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
- Tomoyuki Yamada, Shinichi Morishita:
Accelerated off-target search algorithm for siRNA.
1316-1324
Electronic Edition (link) BibTeX
- Melissa D. Krebs, Robert D. Tingley, Julie E. Zeskind, Joung-Mo Kang, Maria E. Holmboe, Cristina E. Davis:
Autoregressive modeling of analytical sensor data can yield classifiers in the predictor coefficient parameter space.
1325-1331
Electronic Edition (link) BibTeX
- Sven Degroeve, Yvan Saeys, Bernard De Baets, Pierre Rouzé, Yves Van de Peer:
SpliceMachine: predicting splice sites from high-dimensional local context representations.
1332-1338
Electronic Edition (link) BibTeX
- Steven E. Hampson, B. S. Gaut, Pierre Baldi:
Statistical detection of chromosomal homology using shared-gene density alone.
1339-1348
Electronic Edition (link) BibTeX
- John R. Rose, William H. Turkett, Iulia C. Oroian, William W. Laegreid, John W. Keele:
Correlation of amino acid preference and mammalian viral genome type.
1349-1357
Electronic Edition (link) BibTeX
- Yun Lian, Harold R. Garner:
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats.
1358-1364
Electronic Edition (link) BibTeX
- Eric K. Nordberg:
YODA: selecting signature oligonucleotides.
1365-1370
Electronic Edition (link) BibTeX
- Ketil Malde, Eivind Coward, Inge Jonassen:
A graph based algorithm for generating EST consensus sequences.
1371-1375
Electronic Edition (link) BibTeX
- Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo:
Highly specific and accurate selection of siRNAs for high-throughput functional assays.
1376-1382
Electronic Edition (link) BibTeX
- Caroline C. Friedel, Katharina H. V. Jahn, Selina Sommer, Stephen Rudd, Hans-Werner Mewes, Igor V. Tetko:
Support vector machines for separation of mixed plant?Cpathogen EST collections based on codon usage.
1383-1388
Electronic Edition (link) BibTeX
- Matthias B. Wahl, Ulrich Heinzmann, Kenji Imai:
LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome.
1389-1392
Electronic Edition (link) BibTeX
- Matthias B. Wahl, Ulrich Heinzmann, Kenji Imai:
LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse.
1393-1400
Electronic Edition (link) BibTeX
- Xiaochen Bo, Shengqi Wang:
TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA.
1401-1402
Electronic Edition (link) BibTeX
Sequence Analysis
- Elizabeth Jacob, Roschen Sasikumar, K. N. Ramachandran Nair:
A fuzzy guided genetic algorithm for operon prediction.
1403-1407
Electronic Edition (link) BibTeX
- Iain M. Wallace, Orla O'Sullivan, Desmond G. Higgins:
Evaluation of iterative alignment algorithms for multiple alignment.
1408-1414
Electronic Edition (link) BibTeX
- East Zhao, Hsuan-Liang Liu, Chi-Hung Tsai, Huai-Kuang Tsai, Chen-hsiung Chan, Cheng-Yan Kao:
Cysteine separations profiles on protein sequences infer disulfide connectivity.
1415-1420
Electronic Edition (link) BibTeX
- Yasuyuki Nozaki, Matthew I. Bellgard:
Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties.
1421-1428
Electronic Edition (link) BibTeX
- Volkan Atalay, Rengül Çetin-Atalay:
Implicit motif distribution based hybrid computational kernel for sequence classification.
1429-1436
Electronic Edition (link) BibTeX
- Veronique Prigent, Jean-Claude Thierry, Olivier Poch, Frédéric Plewniak:
DbW: automatic update of a functional family-specific multiple alignment.
1437-1442
Electronic Edition (link) BibTeX
- Antonio Cavallo, Andrew C. R. Martin:
Mapping SNPs to protein sequence and structure data.
1443-1450
Electronic Edition (link) BibTeX
- Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, Stephen H. Bryant:
A structure-based method for protein sequence alignment.
1451-1456
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
- Ugis Sarkans, Helen E. Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna-Assunta Sansone, Anna Farne, Tim Rayner, Alvis Brazma:
The ArrayExpress gene expression database: a software engineering and implementation perspective.
1495-1501
Electronic Edition (link) BibTeX
- Chen-An Tsai, Sue-Jane Wang, Dung-Tsa Chen, James J. Chen:
Sample size for gene expression microarray experiments.
1502-1508
Electronic Edition (link) BibTeX
- Jianping Hua, Zixiang Xiong, James Lowey, Edward Suh, Edward R. Dougherty:
Optimal number of features as a function of sample size for various classification rules.
1509-1515
Electronic Edition (link) BibTeX
- Rongwei Fu, Dipak K. Dey, Kent E. Holsinger:
Bayesian models for the analysis of genetic structure when populations are correlated.
1516-1529
Electronic Edition (link) BibTeX
- Yuhang Wang, Fillia Makedon, James C. Ford, Justin D. Pearlman:
HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data.
1530-1537
Electronic Edition (link) BibTeX
- Qinghua Cui, Bing Liu, Tianzi Jiang, Songde Ma:
Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data.
1538-1541
Electronic Edition (link) BibTeX
- Ranadip Pal, Aniruddha Datta, Albert J. Fornace, Michael L. Bittner, Edward R. Dougherty:
Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS.
1542-1549
Electronic Edition (link) BibTeX
- Céline Lefebvre, Jean-Christophe Aude, Eric Glémet, Christian Néri:
Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates.
1550-1558
Electronic Edition (link) BibTeX
- Xin Zhou, K. Z. Mao:
LS Bound based gene selection for DNA microarray data.
1559-1564
Electronic Edition (link) BibTeX
- Baolin Wu:
Differential gene expression detection using penalized linear regression models: the improved SAM statistics.
1565-1571
Electronic Edition (link) BibTeX
- Ursula Sauer, Claudia Preininger, Robert Hany-Schmatzberger:
Quick and simple: quality control of microarray data.
1572-1578
Electronic Edition (link) BibTeX
Genetics And Population Analysis
Systems Biology
- Matthew Holford, Naixin Li, Prakash M. Nadkarni, Hongyu Zhao:
VitaPad: visualization tools for the analysis of pathway data.
1596-1602
Electronic Edition (link) BibTeX
- Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt:
Exploring the diversity of complex metabolic networks.
1603-1609
Electronic Edition (link) BibTeX
- A. Beyer, T. Wilhelm:
Dynamic simulation of protein complex formation on a genomic scale.
1610-1616
Electronic Edition (link) BibTeX
- Marc Daniel Haunschild, Bernd Freisleben, Ralf Takors, Wolfgang Wiechert:
Investigating the dynamic behavior of biochemical networks using model families.
1617-1625
Electronic Edition (link) BibTeX
- Reinhard Guthke, Ulrich Möller, Martin Hoffmann, Frank Thies, Susanne Töpfer:
Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.
1626-1634
Electronic Edition (link) BibTeX
- Joachim Kopka, Nicolas Schauer, Stephan Krueger, Claudia Birkemeyer, Björn Usadel, Eveline Bergmüller, Peter Dörmann, Wolfram Weckwerth, Yves Gibon, Mark Stitt, Lothar Willmitzer, Alisdair R. Fernie, Dirk Steinhauser:
GMD@CSB.DB: the Golm Metabolome Database.
1635-1638
Electronic Edition (link) BibTeX
- Paolo Tieri, Silvana Valensin, Vito Latora, Gastone C. Castellani, Massimo Marchiori, Daniel Remondini, Claudio Franceschi:
Quantifying the relevance of different mediators in the human immune cell network.
