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
- 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
- Hyuna Yang, Gary A. Churchill:
Estimating p-values in small microarray experiments.
38-43
- Paul Fogel, S. Stanley Young, Douglas M. Hawkins, Nathalie Ledirac:
Inferential, robust non-negative matrix factorization analysis of microarray data.
44-49
- Xiaowen Liu, Lusheng Wang:
Computing the maximum similarity bi-clusters of gene expression data.
50-56
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
- 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
- Yujin Chung, Seung Yeoun Lee, Robert C. Elston, Taesung Park:
Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions.
71-76
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
- Dae-Won Kim, Ki Young Lee, Kwang H. Lee, Doheon Lee:
Towards clustering of incomplete microarray data without the use of imputation.
107-113
- Cheolhwan Oh, Stanislaw H. Zak, Hamid Mirzaei, Charles R. Buck, Fred E. Regnier, Xiang Zhang:
Neural network prediction of peptide separation in strong anion exchange chromatography.
114-118
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
- Gabriela G. Loots, Ivan Ovcharenko:
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.
122-124
- C. T. Kuenne, Rohit Ghai, Trinad Chakraborty, Torsten Hain:
GECO-linear visualization for comparative genomics.
125-126
Phylogenetics
- Ivica Letunic, Peer Bork:
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
127-128
Genetics and Population Analysis
Volume 23,
Number 2,
January 2007
ECCB 2006 Conference Proceedings,
January 21-24,
Eilat,
Israel
- ECCB 2006.
1-2
- ECCB 2006 Organization.
3-4
Original Papers
- Sebastian Böcker:
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry.
5-12
- Yanay Ofran, Burkhard Rost:
ISIS: interaction sites identified from sequence.
13-16
- Huzefa Rangwala, George Karypis:
Incremental window-based protein sequence alignment algorithms.
17-23
- Ariel S. Schwartz, Lior Pachter:
Multiple alignment by sequence annealing.
24-29
- Dina Sokol, Gary Benson, Justin Tojeira:
Tandem repeats over the edit distance.
30-35
- Yanni Sun, Jeremy Buhler:
Designing patterns for profile HMM search.
42-43
- Abha Singh Bais, Steffen Grossmann, Martin Vingron:
Simultaneous alignment and annotation of cis-regulatory regions.
44-49
- Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, Thomas Schiex:
A comparative genome approach to marker ordering.
50-56
- Matan Gavish, Amnon Peled, Benny Chor:
Genetic code symmetry and efficient design of GC-constrained coding sequences.
57-63
- Filip Hermans, Elena Tsiporkova:
Merging microarray cell synchronization experiments through curve alignment.
64-70
- Macha Nikolski, David James Sherman:
Family relationships: should consensus reign? - consensus clustering for protein families.
71-76
- Doron Lipson, Zohar Yakhini, Yonatan Aumann:
Optimization of probe coverage for high-resolution oligonucleotide aCGH.
77-83
- Chun Ye, Eleazar Eskin:
Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.
84-90
- 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
- Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, Hans-Peter Lenhof:
Electrostatic potentials of proteins in water: a structured continuum approach.
99-103
- 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
- José Carlos Clemente, Kenji Satou, Gabriel Valiente:
Phylogenetic reconstruction from non-genomic data.
110-115
- Pawel Górecki, Jerzy Tiuryn:
Inferring phylogeny from whole genomes.
116-122
- Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
Efficient parsimony-based methods for phylogenetic network reconstruction.
123-128
- Matthias Bernt, Daniel Merkle, Martin Middendorf:
Using median sets for inferring phylogenetic trees.
129-135
- 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
- Saharon Rosset:
Efficient inference on known phylogenetic trees using Poisson regression.
142-147
- Tomer Hertz, Chen Yanover:
Identifying HLA supertypes by learning distance functions.
148-155
- Keith Noto, Mark Craven:
Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects.
156-162
- Barak Raveh, Ofer Rahat, Ronen Basri, Gideon Schreiber:
Rediscovering secondary structures as network motifs - an unsupervised learning approach.
163-169
- Eitan Hirsh, Roded Sharan:
Identification of conserved protein complexes based on a model of protein network evolution.
170-176
- Natasa Przulj:
Biological network comparison using graphlet degree distribution.
