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 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 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, B. 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, Nick 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, 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
- A. Beyer, T. 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 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