1639-1643
Electronic Edition (link) BibTeX
Data And Text Mining
- Patrick Kemmeren, Thessa T. J. P. Kockelkorn, Theo Bijma, Rogier Donders, Frank Holstege:
Predicting gene function through systematic analysis and quality assessment of high-throughput data.
1644-1652
Electronic Edition (link) BibTeX
- Carlos Santos, Daniela Eggle, David J. States:
Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction.
1653-1658
Electronic Edition (link) BibTeX
- Ying Tao, Carol Friedman, Yves A. Lussier:
Visualizing information across multidimensional post-genomic structured and textual databases.
1659-1667
Electronic Edition (link) BibTeX
- Andrea L. Knorr, Ranjan Srivastava:
Evaluation of HIV-1 kinetic models using quantitative discrimination analysis.
1668-1677
Electronic Edition (link) BibTeX
- Rasmus H. Fogh, Wayne Boucher, Wim F. Vranken, Anne Pajon, Tim J. Stevens, T. N. Bhat, John D. Westbrook, John M. C. Ionides, Ernest D. Laue:
A framework for scientific data modeling and automated software development.
1678-1684
Electronic Edition (link) BibTeX
Databases And Ontologies
Genome Analysis
- Jin Billy Li, Miao Zhang, Susan K. Dutcher, Gary D. Stormo:
Procom: a web-based tool to compare multiple eukaryotic proteomes.
1693-1694
Electronic Edition (link) BibTeX
- Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, Mark L. Farman:
TERMINUS - Telomeric End-Read Mining IN Unassembled Sequences.
1695-1698
Electronic Edition (link) BibTeX
- Tae-Hyung Kim, Yeo-Jin Jeon, Woo-Yeon Kim, Heui-Soo Kim:
HESAS: HERVs Expression and Structure Analysis System.
1699-1700
Electronic Edition (link) BibTeX
- Lauris Kaplinski, Reidar Andreson, Tarmo Puurand, Maido Remm:
MultiPLX: automatic grouping and evaluation of PCR primers.
1701-1702
Electronic Edition (link) BibTeX
- Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, Thomas Schiex:
CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping.
1703-1704
Electronic Edition (link) BibTeX
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Franck Dupuis, Jean-François Sadoc, Rémi Jullien, Borislav Angelov, Jean Paul Mornon:
Voro3D: 3D Voronoi tessellations applied to protein structures.
1715-1716
Electronic Edition (link) BibTeX
- Norihiro Kikuchi, Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Takashi Sato, Toshihide Shikanai, Yoriko Takahashi, Hisashi Narimatsu:
The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.
1717-1718
Electronic Edition (link) BibTeX
- Gianluca Pollastri, Aoife McLysaght:
Porter: a new, accurate server for protein secondary structure prediction.
1719-1720
Electronic Edition (link) BibTeX
- Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura:
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.
1721-1723
Electronic Edition (link) BibTeX
Gene Expression
Genetics And Population Analysis
- Holger Thiele, Peter J. Nürnberg:
HaploPainter: a tool for drawing pedigrees with complex haplotypes.
1730-1732
Electronic Edition (link) BibTeX
- Christian N. K. Anderson, Uma Ramakrishnan, Yvonne L. Chan, Elizabeth A. Hadly:
Serial SimCoal: A population genetics model for data from multiple populations and points in time.
1733-1734
Electronic Edition (link) BibTeX
- Sio Iong Ao, Kevin Y. Yip, Michael K. Ng, David Wai-Lok Cheung, Pui-Yee Fong, Ian Melhado, Pak Chung Sham:
CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs.
1735-1736
Electronic Edition (link) BibTeX
- Pablo Serrano-Fernández, Saleh M. Ibrahim, Dirk Koczan, Uwe K. Zettl, Steffen Möller:
In silico fine-mapping: narrowing disease-associated loci by intergenomics.
1737-1738
Electronic Edition (link) BibTeX
Systems Biology
Data And Text Mining
Databases And Ontologies
Volume 21,
Number 9,
May 1 2005
Databases And Ontologies
Genome Analysis
- Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John Arthur, Jonas S. Almeida:
AGML Central: web based gel proteomic infrastructure.
1754-1757
Electronic Edition (link) BibTeX
- Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita:
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
1758-1763
Electronic Edition (link) BibTeX
- Jeffrey S. Morris, Kevin R. Coombes, John Koomen, Keith A. Baggerly, Ryuji Kobayashi:
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.
1764-1775
Electronic Edition (link) BibTeX
- Darrell Conklin, Betty Haldeman, Zeren Gao:
Gene finding for the helical cytokines.
1776-1781
Electronic Edition (link) BibTeX
- William H. Majoros, Mihaela Pertea, Sihaela Salzberg:
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.
1782-178
Electronic Edition (link) BibTeX
- Maria Stepanova, Tatiana Tiazhelova, Mikle Skoblov, Ancha Baranova:
A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.
1789-1796
Electronic Edition (link) BibTeX
Sequence Analysis
- Dirk Husmeier, Frank Wright, Iain Milne:
Detecting interspecific recombination with a pruned probabilistic divergence measure.
1797-1806
Electronic Edition (link) BibTeX
- Shaun Mahony, David Hendrix, Aaron Golden, Terry J. Smith, Daniel S. Rokhsar:
Transcription factor binding site identification using the self-organizing map.
1807-1814
Electronic Edition (link) BibTeX
- Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin:
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
1815-1824
Electronic Edition (link) BibTeX
- J. M. Cameron, T. Hurd, B. H. Robinson:
Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins.
1825-1830
Electronic Edition (link) BibTeX
- Zheng Rong Yang:
Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks.
1831-1837
Electronic Edition (link) BibTeX
- Han-Lin Li, Chang-Jui Fu:
A linear programming approach for identifying a consensus sequence on DNA sequences.
1838-1845
Electronic Edition (link) BibTeX
- Niklaus Fankhauser, Pascal Mäser:
Identification of GPI anchor attachment signals by a Kohonen self-organizing map.
1846-1852
Electronic Edition (link) BibTeX
- Robel Y. Kahsay, Guang R. Gao, Li Liao:
An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes.
1853-1858
Electronic Edition (link) BibTeX
- Thomas D. Wu, Colin K. Watanabe:
GMAP: a genomic mapping and alignment program for mRNA and EST sequence.
1859-1875
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
Gene Expression
- Håvard Nesvold, Anja Bråthen Kristoffersen, Arne Holst-Jensen, Knut G. Berdal:
Design of a DNA chip for detection of unknown genetically modified organisms (GMOs).
1917-1926
Electronic Edition (link) BibTeX
- Dae-Won Kim, Kwang Hyung Lee, Doheon Lee:
Detecting clusters of different geometrical shapes in microarray gene expression data.
1927-1934
Electronic Edition (link) BibTeX
- Cristian Mircean, Ilya Shmulevich, David Cogdell, Woonyoung Choi, Yu Jia, Ioan Tabus, Stanley R. Hamilton, Wei Zhang:
Robust estimation of protein expression ratios with lysate microarray technology.
1935-1942
Electronic Edition (link) BibTeX
- William T. Barry, Andrew B. Nobel, Fred A. Wright:
Significance analysis of functional categories in gene expression studies: a structured permutation approach.
1943-1949
Electronic Edition (link) BibTeX
- Jelle J. Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob K. Anninga, Hans C. van Houwelingen:
Testing association of a pathway with survival using gene expression data.