177-183
- Oleg Rokhlenko, Ydo Wexler, Zohar Yakhini:
Similarities and differences of gene expression in yeast stress conditions.
184-190
- Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm:
TOPP - the OpenMS proteomics pipeline.
191-197
- Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, Andrew Emili:
Difference detection in LC-MS data for protein biomarker discovery.
198-204
- Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer:
Vorolign - fast structural alignment using Voronoi contacts.
205-211
- Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, Dan Halperin:
Prediction and simulation of motion in pairs of transmembrane alpha-helices.
212-218
- Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik:
Using an alignment of fragment strings for comparing protein structures.
219-224
- Etai Jacob, Ron Unger:
A tale of two tails: why are terminal residues of proteins exposed?
225-230
- 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
- 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
Editorials
Original Papers - Genome Analysis
Sequence Analysis
- Richard J. Dixon, Ian C. Eperon, Nilesh J. Samani:
Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression.
150-155
- Michael Farrar:
Striped Smith-Waterman speeds database searches six times over other SIMD implementations.
156-161
- Xu Zhang, Tamer Kahveci:
QOMA: quasi-optimal multiple alignment of protein sequences.
162-168
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
- Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger Chang, Jizhong Zhou, Richard H. Scheuermann:
Modular organization of protein interaction networks.
207-214
- 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
- Ai Li, Steve Horvath:
Network neighborhood analysis with the multi-node topological overlap measure.
222-231
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
- J. A. Falkner, J. W. Falkner, P. C. Andrews:
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.
262-263
- 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
Corrigendum
- CASPAR: a hierarchical Bayesian approach to predict survival times in cancer from gene expression data.
266
Volume 23,
Number 3,
1 February 2007
Discovery Notes - Sequence Analysis
Structural Bioinformatics
Data and Text Mining
Original Papers - Genome Analysis
Sequence Analysis
- Jaebum Kim, Saurabh Sinha:
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.
289-297
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
- Zhen Jiang, Robert Gentleman:
Extensions to gene set enrichment.
306-313
- 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
- Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H. Scheuermann:
A distribution free summarization method for Affymetrix GeneChip® arrays.
321-327
- Kenneth Lo, Raphael Gottardo:
Flexible empirical Bayes models for differential gene expression.
328-335
Systems Biology
Data and Text Mining
Applications Notes - Sequence Analysis
- Kazutaka Katoh, Hiroyuki Toh:
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
372-374
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
- Lisa Fukui, Yuan Chen:
NvMap: automated analysis of NMR chemical shift perturbation data.
378-380
- 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
- Stephen A. Cammer:
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol.
383-384
- Emidio Capriotti, Rita Casadio:
K-Fold: a tool for the prediction of the protein folding kinetic order and rate.
385-386
Gene Expression
Systems Biology
- Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss, Richard Bonneau:
BioNetBuilder: automatic integration of biological networks.
392-393
- 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
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
- André Müller, Karlheinz Holzmann, Hans A. Kestler:
Visualization of genomic aberrations using Affymetrix SNP arrays.
496-497
- Thomas Derrien, Catherine André, Francis Galibert, Christophe Hitte:
AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps.
498-499
- René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt:
Assembling millions of short DNA sequences using SSAKE.
500-501
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
- Jie Zhou, Hanchuan Peng:
Automatic recognition and annotation of gene expression patterns of fly embryos.
589-596
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
- 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
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
- 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
- Peng Liu, J. T. Gene Hwang:
Quick calculation for sample size while controlling false discovery rate with application to microarray analysis.
739-746
- Dong Hua, Yinglei Lai:
An ensemble approach to microarray data-based gene prioritization after missing value imputation.
747-754
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
- Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Dmitry Skripin, G. D. Bader, Dennis Shasha:
NetMatch: a Cytoscape plugin for searching biological networks.
910-912
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
- Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X. Shirley Liu:
Microarray blob-defect removal improves array analysis.
966-971
- Sijian Wang, Ji Zhu:
Improved centroids estimation for the nearest shrunken centroid classifier.
972-979
- Jelle J. Goeman, Peter Bühlmann:
Analyzing gene expression data in terms of gene sets: methodological issues.
980-987
- Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein:
Assessing the need for sequence-based normalization in tiling microarray experiments.
988-997
- Dorothy S. V. Wong, Frederick K. Wong, Graham R. Wood:
A multi-stage approach to clustering and imputation of gene expression profiles.
