Volume 21, Number 1, January 2005
Editorials
Original Papers - Genome Analysis
- Albert D. G. de Roos:
Origins of introns based on the definition of exon modules and their conserved interfaces.
2-9
Sequence Analysis
- Kuo-Chen Chou:
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes.
10-19
- Chin Lung Lu, Yen Pin Huang:
A memory-efficient algorithm for multiple sequence alignment with constraints.
20-30
- Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang, Michael Q. Zhang:
DWE: Discriminating Word Enumerator.
31-38
- 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
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
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
- David Orrell, Stephen Ramsey, Pedro de Atauri, Hamid Bolouri:
A method for estimating stochastic noise in large genetic regulatory networks.
208-217
- Shawn Martin, Diana C. Roe, Jean-Loup Faulon:
Predicting protein-protein interactions using signature products.
218-226
- Sascha Ott, Annika Hansen, SunYong Kim, Satoru Miyano:
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.
227-238
- Michele Leone, Andrea Pagnani:
Predicting protein functions with message passing algorithms.
239-247
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
- Protein Refinement: A New Challenge For Casp In Its 10th Anniversary.
277
Genome Analysis
Sequence Analysis
Structural Bioinformatics
- Haiquan Li, Jinyan Li:
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets.
314-324
Gene Expression
Genetics And Population Analysis
Systems Biology
- Luca Ferrarini, Luca Bertelli, Jacob D. Feala, Andrew D. McCulloch, Giovanni Paternostro:
A more efficient search strategy for aging genes based on connectivity.
338-348
- 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
- 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
- Vicente Arnau, Sergio Mars, Ignacio Marín:
Iterative Cluster Analysis of Protein Interaction Data.
364-378
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
- Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael L. Creech, Annette Adler:
An architecture for biological information extraction and representation.
430-438
- Daisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara:
Multidimensional support vector machines for visualization of gene expression data.
439-444
- Osman Abul, Reda Alhajj, Faruk Polat, Ken Barker:
Finding differentially expressed genes for pattern generation.
445-450
- Nadia Bolshakova, Francisco Azuaje, Padraig Cunningham:
An integrated tool for microarray data clustering and cluster validity assessment .
451-455
- Alexandros Stamatakis, Thomas Ludwig, Harald Meier:
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
456-463
Genome Analysis
Sequence Analysis
Gene Expression
- Veronica Vinciotti, Raya Khanin, Davide D'Alimonte, Xiaohui Liu, N. Cattini, G. Hotchkiss, G. Bucca, O. de Jesus, J. Rasaiyaah, Colin P. Smith, Paul Kellam, Ernst Wit:
An experimental evaluation of a loop versus a reference design for two-channel microarrays.
492-501
- Paul Delmar, Stéphane Robin, Jean-Jacques Daudin:
VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.
502-508
- Liping Ji, Kian-Lee Tan:
Identifying time-lagged gene clusters using gene expression data.
509-516
- 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
- Zhong Guan, Hongyu Zhao:
A semiparametric approach for marker gene selection based on gene expression data.
529-536
Genome Analysis
Sequence Analysis
- Martín Sarachu, Marc Colet:
wEMBOSS: a web interface for EMBOSS.
540-541
- Derek Kisman, Ming Li, Bin Ma, Li Wang:
tPatternHunter: gapped, fast and sensitive translated homology search .
542-544
- D. Charif, Jean Thioulouse, J. R. Lobry, Guy Perrière:
Online synonymous codon usage analyses with the ade4 and seqinR packages.
545-547
- Jinsoo Kim, Jungmin Seo, Young Seek Lee, Sangsoo Kim:
TFExplorer: integrated analysis database for predicted transcription regulatory elements.
548-550
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
- Jinko Graham, Brad McNeney, Françoise Seillier-Moiseiwitsch:
Stepwise detection of recombination breakpoints in sequence alignments.
589-595
- Yoseph Barash, Gal Elidan, Tommy Kaplan, Nir Friedman:
Y. Barash, G. Elidan, T. Kaplan, , N. Friedman.
596-600
- 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
- Luciano da Fontoura Costa:
Biological sequence analysis through the one-dimensional percolation transform and its enhanced version.
