Volume 19,
Number 1,
January 2003
Editorial
Reviews
- Pietro Liò:
Wavelets in bioinformatics and computational biology: state of art and perspectives.
2-9 BibTeX
Discovery Notes
Original Papers
- Ji-Hong Zhang, Ling-Yun Wu, Xiang-Sun Zhang:
Reconstruction of DNA sequencing by hybridization.
14-21 BibTeX
- Hasan H. Otu, Khalid Sayood:
A divide-and-conquer approach to fragment assembly.
22-29 BibTeX
- João Aires-de-Sousa, Luisa Aires-de-Sousa:
Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps.
30-36 BibTeX
- C. H. Ooi, Patrick Tan:
Genetic algorithms applied to multi-class prediction for the analysis of gene expression data.
37-44 BibTeX
- J. M. Deutsch:
Evolutionary algorithms for finding optimal gene sets in microarray prediction.
45-52 BibTeX
- Lorenz Wernisch, Sharon L. Kendall, Shamit Soneji, Andreas Wietzorrek, Tanya Parish, Jason Hinds, Philip D. Butcher, Neil G. Stoker:
Analysis of whole-genome microarray replicates using mixed models.
53-61 BibTeX
- Rahul Bijlani, Yinhe Cheng, David A. Pearce, Andrew I. Brooks, Mitsunori Ogihara:
Prediction of biologically significant components from microarray data: Independently Consistent Expression Discriminator (ICED).
62-70 BibTeX
- Jinyan Li, Huiqing Liu, James R. Downing, Allen Eng-Juh Yeoh, Limsoon Wong:
Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients.
71-78 BibTeX
- Chad Creighton, Samir Hanash:
Mining gene expression databases for association rules.
79-86 BibTeX
- Richard A. McIndoe, Aaron Lanzen, Kimberly Hurtz:
MADGE: scalable distributed data management software for cDNA microarrays.
87-89 BibTeX
- Kyeong Eun Lee, Naijun Sha, Edward R. Dougherty, Marina Vannucci, Bani K. Mallick:
Gene selection: a Bayesian variable selection approach.
90-97 BibTeX
- Sorin Draghici, R. Brian Potter:
Predicting HIV drug resistance with neural networks.
98-107 BibTeX
- Olivier Perriquet, Hélène Touzet, Max Dauchet:
Finding the common structure shared by two homologous RNAs.
108-116 BibTeX
- Jacek Leluk, Leszek Konieczny, Irena Roterman:
Search for structural similarity in proteins.
117-124 BibTeX
- Joel R. Bock, David A. Gough:
Whole-proteome interaction mining.
125-134 BibTeX
- Robert J. Gaizauskas, George Demetriou, Peter J. Artymiuk, Peter Willett:
Protein Structures and Information Extraction from Biological Texts: The PASTA System.
135-143 BibTeX
- C. Carleos, F. Rodriguez, H. Lamelas, J. A. Baro:
Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations.
144-148 BibTeX
Applications Notes
- Shaun Purcell, Stacey S. Cherny, Pak Chung Sham:
Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits.
149-150 BibTeX
- Yaw-Ling Lin, Xiaoqiu Huang, Tao Jiang, Kun-Mao Chao:
MAVG: locating non-overlapping maximum average segments in a given sequence.
151-152 BibTeX
- T. De Oliveira, R. Miller, M. Tarin, S. Cassol:
An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.
153-154 BibTeX
- Jianhua Zhang, Vincent Carey, Robert Gentleman:
An extensible application for assembling annotation for genomic data.
155-156 BibTeX
- Ramswamy Anbazhagan:
Microarray data assembler.
157-158 BibTeX
- Vivek Gopalan, Tin Wee Tan, Shoba Ranganathan:
XdomView: protein domain and exon position visualization.
159-160 BibTeX
- Patrick Aloy, Robert B. Russell:
InterPreTS: protein Interaction Prediction through Tertiary Structure.
161-162 BibTeX
- Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal:
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.
163-164 BibTeX
- Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Linda McMahan, Andrej Sali:
ModView, visualization of multiple protein sequences and structures.
165-166 BibTeX
- Tejasvini Prasad, M. N. Prathima, Nagasuma Chandra:
Detection of hydrogen-bond signature patterns in protein families.
167-168 BibTeX
Volume 19,
Number 2,
February 2003
Discovery Notes
Original Papers
- Dörte Solle, David Geissler, Eckbert Stärk, Thomas Scheper, Bernd Hitzmann:
Chemometric Modelling based on 2D-Fluorescence Spectra without a Calibration Measurement.
173-177 BibTeX
- Felix Naef, Nicholas D. Socci, Marcelo Magnasco:
A study of accuracy, precision in oligonucleotide arrays: extracting more signal at large concentrations.
178-184 BibTeX
- Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed:
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
185-193 BibTeX
- Chris A. Glasbey, Peter Ghazal:
Combinatorial image analysis of DNA microarray features.
194-203 BibTeX
- Igor Dozmorov, Michael Centola:
An associative analysis of gene expression array data.
204-211 BibTeX
- Neil D. Clarke, Joshua A. Granek:
Rank order metrics for quantifying the association of sequence features with gene regulation.
212-218 BibTeX
- Jakob Skou Pedersen, Jotun Hein:
Gene finding with a hidden Markov model of genome structure and evolution.
219-227 BibTeX
- Xiaoqiu Huang, Kun-Mao Chao:
A generalized global alignment algorithm.
228-233 BibTeX
- Jack Cao, Rosemarie Panetta, Shiyi Yue, Alain Steyaert, Michele Young-Bellido, Sultan Ahmad:
A naive Bayes model to predict coupling between seven transmembrane domain receptors, and G-proteins.
234-240 BibTeX
- Iwei Yeh, Peter D. Karp, Natalya Fridman Noy, Russ B. Altman:
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).
241-248 BibTeX
- Gregory P. Harhay, John W. Keele:
Positional candidate gene selection from livestock EST databases using Gene Ontology.
249-255 BibTeX
- Myung-Hoon Chung, Chul Koo Kim, Kyun Nahm:
Fractional populations in multiple gene inheritance.
256-260 BibTeX
- Steffen Klamt, Jörg Stelling, Martin Ginkel, Ernst Dieter Gilles:
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.
261-269 BibTeX
- Hongwu Ma, An-Ping Zeng:
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms.
270-277 BibTeX
- Peter Ernst, Karl-Heinz Glatting, Sándor Suhai:
A task framework for the web interface W2H.
278-282 BibTeX
Applications Notes
- Felix Kokocinski, Gunnar Wrobel, Meinhard Hahn, Peter Lichter:
QuickLIMS: facilitating the data management for DNA-microarray fabrication.
283-284 BibTeX
- Ming-Hua Hsieh, Wei-Che Hsu, Sung-Kay Chiu, Chi-Meng Tzeng:
An efficient algorithm for minimal primer set selection.
285-286 BibTeX
- Xiayi Ke, Lon R. Cardon:
Efficient selective screening of haplotype tag SNPs.
287-288 BibTeX
- David Posada, Carsten Wiuf:
Simulating haplotype blocks in the human genome.
289-290 BibTeX
- Jeremy M. R. Martin, Lan J. Mackay, Christopher J. Rawlings:
Pedstrip: extracting a maximal subset of available, unrelated individuals from a pedigree.
291-292 BibTeX
- Yihua Zhou, Jingdong Liu:
AVA: visual analysis of gene expression microarray data.
293-294 BibTeX
- Paul Pavlidis, William Stafford Noble:
Matrix2png: a utility for visualizing matrix data.
295-296 BibTeX
- Lusheng Wang, Ying Xu:
SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments.
297-298 BibTeX
- Peter De Rijk, Jan Wuyts, Rupert De Wachter:
RnaViz 2: an improved representation of RNA secondary structure.
299-300 BibTeX
- Michael J. Sanderson:
r8s: inferring absolute rates of molecular evolution, divergence times in the absence of a molecular clock.
301-302 BibTeX
- Jack A. M. Leunissen:
Chimera: construction of chimeric sequences for phylogenetic analysis.
303-304 BibTeX
- Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita:
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining.
305-306 BibTeX
- Zemin Zhang, William I. Wood:
A profile hidden Markov model for signal peptides generated by HMMER.
307-308 BibTeX
- Kunde Ramamoorthy Govindarajan, Pandjassarame Kangueane, Tin Wee Tan, Shoba Ranganathan:
MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules.
309-310 BibTeX
- Charles S. Bond:
TopDraw: a sketchpad for protein structure topology cartoons.
311-321 BibTeX
- Alessandro Pintar, Oliviero Carugo, Sándor Pongor:
DPX: for the analysis of the protein core.
313-314 BibTeX
- Jens P. Linge, Michael Habeck, Wolfgang Rieping, Michael Nilges:
ARIA: automated NOE assignment and NMR structure calculation.
