Volume 21,
Number 1,
January 2005
Editorials
Original Papers - Genome Analysis
Sequence Analysis
- Kuo-Chen Chou:
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes.
10-19
Electronic Edition (link) BibTeX
- Chin Lung Lu, Yen Pin Huang:
A memory-efficient algorithm for multiple sequence alignment with constraints.
20-30
Electronic Edition (link) BibTeX
- Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang, Michael Q. Zhang:
DWE: Discriminating Word Enumerator.
31-38
Electronic Edition (link) BibTeX
- Åsa K. Björklund, Daniel Soeria-Atmadja, Anna Zorzet, Ulf Hammerling, Mats G. Gustafsson:
Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins.
39-50
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Data And Text Mining
Databases And Ontologies
Applications Notes - Sequence Analysis
Gene Expression
Genetics And Population Analysis
Systems Biology
Databases And Ontologies
- Slobodan Vucetic, Zoran Obradovic, Vladimir Vacic, Predrag Radivojac, Kang Peng, Lilia M. Iakoucheva, Marc S. Cortese, J. David Lawson, Celeste J. Brown, Jason G. Sikes, Crystal D. Newton, A. Keith Dunker:
DisProt: a database of protein disorder.
137-140
Electronic Edition (link) BibTeX
Volume 21,
Number 2,
January 2005
Original Papers - Genome Analysis
Sequence Analysis
Gene Expression
Systems Biology
- J. P. Massar, Michael Travers, Jeff Elhai, Jeff Shrager:
BioLingua: a programmable knowledge environment for biologists.
199-207
Electronic Edition (link) BibTeX
- David Orrell, Stephen Ramsey, Pedro de Atauri, Hamid Bolouri:
A method for estimating stochastic noise in large genetic regulatory networks.
208-217
Electronic Edition (link) BibTeX
- Shawn Martin, Diana C. Roe, Jean-Loup Faulon:
Predicting protein-protein interactions using signature products.
218-226
Electronic Edition (link) BibTeX
- Sascha Ott, A. Hansen, SunYong Kim, Satoru Miyano:
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.
227-238
Electronic Edition (link) BibTeX
- Michele Leone, Andrea Pagnani:
Predicting protein functions with message passing algorithms.
239-247
Electronic Edition (link) BibTeX
Data And Text Mining
Applications Notes - Sequence Analysis
Phylogenetics
Genetics And Population Analysis
Systems Biology
Databases And Ontologies
Volume 21,
Number 3,
February 2005
Editorials
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Systems Biology
- Luca Ferrarini, Luca Bertelli, Jacob Feala, Andrew D. McCulloch, Giovanni Paternostro:
A more efficient search strategy for aging genes based on connectivity.
338-348
Electronic Edition (link) BibTeX
- Matthew J. Beal, Francesco Falciani, Zoubin Ghahramani, Claudia Rangel, David L. Wild:
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors.
349-356
Electronic Edition (link) BibTeX
- Antti Pettinen, Tommi Aho, Olli-Pekka Smolander, Tiina Manninen, Antti Saarinen, Kaisa-Leena Taattola, Olli Yli-Harja, Marja-Leena Linne:
Simulation tools for biochemical networks: evaluation of performance and usability.
357-363
Electronic Edition (link) BibTeX
- Vicente Arnau, Sergio Mars, Ignacio Marín:
Iterative Cluster Analysis of Protein Interaction Data.
364-378
Electronic Edition (link) BibTeX
Databases And Ontologies
Genome Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Systems Biology
Data And Text Mining
Databases And Ontologies
Volume 21,
Number 4,
February 2005
SAC 2004 Papers
- Jyotsna Kasturi, Raj Acharya:
Clustering of diverse genomic data using information fusion.
423-429
Electronic Edition (link) BibTeX
- Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael L. Creech, Annette Adler:
An architecture for biological information extraction and representation.
430-438
Electronic Edition (link) BibTeX
- Daisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara:
Multidimensional support vector machines for visualization of gene expression data.
439-444
Electronic Edition (link) BibTeX
- Osman Abul, Reda Alhajj, Faruk Polat, Ken Barker:
Finding differentially expressed genes for pattern generation.