608-616
- 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
Structural Bioinformatics
Gene Expression
- Alexander R. Statnikov, Constantin F. Aliferis, Ioannis Tsamardinos, Douglas P. Hardin, Shawn Levy:
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis.
631-643
- Musa H. Asyali, Musa Alci:
Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods.
644-649
- 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
- Cyril Dalmasso, Philippe Broët, Thierry Moreau:
A simple procedure for estimating the false discovery rate.
660-668
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
- David J. Bakewell, Ernst Wit:
Weighted analysis of microarray gene expression using maximum-likelihood.
723-729
- Y.-h. Taguchi, Y. Oono:
Relational patterns of gene expression via non-metric multidimensional scaling analysis.
730-740
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
- Juliane Schäfer, Korbinian Strimmer:
An empirical Bayes approach to inferring large-scale gene association networks.
754-764
- John Jeremy Rice, Yuhai Tu, Gustavo Stolovitzky:
Reconstructing biological networks using conditional correlation analysis.
765-773
- Chin-Rang Yang, Bruce E. Shapiro, Eric Mjolsness, G. Wesley Hatfield:
An enzyme mechanism language for the mathematical modeling of metabolic pathways.
774-780
Data And Text Mining
- D. Y. Lin:
An efficient Monte Carlo approach to assessing statistical significance in genomic studies.
781-787
- Dilip Rajagopalan, Pankaj Agarwal:
Inferring pathways from gene lists using a literature-derived network of biological relationships.
788-793
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
- Thijs Beuming, Lucy Skrabanek, Masha Y. Niv, Piali Mukherjee, Harel Weinstein:
PDZBase: a protein?Cprotein interaction database for PDZ-domains.
827-828
- Yu Rang Park, Chan Hee Park, Ju Han Kim:
GOChase: correcting errors from Gene Ontology-based annotations for gene products.
829-831
- 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
- Saranyan K. Palaniswamy, Victor X. Jin, Hao Sun, Ramana V. Davuluri:
OMGProm: a database of orthologous mammalian gene promoters.
835-836
Volume 21, Number 7, April 2005
Genome Analysis
- Alexey V. Kochetov:
AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context.
837-840
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
- Daniela Bartels, Sebastian Kespohl, Stefan P. 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
- Roger M. Jarvis, Royston Goodacre:
Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data.
860-868
- Peng Yin, Alexander J. Hartemink:
Theoretical and practical advances in genome halving.
869-879
- Benjamin P. Westover, Jeremy D. Buhler, Justin L. Sonnenburg, Jeffrey I. Gordon:
Operon prediction without a training set.
880-888
- Shahid H. Bokhari, Jon R. Sauer:
A parallel graph decomposition algorithm for DNA sequencing with nanopores.
889-896
- Gideon Dror, Rotem Sorek, Ron Shamir:
Accurate identification of alternatively spliced exons using support vector machine.
897-901
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
- Masumi Itoh, Susumu Goto, Tatsuya Akutsu, Minoru Kanehisa:
Fast and accurate database homology search using upper bounds of local alignment scores.
912-921
- 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
- January Weiner, Geraint Thomas, Erich Bornberg-Bauer:
Rapid motif-based prediction of circular permutations in multi-domain proteins.
932-937
- Wei-Mou Zheng:
Relation between weight matrix and substitution matrix: motif search by similarity.
938-943
- Kuo-Chen Chou, Yu-Dong Cai:
Predicting protein localization in budding Yeast.
944-950
- Johannes Söding:
Protein homology detection by HMM?CHMM comparison.
951-960
- M. Michael Gromiha, Makiko Suwa:
A simple statistical method for discriminating outer membrane proteins with better accuracy.
961-968
Phylogenetics
Structural Bioinformatics
- Dominik Gront, Andrzej Kolinski:
A new approach to prediction of short-range conformational propensities in proteins.
981-987
- John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman:
PDBML: the representation of archival macromolecular structure data in XML.
988-992
- 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
- Erik Sandelin:
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach.
1002-1009
- Xin Yuan, Christopher Bystroff:
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.
1010-1019
- Ilona Kifer, Ori Sasson, Michal Linial:
Predicting fold novelty based on ProtoNet hierarchical classification.
