Volume 25,
Number 1,
January 2009
Discovery Note - Sequence Analysis
Original Papers
- Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones:
Slider - maximum use of probability information for alignment of short sequence reads and SNP detection.
6-13
- Anna Ritz, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael:
Discovery of phosphorylation motif mixtures in phosphoproteomics data.
14-21
- Anton V. Persikov, Robert Osada, Mona Singh:
Predicting DNA recognition by Cys2His2 zinc finger proteins.
22-29
- Jiansheng Wu, Hongde Liu, Xueye Duan, Yan Ding, Hongtao Wu, Yunfei Bai, Xiao Sun:
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.
30-35
Gene Expression
- Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, Tetsuya Yomo:
Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays.
36-41
- A. Marie Fitch, M. Beatrix Jones:
Shortest path analysis using partial correlations for classifying gene functions from gene expression data.
42-47
- Adam L. Asare, Zhong Gao, Vincent J. Carey, Richard Wang, Vicki Seyfert-Margolis:
Power enhancement via multivariate outlier testing with gene expression arrays.
48-53
Genetics and Population Analysis
- James A. Koziol, Anne C. Feng, Zhenyu Jia, Yipeng Wang, Seven Goodison, Michael McClelland, Dan Mercola:
The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis.
54-60
- Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T. C. Wong:
Conditional random pattern algorithm for LOH inference and segmentation.
61-67
- Sharlee Climer, Gerold Jäger, Alan R. Templeton, Weixiong Zhang:
How frugal is mother nature with haplotypes?
68-74
Systems Biology
- Adi L. Tarca, Sorin Draghici, Purvesh Khatri, Sonia S. Hassan, Pooja Mittal, Jung-sun Kim, Chong Jai Kim, Juan Pedro Kusanovic, Roberto Romero:
A novel signaling pathway impact analysis.
75-82
- Hao Zhang, Claus Lundegaard, Morten Nielsen:
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods.
83-89
- Ross P. Carlson:
Decomposition of complex microbial behaviors into resource-based stress responses.
90-97
- Xuebing Wu, Qifang Liu, Rui Jiang:
Align human interactome with phenome to identify causative genes and networks underlying disease families.
98-104
- Jingkai Yu, Russell L. Finley Jr.:
Combining multiple positive training sets to generate confidence scores for protein-protein interactions.
105-111
Data and Text Mining
Applications Note - Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
ISCB News
Letters to the Editor - Phylogenetics
Erratum
Volume 25,
Number 2,
January 2009
Discovery Notes - Sequence Analysis
Databases and Ontologies
Original Papers - Genome Analysis
Sequence Analysis
Phylogenetics
- Yufeng Wu:
A practical method for exact computation of subtree prune and regraft distance.
190-196
- Alex Webb, John M. Hancock, Chris C. Holmes:
Phylogenetic inference under recombination using Bayesian stochastic topology selection.
197-203
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
- F. Van Nieuwerburgh, E. Goetghebeur, M. Vandewoestyne, D. Deforce:
Impact of allelic dropout on evidential value of forensic DNA profiles using RMNE.
225-229
- S. Yilmaz, P. Jonveaux, C. Bicep, L. Pierron, Malika Smaïl-Tabbone, Marie-Dominique Devignes:
Gene-disease relationship discovery based on model-driven data integration and database view definition.
230-236
- Lina Chen, Liangcai Zhang, Yan Zhao, Liangde Xu, Yukui Shang, Qian Wang, Wan Li, Hong Wang, Xia Li:
Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways.
237-242
Systems Biology
- Kevin Y. Yip, Mark Gerstein:
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.
243-250
- Donald A. Barkauskas, Hyun Joo An, Scott R. Kronewitter, Maria Lorna de Leoz, Helen K. Chew, Ralph W. de Vere White, Gary S. Leiserowitz, Suzanne Miyamoto, Carlito B. Lebrilla, David M. Rocke:
Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data.
251-257
Data and Text Mining
- Gavin Brelstaff, Manuele Bicego, Nicola Culeddu, Matilde Chessa:
Bag of Peaks: interpretation of NMR spectrometry.