1950-1957
Electronic Edition (link) BibTeX
- Xiaojun Di, Hajime Matsuzaki, Teresa A. Webster, Earl Hubbell, Guoying Liu, Shoulian Dong, Dan Bartell, Jing Huang, Richard Chiles, Geoffrey Yang, Mei-mei Shen, David Kulp, Giulia C. Kennedy, Rui Mei, Keith W. Jones, Simon Cawley:
Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays.
1958-1963
Electronic Edition (link) BibTeX
- Staal A. Vinterbo, Eun-Young Kim, Lucila Ohno-Machado:
Small, fuzzy and interpretable gene expression based classifiers.
1964-1970
Electronic Edition (link) BibTeX
- Claudio Lottaz, Rainer Spang:
Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.
1971-1978
Electronic Edition (link) BibTeX
- Wenjiang J. Fu, Raymond J. Carroll, Suojin Wang:
Estimating misclassification error with small samples via bootstrap cross-validation.
1979-1986
Electronic Edition (link) BibTeX
- Susmita Datta, Somnath Datta:
Empirical Bayes screening of many p-values with applications to microarray studies.
1987-1994
Electronic Edition (link) BibTeX
- Marie-Laure Martin-Magniette, Julie Aubert, Eric Cabannes, Jean-Jacques Daudin:
Evaluation of the gene-specific dye bias in cDNA microarray experiments.
1995-2000
Electronic Edition (link) BibTeX
Genetics And Population Analysis
Systems Biology
- Marcin Imielinski, Calin Belta, Ádám M. Halász, Harvey Rubin:
Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities.
2008-2016
Electronic Edition (link) BibTeX
- Ross D. King, Simon M. Garrett, George Macleod Coghill:
On the use of qualitative reasoning to simulate and identify metabolic pathway.
2017-2026
Electronic Edition (link) BibTeX
- Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger:
Modeling of signal-response cascades using decision tree analysis.
2027-2035
Electronic Edition (link) BibTeX
- Weijiang Li, Hiroyuki Kurata:
A grid layout algorithm for automatic drawing of biochemical networks.
2036-2042
Electronic Edition (link) BibTeX
- Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai:
Accurate extraction of functional associations between proteins based on common interaction partners and common domains.
2043-2048
Electronic Edition (link) BibTeX
Data And Text Mining
Databases And Ontologies
Genome Analysis
Sequence Analysis
- Morris Michael, Christoph Dieterich, Martin Vingron:
SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors.
2093-2094
Electronic Edition (link) BibTeX
- Frédéric Chalmel, Aurélie Lardenois, Julie Dawn Thompson, Jean Muller, José-Alain Sahel, Thierry Léveillard, Olivier Poch:
GOAnno: GO annotation based on multiple alignment.
2095-2096
Electronic Edition (link) BibTeX
- Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, Mark L. Farman:
TruMatch - a BLAST post-processor that identifies bona fide sequence matches to genome assemblies.
2097-2098
Electronic Edition (link) BibTeX
- Francisco Azuaje:
Integrative data analysis for functional prediction: a multi-objective optimization approach.
2099-2100
Electronic Edition (link) BibTeX
Phylogenetics
- Adi Doron-Faigenboim, Adi Stern, Itay Mayrose, Eran Bacharach, Tal Pupko:
Selecton: a server for detecting evolutionary forces at a single amino-acid site.
2101-2103
Electronic Edition (link) BibTeX
- Federico Abascal, Rafael Zardoya, David Posada:
ProtTest: selection of best-fit models of protein evolution.
2104-2105
Electronic Edition (link) BibTeX
- Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, Thomas Lengauer:
Mtreemix: a software package for learning and using mixture models of mutagenetic trees.
2106-2107
Electronic Edition (link) BibTeX
- Joachim Friedrich, Thomas Dandekar, Matthias Wolf, Tobias Müller:
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.
2108-2109
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
- Joern Toedling, Sebastian Schmeier, Matthias Heinig, Benjamin Georgi, Stefan Roepcke:
MACAT - microarray chromosome analysis tool.
2112-2113
Electronic Edition (link) BibTeX
- Laurie J. Heyer, D. Z. Moskowitz, J. A. Abele, P. Karnik, D. Choi, A. Malcolm Campbell, E. E. Oldham, B. K. Akin:
MAGIC Tool: integrated microarray data analysis.
2114-2115
Electronic Edition (link) BibTeX
- Sek Won Kong, Kyu Baek Hwang, Richard D. Kim, Byoung-Tak Zhang, Steven A. Greenberg, Isaac S. Kohane, Peter J. Park:
CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays.
2116-2117
Electronic Edition (link) BibTeX
- Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, Kevin R. Coombes:
Applications of beta-mixture models in bioinformatics.
2118-2122
Electronic Edition (link) BibTeX
Genetics And Population Analysis
Systems Biology
Data And Text Mining
Databases And Ontologies
- Pedro A. Reche, Hong Zhang, John-Paul Glutting, Ellis L. Reinherz:
EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology.
2140-2141
Electronic Edition (link) BibTeX
- Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Bo-Shu Liu, Jin-Miao Wang, Yi-Xue Li, Yang Zhong:
MPSS: an integrated database system for surveying a set of proteins.
2142-2143
Electronic Edition (link) BibTeX
Volume 21,
Number 10,
May 2005
Review - Structural Bioinformatics
Discovery Notes - Sequence Analysis
Structural Bioinformatics
Original Papers - Genome Analysis
- C. Thach Nguyen, Y. C. Tay, Louxin Zhang:
Divide-and-conquer approach for the exemplar breakpoint distance.
2171-2176
Electronic Edition (link) BibTeX
- Jayson Falkner, Philip Andrews:
Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.
2177-2184
Electronic Edition (link) BibTeX
- Lei Bao, Yan Cui:
Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information.
2185-2190
Electronic Edition (link) BibTeX
- Lee Lancashire, O. Schmid, H. Shah, Graham R. Ball:
Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis.
2191-2199
Electronic Edition (link) BibTeX
- J. S. Yu, S. Ongarello, R. Fiedler, X. W. Chen, G. Toffolo, Claudio Cobelli, Z. Trajanoski:
Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data.
2200-2209
Electronic Edition (link) BibTeX
- Halima Bensmail, Jennifer Golek, Michelle M. Moody, John O. Semmes, Abdelali Haoudi:
A novel approach for clustering proteomics data using Bayesian fast Fourier transform.
2210-2224
Electronic Edition (link) BibTeX
Sequence Analysis
- Valerio Freschi, Alessandro Bogliolo:
Using sequence compression to speedup probabilistic profile matching.
2225-2229
Electronic Edition (link) BibTeX
- Robert G. Beiko, Cheong Xin Chan, Mark A. Ragan:
A word-oriented approach to alignment validation.
2230-2239
Electronic Edition (link) BibTeX
- Alexander V. Favorov, Mikhail S. Gelfand, Anna V. Gerasimova, Dmitry A. Ravcheev, Andrey A. Mironov, Vsevolod Makeev:
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
2240-2245
Electronic Edition (link) BibTeX
- David H. Mathews:
Predicting a set of minimal free energy RNA secondary structures common to two sequences.
2246-2253
Electronic Edition (link) BibTeX
- Ruadhan A. O'Flanagan, Guillaume Paillard, Richard Lavery, Anirvan M. Sengupta:
Non-additivity in protein-DNA binding.
2254-2263
Electronic Edition (link) BibTeX
- Kyounghwa Bae, Bani K. Mallick, Christine G. Elsik:
Prediction of protein interdomain linker regions by a hidden Markov model.