1020-1027
- Carleton L. Kingsford, Bernard Chazelle, Mona Singh:
Solving and analyzing side-chain positioning problems using linear and integer programming.
1028-1039
Gene Expression
- Francisco R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, Bärbel Rohrer, Jonas S. Almeida:
Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method.
1037-1045
- Chao Sima, Ulisses Braga-Neto, Edward R. Dougherty:
Superior feature-set ranking for small samples using bolstered error estimation.
1046-1054
- 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
- Hisanori Kiryu, Taku Oshima, Kiyoshi Asai:
Extracting relations between promoter sequences and their strengths from microarray data.
1062-1068
- Rajarajeswari Balasubramaniyan, Eyke Hüllermeier, Nils Weskamp, Jörg Kämper:
Clustering of gene expression data using a local shape-based similarity measure.
1069-1077
- 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
- Yee Hwa Yang, Yuanyuan Xiao, Mark R. Segal:
Identifying differentially expressed genes from microarray experiments via statistic synthesis.
1084-1093
- Sébastien Rimour, David R. C. Hill, Cécile Militon, Pierre Peyret:
GoArrays: highly dynamic and efficient microarray probe design.
1094-1103
- Gersende Fort, Sophie Lambert-Lacroix:
Classification using partial least squares with penalized logistic regression.
1104-1111
- Antonio Reverter, Wes Barris, Sean McWilliam, Keren A. Byrne, Yong H. Wang, Siok-Hwee Tan, Nicholas J. Hudson, Brian P. Dalrymple:
Validation of alternative methods of data normalization in gene co-expression studies.
1112-1120
- David R. Bickel:
Probabilities of spurious connections in gene networks: application to expression time series.
1121-1128
- Yoram Ben-Shaul, Hagai Bergman, Hermona Soreq:
Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression.
1129-1137
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
- 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
- M. Kloster, C. Tang, N. S. Wingreen:
Finding regulatory modules through large-scale gene-expression data analysis.
1172-1179
- Kuan-Yao Tsai, Feng-Sheng Wang:
Evolutionary optimization with data collocation for reverse engineering of biological networks.
1180-1188
- Syed Asad Rahman, P. Advani, R. Schunk, Rainer Schrader, Dietmar Schomburg:
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC).
1189-1193
- 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
- Robert Urbanczik, C. Wagner:
An improved algorithm for stoichiometric network analysis: theory and applications.
1203-1210
- Ranadip Pal, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty:
Intervention in context-sensitive probabilistic Boolean networks.
1211-1218
- Ina Koch, Björn H. Junker, Monika Heiner:
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.
1219-1226
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
- Julie Chabalier, Cécile Capponi, Yves Quentin, Gwennaele Fichant:
ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems.
1246-1256
- 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
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
- Lars Kiemer, Jannick Dyrløv Bendtsen, Nikolaj Blom:
NetAcet: prediction of N-terminal acetylation sites.
1269-1270
- 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
Phylogenetics
Structural Bioinformatics
Gene Expression
- Victor E. Gerth, Peter D. Vize:
A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns.
1278-1279
- Gilles Caraux, Sylvie Pinloche:
PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order.
1280-1281
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
- 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
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
- 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
- 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
- Steven E. Hampson, B. S. Gaut, Pierre Baldi:
Statistical detection of chromosomal homology using shared-gene density alone.
1339-1348
- John R. Rose, William H. Turkett Jr., Iulia C. Oroian, William W. Laegreid, John W. Keele:
Correlation of amino acid preference and mammalian viral genome type.
1349-1357
- Yun Lian, Harold R. Garner:
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats.
1358-1364
- Eric K. Nordberg:
YODA: selecting signature oligonucleotides.
1365-1370
- Ketil Malde, Eivind Coward, Inge Jonassen:
A graph based algorithm for generating EST consensus sequences.
1371-1375
- Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo:
Highly specific and accurate selection of siRNAs for high-throughput functional assays.
1376-1382
- 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
- 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
- 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
- Xiaochen Bo, Shengqi Wang:
TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA.
