Volume 23,
Number 1,
January 2007
Discovery Note - Genome Analysis
Original Papers - Sequence Analysis
Phylogenetics
Gene Expression
- M. Juanita Martinez, Andrew D. Smith, Bilan Li, Michael Q. Zhang, Kevin S. Harrod:
Computational prediction of novel components of lung transcriptional networks.
21-29
Electronic Edition (link) BibTeX
- Yijun Sun, Steve Goodison, Jian Li, Li Liu, William G. Farmerie:
Improved breast cancer prognosis through the combination of clinical and genetic markers.
30-37
Electronic Edition (link) BibTeX
- Hyuna Yang, Gary A. Churchill:
Estimating p-values in small microarray experiments.
38-43
Electronic Edition (link) BibTeX
- Paul Fogel, S. Stanley Young, Douglas M. Hawkins, Nathalie Ledirac:
Inferential, robust non-negative matrix factorization analysis of microarray data.
44-49
Electronic Edition (link) BibTeX
- Xiaowen Liu, Lusheng Wang:
Computing the maximum similarity bi-clusters of gene expression data.
50-56
Electronic Edition (link) BibTeX
Genetics and Population Analysis
- Jianping Hua, David W. Craig, Marcel Brun, Jennifer Webster, Victoria Zismann, Waibhav Tembe, Keta Joshipura, Matthew J. Huentelman, Edward R. Dougherty, Dietrich A. Stephan:
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.
57-63
Electronic Edition (link) BibTeX
- Johannes Dietter, Manuel Mattheisen, Robert Fürst, Franz Rüschendorf, Thomas F. Wienker, Konstantin Strauch:
Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE.
64-70
Electronic Edition (link) BibTeX
- Yujin Chung, Seung Yeoun Lee, Robert C. Elston, Taesung Park:
Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions.
71-76
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
- Ruhong Zhou, Laxmi Parida, Kush Kapila, Sudhir P. Mudur:
PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.
99-106
Electronic Edition (link) BibTeX
- Dae-Won Kim, Ki Young Lee, Kwang H. Lee, Doheon Lee:
Towards clustering of incomplete microarray data without the use of imputation.
107-113
Electronic Edition (link) BibTeX
- Cheolhwan Oh, Stanislaw H. Zak, Hamid Mirzaei, Charles Buck, Fred E. Regnier, Xiang Zhang:
Neural network prediction of peptide separation in strong anion exchange chromatography.
114-118
Electronic Edition (link) BibTeX
Applications Note - Genome Analysis
- Guillaume Achaz, Frédéric Boyer, Eduardo P. C. Rocha, Alain Viari, Eric Coissac:
Repseek, a tool to retrieve approximate repeats from large DNA sequences.
119-121
Electronic Edition (link) BibTeX
- Gabriela G. Loots, Ivan Ovcharenko:
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.
122-124
Electronic Edition (link) BibTeX
- C. T. Kuenne, Rohit Ghai, Trinad Chakraborty, Torsten Hain:
GECO-linear visualization for comparative genomics.
125-126
Electronic Edition (link) BibTeX
Phylogenetics
Genetics and Population Analysis
Volume 23,
Number 2,
January 2007
ECCB 2006 Conference Proceedings,
January 21-24,
Eilat,
Israel
Original Papers
- Sebastian Böcker:
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry.
5-12
Electronic Edition (link) BibTeX
- Yanay Ofran, Burkhard Rost:
ISIS: interaction sites identified from sequence.
13-16
Electronic Edition (link) BibTeX
- Huzefa Rangwala, George Karypis:
Incremental window-based protein sequence alignment algorithms.
17-23
Electronic Edition (link) BibTeX
- Ariel S. Schwartz, Lior Pachter:
Multiple alignment by sequence annealing.
24-29
Electronic Edition (link) BibTeX
- Dina Sokol, Gary Benson, Justin Tojeira:
Tandem repeats over the edit distance.
30-35
Electronic Edition (link) BibTeX
- Yanni Sun, Jeremy Buhler:
Designing patterns for profile HMM search.
42-43
Electronic Edition (link) BibTeX
- Abha Singh Bais, Steffen Grossmann, Martin Vingron:
Simultaneous alignment and annotation of cis-regulatory regions.
44-49
Electronic Edition (link) BibTeX
- Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, Thomas Schiex:
A comparative genome approach to marker ordering.
50-56
Electronic Edition (link) BibTeX
- Matan Gavish, Amnon Peled, Benny Chor:
Genetic code symmetry and efficient design of GC-constrained coding sequences.
57-63
Electronic Edition (link) BibTeX
- Filip Hermans, Elena Tsiporkova:
Merging microarray cell synchronization experiments through curve alignment.
64-70
Electronic Edition (link) BibTeX
- Macha Nikolski, David James Sherman:
Family relationships: should consensus reign? - consensus clustering for protein families.
71-76
Electronic Edition (link) BibTeX
- Doron Lipson, Zohar Yakhini, Yonatan Aumann:
Optimization of probe coverage for high-resolution oligonucleotide aCGH.
77-83
Electronic Edition (link) BibTeX
- Chun Ye, Eleazar Eskin:
Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.
84-90
Electronic Edition (link) BibTeX
- Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, Roded Sharan:
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data.
91-98
Electronic Edition (link) BibTeX
- Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, Hans-Peter Lenhof:
Electrostatic potentials of proteins in water: a structured continuum approach.
99-103
Electronic Edition (link) BibTeX
- Rafael Najmanovich, Abdellah Allali-Hassani, Richard J. Morris, Ludmila Dombrovsky, Patricia W. Pan, Masoud Vedadi, Alexander N. Plotnikov, Aled M. Edwards, Cheryl H. Arrowsmith, Janet M. Thornton:
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
104-109
Electronic Edition (link) BibTeX
- José Carlos Clemente, Kenji Satou, Gabriel Valiente:
Phylogenetic reconstruction from non-genomic data.
110-115
Electronic Edition (link) BibTeX
- Pawel Górecki, Jerzy Tiuryn:
Inferring phylogeny from whole genomes.
116-122
Electronic Edition (link) BibTeX
- Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
Efficient parsimony-based methods for phylogenetic network reconstruction.
123-128
Electronic Edition (link) BibTeX
- Matthias Bernt, Daniel Merkle, Martin Middendorf:
Using median sets for inferring phylogenetic trees.
129-135
Electronic Edition (link) BibTeX
- Matan Ninio, Eyal Privman, Tal Pupko, Nir Friedman:
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates.