315-316 BibTeX
- Byong-Hyon Ju, Byungkyu Park, Jong H. Park, Kyungsook Han:
Visualization and analysis of protein interactions.
317-318 BibTeX
Volume 19,
Number 3,
February 2003
Jobim Papers
- Arnaud Lefebvre, Thierry Lecroq, H. Dauchel, Joël Alexandre:
FORRepeats: detects repeats on entire chromosomes and between genomes.
319-326 BibTeX
- Michaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset, Michel Termier:
Towards a computational model for -1 eukaryotic frameshifting sites.
327-335 BibTeX
- Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page:
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.
336-344 BibTeX
- Alexandre G. de Brevern, Serge A. Hazout:
`Hybrid Protein Model' for optimally defining 3D protein structure fragments.
345-353 BibTeX
Original Papers:
- Shu-Yun Le, Jih-H. Chen, Danielle Konings, Jacob V. Maizel:
Discovering well-ordered folding patterns in nucleotide sequences.
354-361 BibTeX
- Eugene M. McCarthy, John F. McDonald:
LTR_STRUC: a novel search and identification program for LTR retrotransposons.
362-367 BibTeX
- Anat Reiner, Daniel Yekutieli, Yoav Benjamini:
Identifying differentially expressed genes using false discovery rate controlling procedures.
368-375 BibTeX
- Lance W. Hahn, Marylyn D. Ritchie, Jason H. Moore:
Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions.
376-382 BibTeX
- Blaz Zupan, Janez Demsar, Ivan Bratko, Peter Juvan, John A. Halter, Adam Kuspa, Gad Shaulsky:
GenePath: a system for automated construction of genetic networks from mutant data.
383-389 BibTeX
- John Parkinson, Mark Blaxter:
SimiTri-visualizing similarity relationships for groups of sequences.
390-395 BibTeX
- Soumya Raychaudhuri, Russ B. Altman:
A literature-based method for assessing the functional coherence of a gene group.
396-401 BibTeX
- W. H. Majoros, G. M. Subramanian, M. D. Yandell:
Identification of key concepts in biomedical literature using a modified Markov heuristic.
402-407 BibTeX
- Sudhir Sivakumaran, Sridhar Hariharaputran, Jyoti Mishra, Upinder S. Bhalla:
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.
408-415 BibTeX
Applications Notes
- Zhiwei Fang, Mary L. Polacco, Su-Shing Chen, Steven G. Schroeder, D. Hancock, Hector Sanchez-Villeda, Edward H. Coe:
cMap: the comparative genetic map viewer.
416-417 BibTeX
- William Hsiao, Ivan Wan, Steven J. Jones, Fiona S. L. Brinkman:
IslandPath: aiding detection of genomic islands in prokaryotes.
418-420 BibTeX
- Gary Barker, Jacqueline Batley, Helen O'Sullivan, Keith J. Edwards, David Edwards:
Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP.
421-422 BibTeX
- Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai:
MELINA: motif extraction from promoter regions of potentially co-regulated genes.
423-424 BibTeX
- Burkhard Morgenstern, Sachin Goel, Alexander Sczyrba, Andreas W. M. Dress:
AltAVisT: Comparing alternative multiple sequence alignments.
425-426 BibTeX
- Jimin Pei, Ruslan Sadreyev, Nick V. Grishin:
PCMA: fast and accurate multiple sequence alignment based on profile consistency.
427-428 BibTeX
- Nickolai Alexandrov, Ilya N. Shindyalov:
PDP: protein domain parser.
429-430 BibTeX
- E. Minch, M. de Rinaldis, S. Weiss:
pathSCOUTTM: exploration and analysis of biochemical pathways.
431-432 BibTeX
- Tetsuro Toyoda, Akihiko Konagaya:
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data.
433-434 BibTeX
- Lingchong You, Apirak Hoonlor, John Yin:
Modeling biological systems using Dynetica-a simulator of dynamic networks.
435-436 BibTeX
- Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya:
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs.
437-438 BibTeX
- Björn M. Ursing:
WiGID: wireless genome information database.
439-440 BibTeX
- Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey:
Wrapping up BLAST and other applications for use on Unix clusters.
441-442 BibTeX
Volume 19,
Number 4,
March 2003
Original Papers
- Michael D. Stern, Sergey V. Anisimov, Kenneth R. Boheler:
Can transcriptome size be estimated from SAGE catalogs?
443-448 BibTeX
- Jyotsna Kasturi, Raj Acharya, Murali Ramanathan:
An information theoretic approach for analyzing temporal patterns of gene expression.
449-458 BibTeX
- Susmita Datta, Somnath Datta:
Comparisons and validation of statistical clustering techniques for microarray gene expression data.
459-466 BibTeX
- Daniel Johansson, Petter Lindgren, Anders Berglund:
A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription.
467-473 BibTeX
- Yihui Luan, Hongzhe Li:
Clustering of time-course gene expression data using a mixed-effects model with B-splines.
474-482 BibTeX
- Lee Makowski, Alexei Soares:
Estimating the diversity of peptide populations from limited sequence data.
483-489 BibTeX
- Dirk Metzler:
Statistical alignment based on fragment insertion and deletion models.
490-499 BibTeX
- Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio:
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.
500-505 BibTeX
- Mounir Errami, Christophe Geourjon, Gilbert Deléage:
Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures.
506-512 BibTeX
- Susana Vinga, Jonas S. Almeida:
Alignment-free sequence comparison-a review.
513-523 BibTeX
- Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, J. H. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang:
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
524-531 BibTeX
- Petter Holme, Mikael Huss, Hawoong Jeong:
Subnetwork hierarchies of biochemical pathways.
532-538 BibTeX
Applications Notes
- Stephen Wooding:
PopHist: inferring population history from the spectrum of allele frequencies.
539-540 BibTeX
- Steven P. Bennett, Craig G. Nevill-Manning, Douglas L. Brutlag:
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database.
541-542 BibTeX
- Endre Barta, László Kaján, Sándor Pongor:
IS: a web-site for intron statistics.
543-543 BibTeX
- Jason M. Johnson, Keith Mason, Ciamac Cyrus Moallemi, Hualin Xi, Shyamal Somaroo, Enoch S. Huang:
Protein family annotation in a multiple alignment viewer.
544-545 BibTeX
- Rodrigo Lopez, Stephen Robinson, Asif Kibria, Nicola Harte, Gulam Patel, Rob Harper, Emmanuel Quevillon, Ville Silventoinen, Kimmo Kallio, Petteri Jokinen:
The European Bioinformatics Institute web site: a new view.
546-547 BibTeX
Volume 19,
Number 5,
March 2003
Discovery Notes
Original Papers
- Jesús Angulo, Jean Serra:
Automatic analysis of DNA microarray images using mathematical morphology.
553-562 BibTeX
- A. Antoniadis, S. Lambert-Lacroix, F. Leblanc:
Effective dimension reduction methods for tumor classification using gene expression data.
563-570 BibTeX
- Silvio Bicciato, A. Luchini, Carlo Di Bello:
PCA disjoint models for multiclass cancer analysis using gene expression data.
571-578 BibTeX
- Gernot G. Presting:
Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome.
579-586 BibTeX
- Angela Torres, Juan J. Nieto:
The fuzzy polynucleotide space: basic properties.
587-592 BibTeX
- Chun-Ting Zhang, Ren Zhang, Hong-Yu Ou:
The Z curve database: a graphic representation of genome sequences.
593-599 BibTeX
- David S. Horner, Graziano Pesole:
The estimation of relative site variability among aligned homologous protein sequences.
600-606 BibTeX
- Konstantinos Blekas, Dimitrios I. Fotiadis, Aristidis Likas:
Greedy mixture learning for multiple motif discovery in biological sequences.
607-617 BibTeX
- Stéphane Aris-Brosou:
How Bayes tests of molecular phylogenies compare with frequentist approaches.
618-624 BibTeX
- Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin:
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance.
625-634 BibTeX
- Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak:
Prediction of human protein function according to Gene Ontology categories.
635-642 BibTeX
- Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita:
Dynamic modeling of genetic networks using genetic algorithm and S-system.
643-650 BibTeX
Applications Notes
- Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush:
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
651-652 BibTeX
- Jianxin Wang, Ping Liang:
DigiNorthern, digital expression analysis of query genes based on ESTs.
653-654 BibTeX
- Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo:
Gene expression data preprocessing.
655-656 BibTeX
- Jorge García de la Nava, Daniel Franco Santaella, Jesús Cuenca Alba, José María Carazo, Oswaldo Trelles, Alberto D. Pascual-Montano:
Engene: the processing and exploratory analysis of gene expression data.
657-658 BibTeX
- David Venet:
MatArray: a Matlab toolbox for microarray data.