258-264
- Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed:
Sparse combinatorial inference with an application in cancer biology.
265-271
Applications Note - Genome Analysis
Sequence Analysis
Gene Expression
- Wubin Qu, Zhiyong Shen, Dongsheng Zhao, Yi Yang, Chenggang Zhang:
MFEprimer: multiple factor evaluation of the specificity of PCR primers.
276-278
- Tim F. Rayner, Faisal Ibne Rezwan, Margus Lukk, Xiangqun Zheng Bradley, Anna Farne, Ele Holloway, James Malone, Eleanor Williams, Helen E. Parkinson:
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.
279-280
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Volume 25,
Number 3,
February 2009
Discovery Note - Sequence Analysis
Original Papers
Phylogenetics
Gene Expression
- Stan Pounds, Cheng Cheng, Charles Mullighan, Susana C. Raimondi, Sheila Shurtleff, James R. Downing:
Reference alignment of SNP microarray signals for copy number analysis of tumors.
315-321
- Krzysztof Wabnik, Torgeir R. Hvidsten, Anna Kedzierska, Jelle Van Leene, Geert De Jaeger, Gerrit T. S. Beemster, Henryk Jan Komorowski, Martin T. R. Kuiper:
Gene expression trends and protein features effectively complement each other in gene function prediction.
322-330
- Kun-hong Liu, Chun-Gui Xu:
A genetic programming-based approach to the classification of multiclass microarray datasets.
331-337
Genetics and Population Analysis
Systems Biology
- Ekaterina Myasnikova, Svetlana Surkova, Lena Panok, Maria Samsonova, John Reinitz:
Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila.
346-352
- Mahesh Yaragatti, Ted Sandler, Lyle H. Ungar:
A predictive model for identifying mini-regulatory modules in the mouse genome.
353-357
- Hu Li, Choong Yong Ung, Xiao Hua Ma, Bao Wen Li, Boon Chuan Low, Zhi Wei Cao, Yu Zong Chen:
Simulation of crosstalk between small GTPase RhoA and EGFR-ERK signaling pathway via MEKK1.
358-364
- David Goldberg, Marshall W. Bern, Simon J. North, Stuart M. Haslam, Anne Dell:
Glycan family analysis for deducing N-glycan topology from single MS.
365-371
- Hailiang Huang, Joel S. Bader:
Precision and recall estimates for two-hybrid screens.
372-378
Data and Text Mining
- Anthony Y. C. Kuk, Han Zhang, Yaning Yang:
Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium.
379-386
- Je-Gun Joung, Zhangjun Fei:
Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model.
387-393
- Yusuke Miyao, Kenji Sagae, Rune Sætre, Takuya Matsuzaki, Jun-ichi Tsujii:
Evaluating contributions of natural language parsers to protein-protein interaction extraction.
394-400
- Age K. Smilde, Henk A. L. Kiers, S. Bijlsma, C. M. Rubingh, M. J. van Erk:
Matrix correlations for high-dimensional data: the modified RV-coefficient.
401-405
Databases and Ontologies
Applications Note - Structural Bioinformatics
Gene Expression
Systems Biology
Volume 25,
Number 4,
February 2009
Review - Data and Text Mining
Editorial
Discovery Note - Gene Expression
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Applications Note - Genome Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
- Daniel M. Gatti, Myroslav Sypa, Ivan Rusyn, Fred A. Wright, William T. Barry:
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy.
541-542
- Ryosuke R. Ishiwata, Masaki S. Morioka, Soichi Ogishima, Hiroshi Tanaka:
BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network.
543-544
- Qihao Qi, Yingdong Zhao, Ming-Chung Li, Richard Simon:
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools.
545-547
- E. Ryder, H. Spriggs, E. Drummond, D. St Johnston, S. Russell:
The Flannotator - a gene and protein expression annotation tool for Drosophila melanogaster.
548-549
- Evert-Jan Blom, Jos B. T. M. Roerdink, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data.
550-551
Genetics and Population Analysis
Databases and Ontologies
Volume 25,
Number 5,
March 2009
Discovery Note - Sequence Analysis
Original Papers - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao:
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.