136-141
Electronic Edition (link) BibTeX
- Saharon Rosset:
Efficient inference on known phylogenetic trees using Poisson regression.
142-147
Electronic Edition (link) BibTeX
- Tomer Hertz, Chen Yanover:
Identifying HLA supertypes by learning distance functions.
148-155
Electronic Edition (link) BibTeX
- Keith Noto, Mark Craven:
Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects.
156-162
Electronic Edition (link) BibTeX
- Barak Raveh, Ofer Rahat, Ronen Basri, Gideon Schreiber:
Rediscovering secondary structures as network motifs - an unsupervised learning approach.
163-169
Electronic Edition (link) BibTeX
- Eitan Hirsh, Roded Sharan:
Identification of conserved protein complexes based on a model of protein network evolution.
170-176
Electronic Edition (link) BibTeX
- Natasa Przulj:
Biological network comparison using graphlet degree distribution.
177-183
Electronic Edition (link) BibTeX
- Oleg Rokhlenko, Ydo Wexler, Zohar Yakhini:
Similarities and differences of gene expression in yeast stress conditions.
184-190
Electronic Edition (link) BibTeX
- Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm:
TOPP - the OpenMS proteomics pipeline.
191-197
Electronic Edition (link) BibTeX
- Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, Andrew Emili:
Difference detection in LC-MS data for protein biomarker discovery.
198-204
Electronic Edition (link) BibTeX
- Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer:
Vorolign - fast structural alignment using Voronoi contacts.
205-211
Electronic Edition (link) BibTeX
- Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, Dan Halperin:
Prediction and simulation of motion in pairs of transmembrane alpha-helices.
212-218
Electronic Edition (link) BibTeX
- Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik:
Using an alignment of fragment strings for comparing protein structures.
219-224
Electronic Edition (link) BibTeX
- Etai Jacob, Ron Unger:
A tale of two tails: why are terminal residues of proteins exposed?
225-230
Electronic Edition (link) BibTeX
- Annalisa Marsico, Dirk Labudde, K. Tanuj Sapra, Daniel J. Muller, Michael Schroeder:
A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy.
231-236
Electronic Edition (link) BibTeX
- Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, Peter Stoehr:
EBIMed - text crunching to gather facts for proteins from Medline.
237-244
Electronic Edition (link) BibTeX
Editorials
Original Papers - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Systems Biology
- Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zhang-Zhi Hu, Cathy H. Wu:
Dependence network modeling for biomarker identification.
198-206
Electronic Edition (link) BibTeX
- Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger Chang, Jizhong Zhou, Richard H. Scheuermann:
Modular organization of protein interaction networks.
207-214
Electronic Edition (link) BibTeX
- Xiaotu Ma, Hyunju Lee, Li Wang, Fengzhu Sun:
CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data.
215-221
Electronic Edition (link) BibTeX
- Ai Li, Steve Horvath:
Network neighborhood analysis with the multi-node topological overlap measure.
222-231
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note - Genome Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
- Christopher S. Poultney, Rodrigo A. Gutiérrez, Manpreet S. Katari, Miriam L. Gifford, W. Bradford Paley, Gloria M. Coruzzi, Dennis Shasha:
Sungear: interactive visualization and functional analysis of genomic datasets.
259-261
Electronic Edition (link) BibTeX
- J. A. Falkner, J. W. Falkner, P. C. Andrews:
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.
262-263
Electronic Edition (link) BibTeX
- Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida:
PrepMS: TOF MS data graphical preprocessing tool.
264-265
Electronic Edition (link) BibTeX
Corrigendum
- CASPAR: a hierarchical Bayesian approach to predict survival times in cancer from gene expression data.
266
Electronic Edition (link) BibTeX
Volume 23,
Number 3,
1 February 2007
Discovery Notes - Sequence Analysis
Structural Bioinformatics
Data and Text Mining
Original Papers - Genome Analysis
Sequence Analysis
Gene Expression
- Ian B. Jeffery, Stephen F. Madden, Paul A. McGettigan, Guy Perrière, Aedín C. Culhane, Desmond G. Higgins:
Integrating transcription factor binding site information with gene expression datasets.
298-305
Electronic Edition (link) BibTeX
- Zhen Jiang, Robert Gentleman:
Extensions to gene set enrichment.
306-313
Electronic Edition (link) BibTeX
- Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D. Dynlacht, Guangliang Chen, Bud Mishra:
Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data.
314-320
Electronic Edition (link) BibTeX
- Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H. Scheuermann:
A distribution free summarization method for Affymetrix GeneChip® arrays.
321-327
Electronic Edition (link) BibTeX
- Kenneth Lo, Raphael Gottardo:
Flexible empirical Bayes models for differential gene expression.
328-335
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Applications Notes - Sequence Analysis
Structural Bioinformatics
- Kreshna Gopal, Erik McKee, Tod D. Romo, Reetal Pai, Jacob Smith, James C. Sacchettini, Thomas R. Ioerger:
Crystallographic protein model-building on the web.
375-377
Electronic Edition (link) BibTeX
- Lisa Fukui, Yuan Chen:
NvMap: automated analysis of NMR chemical shift perturbation data.
378-380
Electronic Edition (link) BibTeX
- Wolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Therese E. Malliavin, Michael Nilges:
ARIA2: Automated NOE assignment and data integration in NMR structure calculation.
381-382
Electronic Edition (link) BibTeX
- Stephen A. Cammer:
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol.
383-384
Electronic Edition (link) BibTeX
- Emidio Capriotti, Rita Casadio:
K-Fold: a tool for the prediction of the protein folding kinetic order and rate.
385-386
Electronic Edition (link) BibTeX
Gene Expression
Systems Biology
- Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss, Richard Bonneau:
BioNetBuilder: automatic integration of biological networks.
392-393
Electronic Edition (link) BibTeX
- Olivier Garcia, Cosmin Saveanu, Melissa S. Cline, Micheline Fromont-Racine, Alain Jacquier, Benno Schwikowski, Tero Aittokallio:
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring.
394-396
Electronic Edition (link) BibTeX
Databases and Ontologies
Volume 23,
Number 4,
15 February 2007
Review - Databases and Ontologies
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Applications Notes - Genome Analysis
- Matteo Brilli, Renato Fani, Pietro Liò:
MotifScorer: using a compendium of microarrays to identify regulatory motifs.
493-495
Electronic Edition (link) BibTeX
- André Müller, Karlheinz Holzmann, Hans A. Kestler:
Visualization of genomic aberrations using Affymetrix SNP arrays.