2264-2270
Electronic Edition (link) BibTeX
- Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Prudence W. H. Wong, Siu-Ming Yiu, X. Fan:
The mutated subsequence problem and locating conserved genes.
2271-2278
Electronic Edition (link) BibTeX
- Mikael Bodén, John Hawkins:
Prediction of subcellular localization using sequence-biased recurrent networks.
2279-2286
Electronic Edition (link) BibTeX
- Robel Y. Kahsay, Guoli Wang, Guang R. Gao, Li Liao, Roland L. Dunbrack Jr.:
Quasi-consensus-based comparison of profile hidden Markov models for protein sequences.
2287-2293
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
- Stefan R. Henz, Daniel H. Huson, Alexander F. Auch, Kay Nieselt-Struwe, Stephan C. Schuster:
Whole-genome prokaryotic phylogeny.
2329-2335
Electronic Edition (link) BibTeX
- Fabrizio Ferrè, Peter Clote:
Disulfide connectivity prediction using secondary structure information and diresidue frequencies.
2336-2346
Electronic Edition (link) BibTeX
- Richard J. Morris, Rafael Najmanovich, Abdullah Kahraman, Janet M. Thornton:
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.
2347-2355
Electronic Edition (link) BibTeX
- Jacek Blazewicz, Marta Szachniuk, Adam Wojtowicz:
RNA tertiary structure determination: NOE pathways construction by tabu search.
2356-2361
Electronic Edition (link) BibTeX
- Yuzhen Ye, Adam Godzik:
Multiple flexible structure alignment using partial order graphs.
2362-2369
Electronic Edition (link) BibTeX
- Qidong Zhang, Sukjoon Yoon, William J. Welsh:
Improved method for predicting ?-turn using support vector machine.
2370-2374
Electronic Edition (link) BibTeX
- Markus Leber, Lars Kaderali, Alexander Schönhuth, Rainer Schrader:
A fractional programming approach to efficient DNA melting temperature calculation.
2375-2382
Electronic Edition (link) BibTeX
Gene Expression
- Örjan Carlborg, D. J. De Koning, Kenneth F. Manly, Elissa J. Chesler, Robert W. Williams, C. S. Haley:
Methodological aspects of the genetic dissection of gene expression.
2383-2393
Electronic Edition (link) BibTeX
- Ka Yee Yeung, Roger Eugene Bumgarner, Adrian E. Raftery:
Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data.
2394-2402
Electronic Edition (link) BibTeX
- Hongzhe Li, Yihui Luan:
Boosting proportional hazards models using smoothing splines, with applications to high-dimensional microarray data.
2403-2409
Electronic Edition (link) BibTeX
- Wotao Yin, Terrence Chen, Xiang Sean Zhou, Amit Chakraborty:
Background correction for cDNA microarray images using the TV+L1 model.
2410-2416
Electronic Edition (link) BibTeX
- Muhammad Shoaib B. Sehgal, Iqbal Gondal, Laurence Dooley:
Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data.
2417-2423
Electronic Edition (link) BibTeX
- Christian H. Busold, Stefan Winter, Nicole C. Hauser, Andrea Bauer, Jürgen Dippon, Jörg D. Hoheisel, Kurt Fellenberg:
Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data.
2424-2429
Electronic Edition (link) BibTeX
- K. K. Dobbin, Ernest S. Kawasaki, D. W. Petersen, R. M. Simon:
Characterizing dye bias in microarray experiments.
2430-2437
Electronic Edition (link) BibTeX
Genetics and Population Analysis
- Jörg Rahnenführer, Niko Beerenwinkel, Wolfgang A. Schulz, Christian Hartmann, Andreas von Deimling, Bernd Wullich, Thomas Lengauer:
Estimating cancer survival and clinical outcome based on genetic tumor progression scores.
2438-2446
Electronic Edition (link) BibTeX
- Yuehua Cui, Rongling Wu:
Mapping genome-genome epistasis: a high-dimensional model.
2447-2455
Electronic Edition (link) BibTeX
- Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang:
Haplotype reconstruction from SNP fragments by minimum error correction.
2456-2462
Electronic Edition (link) BibTeX
- Dmitry A. Konovalov, Bruce E. Litow, Nigel Bajema:
Partition-distance via the assignment problem.
2463-2468
Electronic Edition (link) BibTeX
- Wei Zhao, Ying Q. Chen, George Casella, James M. Cheverud, Rongling Wu:
A non-stationary model for functional mapping of complex traits.
2469-2477
Electronic Edition (link) BibTeX
Systems Biology
Databases and Ontologies
Applications Note - Genome Analysis
- Feng-Chi Chen, Trees-Juen Chuang:
ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants.
2510-2513
Electronic Edition (link) BibTeX
- Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, Sun Kim:
PLATCOM: a Platform for Computational Comparative Genomics.
2514-2516
Electronic Edition (link) BibTeX
- Fengkai Zhang, Zhongming Zhao:
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).
2517-2519
Electronic Edition (link) BibTeX
- Igor V. Tetko, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Gisela Fobo, Andreas Ruepp, Alexey V. Antonov, Dimitrij Surmeli, Hans-Werner Mewes:
MIPS bacterial genomes functional annotation benchmark dataset.
2520-2521
Electronic Edition (link) BibTeX
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Carlos J. Camacho, Chao Zhang:
FastContact: rapid estimate of contact and binding free energies.
2534-2536
Electronic Edition (link) BibTeX
- Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead:
Protein structure topological comparison, discovery and matching service.
2537-2538
Electronic Edition (link) BibTeX
- Jason E. Donald, Isaac A. Hubner, Veronica Rotemberg, Eugene I. Shakhnovich, Leonid A. Mirny:
CoC: a database of universally conserved residues in protein folds.
2539-2540
Electronic Edition (link) BibTeX
- Sungsam Gong, Giseok Yoon, Insoo Jang, Dan M. Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, Jonghwa Bhak:
PSIbase: a database of Protein Structural Interactome map (PSIMAP).
2541-2543
Electronic Edition (link) BibTeX
Gene Expression
Genetics and Population Analysis
- Su Young Kim, Suk Woo Nam, Sug Hyung Lee, Won Sang Park, Nam Jin Yoo, Jung Young Lee, Yeun-Jun Chung:
ArrayCyGHt: a web application for analysis and visualization of array-CGH data.
2554-2555
Electronic Edition (link) BibTeX
- Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill, Daniel E. Weeks:
Mega2: data-handling for facilitating genetic linkage and association analyses.
2556-2557
Electronic Edition (link) BibTeX
Data amd Text Mining
Databases and Ontologies
- Pierre-Étienne Jacques, Alain L. Gervais, Mathieu Cantin, Jean-François Lucier, Guillaume Dallaire, Geneviève Drouin, Luc Gaudreau, Jean Goulet, Ryszard Brzezinski:
MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis.
2563-2565
Electronic Edition (link) BibTeX
- Ana Tereza R. Vasconcelos, Ana Carolina R. Guimarães, Carlos Henrique M. Castelletti, Célia S. Caruso, Cristina Ribeiro, Fabiano Yokaichiya, Geraldo R. G. Armôa, Gislaine da Silva P. Pereira, Israel T. da Silva, Carlos G. Schrago, Adélia L. V. Fernandes, Aline R. da Silveira, André G. Carneiro, Bruno M. Carvalho, Carlos Juliano M. Viana, Daniel Gramkow, Franklin J. Lima, Luiz G. G. Corrêa, Maurício de Alvarenga Mudado, Pablo Nehab-Hess, Rangel de Souza, Régis L. Corrêa, Claudia A. M. Russo:
MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies.