1401-1402
Sequence Analysis
- Elizabeth Jacob, Roschen Sasikumar, K. N. Ramachandran Nair:
A fuzzy guided genetic algorithm for operon prediction.
1403-1407
- Iain M. Wallace, Orla O'Sullivan, Desmond G. Higgins:
Evaluation of iterative alignment algorithms for multiple alignment.
1408-1414
- 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
- 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
- Volkan Atalay, Rengül Çetin-Atalay:
Implicit motif distribution based hybrid computational kernel for sequence classification.
1429-1436
- Veronique Prigent, Jean-Claude Thierry, Olivier Poch, Frédéric Plewniak:
DbW: automatic update of a functional family-specific multiple alignment.
1437-1442
- Antonio Cavallo, Andrew C. R. Martin:
Mapping SNPs to protein sequence and structure data.
1443-1450
- 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
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 F. Rayner, Alvis Brazma:
The ArrayExpress gene expression database: a software engineering and implementation perspective.
1495-1501
- Chen-An Tsai, Sue-Jane Wang, Dung-Tsa Chen, James J. Chen:
Sample size for gene expression microarray experiments.
1502-1508
- 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
- Rongwei Fu, Dipak K. Dey, Kent E. Holsinger:
Bayesian models for the analysis of genetic structure when populations are correlated.
1516-1529
- 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
- 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
- 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
- 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
- Xin Zhou, K. Z. Mao:
LS Bound based gene selection for DNA microarray data.
1559-1564
- Baolin Wu:
Differential gene expression detection using penalized linear regression models: the improved SAM statistics.
1565-1571
- Ursula Sauer, Claudia Preininger, Robert Hany-Schmatzberger:
Quick and simple: quality control of microarray data.
1572-1578
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
- 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
- Andreas Beyer, Thomas Wilhelm:
Dynamic simulation of protein complex formation on a genomic scale.
1610-1616
- Marc Daniel Haunschild, Bernd Freisleben, Ralf Takors, Wolfgang Wiechert:
Investigating the dynamic behavior of biochemical networks using model families.
1617-1625
- 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
- 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
- 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
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
- 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
- Ying Tao, Carol Friedman, Yves A. Lussier:
Visualizing information across multidimensional post-genomic structured and textual databases.
1659-1667
- Andrea L. Knorr, Ranjan Srivastava:
Evaluation of HIV-1 kinetic models using quantitative discrimination analysis.
1668-1677
- 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
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
- Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, Mark L. Farman:
TERMINUS - Telomeric End-Read Mining IN Unassembled Sequences.
1695-1698
- Tae-Hyung Kim, Yeo-Jin Jeon, Woo-Yeon Kim, Heui-Soo Kim:
HESAS: HERVs Expression and Structure Analysis System.
1699-1700
- Lauris Kaplinski, Reidar Andreson, Tarmo Puurand, Maido Remm:
MultiPLX: automatic grouping and evaluation of PCR primers.
1701-1702
- Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, Thomas Schiex:
CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping.
1703-1704
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
- 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
- Gianluca Pollastri, Aoife McLysaght:
Porter: a new, accurate server for protein secondary structure prediction.
1719-1720
- Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura:
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.
1721-1723
Gene Expression
Genetics And Population Analysis
- Holger Thiele, Peter J. Nürnberg:
HaploPainter: a tool for drawing pedigrees with complex haplotypes.
1730-1732
- 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
- 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
- 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
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 M. Arthur, Jonas S. Almeida:
AGML Central: web based gel proteomic infrastructure.
1754-1757
- 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
- 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
- Darrell Conklin, Betty Haldeman, Zeren Gao:
Gene finding for the helical cytokines.
1776-1781
- William H. Majoros, Mihaela Pertea, Sihaela Salzberg:
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.
1782-178
- Maria Stepanova, Tatiana Tiazhelova, Mikle Skoblov, Ancha V. Baranova:
A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.
1789-1796
Sequence Analysis
- Dirk Husmeier, Frank Wright, Iain Milne:
Detecting interspecific recombination with a pruned probabilistic divergence measure.
1797-1806
- Shaun Mahony, David Hendrix, Aaron Golden, Terry J. Smith, Daniel S. Rokhsar:
Transcription factor binding site identification using the self-organizing map.