659-660 BibTeX
- Stefano Toppo, Nicola Cannata, Paolo Fontana, Chiara Romualdi, Paolo Laveder, Emanuela Bertocco, Gerolamo Lanfranchi, Giorgio Valle:
TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts.
661-662 BibTeX
- K. Livingstone, L. Rieseberg:
MENDB: a database of polymorphic loci from natural populations.
663-664 BibTeX
- Manoj Bhasin, Harpreet Singh, G. P. S. Raghava:
MHCBN: a comprehensive database of MHC binding and non-binding peptides.
665-666 BibTeX
- Ron Shigeta, Melissa S. Cline, Guoying Liu, Michael A. Siani-Rose:
GPCR-GRAPA-LIB-a refined library of hidden Markov Models for annotating GPCRs.
667-668 BibTeX
- Gianmaria Mancosu, Giuseppe Ledda, Paola M. Melis:
PedNavigator: a pedigree drawing servlet for large and inbred populations.
669-670 BibTeX
- Steve Woolley, Justin Johnson, Matthew J. Smith, Keith A. Crandall, David A. McClellan:
TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees.
671-672 BibTeX
- Mikita Suyama, Osamu Ohara:
DomCut: prediction of inter-domain linker regions in amino acid sequences.
673-674 BibTeX
- Andrew V. Kossenkov, Frank J. Manion, Eugene V. Korotkov, Thomas D. Moloshok, Michael F. Ochs:
ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database.
675-676 BibTeX
- Bruce E. Shapiro, Andre Levchenko, Elliot M. Meyerowitz, Barbara J. Wold, Eric Mjolsness:
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations.
677-678 BibTeX
Volume 19,
Number 6,
April 2003
Editorial
Discovery Notes
Original Papers
- Michael LeBlanc, Charles L. Kooperberg, Thomas M. Grogan, Thomas P. Miller:
Directed indices for exploring gene expression data.
686-693 BibTeX
- Taesung Park, Sung-Gon Yi, Seungmook Lee, Seung Yeoun Lee, Dong-Hyun Yoo, Jun-Ik Ahn, Yong-Sung Lee:
Statistical tests for identifying differentially expressed genes in time-course microarray experiments.
694-703 BibTeX
- Atsushi Kajita, Masayuki Yamamura, Yuji Kohara:
Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans.
704-716 BibTeX
- Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, Vassilis J. Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros J. Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis:
Evaluation of annotation strategies using an entire genome sequence.
717-726 BibTeX
- Michael I. Sadowski, John Howard Parish:
Automated generation and refinement of protein signatures: case study with G-protein coupled receptors.
727-734 BibTeX
- Edward S. C. Shih, Ming-Jing Hwang:
Protein structure comparison by probability-based matching of secondary structure elements.
735-741 BibTeX
- Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik:
A segment alignment approach to protein comparison.
742-749 BibTeX
- Elisabeth R. M. Tillier, Thomas W. H. Lui:
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments.
750-755 BibTeX
- Rintaro Saito, Harukazu Suzuki, Yoshihide Hayashizaki:
Construction of reliable protein-protein interaction networks with a new interaction generality measure.
756-763 BibTeX
- Jason Weston, Fernando Pérez-Cruz, Olivier Bousquet, Olivier Chapelle, André Elisseeff, Bernhard Schölkopf:
Feature selection and transduction for prediction of molecular bioactivity for drug design.
764-771 BibTeX
Applications Notes
- Alexander Sturn, Bernhard Mlecnik, Roland Pieler, Johannes Rainer, Thomas Truskaller, Zlatko Trajanoski:
Client-Server environment for high-performance gene expression data analysis.
772-773 BibTeX
- Marco Masseroli, Pietro Cerveri, P. G. Pelicci, Myriam Alcalay:
GAAS: Gene Array Analyzer Software for management, analysis and visualization of gene expression data.
774-775 BibTeX
- Stephane Rombauts, Yves Van de Peer, Pierre Rouzé:
AFLPinSilico, simulating AFLP fingerprints.
776-777 BibTeX
- Kyungjoon Lee, Isaac S. Kohane, Atul J. Butte:
PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications.
778-779 BibTeX
- Ren Hua Chung, Dan Gusfield:
Perfect phylogeny haplotyper: haplotype inferral using a tree model.
780-781 BibTeX
- Philip Wong, Grigory Kolesov, Dmitrij Frishman, Walid A. Houry:
Phylogenetic Web Profiler.
782-783 BibTeX
- Klaus Reichard, Michael Kaufmann:
EPPS: mining the COG database by an extended phylogenetic patterns search.
784-785 BibTeX
- Elmar Trost, Hubert Hackl, Michael Maurer, Zlatko Trajanoski:
Java editor for biological pathways.
786-787 BibTeX
- Gabriel F. Berriz, James V. White, Oliver D. King, Frederick P. Roth:
GoFish finds genes with combinations of Gene Ontology attributes.
788-789 BibTeX
- Polixeni Dimitropoulou, Chris Cannings:
RECSIM and INDSTATS: probabilities of identity in general genealogies.
790-791 BibTeX
- R. Matthiesen, M. Lundsgaard, K. G. Welinder, G. Bauw:
Interpreting peptide mass spectra by VEMS.
792-793 BibTeX
Volume 19,
Number 7,
May 2003
Editorial
Original Papers
- Xiaowei Wang, Brian Seed:
Selection of Oligonucleotide Probes for Protein Coding Sequences.
796-802 BibTeX
- Kevin Dobbin, Joanna H. Shih, Richard Simon:
Statistical Design of Reverse Dye Microarrays.
803-810 BibTeX
- Li Wuju, Ming Fan, Momiao Xiong:
SamCluster: An Integrated Scheme for Automatic Discovery of Sample Classes Using Gene Expression Profile.
811-817 BibTeX
- David R. Bickel:
Robust Cluster Analysis of Microarray Gene Expression Data with the Number of Clusters Determined Biologically.
818-824 BibTeX
- David Edwards:
Non-linear Normalization and Background Correction in One-channel CDNA Microarray Studies.
825-833 BibTeX
- Shyamal D. Peddada, Edward K. Lobenhofer, Leping Li, Cynthia A. Afshari, Clarice R. Weinberg, David M. Umbach:
Gene Selection and Clustering for Time-course and Dose-response Microarray Experiments Using Order-restricted Inference.
834-841 BibTeX
- Paul M. Magwene, Paul Lizardi, Junhyong Kim:
Reconstructing the Temporal Ordering of Biological Samples Using Microarray Data.
842-850 BibTeX
- Volker Braun, Ricardo B. R. Azevedo, Markus Gumbel, Paul-Michael Agapow, Armand M. Leroi, Hans-Peter Meinzer:
ALES: Cell Lineage Analysis and Mapping of Developmental Events.
851-858 BibTeX
- Mark Hoebeke, Pierre Nicolas, Philippe Bessières:
MuGeN: Simultaneous Exploration of Multiple Genomes and Computer Analysis Results.
859-864 BibTeX
- Sverker Edvardsson, Paul P. Gardner, Anthony M. Poole, Michael D. Hendy, David Penny, Vincent Moulton:
A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction.
865-873 BibTeX
- Liam J. McGuffin, David T. Jones:
Improvement of the GenTHREADER Method for Genomic Fold Recognition.
874-881 BibTeX
- Oscar Sverud, Robert M. MacCallum:
Towards Optimal Views of Proteins.
882-888 BibTeX
Applications Notes
- Karl W. Broman, Hao Wu, Saunak Sen, Gary A. Churchill:
R/qtl: QTL Mapping in Experimental Crosses.
889-890 BibTeX
- Cristian I. Castillo-Davis, Daniel L. Hartl:
GeneMerge - Post-genomic Analysis, Data Mining, and Hypothesis Testing.
891-892 BibTeX
- Kristof Engelen, Bert Coessens, Kathleen Marchal, Bart De Moor:
MARAN: Normalizing Micro-array Data.
893-894 BibTeX
- Antonio Gómez, Núria Domedel-Puig, Juan Cedano, Jaume Piñol, Enrique Querol:
Do Current Sequence Analysis Algorithms Disclose Multifunctional (moonlighting) Proteins?.
895-896 BibTeX
- Peng Yang, Paul A. Craig, David Goodsell, Philip E. Bourne:
BioEditor - Simplifying Macromolecular Structure Annotation.
897-898 BibTeX
- Zsuzsanna Dosztányi, Csaba Magyar, Gábor E. Tusnády, István Simon:
SCide: Identification of Stabilization Centers in Proteins.
899-900 BibTeX
- James M. Brundege, Christopher Dubay:
BioQuery: An Object Framework for Building Queries to Biomedical Databases.
901-902 BibTeX
- Nicolas Goffard, Virginie Garcia, Florian Iragne, Alexis Groppi, Antoine de Daruvar:
IPPRED: Server for Proteins Interactions Inference.