2566-2567
Electronic Edition (link) BibTeX
- Anyuan Guo, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, Liping Wei, Jingchu Luo:
DATF: a database of Arabidopsis transcription factors.
2568-2569
Electronic Edition (link) BibTeX
- Tariq Riaz, Hen Ley Hor, Arun Krishnan, Francis Tang, Kuo-Bin Li:
WebAllergen: a web server for predicting allergenic proteins.
2570-2571
Electronic Edition (link) BibTeX
Volume 21,
Number 11,
June 2005
Original Papers - Genome Analysis
Sequence Analysis
- Jean-François Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, François Rechenmann, Guy Perrière:
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.
2596-2603
Electronic Edition (link) BibTeX
- Hadas Leonov, Isaiah T. Arkin:
A periodicity analysis of transmembrane helices.
2604-2610
Electronic Edition (link) BibTeX
- Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara:
Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
2611-2617
Electronic Edition (link) BibTeX
- Victor Kunin, Sarah A. Teichmann, Martijn A. Huynen, Christos A. Ouzounis:
The properties of protein family space depend on experimental design.
2618-2622
Electronic Edition (link) BibTeX
- Rajesh Chowdhary, R. Ayesha Ali, Werner Albig, Detlef Doenecke, Vladimir B. Bajic:
Promoter modeling: the case study of mammalian histone promoters.
2623-2628
Electronic Edition (link) BibTeX
- Jason E. Donald, Eugene I. Shakhnovich:
Determining functional specificity from protein sequences.
2629-2635
Electronic Edition (link) BibTeX
- Pengyu Hong, X. Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, Wing Hung Wong:
A boosting approach for motif modeling using ChIP-chip data.
2636-2643
Electronic Edition (link) BibTeX
- Zheng Rong Yang:
Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection.
2644-2650
Electronic Edition (link) BibTeX
- Moti Zviling, Hadas Leonov, Isaiah T. Arkin:
Genetic algorithm-based optimization of hydrophobicity tables.
2651-2656
Electronic Edition (link) BibTeX
- Irad E. Ben-Gal, Ayala Shani, Andre Gohr, Jan Grau, S. Arviv, Armin Shmilovici, Stefan Posch, Ivo Grosse:
Identification of transcription factor binding sites with variable-order Bayesian networks.
2657-2666
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Genetics and Populations Analysis
Systems Biology
- Bor-Sen Chen, Yu-Chao Wang, Wei-Sheng Wu, Wen-Hsiung Li:
A new measure of the robustness of biochemical networks.
2698-2705
Electronic Edition (link) BibTeX
- Svetlana Bulashevska, Roland Eils:
Inferring genetic regulatory logic from expression data.
2706-2713
Electronic Edition (link) BibTeX
- Thierry Emonet, Charles M. Macal, Michael J. North, Charles E. Wickersham, Philippe Cluzel:
AgentCell: a digital single-cell assay for bacterial chemotaxis.
2714-2721
Electronic Edition (link) BibTeX
- Luonan Chen, Ruiqi Wang, Tianshou Zhou, Kazuyuki Aihara:
Noise-induced cooperative behavior in a multicell system.
2722-2729
Electronic Edition (link) BibTeX
- Nitin Bhardwaj, Hui Lu:
Correlation between gene expression profiles and protein-protein interactions within and across genomes.
2730-2738
Electronic Edition (link) BibTeX
- Phil Hyoun Lee, Doheon Lee:
Modularized learning of genetic interaction networks from biological annotations and mRNA expression data.
2739-2747
Electronic Edition (link) BibTeX
Data and Text Mining
Databases and Ontologies
Application Notes - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Databases and Ontologies
Volume 21,
Supplement 1,
June 2005
Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005.
2005
Contents BibTeX
Volume 21,
Number 12,
June 2005
Letter to the Editor - Gene Expression
Discovery Note - Sequence Analysis
Original Papers - Genome Analysis
- Alan M. Durham, André Y. Kashiwabara, Fernando T. G. Matsunaga, Paulo H. Ahagon, Flávia Rainone, Leonardo Varuzza, Arthur Gruber:
EGene: a configurable pipeline generation system for automated sequence analysis.
2812-2813
Electronic Edition (link) BibTeX
- Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali:
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
2814-2820
Electronic Edition (link) BibTeX
Sequence Analysis
Structural Bioinformatics
- Guoying Qi, Richard A. Lee, Steven Hayward:
A comprehensive and non-redundant database of protein domain movements.
2832-2838
Electronic Edition (link) BibTeX
- Geraint Thomas, Richard B. Sessions, Martin J. Parker:
Density guided importance sampling: application to a reduced model of protein folding.
2839-2843
Electronic Edition (link) BibTeX
- Jaehyun Sim, Seung-Yeon Kim, Julian Lee:
Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.
2844-2849
Electronic Edition (link) BibTeX
- A. Selim Aytuna, Attila Gürsoy, Ozlem Keskin:
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.
2850-2855
Electronic Edition (link) BibTeX
- Daniele Varrazzo, Andrea Bernini, Ottavia Spiga, Arianna Ciutti, Stefano Chiellini, Vincenzo Venditti, Luisa Bracci, Neri Niccolai:
Three-dimensional computation of atom depth in complex molecular structures.
2856-2860
Electronic Edition (link) BibTeX
Gene Expression
- Dung-Tsa Chen, James J. Chen, Seng-jaw Soong:
Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates.
2861-2866
Electronic Edition (link) BibTeX
- Albert M. Levin, Debashis Ghosh, Kathleen R. Cho, Sharon L. R. Kardia:
A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors.
2867-2874
Electronic Edition (link) BibTeX
- Qunhua Li, Chris Fraley, Roger Eugene Bumgarner, Ka Yee Yeung, Adrian E. Raftery:
Donuts, scratches and blanks: robust model-based segmentation of microarray images.
2875-2882
Electronic Edition (link) BibTeX
Systems Biology
- Kuang-Chi Chen, Tse-Yi Wang, Huei-Hun Tseng, Chi-Ying F. Huang, Cheng-Yan Kao:
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae.
2883-2890
Electronic Edition (link) BibTeX
- Francesco Pappalardo, Pierluigi Lollini, Filippo Castiglione, Santo Motta:
Modeling and simulation of cancer immunoprevention vaccine.
2891-2897
Electronic Edition (link) BibTeX
- Lawrence Cabusora, Electra Sutton, Andy W. Fulmer, Christian V. Forst:
Differential network expression during drug and stress response.
2898-2905
Electronic Edition (link) BibTeX
Application Notes - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
Volume 21,
Number 13,
July 2005
Original Papers - Sequence Analysis
- K. Cartharius, Kornelie Frech, Korbinian Grote, B. Klocke, M. Haltmeier, Andreas Klingenhoff, Matthias Frisch, M. Bayerlein, Thomas Werner:
MatInspector and beyond: promoter analysis based on transcription factor binding sites.
2933-2942
Electronic Edition (link) BibTeX
- G. D'Avenio, M. Grigioni, G. Orefici, R. Creti:
SWIFT (sequence-wide investigation with Fourier transform): a software tool for identifying proteins of a given class from the unannotated genome sequence.
2943-2949
Electronic Edition (link) BibTeX
- Milana Frenkel-Morgenstern, Hillary Voet, Shmuel Pietrokovski:
Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure.
