar Gulukota:
Predicting GPCR-G-protein coupling using hidden Markov models.
3490-3499
Electronic Edition (link) BibTeX
- Soojin Lee, Min-Kyu Cho, Jin-Won Jung, Jai-Hoon Kim, Weontae Lee:
Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform.
3500-3507
Electronic Edition (link) BibTeX
- Natasa Przulj, Derek G. Corneil, Igor Jurisica:
Modeling interactome: scale-free or geometric?.
3508-3515
Electronic Edition (link) BibTeX
- Robert Osada, Elena Zaslavsky, Mona Singh:
Comparative analysis of methods for representing and searching for transcription factor binding sites.
3516-3525
Electronic Edition (link) BibTeX
- Anton Yuryev, Jianping Huang, Kathryn E. Scott, Jennifer Kuebler, Miriam Donaldson, Michael S. Phillips, Mark Pohl, Michael T. Boyce-Jacino:
Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling.
3526-3532
Electronic Edition (link) BibTeX
- Chad L. Myers, Maitreya J. Dunham, Sun-Yuan Kung, Olga G. Troyanskaya:
Accurate detection of aneuploidies in array CGH and gene expression microarray data.
3533-3543
Electronic Edition (link) BibTeX
- Roland Linder, Dawn Dew, Holger Sudhoff, Dirk Theegarten, Klaus Remberger, Siegfried J. Pöppl, Mathias Wagner II:
The 'subsequent artificial neural network' (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses.
3544-3552
Electronic Edition (link) BibTeX
- Markus Neuháuser II, Roswitha Senske:
The Baumgartner-Wei?-Schindler test for the detection of differentially expressed genes in replicated microarray experiments.
3553-3564
Electronic Edition (link) BibTeX
- Alberto de la Fuente, Nan Bing, Ina Hoeschele, Pedro Mendes:
Discovery of meaningful associations in genomic data using partial correlation coefficients.
3565-3574
Electronic Edition (link) BibTeX
- Markus Anderle II, Sushmita Roy, Hua Lin, Christopher Becker, Keith Joho:
Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum.
3575-3582
Electronic Edition (link) BibTeX
- Marcel Dettling:
BagBoosting for tumor classification with gene expression data.
3583-3593
Electronic Edition (link) BibTeX
- Jing Yu, V. Anne Smith, Paul P. Wang, Alexander J. Hartemink, Erich D. Jarvis:
Advances to Bayesian network inference for generating causal networks from observational biological data.
3594-3603
Electronic Edition (link) BibTeX
- Minlie Huang, Xiaoyan Zhu, Hao Yu, Donald G. Payan, Kunbin Qu, Ming Li:
Discovering patterns to extract protein-protein interactions from full texts.
3604-3612
Electronic Edition (link) BibTeX
- Kyoung-Jae Won, Adam Prügel-Bennett, Anders Krogh:
Training HMM structure with genetic algorithm for biological sequence analysis.
3613-3619
Electronic Edition (link) BibTeX
- Matthias Koenig, Niels Grabe:
Highly specific prediction of phosphorylation sites in proteins.
3620-3627
Electronic Edition (link) BibTeX
- Jim Samuelsson, Daniel Dalevi, Fredrik Levander, Thorsteinn S. Rögnvaldsson:
Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting.
3628-3635
Electronic Edition (link) BibTeX
Applications Notes
- Kees Jong, Elena Marchiori, Gerrit Meijer, Aad van der Vaart, Bauke Ylstra:
Breakpoint identification and smoothing of array comparative genomic hybridization data.
3636-3637
Electronic Edition (link) BibTeX
- O. J. Shaw, Colin Harwood, L. Jason Steggles, Anil Wipat:
SARGE: a tool for creation of putative genetic networks.
3638-3640
Electronic Edition (link) BibTeX
- Steffen Durinck, Joke Allemeersch, Vincent Carey, Yves Moreau, Bart De Moor:
Importing MAGE-ML format microarray data into BioConductor.
3641-3642
Electronic Edition (link) BibTeX
- Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven Salzberg:
DAGchainer: a tool for mining segmental genome duplications and synteny.