496-497
Electronic Edition (link) BibTeX
- Thomas Derrien, Catherine André, Francis Galibert, Christophe Hitte:
AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps.
498-499
Electronic Edition (link) BibTeX
- René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt:
Assembling millions of short DNA sequences using SSAKE.
500-501
Electronic Edition (link) BibTeX
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
Volume 23,
Number 5,
March 2007
Discovery Note - Structural Bioinformatics
Original Papers - Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Applications Note - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
- Brian S. Yandell, Tapan Mehta, Samprit Banerjee, Daniel Shriner, Ramprasad Venkataraman, Jee Young Moon, W. Whipple Neely, Hao Wu, Randy von Smith, Nengjun Yi:
R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses.
641-643
Electronic Edition (link) BibTeX
- Juan R. González, Lluís Armengol, Xavier Solé, Elisabet Guinó, Josep M. Mercader, Xavier Estivill, Víctor Moreno:
SNPassoc: an R package to perform whole genome association studies.
654-655
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Databases and Ontologies
Volume 23,
Number 6,
15 March 2007
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- István A. Bogdán, Daniel Coca, Jenny Rivers, Robert J. Beynon:
Hardware acceleration of processing of mass spectrometric data for proteomics.
724-731
Electronic Edition (link) BibTeX
- Shigeyuki Matsui, Masaaki Ito, Hiroyuki Nishiyama, Hajime Uno, Hirokazu Kotani, Jun Watanabe, Parry Guilford, Anthony Reeve, Masanori Fukushima, Osamu Ogawa:
Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models.
732-738
Electronic Edition (link) BibTeX
- Peng Liu, J. T. Gene Hwang:
Quick calculation for sample size while controlling false discovery rate with application to microarray analysis.
739-746
Electronic Edition (link) BibTeX
- Dong Hua, Yinglei Lai:
An ensemble approach to microarray data-based gene prioritization after missing value imputation.
747-754
Electronic Edition (link) BibTeX
Systems Biology
Applications Notes:
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Volume 23,
Number 7,
1 April 2007
Discovery Notes:
Phylogenetics
Structural Bioinformatics
Original Papers:
Genome Analysis
Sequence Analysis
Phylogenetics:
Structural Bioinformatics
Gene Expression
Systems Biology
Databases and Ontologies
Applications Notes - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Systems Biology
- Anuj R. Shah, Mudita Singhal, Kyle R. Klicker, Eric G. Stephan, H. Steven Wiley, Katrina M. Waters:
Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager.
906-909
Electronic Edition (link) BibTeX
- Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, D. Skripin, G. D. Bader, Dennis Shasha:
NetMatch: a Cytoscape plugin for searching biological networks.
910-912
Electronic Edition (link) BibTeX
Databases and Ontologies
Corrigendum
Volume 23,
Number 8,
15 April 2007
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Monica Nicolau, Robert Tibshirani, Anne-Lise Børresen-Dale, Stefanie S. Jeffrey:
Disease-specific genomic analysis: identifying the signature of pathologic biology.
957-965
Electronic Edition (link) BibTeX
- Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X. Shirley Liu:
Microarray blob-defect removal improves array analysis.
966-971
Electronic Edition (link) BibTeX
- Sijian Wang, Ji Zhu:
Improved centroids estimation for the nearest shrunken centroid classifier.
972-979
Electronic Edition (link) BibTeX
- Jelle J. Goeman, Peter Bühlmann:
Analyzing gene expression data in terms of gene sets: methodological issues.
980-987
Electronic Edition (link) BibTeX
- Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein:
Assessing the need for sequence-based normalization in tiling microarray experiments.
988-997
Electronic Edition (link) BibTeX
- Dorothy S. V. Wong, Frederick K. Wong, Graham R. Wood:
A multi-stage approach to clustering and imputation of gene expression profiles.
998-1005
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Data and Text Mining
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Corrigenda
Volume 23,
Number 9,
1 May 2007
Discovery Note:
Systems Biology
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
- Jiusheng Chen, Haoran Zheng, Haiyan Liu, Junqing Niu, Jianping Liu, Tie Shen, Bin Rui, Yunyu Shi:
Improving metabolic flux estimation via evolutionary optimization for convex solution space.
1115-1123
Electronic Edition (link) BibTeX
- Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, Michael Schroeder:
Clustering by common friends finds locally significant proteins mediating modules.
1124-1131
Electronic Edition (link) BibTeX
Data and Text Mining
Databases and Ontologies
Applications Note:
Genome Analysis
Sequence Analysis
Gene Expression
- Evert-Jan Blom, Dinne W. J. Bosman, Sacha A. F. T. van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B. T. M. Roerdink, Oscar P. Kuipers:
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.
1161-1163
Electronic Edition (link) BibTeX
- Wolfram Stacklies, Henning Redestig, Matthias Scholz, Dirk Walther, Joachim Selbig:
pcaMethods - a bioconductor package providing PCA methods for incomplete data.
1164-1167
Electronic Edition (link) BibTeX
- Diego Diez, Rebeca Alvarez, Ana Dopazo:
Codelink: an R package for analysis of GE healthcare gene expression bioarrays.
1168-1169
Electronic Edition (link) BibTeX
- Tancred Frickey, Georg Weiller:
Analyzing microarray data using CLANS.
1170-1171
Electronic Edition (link) BibTeX
Systems Biology
Databases and Ontologies
Volume 23,
Number 10,
15 May 2007
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Wuyan Zhang, Alicia Carriquiry, Dan Nettleton, Jack C. M. Dekkers:
Pooling mRNA in microarray experiments and its effect on power.
1217-1224
Electronic Edition (link) BibTeX
- Jiajun Liu, Jacqueline M. Hughes-Oliver, J. Alan Menius Jr:
Domain-enhanced analysis of microarray data using GO annotations.
1225-1234
Electronic Edition (link) BibTeX
- Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, Yoav Gilad:
Using DNA microarrays to study gene expression in closely related species.
1235-1242
Electronic Edition (link) BibTeX
- Yinglei Lai, Bao-ling Adam, Robert Podolsky, Jin-Xiong She:
A mixture model approach to the tests of concordance and discordance between two large-scale experiments with two-sample groups.
1243-1250
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Applications Notes:
Sequence Analysis
Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
- Sarah Cohen Boulakia, Olivier Biton, Susan B. Davidson, Christine Froidevaux:
BioGuideSRS: querying multiple sources with a user-centric perspective.