903-904 BibTeX
Volume 19,
Number 8,
May 2003
Sac Papers
- Andrew T. Kwon, Holger H. Hoos, Raymond T. Ng:
Inference of Transcriptional Regulation Relationships from Gene Expression Data.
905-912 BibTeX
- Tolga Can, Yujun Wang, Yuan-Fang Wang, Jianwen Su:
FPV: Fast Protein Visualization Using Java 3DTM.
913-922 BibTeX
- See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan:
Integrative Approach for Computationally Inferring Protein Domain Interactions.
923-929 BibTeX
- Larkshmi Krishnamurthy, Joseph H. Nadeau, Gultekin Özsoyoglu, Z. Meral Özsoyoglu, Greg Schaeffer, Murat Tasan, Wanhong Xu:
Pathways Database System: An Integrated System for Biological Pathways.
930-937 BibTeX
- Goran Nenadic, Irena Spasic, Sophia Ananiadou:
Terminology-driven Mining of Biomedical Literature.
938-943 BibTeX
Original Papers
- Marcel Brun, David Sabbagh, Seungchan Kim, Edward R. Dougherty:
Corrected Small-sample Estimation of the Bayes Error.
944-951 BibTeX
- Howard H. Yang, Ying Hu, Michael Edmonson, Kenneth H. Buetow, Maxwell P. Lee:
Computation Method to Identify Differential Allelic Gene Expression and Novel Imprinted Genes.
952-955 BibTeX
- Yudong D. He, Hongyue Dai, Eric E. Schadt, Guy Cavet, Stephen W. Edwards, Sergey B. Stepaniants, Sven Duenwald, Robert Kleinhanz, Allan R. Jones, Daniel D. Shoemaker, Roland B. Stoughton:
Microarray Standard Data Set and Figures of Merit for Comparing Data Processing Methods and Experiment Designs.
956-965 BibTeX
- David M. Rocke, Blythe Durbin:
Approximate Variance-stabilizing Transformations for Gene-expression Microarray Data.
966-972 BibTeX
- Doulaye Dembélé, Philippe Kastner:
Fuzzy C-means Method for Clustering Microarray Data.
973-980 BibTeX
- Sorin Draghici, Frank M. Graziano, Samira Y. Kettoola, Ishwar K. Sethi, George Towfic:
Mining HIV Dynamics Using Independent Component Analysis.
981-986 BibTeX
- Svetlana Boycheva, Georgi Chkodrov, Ivan Ivanov:
Codon Pairs in the Genome of Escherichia Coli.
987-998 BibTeX
- Christopher Lee:
Generating Consensus Sequences from Partial Order Multiple Sequence Alignment Graphs.
999-1008 BibTeX
- Harpreet Singh, G. P. S. Raghava:
ProPred1: Prediction of Promiscuous MHC Class-I Binding Sites.
1009-1014 BibTeX
- Krzysztof Ginalski, Arne Elofsson, Daniel Fischer, Leszek Rychlewski:
3D-Jury: A Simple Approach to Improve Protein Structure Predictions.
1015-1018 BibTeX
- Ralph E. Steuer, Jürgen Kurths, Oliver Fiehn, Wolfram Weckwerth:
Observing and Interpreting Correlations in Metabolic Networks.
1019-1026 BibTeX
- Julien Gagneur, David B. Jackson, Georg Casari:
Hierarchical Analysis of Dependency in Metabolic Networks.
1027-1034 BibTeX
Applications Notes
- Apuã C. M. Paquola, Abimael A. Machado, Eduardo M. Reis, Aline Maria da Silva, Sergio Verjovski-Almeida:
Zerg: A Very Fast BLAST Parser Library.
1035-1036 BibTeX
- David M. A. Martin, Pamela Hill, Geoffrey J. Barton, Andrew J. Flavell:
Visual Representation of Database Search Results: The RHIMS Plot.
1037-1038 BibTeX
- Tao Xie, Leroy E. Hood:
ACGT - A Comparative Genomics Tool.
1039-1040 BibTeX
- Marcin von Grotthuss, Jakub Pas, Leszek Rychlewski:
Ligand-Info, Searching for Similar Small Compounds Using Index Profiles.
1041-1042 BibTeX
- S. S. Sheik, Prasanna Sundararajan, V. Shanthi, Krishna Sekar:
CAP: Conformation Angles Package - Displaying the Conformation Angles of Side Chains in Proteins.
1043-1044 BibTeX
Volume 19,
Number 9,
June 2003
Editorial
- Colin Campbell:
New Analytical Techniques for the Interpretation of Microarray Data.
1045 BibTeX
- Yanli Zhao, Wei Pan:
Modified Nonparametric Approaches to Detecting Differentially Expressed Genes in Replicated Microarray Experiments.
1046-1054 BibTeX
- Ernst Wit, John McClure:
Statistical Adjustment of Signal Censoring in Gene Expression Experiments.
1055-1060 BibTeX
- Marcel Dettling, Peter Bühlmann:
Boosting for Tumor Classification with Gene Expression Data.
1061-1069 BibTeX
- Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi Jaakkola:
K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data.
1070-1078 BibTeX
- Gad Getz, Hilah Gal, Itai Kela, Daniel A. Notterman, Eytan Domany:
Coupled Two-way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data.
1079-1089 BibTeX
- Sandrine Dudoit, Jane Fridlyand:
Bagging to Improve the Accuracy of A Clustering Procedure.
1090-1099 BibTeX
- Rebecka Jörnsten, Bin Yu:
Simultaneous Gene Clustering and Subset Selection for Sample Classification Via MDL.
1100-1109 BibTeX
- David Horn, Inon Axel:
Novel Clustering Algorithm for Microarray Expression Data in A Truncated SVD Space.
1110-1115 BibTeX
- Torgeir R. Hvidsten, Astrid Lægreid, Henryk Jan Komorowski:
Learning Rule-based Models of Biological Process from Gene Expression Time Profiles Using Gene Ontology.
1116-1123 BibTeX
- Hiroyuki Nakahara, Shin-ichi Nishimura, Masato Inoue, Gen Hori, Shun-ichi Amari:
Gene Interaction in DNA Microarray Data Is Decomposed by Information Geometric Measure.
1124-113 BibTeX
- Yoonkyung Lee, Cheol-Koo Lee:
Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Data.
1132-1139 BibTeX
- Dennis J. Michaud, Adam G. Marsh, Prasad S. Dhurjati:
eXPatGen: Generating Dynamic Expression Patterns for the Systematic Evaluation of Analytical Methods.
1140-1146 BibTeX
- Tianjiao Chu, Clark Glymour, Richard Scheines, Peter Spirtes:
A Statistical Problem for Inference to Regulatory Structure from Associations of Gene Expression Measurements with Microarrays.
1147-1152 BibTeX
Applications Note (Microarray Workshop Papers)
Original Papers
Applications Notes
Volume 19,
Number 10,
July 2003
PTC (2000/2001) Papers
- Christoph Helma, Stefan Kramer:
A Survey of the Predictive Toxicology Challenge 2000-2001.
1179-1182 BibTeX
- Hannu Toivonen, Ashwin Srinivasan, Ross D. King, Stefan Kramer, Christoph Helma:
Statistical Evaluation of the Predictive Toxicology Challenge 2000-2001.
1183-1193 BibTeX
- Romualdo Benigni, Alessandro Giuliani:
Putting the Predictive Toxicology Challenge Into Perspective: Reflections on the Results.
1194-1200 BibTeX
- V. G. Blinova, D. A. Dobrynin, V. K. Finn, Sergei O. Kuznetsov, E. S. Pankratova:
Toxicology Analysis by Means of the JSM-method.
1201-1207 BibTeX
- Takashi Okada:
Characteristic Substructures and Properties in Chemical Carcinogens Studied by the Cascade Model.
1208-1215 BibTeX
Discovery Notes
Original Papers
- Ketil Malde, Eivind Coward, Inge Jonassen:
Fast Sequence Clustering Using A Suffix Array Algorithm.
1221-1226 BibTeX
- Joseph Bockhorst, Mark Craven, David Page, Jude W. Shavlik, Jeremy D. Glasner:
A Bayesian Network Approach to Operon Prediction.
1227-1235 BibTeX
- Stan Pounds, Stephan W. Morris:
Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of P-values.
1236-1242 BibTeX
- Minghe Sun, Momiao Xiong:
A Mathematical Programming Approach for Gene Selection and Tissue Classification.
1243-1251 BibTeX
- Efstathia Bura, Ruth M. Pfeiffer:
Graphical Methods for Class Prediction Using Dimension Reduction Techniques on DNA Microarray Data.
1252-1258 BibTeX
- Chris H. Q. Ding:
Unsupervised Feature Selection Via Two-way Ordering in Gene Expression Analysis.