1807-1814
- 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
- J. M. Cameron, T. Hurd, B. H. Robinson:
Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins.
1825-1830
- Zheng Rong Yang:
Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks.
1831-1837
- Han-Lin Li, Chang-Jui Fu:
A linear programming approach for identifying a consensus sequence on DNA sequences.
1838-1845
- Niklaus Fankhauser, Pascal Mäser:
Identification of GPI anchor attachment signals by a Kohonen self-organizing map.
1846-1852
- 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
- Thomas D. Wu, Colin K. Watanabe:
GMAP: a genomic mapping and alignment program for mRNA and EST sequence.
1859-1875
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
- Dae-Won Kim, Kwang Hyung Lee, Doheon Lee:
Detecting clusters of different geometrical shapes in microarray gene expression data.
1927-1934
- 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
- William T. Barry, Andrew B. Nobel, Fred A. Wright:
Significance analysis of functional categories in gene expression studies: a structured permutation approach.
1943-1949
- 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
- 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
- Staal A. Vinterbo, Eun-Young Kim, Lucila Ohno-Machado:
Small, fuzzy and interpretable gene expression based classifiers.
1964-1970
- Claudio Lottaz, Rainer Spang:
Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.
1971-1978
- Wenjiang J. Fu, Raymond J. Carroll, Suojin Wang:
Estimating misclassification error with small samples via bootstrap cross-validation.
1979-1986
- Susmita Datta, Somnath Datta:
Empirical Bayes screening of many p-values with applications to microarray studies.
1987-1994
- Marie-Laure Martin-Magniette, Julie Aubert, Eric Cabannes, Jean-Jacques Daudin:
Evaluation of the gene-specific dye bias in cDNA microarray experiments.
1995-2000
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
- Ross D. King, Simon M. Garrett, George Macleod Coghill:
On the use of qualitative reasoning to simulate and identify metabolic pathway.
2017-2026
- Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger:
Modeling of signal-response cascades using decision tree analysis.
2027-2035
- Weijiang Li, Hiroyuki Kurata:
A grid layout algorithm for automatic drawing of biochemical networks.
2036-2042
- Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai:
Accurate extraction of functional associations between proteins based on common interaction partners and common domains.
2043-2048
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
- 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
- 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
- Francisco Azuaje:
Integrative data analysis for functional prediction: a multi-objective optimization approach.
2099-2100
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
- Federico Abascal, Rafael Zardoya, David Posada:
ProtTest: selection of best-fit models of protein evolution.
2104-2105
- 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
- Joachim Friedrich, Thomas Dandekar, Matthias Wolf, Tobias Müller:
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.
2108-2109
Structural Bioinformatics
Gene Expression
- Joern Toedling, Sebastian Schmeier, Matthias Heinig, Benjamin Georgi, Stefan Roepcke:
MACAT - microarray chromosome analysis tool.
2112-2113
- 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
- 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
- Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, Kevin R. Coombes:
Applications of beta-mixture models in bioinformatics.
2118-2122
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
- Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Boshu Liu, Jin-Miao Wang, Yi-Xue Li, Yang Zhong:
MPSS: an integrated database system for surveying a set of proteins.
2142-2143
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
- Jayson Falkner, Philip Andrews:
Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.
2177-2184
- Lei Bao, Yan Cui:
Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information.
2185-2190
- 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
- J. S. Yu, S. Ongarello, R. Fiedler, X. W. Chen, Gianna Toffolo, Claudio Cobelli, Zlatko Trajanoski:
Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data.
2200-2209
- Halima Bensmail, Jennifer Golek, Michelle M. Moody, O. John Semmes, Abdelali Haoudi:
A novel approach for clustering proteomics data using Bayesian fast Fourier transform.
2210-2224
Sequence Analysis
- Valerio Freschi, Alessandro Bogliolo:
Using sequence compression to speedup probabilistic profile matching.
2225-2229
- Robert G. Beiko, Cheong Xin Chan, Mark A. Ragan:
A word-oriented approach to alignment validation.
2230-2239
- 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
- David H. Mathews:
Predicting a set of minimal free energy RNA secondary structures common to two sequences.