1301-1303
Electronic Edition (link) BibTeX
- Kevin Le Brigand, Pascal Barbry:
Mediante: a web-based microarray data manager.
1304-1306
Electronic Edition (link) BibTeX
- Qihui Zhu, Anyuan Guo, Ge Gao, Yingfu Zhong, Meng Xu, Minren Huang, Jingchu Luo:
DPTF: a database of poplar transcription factors.
1307-1308
Electronic Edition (link) BibTeX
Volume 23,
Number 11,
June 2007
Systems Biology
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Xiuwen Zheng, Hung-Chung Huang, Wenyuan Li, Peng Liu, Quan-Zhen Li, Ying Liu:
Modeling nonlinearity in dilution design microarray data.
1339-1347
Electronic Edition (link) BibTeX
- George Vasmatzis, Eric W. Klee, Dagmar M. Kube, Terry M. Therneau, Farhad Kosari:
Quantitating tissue specificity of human genes to facilitate biomarker discovery.
1348-1355
Electronic Edition (link) BibTeX
- Daniel M. Kemp, N. R. Nirmala, Joseph D. Szustakowski:
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation.
1356-1362
Electronic Edition (link) BibTeX
- Ian A. Wood, Peter M. Visscher, Kerrie L. Mengersen:
Classification based upon gene expression data: bias and precision of error rates.
1363-1370
Electronic Edition (link) BibTeX
Systems Biology
- Filippo Castiglione, Karen Duca, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Donna Hochberg, David Thorley-Lawson:
Simulating Epstein-Barr virus infection with C-ImmSim.
1371-1377
Electronic Edition (link) BibTeX
- Ralf Steuer, Adriano Nunes Nesi, Alisdair R. Fernie, Thilo Gross, Bernd Blasius, Joachim Selbig:
From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle.
1378-1385
Electronic Edition (link) BibTeX
Data and Text Mining
- Alexander V. Alekseyenko, Christopher J. Lee:
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.
1386-1393
Electronic Edition (link) BibTeX
- Peicheng Du, Rajagopalan Sudha, Michael B. Prystowsky, Ruth Hogue Angeletti:
Data reduction of isotope-resolved LC-MS spectra.
1394-1400
Electronic Edition (link) BibTeX
- Martin Sköld, Tobias Rydén, Viktoria Samuelsson, Charlotte Bratt, Lars Ekblad, Håkan Olsson, Bo Baldetorp:
Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry.
1401-1409
Electronic Edition (link) BibTeX
- Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes, Oliver Kohlbacher:
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data.
1410-1417
Electronic Edition (link) BibTeX
Databases and Ontologies
Applications Notes:
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Data and Text Mining
Databases and Ontologies
Volume 23,
Number 12,
15 June 2007
Genetics and Population Analysis
Genome Analysis
- Zhi-Qiang Ye, Shuqi Zhao, Ge Gao, Xiao-Qiao Liu, Robert E. Langlois, Hui Lu, Liping Wei:
Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP).
1444-1450
Electronic Edition (link) BibTeX
- Yuhyun Park, Sean R. Downing, Dohyun Kim, William C. Hahn, Cheng Li, Philip W. Kantoff, L. J. Wei:
Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data.
1451-1458
Electronic Edition (link) BibTeX
- Yuanyuan Xiao, Mark R. Segal, Yee Hwa Yang, Ru-Fang Yeh:
A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays.
1459-1467
Electronic Edition (link) BibTeX
- Avril Coghlan, Richard Durbin:
Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.
1468-1475
Electronic Edition (link) BibTeX
Sequence Anlysis
Gene Expression
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Databases and Ontologies
Erratum
Volume 23,
Number 13,
July 2007
Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007.
2007
Contents BibTeX
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
- Roger Guimerà, Marta Sales-Pardo, Luis A. Nunes Amaral:
A network-based method for target selection in metabolic networks.
1616-1622
Electronic Edition (link) BibTeX
- A. Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Pedro Alberto Morettin, M. C. Sogayar, Carlos Eduardo Ferreira:
Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method.
1623-1630
Electronic Edition (link) BibTeX
- Zhen-Ping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Alignment of molecular networks by integer quadratic programming.
1631-1639
Electronic Edition (link) BibTeX
- Nicola Soranzo, Ginestra Bianconi, Claudio Altafini:
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data.
1640-1647
Electronic Edition (link) BibTeX
Data and Text Mining
- Vladimir Makarenkov, Pablo Zentilli, Dmytro Kevorkov, Andrei V. Gagarin, Nathalie Malo, Robert Nadon:
An efficient method for the detection and elimination of systematic error in high-throughput screening.
1648-1657
Electronic Edition (link) BibTeX
- Vetle I. Torvik, Neil R. Smalheiser:
A quantitative model for linking two disparate sets of articles in MEDLINE.
1658-1665
Electronic Edition (link) BibTeX
- Khuloud Jaqaman, Jonas F. Dorn, E. Marco, Peter K. Sorger, Gaudenz Danuser:
Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics.
1666-1673
Electronic Edition (link) BibTeX
Databases and Ontologies
Genome Analysis
Sequence Analysis
- Anna Gambin, Piotr Wojtalewicz:
CTX-BLAST: context sensitive version of protein BLAST.
1686-1688
Electronic Edition (link) BibTeX
- E. Dicks, J. W. Teague, P. Stephens, K. Raine, A. Yates, C. Mattocks, P. Tarpey, A. Butler, A. Menzies, D. Richardson, A. Jenkinson, H. Davies, S. Edkins, S. Forbes, K. Gray, C. Greenman, R. Shepherd, M. R. Stratton, P. A. Futreal, R. Wooster:
AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.
1689-1691
Electronic Edition (link) BibTeX
- Ben J. Hayes, Kjetil Nilsen, Paul R. Berg, Eli Grindflek, Sigbjørn Lien:
SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates.
1692-1693
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
- Sang-Bae Kim, Sungjin Yang, Seon-Kyu Kim, Sang Cheol Kim, Hyun Goo Woo, David J. Volsky, Seon-Young Kim, In-Sun Chu:
GAzer: gene set analyzer.
1697-1699
Electronic Edition (link) BibTeX
- Hui Zhao, Kristof Engelen, Bart De Moor, Kathleen Marchal:
CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data.
1700-1701
Electronic Edition (link) BibTeX
- Anne-Laure Boulesteix:
WilcoxCV: an R package for fast variable selection in cross-validation.