2950-2956
Electronic Edition (link) BibTeX
- Mark DeLong, Guang Yao, Quanli Wang, Adrian Dobra, Esther P. Black, Jeffrey T. Chang, Andrea Bild, Mike West, Joseph Nevins, Holly Dressman:
DIG - a system for gene annotation and functional discovery.
2957-2959
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
- Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo:
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
2988-2993
Electronic Edition (link) BibTeX
- Omer Demirkaya, Musa H. Asyali, Mohamed M. Shoukri:
Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling.
2994-3000
Electronic Edition (link) BibTeX
- Jiang Gui, Hongzhe Li:
Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data.
3001-3008
Electronic Edition (link) BibTeX
- Yulan Liang, Bamidele Tayo, Xueya Cai, Arpad Kelemen:
Differential and trajectory methods for time course gene expression data.
3009-3016
Electronic Edition (link) BibTeX
- Yudi Pawitan, Stefan Michiels, Serge Koscielny, Arief Gusnanto, Alexander Ploner:
False discovery rate, sensitivity and sample size for microarray studies.
3017-3024
Electronic Edition (link) BibTeX
- Andrew E. Teschendorff, Yanzhong Wang, Nuno L. Barbosa-Morais, James D. Brenton, Carlos H. Caldas:
A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data.
3025-3033
Electronic Edition (link) BibTeX
Genetics And Population Analysis
Systems Biology
Applications Note - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Volume 21,
Number 14,
July 2005
Letter To The Editor
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Systems Biology
Data And Text Mining
Databases And Ontologies
Applications Note - Sequence Analysis
Phylogenetics
Structural Bioinformatics
- C. Paul Barrett, Martin E. M. Noble:
Dynamite extended: two new services to simplify protein dynamic analysis.
3174-3175
Electronic Edition (link) BibTeX
- Carles Ferrer-Costa, Josep Lluis Gelpí, Leire Zamakola, Ivan Parraga, Xavier de la Cruz, Modesto Orozco:
PMUT: a web-based tool for the annotation of pathological mutations on proteins.
3176-3178
Electronic Edition (link) BibTeX
- Dominik Gront, Andrzej Kolinski:
HCPM - program for hierarchical clustering of protein models.
3179-3180
Electronic Edition (link) BibTeX
- Sergi Vives, Bradford Loucas, Mariel Vázquez, David J. Brenner, Rainer K. Sachs, Lynn Hlatky, Michael Cornforth, Javier Arsuaga:
SCHIP: statistics for chromosome interphase positioning based on interchange data.
3181-3182
Electronic Edition (link) BibTeX
Gene Expression
Genetics And Population Analysi
Data And Text Mining
Databases And Ontologies
- Thorsten Henrich, Mirana Ramialison, Beate Wittbrodt, Beatrice Assouline, Franck Bourrat, Anja Berger, Heinz Himmelbauer, Takashi Sasaki, Nobuyoshi Shimizu, Monte Westerfield, Hisato Kondoh, Joachim Wittbrodt:
MEPD: a resource for medaka gene expression patterns.
3195-3197
Electronic Edition (link) BibTeX
- Philip Jones, Nisha Vinod, Thomas Down, Andre Hackmann, Andreas Kähäri, Ernst Kretschmann, Antony F. Quinn, Daniela Wieser, Henning Hermjakob, Rolf Apweiler:
Dasty and UniProt DAS: a perfect pair for protein feature visualization.
3198-3199
Electronic Edition (link) BibTeX
Volume 21,
Number 15,
August 2005
Review - Data And Text Mining
Discovery Note - Genome Analysis
Original Paper - Genome Analysis
Sequence Analysis
Structural Bioinformatics
- Daeui Park, Semin Lee, Dan M. Bolser, Michael Schroeder, Michael Lappe, Donghoon Oh, Jong Bhak:
Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).
3234-3240
Electronic Edition (link) BibTeX
- Jason Weston, Christina S. Leslie, Eugene Ie, Dengyong Zhou, André Elisseeff, William Stafford Noble:
Semi-supervised protein classification using cluster kernels.
3241-3247
Electronic Edition (link) BibTeX
- D. R. Goucher, S. M. Wincovitch, S. H. Garfield, K. M. Carbone, T. H. Malik:
A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm.
3248-3254
Electronic Edition (link) BibTeX
- Dmitry Lupyan, Alejandra Leo-Macias, Angel R. Ortiz:
A new progressive-iterative algorithm for multiple structure alignment.
3255-3263
Electronic Edition (link) BibTeX
Gene Expression
Genetics And Population Analysis
Systems Biology
Data And Text Mining
Applications Note - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Data And Text Mining
Databases And Ontologies
Volume 21,
Number 16,
August 2005
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics And Population Analysis
Systems Biology
Databases And Ontologies
Applications Note - Genome Analysis
Sequence Analysis
Structural Bioinformatics
- Zsuzsanna Dosztányi, Veronika Csizmok, Peter Tompa, István Simon:
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content.
3433-3434
Electronic Edition (link) BibTeX
- Jaime Prilusky, Clifford E. Felder, Tzviya Zeev-Ben-Mordehai, Edwin H. Rydberg, Orna Man, Jacques S. Beckmann, Israel Silman, Joel L. Sussman:
FoldIndex copyright: a simple tool to predict whether a given protein sequence is intrinsically unfolded.
3435-3438
Electronic Edition (link) BibTeX
Gene Expression
Genetics And Population Analysis
Systems Biology
Data And Text Mining
Databases And Ontologies
Volume 21,
Number 17,
September 2005
Editorials
Original Papers
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- Niels Grabe, Karsten Neuber:
A multicellular systems biology model predicts epidermal morphology, kinetics and Ca2+ flow.
3541-3547
Electronic Edition (link) BibTeX
- Denise Scholtens, Marc Vidal, Robert Gentleman:
Local modeling of global interactome networks.
3548-3557
Electronic Edition (link) BibTeX
- Vitaly A. Selivanov, Ludmilla E. Meshalkina, Olga N. Solovjeva, Philip W. Kuchel, Antonio Ramos-Montoya, German A. Kochetov, Paul W.-N. Lee, Marta Cascante:
Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells.
3558-3564
Electronic Edition (link) BibTeX
Applications Note
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Data and Text Mining
Databases and Ontologies
Volume 21,
Number 18,
September 2005
Review - Databases and Ontologies
Sequence Analysis
- Jonathan E. Allen, Steven Salzberg:
JIGSAW: integration of multiple sources of evidence for gene prediction.
3596-3603
Electronic Edition (link) BibTeX
- Robert Petryszak, Ernst Kretschmann, Daniela Wieser, Rolf Apweiler:
The predictive power of the CluSTr database.
3604-3609
Electronic Edition (link) BibTeX
- Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li:
MicroRNA identification based on sequence and structure alignment.
3610-3614
Electronic Edition (link) BibTeX
- Hongyi Zhou, Yaoqi Zhou:
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
3615-3621
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Applications Note - Genome Analysis
- J. C. Abbott, David M. Aanensen, Kim Rutherford, S. Butcher, Brian G. Spratt:
WebACT - an online companion for the Artemis Comparison Tool.
3665-3666
Electronic Edition (link) BibTeX
- Marcus J. Claesson, Douwe van Sinderen:
BlastXtract - a new way of exploring translated searches.
3667-3668
Electronic Edition (link) BibTeX
- Alessandro Romualdi, Roman Siddiqui, Gernot Glöckner, Rüdiger Lehmann, Jürgen Sühnel:
GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.