2246-2253
- Ruadhan A. O'Flanagan, Guillaume Paillard, Richard Lavery, Anirvan M. Sengupta:
Non-additivity in protein-DNA binding.
2254-2263
- Kyounghwa Bae, Bani K. Mallick, Christine G. Elsik:
Prediction of protein interdomain linker regions by a hidden Markov model.
2264-2270
- 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
- Mikael Bodén, John Hawkins:
Prediction of subcellular localization using sequence-biased recurrent networks.
2279-2286
- 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
Phylogenetics
Structural Bioinformatics
- Stefan R. Henz, Daniel H. Huson, Alexander F. Auch, Kay Nieselt-Struwe, Stephan C. Schuster:
Whole-genome prokaryotic phylogeny.
2329-2335
- Fabrizio Ferrè, Peter Clote:
Disulfide connectivity prediction using secondary structure information and diresidue frequencies.
2336-2346
- 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
- Jacek Blazewicz, Marta Szachniuk, Adam Wojtowicz:
RNA tertiary structure determination: NOE pathways construction by tabu search.
2356-2361
- Yuzhen Ye, Adam Godzik:
Multiple flexible structure alignment using partial order graphs.
2362-2369
- Qidong Zhang, Sukjoon Yoon, William J. Welsh:
Improved method for predicting ?-turn using support vector machine.
2370-2374
- Markus Leber, Lars Kaderali, Alexander Schönhuth, Rainer Schrader:
A fractional programming approach to efficient DNA melting temperature calculation.
2375-2382
Gene Expression
- Örjan Carlborg, D. J. De Koning, Kenneth F. Manly, Elissa J. Chesler, Robert W. Williams, Chris S. Haley:
Methodological aspects of the genetic dissection of gene expression.
2383-2393
- 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
- Hongzhe Li, Yihui Luan:
Boosting proportional hazards models using smoothing splines, with applications to high-dimensional microarray data.
2403-2409
- Wotao Yin, Terrence Chen, Xiang Sean Zhou, Amit Chakraborty:
Background correction for cDNA microarray images using the TV+L1 model.
2410-2416
- Muhammad Shoaib B. Sehgal, Iqbal Gondal, Laurence Dooley:
Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data.
2417-2423
- 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
- K. K. Dobbin, Ernest S. Kawasaki, D. W. Petersen, R. M. Simon:
Characterizing dye bias in microarray experiments.
2430-2437
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
- Yuehua Cui, Rongling Wu:
Mapping genome-genome epistasis: a high-dimensional model.
2447-2455
- Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang:
Haplotype reconstruction from SNP fragments by minimum error correction.
2456-2462
- Dmitry A. Konovalov, Bruce E. Litow, Nigel Bajema:
Partition-distance via the assignment problem.
2463-2468
- Wei Zhao, Ying Q. Chen, George Casella, James M. Cheverud, Rongling Wu:
A non-stationary model for functional mapping of complex traits.
2469-2477
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
- Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, Sun Kim:
PLATCOM: a Platform for Computational Comparative Genomics.
2514-2516
- Fengkai Zhang, Zhongming Zhao:
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).
2517-2519
- 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
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Carlos J. Camacho, Chao Zhang:
FastContact: rapid estimate of contact and binding free energies.
2534-2536
- Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead:
Protein structure topological comparison, discovery and matching service.
2537-2538
- 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
- 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
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
- Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill, Daniel E. Weeks:
Mega2: data-handling for facilitating genetic linkage and association analyses.
2556-2557
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
- 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
- Anyuan Guo, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, Liping Wei, Jingchu Luo:
DATF: a database of Arabidopsis transcription factors.
2568-2569
- Tariq Riaz, Hen Ley Hor, Arun Krishnan, Francis Tang, Kuo-Bin Li:
WebAllergen: a web server for predicting allergenic proteins.
2570-2571
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
- Hadas Leonov, Isaiah T. Arkin:
A periodicity analysis of transmembrane helices.
2604-2610
- Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara:
Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
2611-2617
- Victor Kunin, Sarah A. Teichmann, Martijn A. Huynen, Christos A. Ouzounis:
The properties of protein family space depend on experimental design.