1702-1704
Electronic Edition (link) BibTeX
Systems Biology
Databases and Ontologies
Volume 23,
Number 14,
15 July 2007
REVIEW:
Sequence Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
- Martin Schumacher, Harald Binder, Thomas Gerds:
Assessment of survival prediction models based on microarray data.
1768-1774
Electronic Edition (link) BibTeX
- Feng Tai, Wei Pan:
Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms.
1775-1782
Electronic Edition (link) BibTeX
- Mark P. Brynildsen, Tung-Yun Wu, Shi-Shang Jang, James C. Liao:
Biological network mapping and source signal deduction.
1783-1791
Electronic Edition (link) BibTeX
- María José Nueda, Ana Conesa, Johan A. Westerhuis, Huub C. J. Hoefsloot, Age K. Smilde, Manuel Talón, Alberto Ferrer:
Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA.
1792-1800
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Databases and Ontologies
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
- T. Antao, A. Beja-Pereira, G. Luikart:
MODELER4SIMCOAL2: A user-friendly, extensible modeler of demography and linked loci for coalescent simulations.
1848-1850
Electronic Edition (link) BibTeX
- August E. Woerner, Murray P. Cox, Michael F. Hammer:
Recombination-filtered genomic datasets by information maximization.
1851-1853
Electronic Edition (link) BibTeX
- Edward H. Trager, Ritu Khanna, Adrian Marrs, Lawrence Siden, Kari E. H. Branham, Anand Swaroop, Julia E. Richards:
Madeline 2.0 PDE: a new program for local and web-based pedigree drawing.
1854-1856
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Databases and Ontologies
Volume 23,
Number 15,
August 2007
Sequence Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Data and Text Mining
- Matthew E. Monroe, Nikola Tolic, Navdeep Jaitly, Jason L. Shaw, Joshua N. Adkins, Richard D. Smith:
VIPER: an advanced software package to support high-throughput LC-MS peptide identification.
2021-2023
Electronic Edition (link) BibTeX
- Jiajing Wang, Huai Li, Yitan Zhu, Malik Yousef, Michael Nebozhyn, Michael M. Showe, Louise C. Showe, Jianhua Xuan, Robert Clarke, Yue Wang:
VISDA: an open-source caBIGTM analytical tool for data clustering and beyond.
2024-2027
Electronic Edition (link) BibTeX
Corrigendum
Volume 23,
Number 16,
15 August 2007
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Rosalia Maglietta, Ada Piepoli, Domenico Catalano, Piepoli Licciulli, Massimo Carella, Sabino Liuni, Graziano Pesole, Francesco Perri, Nicola Ancona:
Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data.
2063-2072
Electronic Edition (link) BibTeX
- Yiyong Zhou, Corentin Cras-Méneur, Mitsuru Ohsugi, Gary D. Stormo, M. Alan Permutt:
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments.
2073-2079
Electronic Edition (link) BibTeX
- H. M. Bøvelstad, S. Nygård, H. L. Størvold, Magne Aldrin, Ø. Borgan, Arnoldo Frigessi, Ole Christian Lingjærde:
Predicting survival from microarray data - a comparative study.
2080-2087
Electronic Edition (link) BibTeX
- Yonghong Wang, Ze-Hong Miao, Yves Pommier, Ernest S. Kawasaki, Audrey Player:
Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips.
2088-2095
Electronic Edition (link) BibTeX
- Laura Elo, Henna Järvenpää, Matej Oresic, Riitta Lahesmaa, Tero Aittokallio:
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process.
2096-2103
Electronic Edition (link) BibTeX
- James J. Chen, Taewon Lee, Robert R. Delongchamp, Tao Chen, Chen-An Tsai:
Significance analysis of groups of genes in expression profiling studies.
2104-2112
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
- Zheng Guo, Yongjin Li, Xue Gong, Chen Yao, Wencai Ma, Dong Wang, Yanhui Li, Jing Zhu, Min Zhang, Da Yang, Jing Wang:
Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network.
2121-2128
Electronic Edition (link) BibTeX
- Vachiranee Limviphuvadh, Seigo Tanaka, Susumu Goto, Kunihiro Ueda, Minoru Kanehisa:
The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs).
2129-2138
Electronic Edition (link) BibTeX
- Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter:
Constraint-based functional similarity of metabolic genes: going beyond network topology.
2139-2146
Electronic Edition (link) BibTeX
Data and Text Mining
- Minca Mramor, Gregor Leban, Janez Demsar, Blaz Zupan:
Visualization-based cancer microarray data classification analysis.
2147-2154
Electronic Edition (link) BibTeX
- Kyu-Won Kim, Hun-Ki Chung, Gyu-Taek Cho, Kyung-Ho Ma, Dorothy Chandrabalan, Jae-Gyun Gwag, Tae-San Kim, Eun-Gi Cho, Yong-Jin Park:
PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets.
2155-2162
Electronic Edition (link) BibTeX
Databases and Ontologies
Genome Analysis
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Corrigendum
Erratum
Volume 23,
Number 17,
1 September 2007
Structural Bioinformatics
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Anat Reiner-Benaim, Daniel Yekutieli, Noah E. Letwin, Gregory I. Elmer, Norman H. Lee, Neri Kafkafi, Yoav Benjamini:
Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay.
2239-2246
Electronic Edition (link) BibTeX
- George C. Tseng:
Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data.
2247-2255
Electronic Edition (link) BibTeX
- Claudio Lottaz, Joern Toedling, Rainer Spang:
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies.
2256-2264
Electronic Edition (link) BibTeX
- Antonis Daskalakis, Dionisis Cavouras, Panagiotis Bougioukos, Spiros Kostopoulos, Dimitris Glotsos, Ioannis Kalatzis, George C. Kagadis, Christos Argyropoulos, George Nikiforidis:
Improving gene quantification by adjustable spot-image restoration.
2265-2272
Electronic Edition (link) BibTeX
- Andreas Buness, Ruprecht Kuner, Markus Ruschhaupt, Annemarie Poustka, Holger Sültmann, Achim Tresch:
Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer.
2273-2280
Electronic Edition (link) BibTeX
Systems Biology
- Julio Vera, Raul Curto, Marta Cascante, Néstor V. Torres:
Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy.
2281-2289
Electronic Edition (link) BibTeX
- Wei Sun, Tianwei Yu, Ker-Chau Li:
Detection of eQTL modules mediated by activity levels of transcription factors.
2290-2297
Electronic Edition (link) BibTeX
- Dongxiao Zhu, Youjuan Li, Hua Li:
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data.