1259-1266 BibTeX
- An-Suei Yang, Lu-Yong Wang:
Local Structure Prediction with Local Structure-based Sequence Profiles.
1267-1274 BibTeX
- Phillip W. Lord, Robert D. Stevens, Andy Brass, Carole A. Goble:
Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation.
1275-1283 BibTeX
- Ronghui Xu, Xiaochun Li:
A Comparison of Parametric Versus Permutation Methods with Applications to General and Temporal Microarray Gene Expression Data.
1284-1289 BibTeX
Applications Notes
- Richard A. Lee, Moe Razaz, Steven Hayward:
The DynDom Database of Protein Domain Motions.
1290-1291 BibTeX
- James E. Johnson, Martina V. Stromvik, Kevin A. T. Silverstein, John A. Crow, Elizabeth Shoop, Ernest F. Retzel:
TableView: Portable Genomic Data Visualization.
1292-1293 BibTeX
- Lloyd Allison:
Longest Biased Interval and Longest Non-negative Sum Interval.
1294-1295 BibTeX
- Sohrab P. Shah, Graham P. McVicker, Alan K. Mackworth, Sanja Rogic, B. F. Francis Ouellette:
GeneComber: Combining Outputs of Gene Prediction Programs for Improved Results.
1296-1297 BibTeX
- James A. R. Dalton, Ioannis Michalopoulos, David R. Westhead:
Calculation of Helix Packing Angles in Protein Structures.
1298-1299 BibTeX
- Kun Zhang, Li Jin:
HaploBlockFinder: Haplotype Block Analyses.
1300-1301 BibTeX
Volume 19,
Number 11,
July 2003
Original Papers
- Jinling Huang, Suchendra M. Bhandarkar:
A Comparison of Physical Mapping Algorithms Based on the Maximum Likelihood Model.
1303-1310 BibTeX
- Pei-chin Chang, Konan Peck:
Design and Assessment of A Fast Algorithm for Identifying Specific Probes for Human and Mouse Genes.
1311-1317 BibTeX
- Todd E. Scheetz, Nishank Trivedi, Chad A. Roberts, Tamara Kucaba, Brian Berger, Natalie L. Robinson, Clayton L. Birkett, Allen J. Gavin, Brian O'Leary, Terry A. Braun, Maria F. Bonaldo, John P. Robinson, Val C. Sheffield, Marcelo Bento Soares, Thomas L. Casavant:
ESTprep: Preprocessing CDNA Sequence Reads.
1318-1324 BibTeX
- Dale L. Wilson, Michael J. Buckley, Chris A. Helliwell, I. W. Wilson:
New Normalization Methods for CDNA Microarray Data.
1325-1332 BibTeX
- Wei Pan:
On the Use of Permutation in and the Performance of A Class of Nonparametric Methods to Detect Differential Gene Expression.
1333-1340 BibTeX
- Xujing Wang, Martin J. Hessner, Yan Wu, Nirupma Pati, Soumitra Ghosh:
Quantitative Quality Control in Microarray Experiments and the Application in Data Filtering, Normalization and False Positive Rate Prediction.
1341-1347 BibTeX
- Sorin Draghici, Olga Kulaeva, Bruce Hoff, Anton Petrov, Soheil Shams, Michael A. Tainsky:
Noise Sampling Method: An ANOVA Approach Allowing Robust Selection of Differentially Regulated Genes Measured by DNA Microarrays.
1348-1359 BibTeX
- Blythe Durbin, David M. Rocke:
Estimation of Transformation Parameters for Microarray Data.
1360-1367 BibTeX
- Mark Spencer:
Exact Significance Levels for the Maximum 2 Method of Detecting Recombination.
1368-1370 BibTeX
- Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita:
Computational Analysis of Stop Codon Readthrough in D.melanogaster.
1371-1380 BibTeX
- Venkatarajan S. Mathura, Catherine H. Schein, Werner Braun:
Identifying Property Based Sequence Motifs in Protein Families and Superfamilies: Application to DNase-1 Related Endonucleases.
1381-1390 BibTeX
- Hongyu Zhang:
Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm.
1391-1396 BibTeX
- Caleb Webber, Geoffrey J. Barton:
Increased Coverage Obtained by Combination of Methods for Protein Sequence Database Searching.
1397-1403 BibTeX
- Robert C. Edgar, Kimmen Sjölander:
SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models.
1404-1411 BibTeX
- Victor Kunin, Christos A. Ouzounis:
GeneTRACE - Reconstruction of Gene Content of Ancestral Species.
1412-1416 BibTeX
- Jung-Hsien Chiang, Hsu-Chun Yu:
MeKE: Discovering the Functions of Gene Products from Biomedical Literature Via Sentence Alignment.
1417-1422 BibTeX
- Hongwu Ma, An-Ping Zeng:
The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks.
1423-1430 BibTeX
- Artem L. Ponomarev, Ronald L. Davis:
An Adjustable-threshold Algorithm for the Identification of Objects in Three-dimensional Images.
1431-1435 BibTeX
Applications Notes
- Michael A. Banks, Will Eichert, Jeffrey B. Olsen:
Which Genetic Loci Have Greater Population Assignment Power?.
1436-1438 BibTeX
- Perikles Simon Q-Gene:
Processing Quantitative Real-time RT-PCR Data.
1439-1440 BibTeX
- Yong Li, Mario G. Rosso, Nicolai Strizhov, Prisca Viehoever, Bernd Weisshaar:
GABI-Kat SimpleSearch: A Flanking Sequence Tag (FST) Database for the Identification of T-DNA Insertion Mutants in Arabidopsis Thaliana.
1441-1442 BibTeX
- J. Lynn Fink, Scott Drewes, Hiren Patel, John B. Welsh, Daniel R. Masys, Jacques Corbeil, Michael Gribskov:
2HAPI: A Microarray Data Analysis System.
1443-1445 BibTeX
- Catherine Grasso, Michael Quist, Kevin Ke, Christopher Lee:
POAVIZ: A Partial Order Multiple Sequence Alignment Visualizer.
1446-1448 BibTeX
- René Gibson, Douglas R. Smith:
Genome Visualization Made Fast and Simple.
1449-1450 BibTeX
- Paul Janssen, Anton J. Enright, Benjamin Audit, Ildefonso Cases, Leon Goldovsky, Nicola Harte, Victor Kunin, Christos A. Ouzounis:
COmplete GENome Tracking (COGENT): A Flexible Data Environment for Computational Genomics.
1451-1452 BibTeX
- T. B. Fischer, K. V. Arunachalam, D. Bailey, V. Mangual, S. Bakhru, R. Russo, D. Huang, M. Paczkowski, V. Lalchandani, C. Ramachandra, B. Ellison, S. Galer, J. Shapley, E. Fuentes, J. Tsai:
The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfaces.
1453-1454 BibTeX
Volume 19,
Number 12,
August 2003
Discovery Notes
Original Papers
- T. Z. DeSantis Jr., I. Dubosarskiy, S. R. Murray, G. L. Andersen:
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA.
1461-1468 BibTeX
- Dilip Rajagopalan:
A comparison of statistical methods for analysis of high density oligonucleotide array data.
1469-1476 BibTeX
- Keith A. Baggerly, Li Deng, Jeffrey S. Morris, C. Marcelo Aldaz:
Differential expression in SAGE: accounting for normal between-library variation.
1477-1483 BibTeX
- Ray L. Somorjai, B. Dolenko, Richard Baumgartner:
Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions.
1484-1491 BibTeX
- Ian Korf:
Serial BLAST searching.
1492-1496 BibTeX
- Louxin Zhang, Bin Ma, Lusheng Wang, Ying Xu:
Greedy method for inferring tandem duplication history.
1497-1504 BibTeX
- Ari Löytynoja, Michel C. Milinkovitch:
A hidden Markov model for progressive multiple alignment.
1505-1513 BibTeX
- Yoshiharu Hayashi, Katsuyoshi Sakaguchi, Mime Kobayashi, Masaki Kobayashi, Yo Kikuchi, Eiichiro Ichiishi:
Molecular evaluation using in silico protein interaction profiles.
1514-1523 BibTeX
- Jie Wu, Simon Kasif, Charles DeLisi:
Identification of functional links between genes using phylogenetic profiles.
1524-1530 BibTeX
- David Mittelman, Ruslan Sadreyev, Nick V. Grishin:
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.
1531-1539 BibTeX
- Bala Krishnamoorthy, Alexander Tropsha:
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations.
1540-1548 BibTeX
- Homayoun Valafar, James H. Prestegard:
Rapid classification of a protein fold family using a statistical analysis of dipolar couplings.
1549-1555 BibTeX
- Simon Whelan, Paul I. W. de Bakker, Nick Goldman:
Pandit: a database of protein and associated nucleotide domains with inferred trees.