445-450
Electronic Edition (link) BibTeX
- Nadia Bolshakova, Francisco Azuaje, Padraig Cunningham:
An integrated tool for microarray data clustering and cluster validity assessment .
451-455
Electronic Edition (link) BibTeX
- Alexandros Stamatakis, Thomas Ludwig, Harald Meier:
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
456-463
Electronic Edition (link) BibTeX
Genome Analysis
Sequence Analysis
Gene Expression
- Veronica Vinciotti, Raya Khanin, David D'Alimonte, Xiaohui Liu, N. Cattini, G. Hotchkiss, G. Bucca, O. de Jesus, J. Rasaiyaah, C. P. Smith, Paul Kellam, Ernst Wit:
An experimental evaluation of a loop versus a reference design for two-channel microarrays.
492-501
Electronic Edition (link) BibTeX
- Paul Delmar, Stéphane Robin, Jean-Jacques Daudin:
VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.
502-508
Electronic Edition (link) BibTeX
- Liping Ji, Kian-Lee Tan:
Identifying time-lagged gene clusters using gene expression data.
509-516
Electronic Edition (link) BibTeX
- Byung Soo Kim, Inyoung Kim, Sunho Lee, Sangcheol Kim, Sun Young Rha, Hyun Cheol Chung:
Statistical methods of translating microarray data into clinically relevant diagnostic information in colorectal cancer.
517-528
Electronic Edition (link) BibTeX
- Zhong Guan, Hongyu Zhao:
A semiparametric approach for marker gene selection based on gene expression data.
529-536
Electronic Edition (link) BibTeX
Genome Analysis
Sequence Analysis
- Martín Sarachu, Marc Colet:
wEMBOSS: a web interface for EMBOSS.
540-541
Electronic Edition (link) BibTeX
- Derek Kisman, Ming Li, Bin Ma, Li Wang:
tPatternHunter: gapped, fast and sensitive translated homology search .
542-544
Electronic Edition (link) BibTeX
- D. Charif, Jean Thioulouse, J. R. Lobry, Guy Perrière:
Online synonymous codon usage analyses with the ade4 and seqinR packages.
545-547
Electronic Edition (link) BibTeX
- Jinsoo Kim, Jungmin Seo, Young Seek Lee, Sangsoo Kim:
TFExplorer: integrated analysis database for predicted transcription regulatory elements.
548-550
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Systems Biology
Volume 21,
Number 5,
March 2005
Genome Analysis
Sequence Analysis
- Davide Campagna, Chiara Romualdi, Nicola Vitulo, Micky Del Favero, Matej Lexa, Nicola Cannata, Giorgio Valle:
RAP: a new computer program for de novo identification of repeated sequences in whole genomes.
582-588
Electronic Edition (link) BibTeX
- Jinko Graham, Brad McNeney, Françoise Seillier-Moiseiwitsch:
Stepwise detection of recombination breakpoints in sequence alignments.
589-595
Electronic Edition (link) BibTeX
- Yoseph Barash, Gal Elidan, Tommy Kaplan, Nir Friedman:
Y. Barash, G. Elidan, T. Kaplan, , N. Friedman.
596-600
Electronic Edition (link) BibTeX
- S. Burden, Y.-X. Lin, R. Zhang:
Improving promoter prediction Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences.
601-607
Electronic Edition (link) BibTeX
- Luciano da Fontoura Costa:
Biological sequence analysis through the one-dimensional percolation transform and its enhanced version.
608-616
Electronic Edition (link) BibTeX
- Jennifer L. Gardy, Matthew R. Laird, Fei Chen, Sébastien Rey, C. J. Walsh, Martin Ester, Fiona S. L. Brinkman:
PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis.
617-623
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
- Alexander R. Statnikov, Constantin F. Aliferis, Ioannis Tsamardinos, Douglas Hardin, Shawn Levy:
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis.
631-643
Electronic Edition (link) BibTeX
- Musa H. Asyali, Musa Alci:
Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods.
644-649
Electronic Edition (link) BibTeX
- Itai Yanai, Hila Benjamin-Rodrig, Michael Shmoish, Vered Chalifa-Caspi, Maxim Shklar, Ron Ophir, Arren Bar-Even, Shirley Horn-Saban, Marilyn Safran, Eytan Domany, Doron Lancet, Orit Shmueli:
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.