2298-2305
Electronic Edition (link) BibTeX
- E. Yang, P. T. Foteinou, K. R. King, M. L. Yarmush, Ioannis P. Androulakis:
A novel non-overlapping bi-clustering algorithm for network generation using living cell array data.
2306-2313
Electronic Edition (link) BibTeX
- Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert:
A statistical approach using network structure in the prediction of protein characteristics.
2314-2321
Electronic Edition (link) BibTeX
Data and Text Mining
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Databases and Ontologies
Volume 23,
Number 18,
15 September 2007
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
- Hongfang Liu, Barry Zeeberg, Gang Qu, Akif Günes Koru, Alessandro Ferrucci, Ari Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein:
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.
2385-2390
Electronic Edition (link) BibTeX
- Jianqing Fan, Yue Niu:
Selection and validation of normalization methods for c-DNA microarrays using within-array replications.
2391-2398
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
- Mohamed Elati, Pierre Neuvial, Monique Bolotin-Fukuhara, Emmanuel Barillot, François Radvanyi, Céline Rouveirol:
LICORN: learning cooperative regulation networks from gene expression data.
2407-2414
Electronic Edition (link) BibTeX
- Grégory Batt, Boyan Yordanov, Ron Weiss, Calin Belta:
Robustness analysis and tuning of synthetic gene networks.
2415-2422
Electronic Edition (link) BibTeX
- Zuoshuang Xiang, Rebecca M. Minter, Xiaoming Bi, Peter J. Woolf, Yongqun He:
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis.
2423-2432
Electronic Edition (link) BibTeX
- Jeongah Yoon, Yaguang Si, Ryan Nolan, Kyongbum Lee:
Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection.
2433-2440
Electronic Edition (link) BibTeX
Data and Text Mining
- Jaroslaw Harezlak, Mike Wang, David Christiani, Xihong Lin:
Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments.
2441-2448
Electronic Edition (link) BibTeX
- Ziliang Qian, Lingyi Lu, Xiao-Jun Liu, Yu-Dong Cai, Yixue Li:
An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization.
2449-2454
Electronic Edition (link) BibTeX
- Hiroto Saigo, Takeaki Uno, Koji Tsuda:
Mining complex genotypic features for predicting HIV-1 drug resistance.
2455-2462
Electronic Edition (link) BibTeX
- Jian Huang, Arief Gusnanto, Kathleen O'Sullivan, Johan Staaf, Åke Borg, Yudi Pawitan:
Robust smooth segmentation approach for array CGH data analysis.
2463-2469
Electronic Edition (link) BibTeX
- Youjuan Li, Ji Zhu:
Analysis of array CGH data for cancer studies using fused quantile regression.
2470-2476
Electronic Edition (link) BibTeX
- Weijian Xuan, Pinglang Wang, Stanley J. Watson, Fan Meng:
Medline search engine for finding genetic markers with biological significance.
2477-2484
Electronic Edition (link) BibTeX
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
- Hongseok Yun, Jeong Wook Lee, Joonwoo Jeong, Jaesung Chung, Jong Myoung Park, Han Na Myoung, Sang Yup Lee:
EcoProDB: the Escherichia coli protein database.
2501-2503
Electronic Edition (link) BibTeX
- C. Voegele, S. V. Tavtigian, D. de Silva, S. Cuber, A. Thomas, F. Le Calvez-Kelm:
A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening.
2504-2506
Electronic Edition (link) BibTeX
Volume 23,
Number 19,
1 October 2007
REVIEW:
Gene Expression
Sequence Analysis
Structural Bioinformatics
Genome Analysis
Sequence Analysis
- Pawel Smialowski, Antonio J. Martin-Galiano, Aleksandra Mikolajka, Tobias Girschick, Tad A. Holak, Dmitrij Frishman:
Protein solubility: sequence based prediction and experimental verification.
2536-2542
Electronic Edition (link) BibTeX
- J. Zucko, N. Skunca, Tomaz Curk, Blaz Zupan, P. F. Long, J. Cullum, R. H. Kessin, D. Hranueli:
Polyketide synthase genes and the natural products potential of Dictyostelium discoideum.
2543-2549
Electronic Edition (link) BibTeX
- Cécile Militon, Sébastien Rimour, Mohieddine Missaoui, Corinne Biderre, Vincent Barra, David R. C. Hill, Anne Moné, Geneviève Gagne, Harald Meier, Eric Peyretaillade, Pierre Peyret:
PhylArray: phylogenetic probe design algorithm for microarray.
2550-2557
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
- Fred A. Wright, Hanwen Huang, Xiaojun Guan, Kevin Gamiel, Clark Jeffries, William T. Barry, Fernando Pardo-Manuel de Villena, Patrick F. Sullivan, Kirk C. Wilhelmsen, Fei Zou:
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans.
2581-2588
Electronic Edition (link) BibTeX
- Seung Yeoun Lee, Yujin Chung, Robert C. Elston, Youngchul Kim, Taesung Park:
Log-linear model-based multifactor dimensionality reduction method to detect gene-gene interactions.
2589-2595
Electronic Edition (link) BibTeX
Systems Biology
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Volume 23,
Number 20,
15 October 2007
Systems Biology
Sequence Analysis
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Thomas Tang, Nicolas François, Annie Glatigny, Nicolas Agier, Marie-Hélène Mucchielli-Giorgi, Lawrence Aggerbeck, Hervé Delacroix:
Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment.
2686-2691
Electronic Edition (link) BibTeX
- Matthew A. Hibbs, David C. Hess, Chad L. Myers, Curtis Huttenhower, Kai Li, Olga G. Troyanskaya:
Exploring the functional landscape of gene expression: directed search of large microarray compendia.
2692-2699
Electronic Edition (link) BibTeX
- Matthew E. Ritchie, Jeremy Silver, Alicia Oshlack, Melissa Holmes, Dileepa Diyagama, Andrew Holloway, Gordon K. Smyth:
A comparison of background correction methods for two-colour microarrays.
2700-2707
Electronic Edition (link) BibTeX
- Michele Leone, Sumedha, Martin Weigt:
Clustering by soft-constraint affinity propagation: applications to gene-expression data.
2708-2715
Electronic Edition (link) BibTeX
- Duygu Ucar, Isaac Neuhaus, Petra Ross-MacDonald, Charles Tilford, Srinivasan Parthasarathy, Nathan Siemers, Rui-Ru Ji:
Construction of a reference gene association network from multiple profiling data: application to data analysis.