1556-1563 BibTeX
- Patrick Lambrix, Manal Habbouche, Marta Pérez:
Evaluation of ontology development tools for bioinformatics.
1564-1571 BibTeX
Applications Notes
- Fredrik Ronquist, John P. Huelsenbeck:
MrBayes 3: Bayesian phylogenetic inference under mixed models.
1572-1574 BibTeX
- Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern:
AGenDA: homology-based gene prediction.
1575-1577 BibTeX
- Yang Su, T. M. Murali, Vladimir Pavlovic, Michael Schaffer, Simon Kasif:
RankGene: identification of diagnostic genes based on expression data.
1578-1579 BibTeX
- Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Jan Kok, Oscar P. Kuipers:
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons.
1580-1582 BibTeX
- Naoki Sato, Shigeki Ehira:
GenoMap, a circular genome data viewer.
1583-1584 BibTeX
- Kuo-Bin Li:
ClustalW-MPI: ClustalW analysis using distributed and parallel computing.
1585-1586 BibTeX
- Apuã C. M. Paquola, Milton Y. Nishyiama Jr., Eduardo M. Reis, Aline Maria da Silva, Sergio Verjovski-Almeida:
ESTWeb: bioinformatics services for EST sequencing projects.
1587-1588 BibTeX
- Guoli Wang, Roland L. Dunbrack Jr.:
PISCES: a protein sequence culling server.
1589-1591 BibTeX
- Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen:
Digital extractor: analysis of digital differential display output.
1592-1593 BibTeX
- Stephen F. Madden, Barry O'Donovan, Simon J. Furney, Hugh R. Brady, Guenole C. M. Silvestre, Peter P. Doran:
Digital extractor: analysis of digital differential display output.
1594-1595 BibTeX
Volume 19,
Number 13,
September 2003
Original Papers
- Shuyu Li, Gene Cutler, Jane Jijun Liu, Timothy Hoey, Liangbiao Chen, Peter G. Schultz, Jia yu Liao, Xuefeng Bruce Ling:
A comparative analysis of HGSC and Celera human genome assemblies and gene sets.
1597-1605 BibTeX
- Diego di Bernardo, Thomas Down, Tim J. P. Hubbard:
ddbRNA: detection of conserved secondary structures in multiple alignments.
1606-1611 BibTeX
- Inderjit S. Dhillon, Edward M. Marcotte, Usman Roshan:
Diametrical clustering for identifying anti-correlated gene clusters.
1612-1619 BibTeX
- Paul Pavlidis, Qinghong Li, William Stafford Noble:
The effect of replication on gene expression microarray experiments.
1620-1627 BibTeX
- Xu Guo, Huilin Qi, Catherine M. Verfaillie, Wei Pan:
Statistical significance analysis of longitudinal gene expression data.
1628-1635 BibTeX
- Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn Stone, David Ward, Kenneth Williams, Hongyu Zhao:
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data.
1636-1643 BibTeX
- Jonathan A. Barker, Janet M. Thornton:
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
1644-1649 BibTeX
- Jonathan J. Ward, Liam J. McGuffin, Bernard F. Buxton, David T. Jones:
Secondary structure prediction with support vector machines.
1650-1655 BibTeX
- Keun-Joon Park, Minoru Kanehisa:
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs.
1656-1663 BibTeX
- Alex Mitchell, Jacqueline Renée Reich, Terri K. Attwood:
PRECIS: Protein reports engineered from concise information in SWISS-PROT.
1664-1671 BibTeX
- David P. Kreil, Christos A. Ouzounis:
Comparison of sequence masking algorithms and the detection of biased protein sequence regions.
1672-1681 BibTeX
- Jahnavi C. Prasad, Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho:
Consensus alignment for reliable framework prediction in homology modeling.
1682-1691 BibTeX
- D. C. McShan, S. Rao, Imran Shah:
PathMiner: predicting metabolic pathways by heuristic search.
1692-1698 BibTeX
- Svetlana Novichkova, Sergei Egorov, Nikolai Daraselia:
MedScan, a natural language processing engine for MEDLINE abstracts.
1699-1706 BibTeX
Applications Notes
- Christophe Pichon, Brice Felden:
Intergenic sequence inspector: searching and identifying bacterial RNAs.
1707-1709 BibTeX
- D. P. Wall, H. B. Fraser, A. E. Hirsh:
Detecting putative orthologs.
1710-1711 BibTeX
- Jian Wang, Eileen Kraemer:
GFPE: gene-finding program evaluation.
1712-1713 BibTeX
- Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi:
CGH-Plotter: MATLAB toolbox for CGH-data analysis.
1714-1715 BibTeX
- R. J. Laws, Tracy L. Bergemann, Filemon Quiaoit, Lue Ping Zhao:
SignalViewer: analyzing microarray images.
1716-1717 BibTeX
- Robert J. Blick, Andrew T. Revel, Eric J. Hansen:
FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis.
1718-1719 BibTeX
- Chunhong Mao, John C. Cushman, Gregory D. May, Jennifer W. Weller:
ESTAP-an automated system for the analysis of EST data.
1720-1722 BibTeX
- Razif R. Gabdoulline, René Hoffmann, Florian Leitner, Rebecca C. Wade:
ProSAT: functional annotation of protein 3D structures.
1723-1725 BibTeX
- C. J. Creevey, James O. McInerney:
CRANN: detecting adaptive evolution in protein-coding DNA sequences.
1726 BibTeX
- Koichi Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, Fumihiko Miyoshi, Yasuhiro Naito, Yoichi Nakayama, Masaru Tomita:
E-Cell 2: Multi-platform E-Cell simulation system.
1727-1729 BibTeX
- Sinan Güler, Andreas Eberhart, Isabel Rojas:
Web-based exchange of biochemical information.
1730-1731 BibTeX
Volume 19,
Number 14,
September 2003
Chia Papers
Original Papers
- Rebecca Thomson, T. Charles Hodgman, Zheng Rong Yang, Austin K. Doyle:
Characterizing proteolytic cleavage site activity using bio-basis function neural networks.
1741-1747 BibTeX
- Andrew P. Harrison, Frances M. G. Pearl, Ian Sillitoe, Tim Slidel, Richard Mott, Janet M. Thornton, Christine A. Orengo:
Recognizing the fold of a protein structure.
1748-1759 BibTeX
- A. Vinayagam, J. Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini:
DDBASE2.0: updated domain database with improved identification of structural domains.
1760-1764 BibTeX
- Björn Peters, Weiwei Tong, John Sidney, Alessandro Sette, Zhiping Weng:
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules.
1765-1772 BibTeX
- Lusheng Wang, Ying Xu:
Haplotype inference by maximum parsimony.
1773-1780 BibTeX
- Gábor Firneisz, Idit Zehavi, Csaba Vermes, Anita Hanyecz, Joshua A. Frieman, Tibor T. Glant:
Identification and quantification of disease-related gene clusters.
1781-1786 BibTeX
- Roded Sharan, Adi Maron-Katz, Ron Shamir:
CLICK and EXPANDER: a system for clustering and visualizing gene expression data.
1787-1799 BibTeX
- Adil M. Bagirov, Brent Ferguson, Sasha Ivkovic, G. Saunders, John Yearwood:
New algorithms for multi-class cancer diagnosis using tumor gene expression signatures.
1800-1807 BibTeX
- Sue C. Geller, Jeff P. Gregg, Paul Hagerman, David M. Rocke:
Transformation and normalization of oligonucleotide microarray data.
1817-1823 BibTeX
- Vitaly L. Galinsky:
Automatic registration of microarray images. I. Rectangular grid.
1824-1831 BibTeX
- Vitaly L. Galinsky:
Automatic registration of microarray images. II. Hexagonal grid.
1832-1836 BibTeX
- Tim Carver, Alan J. Bleasby:
The design of Jemboss: a graphical user interface to EMBOSS.
1837-1843 BibTeX
Applications Notes
- Donny Tjandra, Stephen T. C. Wong, Weimin Shen, Brian Pulliam, Elaine Yu, Laura Esserman:
An XML message broker framework for exchange and integration of microarray data.
1844-1845 BibTeX
- N. H. Shah, D. C. King, P. N. Shah, Nina V. Fedoroff:
A tool-kit for cDNA microarray and promoter analysis.
1846-1848 BibTeX
- Shandar Ahmad, M. Michael Gromiha, Akinori Sarai:
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences.
1849-1851 BibTeX
- Alan A. Dombkowski:
Disulfide by DesignTM: a computational method for the rational design of disulfide bonds in proteins.
1852-1853 BibTeX
- Fabien Campagne, Emmanuel Bettler, Gert Vriend, Harel Weinstein:
Batch mode generation of residue-based diagrams of proteins.
1854-1855 BibTeX
- Dushyanthan Puvanendrampillai, John B. O. Mitchell:
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes.