2618-2622
- Rajesh Chowdhary, R. Ayesha Ali, Werner Albig, Detlef Doenecke, Vladimir B. Bajic:
Promoter modeling: the case study of mammalian histone promoters.
2623-2628
- Jason E. Donald, Eugene I. Shakhnovich:
Determining functional specificity from protein sequences.
2629-2635
- 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
- Zheng Rong Yang:
Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection.
2644-2650
- Moti Zviling, Hadas Leonov, Isaiah T. Arkin:
Genetic algorithm-based optimization of hydrophobicity tables.
2651-2656
- Irad E. Ben-Gal, Ayala Shani, André Gohr, Jan Grau, S. Arviv, Armin Shmilovici, Stefan Posch, Ivo Grosse:
Identification of transcription factor binding sites with variable-order Bayesian networks.
2657-2666
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
- Svetlana Bulashevska, Roland Eils:
Inferring genetic regulatory logic from expression data.
2706-2713
- Thierry Emonet, Charles M. Macal, Michael J. North, Charles E. Wickersham, Philippe Cluzel:
AgentCell: a digital single-cell assay for bacterial chemotaxis.
2714-2721
- Luonan Chen, Ruiqi Wang, Tianshou Zhou, Kazuyuki Aihara:
Noise-induced cooperative behavior in a multicell system.
2722-2729
- Nitin Bhardwaj, Hui Lu:
Correlation between gene expression profiles and protein-protein interactions within and across genomes.
2730-2738
- Phil Hyoun Lee, Doheon Lee:
Modularized learning of genetic interaction networks from biological annotations and mRNA expression data.
2739-2747
Data and Text Mining
Databases and Ontologies
- J. Stuart Aitken:
Formalizing concepts of species, sex and developmental stage in anatomical ontologies.
2773-2779
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
Volume 21, Number 12, June 2005
Letter to the Editor - Gene Expression
Discovery Note - Sequence Analysis
- Vivek Anantharaman, L. Aravind:
MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems.
2805-2811
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
- 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
Sequence Analysis
Structural Bioinformatics
- Guoying Qi, Richard A. Lee, Steven Hayward:
A comprehensive and non-redundant database of protein domain movements.
2832-2838
- Geraint Thomas, Richard B. Sessions, Martin J. Parker:
Density guided importance sampling: application to a reduced model of protein folding.
2839-2843
- Jaehyun Sim, Seung-Yeon Kim, Julian Lee:
Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.
2844-2849
- A. Selim Aytuna, Attila Gürsoy, Ozlem Keskin:
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.
2850-2855
- 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
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
- 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
- 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
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
- Francesco Pappalardo, Pierluigi Lollini, Filippo Castiglione, Santo Motta:
Modeling and simulation of cancer immunoprevention vaccine.
2891-2897
- Lawrence Cabusora, Electra Sutton, Andy W. Fulmer, Christian V. Forst:
Differential network expression during drug and stress response.
2898-2905
Application Notes - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
- Yu Zheng, Daiwen Yang:
STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures.
2925-2926
Databases and Ontologies
Volume 21, Number 13, July 2005
Original Papers - Sequence Analysis
- K. Cartharius, Kornelie Frech, Korbinian Grote, Bernward Klocke, Manuela Haltmeier, Andreas Klingenhoff, Matthias Frisch, M. Bayerlein, Thomas Werner:
MatInspector and beyond: promoter analysis based on transcription factor binding sites.
2933-2942
- 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
- Milana Frenkel-Morgenstern, Hillary Voet, Shmuel Pietrokovski:
Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure.
2950-2956
- 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
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
- Omer Demirkaya, Musa H. Asyali, Mohamed M. Shoukri:
Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling.
2994-3000
- 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
- Yulan Liang, Bamidele Tayo, Xueya Cai, Arpad Kelemen:
Differential and trajectory methods for time course gene expression data.
3009-3016
- Yudi Pawitan, Stefan Michiels, Serge Koscielny, Arief Gusnanto, Alexander Ploner:
False discovery rate, sensitivity and sample size for microarray studies.
3017-3024
- Andrew E. Teschendorff, Yanzhong Wang, Nuno L. Barbosa-Morais, James D. Brenton, Carlos Caldas:
A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data.