2716-2724
Electronic Edition (link) BibTeX
- Giacomo Gamberoni, Evelina Lamma, Gianluca Lodo, Jlenia Marchesini, Nicoletta Mascellani, Simona Rossi, Sergio Storari, Luca Tagliavini, Stefano Volinia:
Fun&Co: identification of key functional differences in transcriptomes.
2725-2732
Electronic Edition (link) BibTeX
- Carla S. Möller-Levet, Catharine M. West, Crispin J. Miller:
Exploiting sample variability to enhance multivariate analysis of microarray data.
2733-2740
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
- C. Kreutz, M. M. Bartolome Rodriguez, Thomas Maiwald, M. Seidl, H. E. Blum, L. Mohr, Jens Timmer:
An error model for protein quantification.
2747-2753
Electronic Edition (link) BibTeX
- Raman Lall, Julie Mitchell:
Metal reduction kinetics in Shewanella.
2754-2759
Electronic Edition (link) BibTeX
- Yizhi Cai, Brian Hartnett, Claes Gustafsson, Jean Peccoud:
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts.
2760-2767
Electronic Edition (link) BibTeX
Data and Text Mining
- Yoshimasa Tsuruoka, John McNaught, Jun-ichi Tsujii, Sophia Ananiadou:
Learning string similarity measures for gene/protein name dictionary look-up using logistic regression.
2768-2774
Electronic Edition (link) BibTeX
- Ali Cakmak, Gultekin Özsoyoglu:
Mining biological networks for unknown pathways.
2775-2783
Electronic Edition (link) BibTeX
- Norman Warthmann, Joffrey Fitz, Detlef Weigel:
MSQT for choosing SNP assays from multiple DNA alignments.
2784-2787
Electronic Edition (link) BibTeX
- Zhanfeng Wang, Yuan-chin I. Chang, Zhiliang Ying, Liang Zhu, Yaning Yang:
A parsimonious threshold-independent protein feature selection method through the area under receiver operating characteristic curve.
2788-2794
Electronic Edition (link) BibTeX
Sequence Analysis
Structural Bioinformatics
Systems Biology
Volume 23,
Number 21,
1 November 2007
Genome Analysis
Sequence Analysis
Structural Bioinformatics
- Michael J. Sweredoski, Kevin J. Donovan, Bao D. Nguyen, A. J. Shaka, Pierre Baldi:
Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling.
2829-2835
Electronic Edition (link) BibTeX
- Hung-Pin Peng, An-Suei Yang:
Modeling protein loops with knowledge-based prediction of sequence-structure alignment.
2836-2842
Electronic Edition (link) BibTeX
- Ke Chen, Lukasz A. Kurgan:
PFRES: protein fold classification by using evolutionary information and predicted secondary structure.
2843-2850
Electronic Edition (link) BibTeX
- Frank DiMaio, Dmitry A. Kondrashov, Eduard Bitto, Ameet Soni, Craig A. Bingman, George N. Phillips Jr., Jude W. Shavlik:
Creating protein models from electron-density maps using particle-filtering methods.
2851-2858
Electronic Edition (link) BibTeX
Gene Expression
- Sanghamitra Bandyopadhyay, Anirban Mukhopadhyay, Ujjwal Maulik:
An improved algorithm for clustering gene expression data.
2859-2865
Electronic Edition (link) BibTeX
- Blaise Hanczar, Jean-Daniel Zucker, Corneliu Henegar, Lorenza Saitta:
Feature construction from synergic pairs to improve microarray-based classification.
2866-2872
Electronic Edition (link) BibTeX
- Kathe E. Bjork, Karen Kafadar:
Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips®.
2873-2880
Electronic Edition (link) BibTeX
- Mark D. Robinson, Gordon K. Smyth:
Moderated statistical tests for assessing differences in tag abundance.
2881-2887
Electronic Edition (link) BibTeX
- Zhiwen Yu, Hau-San Wong, Hongqiang Wang:
Graph-based consensus clustering for class discovery from gene expression data.
2888-2896
Electronic Edition (link) BibTeX
- Willem Talloen, Djork-Arné Clevert, Sepp Hochreiter, Dhammika Amaratunga, Luc Bijnens, Stefan Kass, Hinrich W. H. Göhlmann:
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data.
2897-2902
Electronic Edition (link) BibTeX
- Jiexin Zhang, Yuan Ji, Li Zhang:
Extracting three-way gene interactions from microarray data.
2903-2909
Electronic Edition (link) BibTeX
- Sangeeta B. English, Atul J. Butte:
Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes.
2910-2917
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
- Atsushi Hijikata, Hiroshi Kitamura, Yayoi Kimura, Ryo Yokoyama, Yuichi Aiba, Yanyuan Bao, Shigeharu Fujita, Koji Hase, Shohei Hori, Yasuyuki Ishii, Osami Kanagawa, Hiroshi Kawamoto, Kazuya Kawano, Haruhiko Koseki, Masato Kubo, Ai Kurita-Miki, Tomohiro Kurosaki, Kyoko Masuda, Mitsumasa Nakata, Keisuke Oboki, Hiroshi Ohno, Mariko Okamoto, Yoshimichi Okayama, Jiyang O-Wang, Hirohisa Saito, Takashi Saito, Machie Sakuma, Katsuaki Sato, Kaori Sato, Ken-ichiro Seino, Ruka Setoguchi, Yuki Tamura, Masato Tanaka, Masaru Taniguchi, Ichiro Taniuchi, Annabelle Teng, Takeshi Watanabe, Hiroshi Watarai, Sho Yamasaki, Osamu Ohara:
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells.
2934-2941
Electronic Edition (link) BibTeX
Genome Analysis
Sequence Analysis
- M. A. Larkin, Gordon Blackshields, N. P. Brown, R. Chenna, Paul A. McGettigan, Hamish McWilliam, Franck Valentin, Iain M. Wallace, Andreas Wilm, Rodrigo Lopez, Julie Dawn Thompson, Toby J. Gibson, Desmond G. Higgins:
Clustal W and Clustal X version 2.0.
2947-2948
Electronic Edition (link) BibTeX
- Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, Richa Agarwala:
Improved BLAST searches using longer words for protein seeding.
2949-2951
Electronic Edition (link) BibTeX
Phylogenetics
- John Archer, David L. Robertson:
CTree: comparison of clusters between phylogenetic trees made easy.
2952-2953
Electronic Edition (link) BibTeX
- Víctor Soria-Carrasco, Gerard Talavera, Javier Igea, Jose Castresana:
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.