3669-3671
Electronic Edition (link) BibTeX
- Elias Zintzaras, John P. A. Ioannidis:
HEGESMA: genome search meta-analysis and heterogeneity testing.
3672-3673
Electronic Edition (link) BibTeX
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
- J. Michael Brockman, Priyam Singh, Donglin Liu, Sean Quinlan, Jesse Salisbury, Joel H. Graber:
PACdb: PolyA Cleavage Site and 3'-UTR Database.
3691-3693
Electronic Edition (link) BibTeX
- Quan-Yuan He, Jing Cao, Xiang-Hua Liu, Miao-Xin Li, Yi-Song Liu, Jin-Yun Xie, Song-Ping Liang:
DEPD: a novel database for differentially expressed proteins.
3694-3696
Electronic Edition (link) BibTeX
- Min He, John K. Tomfohr, Blythe H. Devlin, Marcella Sarzotti, M. Louise Markert, Thomas B. Kepler:
SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.
3697-3699
Electronic Edition (link) BibTeX
- Erratum.
3700
Electronic Edition (link) BibTeX
Volume 21,
Supplement 2,
September 2005
ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28 - October 1, 2005.
2005
Contents BibTeX
Volume 21,
Number 19,
October 2005
Discovery Note Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Imola K. Fodor, David O. Nelson, Michelle Alegria-Hartman, Kristin Robbins, Richard G. Langlois, Kenneth W. Turteltaub, Todd H. Corzett, Sandra L. McCutchen-Maloney:
Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyderTM.
3733-3740
Electronic Edition (link) BibTeX
- Fan Li, Yiming Yang:
Analysis of recursive gene selection approaches from microarray data.
3741-3747
Electronic Edition (link) BibTeX
- Guido Sanguinetti, Marta Milo, Magnus Rattray, Neil D. Lawrence:
Accounting for probe-level noise in principal component analysis of microarray data.
3748-3754
Electronic Edition (link) BibTeX
- Lodewyk F. A. Wessels, Marcel J. T. Reinders, Augustinus A. M. Hart, Cor J. Veenman, Hongyue Dai, Yudong D. He, Laura J. van't Veer:
A protocol for building and evaluating predictors of disease state based on microarray data.
3755-3762
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Applications Note Phylogenetics
- Bui Quang Minh, Le Sy Vinh, Arndt von Haeseler, Heiko A. Schmidt:
pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies.
3794-3796
Electronic Edition (link) BibTeX
- Tulio de Oliveira, Koen Deforche, Sharon Cassol, Mika Salminen, Dimitris Paraskevis, Chris Seebregts, Joe Snoeck, Estrelita J. Janse van Rensburg, Annemarie M. J. Wensing, David A. van de Vijver, Charles A. Boucher, Ricardo Camacho, Anne-Mieke Vandamme:
An automated genotyping system for analysis of HIV-1 and other microbial sequences.
3797-3800
Electronic Edition (link) BibTeX
- Geert Trooskens, David De Beule, Frederik Decouttere, Wim Van Criekinge:
Phylogenetic trees: visualizing, customizing and detecting incongruence.
3801-3802
Electronic Edition (link) BibTeX
Structural Bioinformaics
Databases and Ontologies
- Leon Goldovsky, Paul Janssen, Dag G. Ahrén, Benjamin Audit, Ildefonso Cases, Nikos Darzentas, Anton J. Enright, Núria López-Bigas, José M. Peregrin-Alvarez, Mike Smith, Sophia Tsoka, Victor Kunin, Christos A. Ouzounis:
CoGenT++: an extensive and extensible data environment for computational genomics.
3806-3810
Electronic Edition (link) BibTeX
Volume 21,
Number 20,
October 2005
Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
- Jesús S. Aguilar-Ruiz:
Shifting and scaling patterns from gene expression data.
3840-3845
Electronic Edition (link) BibTeX
- L. Diambra, L. da F. Costa:
Complex networks approach to gene expression driven phenotype imaging.
3846-3851
Electronic Edition (link) BibTeX
- Xinping Cui, Jin Xu, Rehana Asghar, Pascal Condamine, Jan T. Svensson, Steve Wanamaker, Nils Stein, Mikeal Roose, Timothy J. Close:
Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit.
3852-3858
Electronic Edition (link) BibTeX
- Karen Willbrand, François Radvanyi, Jean-Pierre Nadal, Jean-Paul Thiery, Thomas M. A. Fink:
Identifying genes from up-down properties of microarray expression series.
3859-3864
Electronic Edition (link) BibTeX
- Yudi Pawitan, Karuturi R. Krishna Murthy, Stefan Michiels, Alexander Ploner:
Bias in the estimation of false discovery rate in microarray studies.
3865-3872
Electronic Edition (link) BibTeX
- Kavitha Bhasi, Alan Forrest, Murali Ramanathan:
SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles.
3873-3879
Electronic Edition (link) BibTeX
- David Meintrup, Ellen Reisinger:
A statistical model providing comprehensive predictions for the mRNA differential display.
3880-3886
Electronic Edition (link) BibTeX
- Matthias Scholz, Fatma Kaplan, Charles L. Guy, Joachim Kopka, Joachim Selbig:
Non-linear PCA: a missing data approach.
3887-3895
Electronic Edition (link) BibTeX
- Aik Choon Tan, Daniel Q. Naiman, Lei Xu, Raimond L. Winslow, Donald Geman:
Simple decision rules for classifying human cancers from gene expression profiles.
3896-3904
Electronic Edition (link) BibTeX
- Lei Xu, Aik Choon Tan, Daniel Q. Naiman, Donald Geman, Raimond L. Winslow:
Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data.
3905-3911
Electronic Edition (link) BibTeX
Genetics And Population Analysis
Data and Text Mining
Applications Note Structural Bioinformatics
- Chi Yu Chan, Charles E. Lawrence, Ye Ding:
Structure clustering features on the Sfold Web server.
3926-3928
Electronic Edition (link) BibTeX
- Martin Jambon, Olivier Andrieu, Christophe Combet, Gilbert Deléage, François Delfaud, Christophe Geourjon:
The SuMo server: 3D search for protein functional sites.
3929-3930
Electronic Edition (link) BibTeX
- Nir Kalisman, Ami Levi, Tetyana Maximova, Dan Reshef, Sharon Zafriri-Lynn, Yan Gleyzer, Chen Keasar:
MESHI: a new library of Java classes for molecular modeling.
3931-3932
Electronic Edition (link) BibTeX
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Volume 21,
Number 21,
November 2005
Review - Data and Text Mining
- Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, Roman Fischer, Daniel Hoffmann, Joachim Selbig, Klaus Korn, Hauke Walter, Thomas Berg, Patrick Braun, Gerd Fätkenheuer, Mark Oette, Jürgen K. Rockstroh, Bernd Kupfer, Rolf Kaiser, Martin Däumer:
Computational methods for the design of effective therapies against drug resistant HIV strains.
3943-3950
Electronic Edition (link) BibTeX
Discovery Notes - Genome Analysis
Structural Bioinformatics
Sequence Analysis
Gene Expression
- Yuan Gao, George Church:
Improving molecular cancer class discovery through sparse non-negative matrix factorization.
3970-3975
Electronic Edition (link) BibTeX
- Shin Kawano, Kosuke Hashimoto, Takashi Miyama, Susumu Goto, Minoru Kanehisa:
Prediction of glycan structures from gene expression data based on glycosyltransferase reactions.
3976-3982
Electronic Edition (link) BibTeX
- Lei Zhou, David M. Rocke:
An expression index for Affymetrix GeneChips based on the generalized logarithm.