650-659
Electronic Edition (link) BibTeX
- Cyril Dalmasso, Philippe Broët, Thierry Moreau:
A simple procedure for estimating the false discovery rate.
660-668
Electronic Edition (link) BibTeX
Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Data And Text Mining
Databases And Ontologies:
Volume 21,
Number 6,
March 2005
Sequence Analysis
Genome Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
- Peter J. Woolf, Wendy Prudhomme, Laurence Daheron, George Q. Daley, Douglas A. Lauffenburger:
Bayesian analysis of signaling networks governing embryonic stem cell fate decisions.
741-753
Electronic Edition (link) BibTeX
- Juliane Schäfer, Korbinian Strimmer:
An empirical Bayes approach to inferring large-scale gene association networks.
754-764
Electronic Edition (link) BibTeX
- John Jeremy Rice, Yuhai Tu, Gustavo Stolovitzky:
Reconstructing biological networks using conditional correlation analysis.
765-773
Electronic Edition (link) BibTeX
- Chin-Rang Yang, Bruce E. Shapiro, Eric Mjolsness, G. Wesley Hatfield:
An enzyme mechanism language for the mathematical modeling of metabolic pathways.
774-780
Electronic Edition (link) BibTeX
Data And Text Mining
Databases And Ontologies
Genome Analysis
Genetics And Population Analysis
Systems Biology
Databases And Ontologies
- J. Stuart Aitken, Roman Korf, Bonnie L. Webber, Jonathan Bard:
COBrA: a bio-ontology editor.
825-826
Electronic Edition (link) BibTeX
- Thijs Beuming, Lucy Skrabanek, Masha Y. Niv, Piali Mukherjee, Harel Weinstein:
PDZBase: a protein?Cprotein interaction database for PDZ-domains.
827-828
Electronic Edition (link) BibTeX
- Yu Rang Park, Chan Hee Park, Ju Han Kim:
GOChase: correcting errors from Gene Ontology-based annotations for gene products.
829-831
Electronic Edition (link) BibTeX
- Philipp Pagel, Stefan Kovac, Matthias Oesterheld, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Pekka Mark, Volker Stümpflen, Hans-Werner Mewes, Andreas Ruepp, Dmitrij Frishman:
The MIPS mammalian protein?Cprotein interaction database.
832-834
Electronic Edition (link) BibTeX
- Saranyan K. Palaniswamy, Victor X. Jin, Hao Sun, Ramana V. Davuluri:
OMGProm: a database of orthologous mammalian gene promoters.
835-836
Electronic Edition (link) BibTeX
Volume 21,
Number 7,
April 2005
Genome Analysis
Sequence Analysis
Genome Analysis
- Vladimir Paar, Nenad Pavin, Marija Rosandic, Matko Gluncic, Ivan Basar, Robert Pezer, Sonja Durajlija Zinic:
ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome.
846-852
Electronic Edition (link) BibTeX
- Daniela Bartels, Sebastian Kespohl, Stefan Albaum, Tanja Drüke, Alexander Goesmann, Julia Herold, Olaf Kaiser, Alfred Pühler, Friedhelm Pfeiffer, Günter Raddatz, Jens Stoye, Folker Meyer, Stephan C. Schuster:
BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
853-859
Electronic Edition (link) BibTeX
- Roger M. Jarvis, Royston Goodacre:
Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data.
860-868
Electronic Edition (link) BibTeX
- Peng Yin, Alexander J. Hartemink:
Theoretical and practical advances in genome halving.
869-879
Electronic Edition (link) BibTeX
- Benjamin P. Westover, Jeremy D. Buhler, Justin L. Sonnenburg, Jeffrey I. Gordon:
Operon prediction without a training set.
880-888
Electronic Edition (link) BibTeX
- Shahid H. Bokhari, Jon R. Sauer:
A parallel graph decomposition algorithm for DNA sequencing with nanopores.
889-896
Electronic Edition (link) BibTeX
- Gideon Dror, Rotem Sorek, Ron Shamir:
Accurate identification of alternatively spliced exons using support vector machine.