606-614
- Izhar Wallach, Ryan H. Lilien:
The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding.
615-620
- Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David Hall, Melissa R. Landon, Carla Mattos, Sandor Vajda:
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.
621-627
Structural Bioinformatics and Data Mining
Gene Expression
- Satwik Rajaram:
A novel meta-analysis method exploiting consistency of high-throughput experiments.
636-642
Data and Text Mining
- Theodore Alexandrov, Jens Decker, Bart J. A. Mertens, André M. Deelder, Rob A. E. M. Tollenaar, Peter Maass, Herbert Thiele:
Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation.
643-649
- Li Zhang, Qingyi Wei, Li Mao, Wenbin Liu, Gordon B. Mills, Kevin R. Coombes:
Serial dilution curve: a new method for analysis of reverse phase protein array data.
650-654
Databases and Ontologies
Applications Note - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- Nils Gehlenborg, Wei Yan, Inyoul Y. Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, Leroy Hood:
Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.
682-683
- Alexander Lachmann, Avi Ma'ayan:
KEA: kinase enrichment analysis.
684-686
- Sebastian Mirschel, Katrin Steinmetz, Michael Rempel, Martin Ginkel, Ernst Dieter Gilles:
PROMOT: modular modeling for systems biology.
687-689
Databases and Ontologies
Letter to the Editor - Gene Expression
Volume 25,
Number 6,
March 2009
Editorial
Original Papers - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Jinyan Li, Qian Liu:
'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces.
743-750
Gene Expression
- Yang Xie, Xinlei Wang, Michael Story:
Statistical methods of background correction for Illumina BeadArray data.
751-757
- Katharina Podwojski, Arno Fritsch, Daniel C. Chamrad, Wolfgang Paul, Barbara Sitek, Kai Stühler, Petra Mutzel, Christian Stephan, Helmut E. Meyer, Wolfgang Urfer, Katja Ickstadt, Jörg Rahnenführer:
Retention time alignment algorithms for LC/MS data must consider non-linear shifts.
758-764
- Davis J. McCarthy, Gordon K. Smyth:
Testing significance relative to a fold-change threshold is a TREAT.
765-771
Systems Biology
- David R. Bickel, Zahra Montazeri, Pei-Chun Hsieh, Mary Beatty, Shai J. Lawit, Nicholas J. Bate:
Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative.
772-779
- Peter Gennemark, Dag Wedelin:
Benchmarks for identification of ordinary differential equations from time series data.
780-786
- V. V. Mihaleva, H. A. Verhoeven, R. C. H. de Vos, R. D. Hall, Roeland C. H. J. van Ham:
Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index.
787-794
- Zhirong Sun, Jie Luo, Yun Zhou, Junjie Luo, Ke Liu, Wenting Li:
Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework.
795-800
- Brian C. Haynes, Michael R. Brent:
Benchmarking regulatory network reconstruction with GRENDEL.
801-807
Data and Text Mining
Applications Note - Sequence Analysis
Gene Expression
Systems Biology
- Sabine Dietmann, Elisabeth Georgii, Alexey V. Antonov, Koji Tsuda, Hans-Werner Mewes:
The DICS repository: module-assisted analysis of disease-related gene lists.
830-831
- X. Wu, M. Watson:
CORNA: testing gene lists for regulation by microRNAs.
832-833
- Armando Reyes-Palomares, Raúl Montañez, Alejando Real-Chicharro, Othmane Chniber, Amine Kerzazi, Ismael Navas Delgado, Miguel Angel Medina, José Francisco Aldana Montes, Francisca Sánchez-Jiménez:
Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling.
834-835
- J. Vanlier, F. Wu, Feng Qi, K. C. Vinnakota, Yu Han, Ranjan K. Dash, F. Yang, Daniel A. Beard:
BISEN: Biochemical Simulation Environment.
836-837
Data and Text Mining
Volume 25,
Number 7,
April 2009
Discovery Note - Genome Analysis
Original Papers
- Kuo-Ho Yen, Chung-Liang Ho, Chiang Lee:
The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding.