3643-3646
Electronic Edition (link) BibTeX
- Dirk Steinhauser, Björn Usadel, Alexander Lüdemann, Oliver Thimm, Joachim Kopka:
CSB.DB: a comprehensive systems-biology database.
3647-3651
Electronic Edition (link) BibTeX
- Paolo Di Giovine:
PLPMDB: Pyridoxal-5'-phosphate dependent enzymes mutants database.
3652-3653
Electronic Edition (link) BibTeX
- Kristoffer Forslund, Daniel H. Huson, Vincent Moulton:
VisRD--visual recombination detection.
3654-3655
Electronic Edition (link) BibTeX
- Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte:
DNMAD: web-based diagnosis and normalization for microarray data.
3656-3658
Electronic Edition (link) BibTeX
- Simon M. Lin, Patrick McConnell, Kimberly F. Johnson, Jennifer Shoemaker:
MedlineR: an open source library in R for Medline literature data mining.
3659-3661
Electronic Edition (link) BibTeX
- Aaron Kaluszka, Cynthia Gibas:
Interactive gene-order comparison for multiple small genomes.
3662-3664
Electronic Edition (link) BibTeX
- Christophe Hitte, Thomas Derrien, Catherine André, Elaine A. Ostrander, Francis Galibert:
CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome.
3665-3667
Electronic Edition (link) BibTeX
- Shaolin Liu, Nicholas A. Tinker, Stephen J. Molnar, Diane E. Mather:
EC_oligos: automated and whole-genome primer design for exons within one or between two genomes.
3668-3669
Electronic Edition (link) BibTeX
- Giacomo Finocchiaro, Paola Parise, Simone P. Minardi, Myriam Alcalay, Heiko Mueller:
GenePicker: replicate analysis of Affymetrix gene expression microarrays.
3670-3672
Electronic Edition (link) BibTeX
- Chris C. A. Spencer, Graham Coop:
SelSim: a program to simulate population genetic data with natural selection and recombination.
3673-3675
Electronic Edition (link) BibTeX
- Andreas Gisel, Maria Panetta, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Cecilia Saccone, Graziano Pesole:
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions.
3676-3679
Electronic Edition (link) BibTeX
- Marc Vass, Nicholas Allen, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson:
The JigCell Model Builder and Run Manager.
3680-3681
Electronic Edition (link) BibTeX
- Peter F. Hallin, David Ussery:
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.
3682-3686
Electronic Edition (link) BibTeX
- Nicholas Knowlton, Igor Dozmorov, Michael Centola:
Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data.
3687-3690
Electronic Edition (link) BibTeX
- Chia-Chin Wu, Hsuan-Cheng Huang, Hsueh-Fen Juan, Shui-Tein Chen:
GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data.
3691-3693
Electronic Edition (link) BibTeX
- Vincent Catherinot, Gilles Labesse:
ViTO: tool for refinement of protein sequence-structure alignments.
3694-3696
Electronic Edition (link) BibTeX
- Yuan Qi, Nick V. Grishin:
PCOAT: positional correlation analysis using multiple methods.
3697-3699
Electronic Edition (link) BibTeX
- Peter E. Midford:
Ontologies for Behavior.
3700-3701
Electronic Edition (link) BibTeX
- Tancred Frickey, Andrei N. Lupas:
CLANS: a Java application for visualizing protein families based on pairwise similarity.
3702-3704
Electronic Edition (link) BibTeX
- James M. Wettenhall, Gordon K. Smyth:
limmaGUI: A graphical user interface for linear modeling of microarray data.
3705-3706
Electronic Edition (link) BibTeX
- Jean-Luc Pons, Therese E. Malliavin, Dominique Tramesel, Marc-André Delsuc:
NMRb: a web-site repository for raw NMR datasets.
3707-3709
Electronic Edition (link) BibTeX
- Elizabeth I. Boyle, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, J. Michael Cherry, Gavin Sherlock:
GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.
3710-3715
Electronic Edition (link) BibTeX
Errata
Volume 20,
Supplement August 2004
Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, Glasgow, UK, July 31-August 4, 2004.
2004
Contents BibTeX
Copyright © Sat May 16 23:51:30 2009
by Michael Ley (ley@uni-trier.de)