2954-2956
Electronic Edition (link) BibTeX
- Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf:
CREx: inferring genomic rearrangements based on common intervals.
2957-2958
Electronic Edition (link) BibTeX
Structural Bioinformatics
Volume 23,
Number 22,
15 November 2007
Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
- Franz F. Roos, Riko Jacob, Jonas Grossmann, Bernd Fischer, Joachim M. Buhmann, Wilhelm Gruissem, Sacha Baginsky, Peter Widmayer:
PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra.
3016-3023
Electronic Edition (link) BibTeX
- Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron:
Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis.
3024-3031
Electronic Edition (link) BibTeX
- Nandini Raghavan, An M. I. M. De Bondt, Willem Talloen, Dieder Moechars, Hinrich W. H. Göhlmann, Dhammika Amaratunga:
The high-level similarity of some disparate gene expression measures.
3032-3038
Electronic Edition (link) BibTeX
- Shinsheng Yuan, Ker-Chau Li:
Context-dependent clustering for dynamic cellular state modeling of microarray gene expression.
3039-3047
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Databases and Ontologies
Volume 23,
Number 23,
1 December 2007
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Mehdi Poursheikhali Asgary, Samad Jahandideh, Parviz Abdolmaleki, Anoshirvan Kazemnejad:
Analysis and identification of beta-turn types using multinomial logistic regression and artificial neural network.
3125-3130
Electronic Edition (link) BibTeX
- Francisco S. Domingues, Jörg Rahnenführer, Thomas Lengauer:
Conformational analysis of alternative protein structures.
3131-3138
Electronic Edition (link) BibTeX
- Ingolf Sommer, Oliver Müller, Francisco S. Domingues, Oliver Sander, Joachim Weickert, Thomas Lengauer:
Moment invariants as shape recognition technique for comparing protein binding sites.
3139-3146
Electronic Edition (link) BibTeX
- Jiangning Song, Zheng Yuan, Hao Tan, Thomas Huber, Kevin Burrage:
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.
3147-3154
Electronic Edition (link) BibTeX
- Majid Masso, Iosif I. Vaisman:
Accurate prediction of enzyme mutant activity based on a multibody statistical potential.
3155-3161
Electronic Edition (link) BibTeX
Gene Expression
- Gabriela V. Cohen Freue, Zsuzsanna Hollander, Enqing Shen, Ruben H. Zamar, Robert Balshaw, Andreas Scherer, Bruce McManus, Paul Keown, W. Robert McMaster, Raymond T. Ng:
MDQC: a new quality assessment method for microarrays based on quality control reports.
3162-3169
Electronic Edition (link) BibTeX
- Feng Tai, Wei Pan:
Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data.
3170-3177
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
- Thomas Fournier, Jean-Pierre Gabriel, Christian Mazza, Jerome Pasquier, Jose L. Galbete, Nicolas Mermod:
Steady-state expression of self-regulated genes.
3185-3192
Electronic Edition (link) BibTeX
- Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, William S. Hlavacek:
Carbon-fate maps for metabolic reactions.
3193-3199
Electronic Edition (link) BibTeX
- Niels Grabe, Thora Pommerencke, Thorsten Steinberg, Hartmut Dickhaus, Pascal Tomakidi:
Reconstructing protein networks of epithelial differentiation from histological sections.
3200-3208
Electronic Edition (link) BibTeX
- Minh Quach, Nicolas Brunel, Florence d'Alché-Buc:
Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference.
3209-3216
Electronic Edition (link) BibTeX
- Hyunjung Shin, Andreas Martin Lisewski, Olivier Lichtarge:
Graph sharpening plus graph integration: a synergy that improves protein functional classification.
3217-3224
Electronic Edition (link) BibTeX
- Dougu Nam, Sung Ho Yoon, Jihyun F. Kim:
Ensemble learning of genetic networks from time-series expression data.
3225-3231
Electronic Edition (link) BibTeX
Data and Text Mining
Sequence Analysis
Structural Bioinformatics
- Itay Mayrose, Osnat Penn, Elana Erez, Nimrod D. Rubinstein, Tomer Shlomi, Natalia Tarnovitski Freund, Erez M. Bublil, Eytan Ruppin, Roded Sharan, Jonathan M. Gershoni, Eric Martz, Tal Pupko:
Pepitope: epitope mapping from affinity-selected peptides.
3244-3246
Electronic Edition (link) BibTeX
- Sergei Spirin, Mikhail Titov, Anna Karyagina, Andrei Alexeevski:
NPIDB: a Database of Nucleic Acids-Protein Interactions.
3247-3248
Electronic Edition (link) BibTeX
Gene Expression
Genetics and Population Analysis
Databases and Ontologies
Letter to the Editor
Phylogenetics
Volume 23,
Number 24,
15 December 2007
REVIEW:
Sequence Analysis
Structural Bioinformatics
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Sanbo Qin, Huan-Xiang Zhou:
meta-PPISP: a meta web server for protein-protein interaction site prediction.
3386-3387
Electronic Edition (link) BibTeX
- D. Fusco, B. Bassetti, P. Jona, M. Cosentino Lagomarsino:
DIA-MCIS: an importance sampling network randomizer for network motif discovery and other topological observables in transcription networks.
3388-3390
Electronic Edition (link) BibTeX
- Jose-Roman Bilbao-Castro, Inmaculada García, José-Jesús Fernández:
EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography.
3391-3393
Electronic Edition (link) BibTeX
- Ted Laderas, Cory Bystrom, Debra McMillen, Guang Fan, Shannon K. McWeeney:
TandTRAQ: an open-source tool for integrated protein identification and quantitation.
3394-3396
Electronic Edition (link) BibTeX
- Surendra S. Negi, Catherine H. Schein, Numan Özgün, Trevor D. Power, Werner Braun:
InterProSurf: a web server for predicting interacting sites on protein surfaces.
3397-3399
Electronic Edition (link) BibTeX
- Min Hu, Junhui Wang, Qunsheng Peng:
Identification and visualization of cage-shaped proteins.
3400-3402
Electronic Edition (link) BibTeX
- Lukasz Slabinski, Lukasz Jaroszewski, Leszek Rychlewski, Ian A. Wilson, Scott A. Lesley, Adam Godzik:
XtalPred: a web server for prediction of protein crystallizability.
3403-3405
Electronic Edition (link) BibTeX
Gene Expression
Systems Biology
Copyright © Sat May 16 23:51:33 2009
by Michael Ley (ley@uni-trier.de)