1856-1857 BibTeX
- Sean D. Mooney, Russ B. Altman:
MutDB: annotating human variation with functionally relevant data.
1858-1860 BibTeX
- Rasko Leinonen, Francesco Nardone, Olalekan Oyewole, Nicole Redaschi, Peter Stoehr:
The EMBL sequence version archive.
1861-1862 BibTeX
- Jiren Wang, Qing Mu:
Soap-HT-BLAST: high throughput BLAST based on Web services.
1863-1864 BibTeX
- David R. Mathog:
Parallel BLAST on split databases.
1865-1866 BibTeX
Volume 19,
Number 15,
October 2003
Editorials
- The Fourth Georgia Tech-University of Georgia International Conference in Bioinformatics: in silico Biology, Biological Networks, from Genomics to Epidemiology (November 13-16, 2003, Atlanta, Georgia, USA).
1867-1868 BibTeX
Atlanta Conference Papers
- Joel S. Bader:
Greedily building protein networks with confidence.
1869-1874 BibTeX
- Shawn M. Gomez, William Stafford Noble, Andrey Rzhetsky:
Learning to predict protein-protein interactions from protein sequences.
1875-1881 BibTeX
- Kyungsook Han, Byong-Hyon Ju:
A fast layout algorithm for protein interaction networks.
1882-1888 BibTeX
- Georgy P. Karev, Yuri I. Wolf, Eugene V. Koonin:
Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve?
1889-1900 BibTeX
- Roland Krause, Christian von Mering, Peer Bork:
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
1901-1908 BibTeX
- Alexander V. Lukashin, Matvey E. Lukashev, Rainer Fuchs:
Topology of gene expression networks as revealed by data mining and modeling.
1909-1916 BibTeX
- Jiang Qian, Jimmy Lin, Nicholas M. Luscombe, Haiyuan Yu, Mark Gerstein:
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
1917-1926 BibTeX
- Daniel Rocco, Terence Critchlow:
Automatic discovery and classification of bioinformatics Web sources.
1927-1933 BibTeX
Commentaries
Original Papers
- Xueli Liu, Hans-Georg Müller:
Modes and clustering for time-warped gene expression profile data.
1937-1944 BibTeX
- Nitin Jain, Jayant Thatte, Thomas Braciale, Klaus Ley, Michael O'Connell, Jae K. Lee:
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays.
1945-1951 BibTeX
- Chandrasegaran Narasimhan, Philip F. LoCascio, Edward C. Uberbacher:
Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection.
1952-1963 BibTeX
- Leo Gordon, Alexey Ya. Chervonenkis, Alex J. Gammerman, Ilham A. Shahmuradov, Victor V. Solovyev:
Sequence alignment kernel for recognition of promoter regions.
1964-1971 BibTeX
- Yonghong Wang, Jinwei Liu, Tongju Zhao, Qing Ji:
Recognizing translation initiation sites of eukaryotic genes based on the cooperatively scanning model.
1972-1977 BibTeX
- Yingdong Zhao, Clemencia Pinilla, Danila Valmori, Roland Martin, Richard Simon:
Application of support vector machines for T-cell epitopes prediction.
1978-1984 BibTeX
- Manesh J. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong Xu, Ying Xu:
A computational pipeline for protein structure prediction and analysis at genome scale.
1985-1996 BibTeX
Applications Notes
Volume 19,
Number 16,
November 2003
Original Papers
- Alessandra Carbone, Andrey Zinovyev, François Képès:
Codon adaptation index as a measure of dominating codon bias.
2005-2015 BibTeX
- Gerhard Kauer, Helmut Blöcker:
Applying signal theory to the analysis of biomolecules.
2016-2021 BibTeX
- Hector Sanchez-Villeda, Steven G. Schroeder, Mary L. Polacco, Michael D. McMullen, Seth A. Havermann, Georgia L. Davis, Irie Vroh-Bi, Karen C. Cone, Natasha Sharopova, Young-Sun Yim, Linda Schultz, Ngozi A. Duru, Theresa A. Musket, Kate Houchins, Zhiwei Fang, Jack M. Gardiner, Edward H. Coe:
Development of an integrated laboratory information management system for the maize mapping project.
2022-2030 BibTeX
- Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni:
A novel strategy for microarray quality control using Bayesian networks.
2031-2038 BibTeX
- Jason Gertz, Georgiy Elfond, Anna Shustrova, Matt Weisinger, Matteo Pellegrini, Shawn Cokus, Bruce Rothschild:
Inferring protein interactions from phylogenetic distance matrices.
2039-2045 BibTeX
- Joshua M. Temkin, Mark R. Gilder:
Extraction of protein interaction information from unstructured text using a context-free grammar.
2046-2053 BibTeX
- S. P. Mielke, V. V. Krishnan:
Protein structural class identification directly from NMR spectra using averaged chemical shifts.
2054-2064 BibTeX
- Marcel Smid, Lambert C. J. Dorssers, Guido Jenster:
Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes.
2065-2071 BibTeX
- Xiaohong Huang, Wei Pan:
Linear regression and two-class classification with gene expression data.
2072-2078 BibTeX
- Humberto González Díaz, Ronal Ramos de Armas, Reinaldo Molina Ruiz:
Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 -RNA packaging region with drugs.
2079-2087 BibTeX
- Shigeyuki Oba, Masa-aki Sato, Ichiro Takemasa, Morito Monden, Ken-ichi Matsubara, Shin Ishii:
A Bayesian missing value estimation method for gene expression profile data.
2088-2096 BibTeX
- Jie Qin, Darrin P. Lewis, William Stafford Noble:
Kernel hierarchical gene clustering from microarray expression data.
2097-2104 BibTeX
- Zhiwei Fang, Karen C. Cone, Hector Sanchez-Villeda, Mary L. Polacco, Michael D. McMullen, Steven G. Schroeder, Jack M. Gardiner, Georgia L. Davis, Seth A. Havermann, Young-Sun Yim, Irie Vroh-Bi, Edward H. Coe:
iMap: a database-driven utility to integrate and access the genetic and physical maps of maize.
2105-2111 BibTeX
- Kristian Rother, Robert Preissner, Andrean Goede, Cornelius Frömmel:
Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins.
2112-2121 BibTeX
- Hasan H. Otu, Khalid Sayood:
A new sequence distance measure for phylogenetic tree construction.
2122-2130 BibTeX
- Arthur L. Hsu, Sen-Lin Tang, Saman K. Halgamuge:
An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data.
2131-2140 BibTeX
Applications Notes
- Mark Harris, Jeremy M. R. Martin, John F. Peden, Christopher J. Rawlings:
SNP cherry picker: maximizing the chance of finding an association with a disease SNP.
2141-2143 BibTeX
- Dong-Yup Lee, Hongsoek Yun, Sunwon Park, Sang Yup Lee:
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis.
2144-2146 BibTeX
- Keyue Ding, Kaixin Zhou, Fuchu He, Yan Shen:
LDA - a java-based linkage disequilibrium analyzer.
2147-2148 BibTeX
- Aubrey E. Hill, Helen Kim:
The UAB Proteomics Database.
2149-2151 BibTeX
- Kamyar Farahi, William B. Whitman, Eileen Kraemer:
RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events.
2152-2154 BibTeX
- Alexander Nikitin, Sergei Egorov, Nikolai Daraselia, Ilya Mazo:
Pathway studio - the analysis and navigation of molecular networks.
2155-2157 BibTeX
- Luis A. Martínez-Cruz, Angel Rubio, María L. Martínez-Chantar, Alberto Labarga, Isabel Barrio, Adam Podhorski, Victor Segura, José L. Sevilla Campo, Matías A. Avila, Jose M. Mato:
GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data.
2158-2160 BibTeX
- Bairong Shen, Mauno Vihinen:
RankViaContact: ranking and visualization of amino acid contacts.
2161-2162 BibTeX
- Gianluigi Cardinali, Francesco Maraziti, Sabrina Selvi:
Electrophoretic data classification for phylogenetics and biostatistics.
2163-2165 BibTeX
Volume 19,
Number 17,
November 2003
Discovery Notes
Reviews
Original Papers
- Vincent Thareau, Patrice Déhais, Carine Serizet, Pierre Hilson, Pierre Rouzé, Sébastien Aubourg:
Automatic design of gene-specific sequence tags for genome-wide functional studies.
2191-2198 BibTeX
- Vidhya Gomathi Krishnan, David R. Westhead:
A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function.
2199-2209 BibTeX
- Junbai Wang, Ola Myklebost, Eivind Hovig:
MGraph: graphical models for microarray data analysis.
2210-2211 BibTeX
- Anders Wallqvist, Alfred A. Rabow, Robert H. Shoemaker, Edward A. Sausville, David G. Covell:
Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data.