845-852
- Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, Yasubumi Sakakibara:
Accurate identification of orthologous segments among multiple genomes.
853-860
- Henrik Bengtsson, Amrita Ray, Paul T. Spellman, Terence P. Speed:
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.
861-867
- Chen Yanover, Mona Singh, Elena Zaslavsky:
M are better than one: an ensemble-based motif finder and its application to regulatory element prediction.
868-874
Gene Expression
Systems Biology
Data and Text Mining
- Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda:
Enumeration of condition-dependent dense modules in protein interaction networks.
933-940
- M. Netzer, G. Millonig, Melanie Osl, Bernhard Pfeifer, S. Praun, J. Villinger, W. Vogel, Christian Baumgartner:
A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry.
941-947
Structural Bioinformatics
Applications Note - Genome Analysis
- Touati Benoukraf, Pierre Cauchy, Romain Fenouil, Adrien Jeanniard, Frederic Koch, Sébastien Jaeger, Denis Thieffry, Jean Imbert, Jean-Christophe Andrau, Salvatore Spicuglia, Pierre Ferrier:
CoCAS: a ChIP-on-chip analysis suite.
954-955
- Kashi Vishwanath Revanna, Vivek Krishnakumar, Qunfeng Dong:
A web-based software system for dynamic gene cluster comparison across multiple genomes.
956-957
- Masumi Itoh, Hidemi Watanabe:
CGAS: comparative genomic analysis server.
958-959
- Andrés Esteban-Marcos, Aaron E. Darling, Mark A. Ragan:
Seevolution: visualizing chromosome evolution.
960-961
- Andrew C. Stewart, Brian Osborne, Timothy D. Read:
DIYA: a bacterial annotation pipeline for any genomics lab.
962-963
- Lukas Käll, John D. Storey, William Stafford Noble:
QVALITY: non-parametric estimation of q-values and posterior error probabilities.
964-966
Sequence Analysis
Phylogenetics
Data and Text Mining
Databases and Ontologies
Volume 25,
Number 8,
April 2009
Original Papers - Genome Analysis
Structural Bioinformatics
Gene Expression
- Claudia Hundertmark, R. Fischer, T. Reinl, S. May, Frank Klawonn, Lothar Jänsch:
MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics.
1004-1011
- Trevis M. Alleyne, Lourdes Peña Castillo, Gwenael Badis, Shaheynoor Talukder, Michael F. Berger, Andrew R. Gehrke, Anthony A. Philippakis, Martha L. Bulyk, Quaid Morris, Timothy R. Hughes:
Predicting the binding preference of transcription factors to individual DNA k-mers.
1012-1018
- Ruth Heller, Elisabetta Manduchi, Gregory R. Grant, Warren J. Ewens:
A flexible two-stage procedure for identifying gene sets that are differentially expressed.
1019-1025
- Hui Jiang, Wing Hung Wong:
Statistical inferences for isoform expression in RNA-Seq.
1026-1032
Genetics and Population Analysis
- Runqing Yang, Xin Wang, Jian Li, Hongwen Deng:
Bayesian robust analysis for genetic architecture of quantitative traits.
1033-1039
- Mattia C. F. Prosperi, Roberto D'Autilia, Francesca Incardona, Andrea De Luca, Maurizio Zazzi, Giovanni Ulivi:
Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization.
1040-1047
- Phil Hyoun Lee, Hagit Shatkay:
An integrative scoring system for ranking SNPs by their potential deleterious effects.
1048-1055
- Richard Bourgon, Eugenio Mancera, Alessandro Brozzi, Lars M. Steinmetz, Wolfgang Huber:
Array-based genotyping in S.cerevisiae using semi-supervised clustering.
1056-1062
Systems Biology
Data and Text Mining
Applications Note - Gene Expression
- Jan Gertheiss, Gerhard Tutz:
Supervised feature selection in mass spectrometry-based proteomic profiling by blockwise boosting.
1076-1077
Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
Volume 25,
Number 9,
May 2009
Original Papers - Genome Analysis
Sequence Analysis
- Cole Trapnell, Lior Pachter, Steven L. Salzberg:
TopHat: discovering splice junctions with RNA-Seq.