3025-3033
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
- Simon Rogers, Mark Girolami:
A Bayesian regression approach to the inference of regulatory networks from gene expression data.
3131-3137
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
- 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
- Dominik Gront, Andrzej Kolinski:
HCPM - program for hierarchical clustering of protein models.
3179-3180
- 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
Gene Expression
Genetics And Population Analysi
- Alun Thomas:
GMCheck: Bayesian error checking for pedigreegenotypes and phenotypes.
3187-3188
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
- 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
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
- Jason Weston, Christina S. Leslie, Eugene Ie, Dengyong Zhou, André Elisseeff, William Stafford Noble:
Semi-supervised protein classification using cluster kernels.
3241-3247
- 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
- Dmitry Lupyan, Alejandra Leo-Macias, Angel R. Ortiz:
A new progressive-iterative algorithm for multiple structure alignment.
3255-3263
Gene Expression
Genetics And Population Analysis
- Andrei S. Rodin, Eric Boerwinkle:
Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels).
3273-3278
Systems Biology
- Yin Liu, Nianjun Liu, Hongyu Zhao:
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms.
3279-3285
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
- 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
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
- Denise Scholtens, Marc Vidal, Robert Gentleman:
Local modeling of global interactome networks.
3548-3557
- 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
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
- Robert Petryszak, Ernst Kretschmann, Daniela Wieser, Rolf Apweiler:
The predictive power of the CluSTr database.
3604-3609
- Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li:
MicroRNA identification based on sequence and structure alignment.
3610-3614
- Hongyi Zhou, Yaoqi Zhou:
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
3615-3621
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Applications Note - Genome Analysis
- J. C. Abbott, David M. Aanensen, Kim Rutherford, Sarah A. Butcher, Brian G. Spratt:
WebACT - an online companion for the Artemis Comparison Tool.
3665-3666
- Marcus J. Claesson, Douwe van Sinderen:
BlastXtract - a new way of exploring translated searches.
3667-3668
- 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
- Elias Zintzaras, John P. A. Ioannidis:
HEGESMA: genome search meta-analysis and heterogeneity testing.
3672-3673
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
- Bo Peng, Marek Kimmel:
simuPOP: a forward-time population genetics simulation environment.
3686-3687
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
- 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
- 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
- Erratum.
3700
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
Volume 21, Number 19, October 2005
Discovery Note Genome Analysis
- Yi Xing, Christopher Lee:
Assessing the application of Ka/Ks ratio test to alternatively spliced exons.
3701-3703
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
- Fan Li, Yiming Yang:
Analysis of recursive gene selection approaches from microarray data.
3741-3747
- Guido Sanguinetti, Marta Milo, Magnus Rattray, Neil D. Lawrence:
Accounting for probe-level noise in principal component analysis of microarray data.
3748-3754
- 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
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
- 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
- Geert Trooskens, David De Beule, Frederik Decouttere, Wim Van Criekinge:
Phylogenetic trees: visualizing, customizing and detecting incongruence.
3801-3802
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
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
- L. Diambra, L. da F. Costa:
Complex networks approach to gene expression driven phenotype imaging.
3846-3851
- 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
- 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
- Yudi Pawitan, Karuturi R. Krishna Murthy, Stefan Michiels, Alexander Ploner:
Bias in the estimation of false discovery rate in microarray studies.
3865-3872
- 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
- David Meintrup, Ellen Reisinger:
A statistical model providing comprehensive predictions for the mRNA differential display.
3880-3886
- Matthias Scholz, Fatma Kaplan, Charles L. Guy, Joachim Kopka, Joachim Selbig:
Non-linear PCA: a missing data approach.
3887-3895
- 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
- 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
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
- Martin Jambon, Olivier Andrieu, Christophe Combet, Gilbert Deléage, François Delfaud, Christophe Geourjon:
The SuMo server: 3D search for protein functional sites.
3929-3930
- 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
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
Discovery Notes - Genome Analysis
- Liang Chen, Hongyu Zhao:
Negative correlation between compositional symmetries and local recombination rates.
3951-3958
Structural Bioinformatics
Sequence Analysis
Gene Expression