998-1005
Genetics and Population Analysis
Data and Text Mining
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Genetics and Population Analysis
- D. A. Tregouet, V. Garelle:
A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.
1038-1039
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
- Xin Zhou, David P. Tuck:
MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data.
1106-1114
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
- Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, Michael Schroeder:
Clustering by common friends finds locally significant proteins mediating modules.
1124-1131
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
- Wolfram Stacklies, Henning Redestig, Matthias Scholz, Dirk Walther, Joachim Selbig:
pcaMethods - a bioconductor package providing PCA methods for incomplete data.
1164-1167
- Diego Diez, Rebeca Alvarez, Ana Dopazo:
Codelink: an R package for analysis of GE healthcare gene expression bioarrays.
1168-1169
- Tancred Frickey, Georg Weiller:
Analyzing microarray data using CLANS.
1170-1171
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
- Jiajun Liu, Jacqueline M. Hughes-Oliver, J. Alan Menius Jr.:
Domain-enhanced analysis of microarray data using GO annotations.
1225-1234
- Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, Yoav Gilad:
Using DNA microarrays to study gene expression in closely related species.
1235-1242
- 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
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
- Kevin Le Brigand, Pascal Barbry:
Mediante: a web-based microarray data manager.
1304-1306
- Qihui Zhu, Anyuan Guo, Ge Gao, Yingfu Zhong, Meng Xu, Minren Huang, Jingchu Luo:
DPTF: a database of poplar transcription factors.
1307-1308
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
- 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
- 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
- Ian A. Wood, Peter M. Visscher, Kerrie L. Mengersen:
Classification based upon gene expression data: bias and precision of error rates.
1363-1370
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
- 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
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
- Peicheng Du, Rajagopalan Sudha, Michael B. Prystowsky, Ruth Hogue Angeletti:
Data reduction of isotope-resolved LC-MS spectra.
1394-1400
- 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
- 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
Databases and Ontologies
Applications Notes:
Genome Analysis
Sequence Analysis
- Reed A. Cartwright:
Ngila: global pairwise alignments with logarithmic and affine gap costs.
1427-1428
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
- 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
- Yuanyuan Xiao, Mark R. Segal, Yee Hwa Yang, Ru-Fang Yeh:
A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays.
1459-1467
- Avril Coghlan, Richard Durbin:
Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.
1468-1475
Sequence Anlysis
Gene Expression
- Lifeng Wang, Guang Chen, Hongzhe Li:
Group SCAD regression analysis for microarray time course gene expression data.
1486-1494
- Hyunsoo Kim, Haesun Park:
Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis.
1495-1502
- D. Huang, Tommy W. S. Chow:
Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer.
1503-1510
- Wai-Ki Ching, Shuqin Zhang, Michael K. Ng, Tatsuya Akutsu:
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks.
1511-1518
Genetics and Population Analysis
Systems Biology
- Zhi Wei, Hongzhe Li:
A Markov random field model for network-based analysis of genomic data.
1537-1544
Databases and Ontologies
Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Databases and Ontologies
Erratum
- Jie Zhou, Hanchuan Peng:
Automatic recognition and annotation of gene expression patterns of fly embryos.
1571-1572
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
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
- André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Pedro Alberto Morettin, Mari Cleide Sogayar, Carlos Eduardo Ferreira:
Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method.
1623-1630
- Zhen-Ping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Alignment of molecular networks by integer quadratic programming.
1631-1639
- 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
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
- Vetle I. Torvik, Neil R. Smalheiser:
A quantitative model for linking two disparate sets of articles in MEDLINE.
1658-1665
- Khuloud Jaqaman, Jonas F. Dorn, E. Marco, Peter K. Sorger, Gaudenz Danuser:
Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics.
1666-1673
Databases and Ontologies
Genome Analysis
Sequence Analysis
- Anna Gambin, Piotr Wojtalewicz:
CTX-BLAST: context sensitive version of protein BLAST.
1686-1688
- 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
- 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
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
- 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
- Anne-Laure Boulesteix:
WilcoxCV: an R package for fast variable selection in cross-validation.
1702-1704
Systems Biology
Databases and Ontologies
Volume 23,
Number 14,
15 July 2007
REVIEW:
Sequence Analysis
Sequence Analysis
