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