3983-3989
Electronic Edition (link) BibTeX
- David M. Rocke, Zelanna Goldberg, Chad Schweitert, Alison Santana:
A method for detection of differential gene expression in the presence of inter-individual variability in response.
3990-3992
Electronic Edition (link) BibTeX
- Aurora Torrente, Misha Kapushesky, Alvis Brazma:
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
3993-3999
Electronic Edition (link) BibTeX
- Li-yu D. Liu, Naisyin Wang, Joanne R. Lupton, Nancy D. Turner, Robert S. Chapkin, Laurie A. Davidson:
A two-stage normalization method for partially degraded mRNA microarray data.
4000-4006
Electronic Edition (link) BibTeX
- Biao Xing, Mark J. van der Laan:
A causal inference approach for constructing transcriptional regulatory networks.
4007-4013
Electronic Edition (link) BibTeX
- Dongxiao Zhu, Alfred O. Hero, Hong Cheng, Ritu Khanna, Anand Swaroop:
Network constrained clustering for gene microarray data.
4014-4020
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
- Habtom W. Ressom, Rency S. Varghese, Mohamed Abdel-Hamid, Sohair Abdel-Latif Eissa, Daniel Saha, Lenka Goldman, Emanuel F. Petricoin, Thomas P. Conrads, Timothy D. Veenstra, Christopher A. Loffredo, Radoslav Goldman:
Analysis of mass spectral serum profiles for biomarker selection.
4039-4045
Electronic Edition (link) BibTeX
- Jonathan D. Wren, William H. Hildebrand, Sreedevi Chandrasekaran, Ulrich Melcher:
Markov model recognition and classification of DNA/protein sequences within large text databases.
4046-4053
Electronic Edition (link) BibTeX
- Xiang Zhang, John M. Asara, Jiri Adamec, Mourad Ouzzani, Ahmed K. Elmagarmid:
Data pre-processing in liquid chromatography-mass spectrometry-based proteomics.
4054-4059
Electronic Edition (link) BibTeX
Databases and Ontologies
Applications Note - Sequence Analysis
Gene Expression
Volume 21,
Number 22,
November 2005
Editorials
Genome Analysis
Sequence Analysis
- Won-Hyong Chung, Sung-Keun Rhee, Xiu-Feng Wan, Jin-Woo Bae, Zhe-Xue Quan, Yong-Ha Park:
Design of long oligonucleotide probes for functional gene detection in a microbial community.
4092-4100
Electronic Edition (link) BibTeX
- Nikolaos G. Sgourakis, Pantelis G. Bagos, Stavros J. Hamodrakas:
Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.
4101-4106
Electronic Edition (link) BibTeX
- Kevin Karplus, Rachel Karchin, George Shackelford, Richard Hughey:
Calibrating E-values for hidden Markov models using reverse-sequence null models.
4107-4115
Electronic Edition (link) BibTeX
- L. C. Martin, G. B. Gloor, S. D. Dunn, L. M. Wahl:
Using information theory to search for co-evolving residues in proteins.
4116-4124
Electronic Edition (link) BibTeX
- Tiee-Jian Wu, Ying-Hsueh Huang, Lung-An Li:
Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences.
4125-4132
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Systems Biology
Databases and Ontologies
Applications Note - Genome Analysis
Sequence Analysis
Gene Expression
Data and Text Mining
Volume 21,
Supplement 3,
November 2005
The Fifth Georgia Tech - Oak Ridge National Lab International Conference in Bioinformatics:
In Silico Biology,
Computational Genomics and Evolutionary Biology,
Atlanta,
Georgia,
USA,
November 17-19,
2005
- Mark Borodovsky, Andrey Rzhetsky, Dmitrij Frishman:
The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology.
1
Electronic Edition (link) BibTeX
- Galina Glazko, Alexander Gordon, Arcady R. Mushegian:
The choice of optimal distance measure in genome-wide datasets.
11
Electronic Edition (link) BibTeX
- Georgy P. Karev, Faina S. Berezovskaya, Eugene V. Koonin:
Modeling genome evolution with a diffusion approximation of a birth-and-death process.
19
Electronic Edition (link) BibTeX
- Michael E. Sparks, Volker Brendel:
Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants.
30
Electronic Edition (link) BibTeX
- Reed A. Cartwright:
DNA assembly with gaps (Dawg): simulating sequence evolution.
38
Electronic Edition (link) BibTeX
- Austin L. Hughes, Helen Piontkivska, Kendall C. Krebs, David H. O'Connor, David I. Watkins:
Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus.
44
Electronic Edition (link) BibTeX
- Luke E. Ulrich, Igor B. Zhulin:
Four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction.
48
Electronic Edition (link) BibTeX
- Irena I. Artamonova, Goar Frishman, Mikhail S. Gelfand, Dmitrij Frishman:
Mining sequence annotation databanks for association patterns.
57
Electronic Edition (link) BibTeX
Volume 21,
Number 23,
December 2005
Letter to the Editor - Data and Text Mining
Discovery Note - Structural Bioinformatics
Systems Biology
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Databases and Ontologies
Applications Note Genome Analysis
- Alberto M. R. Dávila, Daniel M. Lorenzini, Pablo N. Mendes, Thiago S. Satake, Gabriel R. Sousa, Linair Maria Campos, Camila J. Mazzoni, Glauber Wagner, Paulo F. Pires, Edmundo C. Grisard, Maria Cláudia Reis Cavalcanti, Maria Luiza Machado Campos:
GARSA: genomic analysis resources for sequence annotation.
4302-4303
Electronic Edition (link) BibTeX
Sequence Analysis
Genetics and Population Analysis
Databases and Ontologies
Volume 21,
Number 24,
December 2005
Editorials
Letter to the Editor
Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
- Jung Kyoon Choi, Ungsik Yu, Ook Joon Yoo, Sangsoo Kim:
Differential coexpression analysis using microarray data and its application to human cancer.
4348-4355
Electronic Edition (link) BibTeX
- Shuangge Ma, Jian Huang:
Regularized ROC method for disease classification and biomarker selection with microarray data.
4356-4362
Electronic Edition (link) BibTeX
- Fumihito Miura, Chihiro Uematsu, Yoshiyuki Sakaki, Takashi Ito:
A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences.
4363-4370
Electronic Edition (link) BibTeX
- Ezgi O. Booth, Nancy Van Driessche, Olga Zhuchenko, Adam Kuspa, Gad Shaulsky:
Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes.
4371-4377
Electronic Edition (link) BibTeX
- Shu-Dong Zhang, Timothy W. Gant:
Effect of pooling samples on the efficiency of comparative studies using microarrays.
4378-4383
Electronic Edition (link) BibTeX
Genetics And Population Analysis
Systems Biology
Databases and Ontologies
Applications Note Genome Analysis
Sequence Analysis
- Celine A. Hayden, Travis J. Wheeler, Richard A. Jorgensen:
Evaluating and improving cDNA sequence quality with cQC.
4414-4415
Electronic Edition (link) BibTeX
- Chi-Hung Tsai, Bo-Juen Chen, Chen-hsiung Chan, Hsuan-Liang Liu, Cheng-Yan Kao:
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines.
4416-4419
Electronic Edition (link) BibTeX
- James A. Smagala, Erica D. Dawson, Martin Mehlmann, Michael B. Townsend, Robert D. Kuchta, Kathy L. Rowlen:
ConFind: a robust tool for conserved sequence identification.
4420-4422
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Copyright © Sat May 16 23:51:31 2009
by Michael Ley (ley@uni-trier.de)