897-901
Electronic Edition (link) BibTeX
Sequence Analysis
- Yi-Kuo Yu, Stephen F. Altschul:
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions.
902-911
Electronic Edition (link) BibTeX
- Masumi Itoh, Susumu Goto, Tatsuya Akutsu, Minoru Kanehisa:
Fast and accurate database homology search using upper bounds of local alignment scores.
912-921
Electronic Edition (link) BibTeX
- Chiara Sabatti, Lars Rohlin, Kenneth Lange, James C. Liao:
Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites.
922-931
Electronic Edition (link) BibTeX
- January Weiner, Geraint Thomas, Erich Bornberg-Bauer:
Rapid motif-based prediction of circular permutations in multi-domain proteins.
932-937
Electronic Edition (link) BibTeX
- Wei-Mou Zheng:
Relation between weight matrix and substitution matrix: motif search by similarity.
938-943
Electronic Edition (link) BibTeX
- Kuo-Chen Chou, Yu-Dong Cai:
Predicting protein localization in budding Yeast.
944-950
Electronic Edition (link) BibTeX
- Johannes Söding:
Protein homology detection by HMM?CHMM comparison.
951-960
Electronic Edition (link) BibTeX
- M. Michael Gromiha, Makiko Suwa:
A simple statistical method for discriminating outer membrane proteins with better accuracy.
961-968
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
- Dominik Gront, Andrzej Kolinski:
A new approach to prediction of short-range conformational propensities in proteins.
981-987
Electronic Edition (link) BibTeX
- John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman:
PDBML: the representation of archival macromolecular structure data in XML.
988-992
Electronic Edition (link) BibTeX
- Tom M. W. Nye, Carlo Berzuini, Walter R. Gilks, M. Madan Babu, Sarah A. Teichmann:
Statistical analysis of domains in interacting protein pairs.
993-1001
Electronic Edition (link) BibTeX
- Erik Sandelin:
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach.
1002-1009
Electronic Edition (link) BibTeX
- Xin Yuan, Christopher Bystroff:
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.
1010-1019
Electronic Edition (link) BibTeX
- Ilona Kifer, Ori Sasson, Michal Linial:
Predicting fold novelty based on ProtoNet hierarchical classification.
1020-1027
Electronic Edition (link) BibTeX
- Carleton L. Kingsford, Bernard Chazelle, Mona Singh:
Solving and analyzing side-chain positioning problems using linear and integer programming.
1028-1039
Electronic Edition (link) BibTeX
Gene Expression
- F. R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, B. Rohrer, Jonas S. Almeida:
Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method.
1037-1045
Electronic Edition (link) BibTeX
- Chao Sima, Ulisses Braga-Neto, Edward R. Dougherty:
Superior feature-set ranking for small samples using bolstered error estimation.
1046-1054
Electronic Edition (link) BibTeX
- Yuan Ji, Kam-Wah Tsui, KyungMann Kim:
A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples.
1055-1061
Electronic Edition (link) BibTeX
- Hisanori Kiryu, Taku Oshima, Kiyoshi Asai:
Extracting relations between promoter sequences and their strengths from microarray data.
1062-1068
Electronic Edition (link) BibTeX
- Rajarajeswari Balasubramaniyan, Eyke Hüllermeier, Nils Weskamp, Jörg Kämper:
Clustering of gene expression data using a local shape-based similarity measure.
1069-1077
Electronic Edition (link) BibTeX
- J. E. Eckel, C. Gennings, Terry M. Therneau, L. D. Burgoon, D. R. Boverhof, T. R. Zacharewski:
Normalization of two-channel microarray experiments: a semiparametric approach.
1078-1083
Electronic Edition (link) BibTeX
- Yee Hwa Yang, Yuanyuan Xiao, Mark R. Segal:
Identifying differentially expressed genes from microarray experiments via statistic synthesis.
1084-1093
Electronic Edition (link) BibTeX
- Sébastien Rimour, David R. C. Hill, Cécile Militon, Pierre Peyret:
GoArrays: highly dynamic and efficient microarray probe design.
1094-1103
Electronic Edition (link) BibTeX
- Gersende Fort, Sophie Lambert-Lacroix:
Classification using partial least squares with penalized logistic regression.