1105-1111
- Zhu-Jin Zhang:
DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences.
1112-1117
- Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert:
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
1118-1124
- Cristina Marino Buslje, Javier Santos, Jose M. Delfino, Morten Nielsen:
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information.
1125-1131
Structural Bioinformatics
Gene Expression
Systems Biology
- Igor Ulitsky, Ron Shamir:
Identifying functional modules using expression profiles and confidence-scored protein interactions.
1158-1164
Data and Text Mining
Applications Note - Genome Analysis
Sequence Analysis
- Andrew M. Waterhouse, James B. Procter, David M. A. Martin, Michele E. Clamp, Geoffrey J. Barton:
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench.
1189-1191
- David Talavera, Roman A. Laskowski, Janet M. Thornton:
WSsas: a web service for the annotation of functional residues through structural homologues.
1192-1194
- Yongjian Guo, Jose M. C. Ribeiro, Jennifer M. Anderson, Stephan Bour:
dCAS: a desktop application for cDNA sequence annotation.
1195-1196
- Robert J. Gifford, Tommy F. Liu, Soo-Yon Rhee, Mark Kiuchi, Stephane Hue, Deenan Pillay, Robert W. Shafer:
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance.
1197-1198
Phylogenetics
Structural Bioinformatics
Gene Expression
- Jeffrey T. Leek:
The tspair package for finding top scoring pair classifiers in R.
1203-1204
Systems Biology
Databases and Ontologies
Corrigendum
Volume 25,
Number 10,
May 2009
Discovery Note - Genome Analysis
Sequence Analysis
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
- Mingyue Zheng, Xiaomin Luo, Qiancheng Shen, Yong Wang, Yun Du, Weiliang Zhu, Hualiang Jiang:
Site of metabolism prediction for six biotransformations mediated by cytochromes P450.
1251-1258
- Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin:
Structure similarity measure with penalty for close non-equivalent residues.
1259-1263
- Patrik Björkholm, Pawel Daniluk, Andriy Kryshtafovych, Krzysztof Fidelis, Robin Andersson, Torgeir R. Hvidsten:
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.
1264-1270
- Julia Handl, Joshua D. Knowles, Simon C. Lovell:
Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction.
1271-1279
Gene Expression
Genetics and Population Analysis
- Alun Thomas:
A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation.
1287-1292
Systems Biology
- Hao Zhang, Ole Lund, Morten Nielsen:
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.
1293-1299
- Paul D. W. Kirk, Michael P. H. Stumpf:
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.
1300-1306
Data and Text Mining
Databases and Ontologies
- Hagen Blankenburg, Robert D. Finn, Andreas Prlic, Andrew M. Jenkinson, Fidel Ramírez, Dorothea Emig, Sven-Eric Schelhorn, Joachim Büch, Thomas Lengauer, Mario Albrecht:
DASMI: exchanging, annotating and assessing molecular interaction data.
1321-1328
Applications Note - Sequence Analysis
- György Abrusán, Norbert Grundmann, Luc DeMester, Wojciech Makalowski:
TEclass - a tool for automated classification of unknown eukaryotic transposable elements.
1329-1330
- Micah Hamady, Stephanie A. Wilson, Jesse Zaneveld, Noboru Sueoka, Rob Knight:
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.
1331-1332
- David N. Messina, Erik L. L. Sonnhammer:
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.
1333-1334
- Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy:
Infernal 1.0: inference of RNA alignments.
1335-1337
- Ying Huang, Paul Gilna, Weizhong Li:
Identification of ribosomal RNA genes in metagenomic fragments.
1338-1340
Data and Text Mining
Volume 25,
Number 11,
June 2009
Discovery Note - Sequence Analysis
Original Papers - Genome Analysis
- Triinu Koressaar, Kai Jõers, Maido Remm:
Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms.