2212-2224 BibTeX
- Ivan Erill, Marcos Escribano, Susana Campoy, Jordi Barbé:
In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon.
2225-2236 BibTeX
- Lusheng Wang, Jianyun Zhao:
Parametric alignment of ordered trees.
2237-2245 BibTeX
- Shirish Krishnaj Shevade, S. Sathiya Keerthi:
A simple and efficient algorithm for gene selection using sparse logistic regression.
2246-2253 BibTeX
- Peter J. Giles, David Kipling:
Normality of oligonucleotide microarray data and implications for parametric statistical analyses.
2254-2262 BibTeX
- Irini A. Doytchinova, Darren R. Flower:
Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction.
2263-2270 BibTeX
- Dirk Husmeier:
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks.
2271-2282 BibTeX
- Anthony L. Duran, Jian Yang, Liangjiang Wang, Lloyd W. Sumner:
Metabolomics spectral formatting, alignment and conversion tools (MSFACTs).
2283-2293 BibTeX
- Yuna Hou, Wynne Hsu, Mong-Li Lee, Chris Bystroff:
Efficient remote homology detection using local structure.
2294-2301 BibTeX
- Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty:
Missing-value estimation using linear and non-linear regression with Bayesian gene selection.
2302-2307 BibTeX
Applications Notes
- Thomas Hamelryck, Bernard Manderick:
PDB file parser and structure class implemented in Python.
2308-2310 BibTeX
- Yanming Yang, Li M. Fu:
TSGDB: a database system for tumor suppressor genes.
2311-2312 BibTeX
- Kim Carter, Matthew I. Bellgard:
MASV - Multiple (BLAST) Annotation System Viewer.
2313-2315 BibTeX
- Jason S. Iacovoni:
GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome.
2316-2318 BibTeX
- Mads Wichmann Matthiessen:
BioWareDB: the biomedical software and database search engine.
2319-2320 BibTeX
- Gabriel S. Eichler, Sui Huang, Donald E. Ingber:
Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles.
2321-2322 BibTeX
- Hao Wang, Beng Chin Ooi, Kian-Lee Tan, Twee-Hee Ong, Lei Zhou:
BLAST++: BLASTing queries in batches.
2323-2324 BibTeX
- Kevin Thornton:
libsequence: a C++ class library for evolutionary genetic analysis.
2325-2327 BibTeX
- Jorge García de la Nava, Sacha A. F. T. van Hijum, Oswaldo Trelles:
PreP: gene expression data pre-processing.
2328-2329 BibTeX
- Paul O. Lewis:
NCL: a C++ class library for interpreting data files in NEXUS format.
2330-2331 BibTeX
- Carsten O. Daub, Sebastian Kloska, Joachim Selbig:
MetaGeneAlyse: analysis of integrated transcriptional and metabolite data.
2332-2333 BibTeX
Volume 19,
Number 18,
December 2003
Original Papers
- Johannes Hüsing, Michael Zeschnigk, Tanja Boes, Karl-Heinz Jöckel:
Combining DNA expression with positional information to detect functional silencing of chromosomal regions.
2335-2342 BibTeX
- Igor Landais, M. Ogliastro, Kazuei Mita, Junko Nohata, Miguel López-Ferber, Martine Duonor-Cérutti, Toru Shimada, Philippe Fournier, Gérard Devauchelle:
Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias.
2343-2350 BibTeX
- Yihua Huang, Tianyun Ni, Lei Zhou, Stanley Y. W. Su:
JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.
2351-2358 BibTeX
- Virpi Ahola, Tero Aittokallio, Esa Uusipaikka, Mauno Vihinen:
Efficient estimation of emission probabilities in profile hidden Markov models.
2359-2368 BibTeX
- Ting Wang, Gary D. Stormo:
Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
2369-2380 BibTeX
- Irit Gat-Viks, Roded Sharan, Ron Shamir:
Scoring clustering solutions by their biological relevance.
2381-2389 BibTeX
- Shao-Wu Zhang, Quan Pan, Hongcai Zhang, Yun-Long Zhang, Hai-Yu Wang:
Classification of protein quaternary structure with support vector machine.
2390-2396 BibTeX
- Wei-Min Liu, Xiaojun Di, Geoffrey Yang, Hajime Matsuzaki, Jing Huang, Rui Mei, Thomas B. Ryder, Teresa A. Webster, Shoulian Dong, Guoying Liu, Keith W. Jones, Giulia C. Kennedy, David Kulp:
Algorithms for large-scale genotyping microarrays.
2397-2403 BibTeX
- Peter A. Covitz, Frank W. Hartel, Carl Schaefer, Sherri de Coronado, Gilberto Fragoso, Himanso Sahni, Scott Gustafson, Kenneth H. Buetow:
caCORE: A common infrastructure for cancer informatics.
2404-2412 BibTeX
- Chen-Shan Chin, Manoj Pratim Samanta:
Global snapshot of a protein interaction network - a percolation based approach.
2413-2419 BibTeX
- Jacob Köhler, Stephan Philippi, Matthias Lange:
SEMEDA: ontology based semantic integration of biological databases.
2420-2427 BibTeX
- Antonio S. Torralba:
Susceptibility of non-linear systems as an approach to metabolic responses.
2428-2435 BibTeX
- Igor Rojdestvenski:
Metabolic pathways in three dimensions.
2436-2441 BibTeX
- Cornelius Frömmel, Christoph Gille, Andrean Goede, Clemens Gröpl, Stefan Hougardy, Till Nierhoff, Robert Preissner, Martin Thimm:
Accelerating screening of 3D protein data with a graph theoretical approach.
2442-2447 BibTeX
- George W. Wright, Richard Simon:
A random variance model for detection of differential gene expression in small microarray experiments.
2448-2455 BibTeX
- Zhuoran Chen:
Assessing sequence comparison methods with the average precision criterion.
2456-2460 BibTeX
- Ricardo Z. N. Vêncio, Helena Brentani, Carlos A. B. Pereira:
Using credibility intervals instead of hypothesis tests in SAGE analysis.
2461-2464 BibTeX
- Anne-Laure Boulesteix, Gerhard Tutz, Korbinian Strimmer:
A CART-based approach to discover emerging patterns in microarray data.
2465-2472 BibTeX
Applications Notes
- Gary L. Argraves, Jeremy L. Barth, W. Scott Argraves:
The MUSC DNA Microarray Database.
2473-2474 BibTeX
- Roman Roset, Juan A. Subirana, Xavier Messeguer:
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences.
2475-2476 BibTeX
- Josep F. Abril, Roderic Guigó, Thomas Wiehe:
gff2aplot: Plotting sequence comparisons.
2477-2479 BibTeX
- Kim Brügger, Peter Redder, Marie Skovgaard:
MUTAGEN: Multi-User Tool for Annotating GENomes.
2480-2481 BibTeX
- Thomas Lütteke, Peter Krieg, Gerhard Fürstenberger, Claus-Wilhelm von der Lieth:
LOX-DB - a database on lipoxygenases.
2482-2483 BibTeX
- Salim Khan, Gang Situ, Keith Decker, Carl Schmidt:
GoFigure: Automated Gene OntologyTM annotation.
2484-2485 BibTeX
- Matej Lexa, Giorgio Valle:
PRIMEX: rapid identification of oligonucleotide matches in whole genomes.
2486-2488 BibTeX
- Christoph Gille, Stephan Lorenzen, Elke Michalsky, Cornelius Frömmel:
KISS for STRAP: user extensions for a protein alignment editor.
2489-2491 BibTeX
- Daniel Aguilar, Baldomero Oliva, Francesc X. Avilés, Enrique Querol:
SNOW: Standard NOmenclature Wizard to help searching for (bio) chemical standardized names.
2492-2493 BibTeX
- Nadia Bolshakova, Francisco Azuaje:
Machaon CVE: cluster validation for gene expression data.
2494-2495 BibTeX
- Julio Rozas, Juan C. Sánchez-DelBarrio, Xavier Messeguer, Ricardo Rozas:
DnaSP, DNA polymorphism analyses by the coalescent and other methods.
2496-2497 BibTeX
- Piero Fariselli, Giacomo Finocchiaro, Rita Casadio:
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites.
2498-2499 BibTeX
- András Fiser, Andrej Sali:
ModLoop: automated modeling of loops in protein structures.
2500-2501 BibTeX
- Gabriel F. Berriz, Oliver D. King, Barbara Bryant, Chris Sander, Frederick P. Roth:
Characterizing gene sets with FuncAssociate.
2502-2504 BibTeX
Supplements
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29 - July 3, 2003, Brisbane, Australia.
2003
Contents BibTeX
Proceedings of the European Conference on Computational Biology (ECCB 2003), September 27-30, 2003, Paris, France.
2003
Contents BibTeX
Copyright © Sat May 16 23:51:29 2009
by Michael Ley (ley@uni-trier.de)