1104-1111
Electronic Edition (link) BibTeX
- Antonio Reverter, Wes Barris, Sean McWilliam, Keren A. Byrne, Yong H. Wang, Siok-Hwee Tan, Nick Hudson, Brian P. Dalrymple:
Validation of alternative methods of data normalization in gene co-expression studies.
1112-1120
Electronic Edition (link) BibTeX
- David R. Bickel:
Probabilities of spurious connections in gene networks: application to expression time series.
1121-1128
Electronic Edition (link) BibTeX
- Yoram Ben-Shaul, Hagai Bergman, Hermona Soreq:
Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression.
1129-1137
Electronic Edition (link) BibTeX
Genetics And Population Analysis
Systems Biology
- Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya:
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.
1154-1163
Electronic Edition (link) BibTeX
- Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak:
Comparison of computational methods for the identification of cell cycle-regulated genes.
1164-1171
Electronic Edition (link) BibTeX
- M. Kloster, C. Tang, N. S. Wingreen:
Finding regulatory modules through large-scale gene-expression data analysis.
1172-1179
Electronic Edition (link) BibTeX
- Kuan-Yao Tsai, Feng-Sheng Wang:
Evolutionary optimization with data collocation for reverse engineering of biological networks.
1180-1188
Electronic Edition (link) BibTeX
- Syed Asad Rahman, P. Advani, R. Schunk, Rainer Schrader, Dietmar Schomburg:
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC).
1189-1193
Electronic Edition (link) BibTeX
- Gang Liu, Mark T. Swihart, Sriram Neelamegham:
Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling.
1194-1202
Electronic Edition (link) BibTeX
- Robert Urbanczik, C. Wagner:
An improved algorithm for stoichiometric network analysis: theory and applications.
1203-1210
Electronic Edition (link) BibTeX
- Ranadip Pal, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty:
Intervention in context-sensitive probabilistic Boolean networks.
1211-1218
Electronic Edition (link) BibTeX
- Ina Koch, Bjørn H. Junker, Monika Heiner:
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.
1219-1226
Electronic Edition (link) BibTeX
Data And Text Mining
Databases And Ontologies
- Yingyao Zhou, Jason A. Young, Andrey Santrosyan, Kaisheng Chen, S. Frank Yan, Elizabeth A. Winzeler:
In silico gene function prediction using ontology-based pattern identification.
1237-1245
Electronic Edition (link) BibTeX
- Julie Chabalier, Cécile Capponi, Yves Quentin, Gwennaele Fichant:
ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems.
1246-1256
Electronic Edition (link) BibTeX
- Georgios V. Gkoutos, Eain C. J. Green, Simon Greenaway, Andrew Blake, Ann-Marie Mallon, John M. Hancock:
CRAVE: a database, middleware and visualization system for phenotype ontologies.
1257-1262
Electronic Edition (link) BibTeX
Genome Analysis
Sequence Analysis
- Ivo Van Walle, Ignace Lasters, Lode Wyns:
SABmark- a benchmark for sequence alignment that covers the entire known fold space.
1267-1268
Electronic Edition (link) BibTeX
- Lars Kiemer, Jannick Dyrløv Bendtsen, Nikolaj Blom:
NetAcet: prediction of N-terminal acetylation sites.
1269-1270
Electronic Edition (link) BibTeX
- Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff:
Multiple sequence alignment with user-defined constraints at GOBICS.
1271-1273
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Systems Biology
Databases And Ontologies
- Chung-Yen Lin, Chia-Ling Chen, Chi-Shiang Cho, Li-Ming Wang, Chia-Ming Chang, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung:
hp-DPI: Helicobacter pylori Database of Protein Interactomes-embracing experimental and inferred interactions.
1288-1290
Electronic Edition (link) BibTeX
- Joachim Reichelt, Guido Dieterich, Marsel Kvesic, Dietmar Schomburg, Dirk W. Heinz:
BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.
1291-1293
Electronic Edition (link) BibTeX
Volume 21,
Number 8,
April 2005
Sequence Analysis
Structural Bioinformatics
Systems Biology
Genome Analysis