1349-1355
Sequence Analysis
Phylogenetics
Genetics and Population Analysis
Systems Biology
Data and Text Mining
- Smriti R. Ramakrishnan, Christine Vogel, John T. Prince, Rong Wang, Zhihua Li, Luiz O. Penalva, Margaret Myers, Edward M. Marcotte, Daniel P. Miranker:
Integrating shotgun proteomics and mRNA expression data to improve protein identification.
1397-1403
- Irena Spasic, Evangelos Simeonidis, Hanan L. Messiha, Norman W. Paton, Douglas B. Kell:
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways.
1404-1411
- Dolf Trieschnigg, Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel Kraaij, Dietrich Rebholz-Schuhmann:
MeSH Up: effective MeSH text classification for improved document retrieval.
1412-1418
Applications Note - Genome Analysis
Sequence Analysis
- Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon:
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
1422-1423
- You Jung Kim, Nikhil Teletia, Victor Ruotti, Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson, Jignesh M. Patel:
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
1424-1425
Structural Bioinformatics
- R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin, David M. Kristensen, Olivier Lichtarge:
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.
1426-1427
- Massimo Sandal, Fabrizio Benedetti, Marco Brucale, Alberto Gomez-Casado, Bruno Samorì:
Hooke: an open software platform for force spectroscopy.
1428-1430
- Michael Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin:
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.
1431-1432
- Xuefeng Xia, Song Zhang, Yu Su, Zhirong Sun:
MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields.
1433-1434
- Yanga Byun, Kyungsook Han:
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots.
1435-1437
Gene Expression
Genetics and Population Analysis
- Ambra Giovannini, Gaetano Zanghirati, Mark A. Beaumont, Lounès Chikhi, Guido Barbujani:
A novel parallel approach to the likelihood-based estimation of admixture in population genetics.
1440-1441
- Xavier Didelot, Daniel Lawson, Daniel Falush:
SimMLST: simulation of multi-locus sequence typing data under a neutral model.
1442-1444
- John Watkinson, Dimitris Anastassiou:
Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype.
1445-1446
- Vincent J. Carey, Adam R. Davis, Michael F. Lawrence, Robert Gentleman, Benjamin A. Raby:
Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.
1447-1448
- Miao-Xin Li, Lin Jiang, Patrick Yu-Ping Kao, Pak Chung Sham, You-Qiang Song:
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis.
1449-1450
- P. Librado, J. Rozas:
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.
1451-1452
Systems Biology
- Frédéric Y. Bois:
GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models.
1453-1454
- Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell:
SBML2LATEX: Conversion of SBML files into human-readable reports.
1455-1456
- Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek:
GetBonNie for building, analyzing and sharing rule-based models.
1457-1460
- Xuefeng Bruce Ling, Harvey Cohen, Joseph Jin, Irwin Lau, James Schilling:
FDR made easy in differential feature discovery and correlation analyses.
1461-1462
- Stephan Preibisch, Stephan Saalfeld, Pavel Tomancak:
Globally optimal stitching of tiled 3D microscopic image acquisitions.
1463-1465
- Giorgio F. Gilestro, Chiara Cirelli:
pySolo: a complete suite for sleep analysis in Drosophila.
1466-1467
- Mauro A. A. Castro, José L. Rybarczyk Filho, Rodrigo J. S. Dalmolin, Marialva Sinigaglia, José C. F. Moreira, José C. M. Mombach, Rita M. C. de Almeida:
ViaComplex: software for landscape analysis of gene expression networks in genomic context.
1468-1469
Data and Text Mining
Erratum
Volume 25,
Number 12,
June 2009
ISMB/ECCB 2009 Conference Proceedings,
June 27 TO July 2,
2009,
Stockholm,
Sweden - Editorial
Original Papers
- Ivan G. Costa, Alexander Schönhuth, Christoph Hafemeister, Alexander Schliep:
Constrained mixture estimation for analysis and robust classification of clinical time series.
- Yang Huang, Stefan Wuchty, Michael T. Ferdig, Teresa M. Przytycka:
Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum.
- Marc A. Schaub, Irene M. Kaplow, Marina Sirota, Chuong B. Do, Atul J. Butte, Serafim Batzoglou:
A Classifier-based approach to identify genetic similarities between diseases.
- Sohrab P. Shah, K-John Cheung Jr., Nathalie A. Johnson, Guillaume Alain, Randy D. Gascoyne, Douglas E. Horsman, Raymond T. Ng, Kevin P. Murphy:
Model-based clustering of array CGH data.
- Tal Vider-Shalit, Ronit Sarid, Kobi Maman, Lea Tsaban, Ran Levi, Yoram Louzoun:
Viruses selectively mutate their CD8+ T-cell epitopes - a large-scale immunomic analysis.
Comparative genomics
Databases and Ontologies
- Pan Du, Gang Feng, Jared Flatow, Jie Song, Michelle Holko, Warren A. Kibbe, Simon M. Lin:
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.
- Stefan Schulz, Elena Beisswanger, László van den Hoek, Olivier Bodenreider, Erik M. van Mulligen:
Alignment of the UMLS semantic network with BioTop: methodology and assessment.
- Karin Verspoor, Daniel Dvorkin, K. Bretonnel Cohen, Lawrence Hunter:
Ontology quality assurance through analysis of term transformations.
Evolution and Phylogeny
Gene Regulation and transcriptomics
- Abhishek Garg, Kartik Mohanram, Alessandro Di Cara, Giovanni De Micheli, Ioannis Xenarios:
Modeling stochasticity and robustness in gene regulatory networks.
- Aurelie C. Lozano, Naoki Abe, Yan Liu, Saharon Rosset:
Grouped graphical Granger modeling for gene expression regulatory networks discovery.
- Adam A. Smith, Aaron Vollrath, Christopher A. Bradfield, Mark Craven:
Clustered alignments of gene-expression time series data.
- Le Song, Mladen Kolar, Eric P. Xing:
KELLER: estimating time-varying interactions between genes.
- Duygu Ucar, Andreas Beyer, Srinivasan Parthasarathy, Christopher T. Workman:
Predicting functionality of protein-DNA interactions by integrating diverse evidence.
Other Bioinformatics Applications and Methods
- José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski:
Probabilistic retrieval and visualization of biologically relevant microarray experiments.
- Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann:
Proteome coverage prediction with infinite Markov models.
- Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich:
Fewer permutations, more accurate P-values.
- Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
A general computational method for robustness analysis with applications to synthetic gene networks.
- Yoshihiro Yamanishi, Masahiro Hattori, Masaaki Kotera, Susumu Goto, Minoru Kanehisa:
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
Population genomics
- Anand Bhaskar, Yun S. Song:
Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models.
- Dan Geiger, Christopher Meek, Ydo Wexler:
Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space.
- Seyoung Kim, Kyung-Ah Sohn, Eric P. Xing:
A multivariate regression approach to association analysis of a quantitative trait network.
- Bogdan Pasaniuc, Sriram Sankararaman, Gad Kimmel, Eran Halperin:
Inference of locus-specific ancestry in closely related populations.
- Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael:
A geometric approach for classification and comparison of structural variants.
- Junming Yin, Michael I. Jordan, Yun S. Song:
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.
Protein Interactions and Molecular Networks
- Xin Guo, Alexander J. Hartemink:
Domain-oriented edge-based alignment of protein interaction networks.
- Shira Mintz-Oron, Asaph Aharoni, Eytan Ruppin, Tomer Shlomi:
Network-based prediction of metabolic enzymes' subcellular localization.
- Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, Bonnie Berger:
IsoRankN: spectral methods for global alignment of multiple protein networks.
- Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert:
Global alignment of protein-protein interaction networks by graph matching methods.
Protein Structure and Function
- Babak Alipanahi, Xin Gao, Emre Karakoç, Logan Donaldson, Ming Li:
PICKY: a novel SVD-based NMR spectra peak picking method.
- Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu:
A framework to refine particle clusters produced by EMAN.
- Firas Khatib, Carol A. Rohl, Kevin Karplus:
Pokefind: a novel topological filter for use with protein structure prediction.
- Luca Marsella, Francesco Sirocco, Antonio Trovato, Flavio Seno, Silvio C. E. Tosatto:
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform.
- Izhar Wallach, Ryan H. Lilien:
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation.
