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Bioinformatics, Volume 24
Volume 24, Number 1, 1 January 2008
- Christoph Bock
, Thomas Lengauer:
Computational epigenetics. 1-10
- Michael L. Tress
, Jan-Jaap Wesselink, Adam Frankish
, Gonzalo López
, Nick Goldman
, Ari Löytynoja
, Tim Massingham, Fabio Pardi, Simon Whelan, Jennifer L. Harrow
, Alfonso Valencia:
Determination and validation of principal gene products. 11-17
- Kai Ye
, K. Anton Feenstra
, Jaap Heringa, Adriaan P. IJzerman
, Elena Marchiori:
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. 18-25 - Aalt D. J. van Dijk, Cajo J. F. ter Braak
, Richard G. H. Immink
, Gerco C. Angenent, Roeland C. H. J. van Ham:
Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control. 26-33 - Koen Deforche, Ricardo Camacho
, Kristel Van Laethem
, Philippe Lemey, Andrew Rambaut
, Yves Moreau
, Anne-Mieke Vandamme
:
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. 34-41 - Aleksey V. Zimin, Douglas R. Smith, Granger G. Sutton, James A. Yorke:
Assembly reconciliation. 42-45 - Kuo-ching Liang, Xiaodong Wang, Dimitris Anastassiou:
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery. 46-55
- Nicolas Rodrigue, Hervé Philippe, Nicolas Lartillot:
Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models. 56-62
- Dante Mantini
, Francesca Petrucci, Piero Del Boccio
, Damiana Pieragostino
, Marta Di Nicola
, Alessandra Lugaresi
, Giorgio Federici, Paolo Sacchetta, Carmine Di Ilio, Andrea Urbani:
Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra. 63-70
- Ryan M. Kelley, Hoda Feizi, Trey Ideker
:
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. 71-77 - Manuela Hummel, Reinhard Meister, Ulrich Mansmann:
GlobalANCOVA: exploration and assessment of gene group effects. 78-85
- Guohui Lin, Zhanyong Wang, Lusheng Wang
, Yu-Lung Lau, Wanling Yang:
Identification of linked regions using high-density SNP genotype data in linkage analysis. 86-93
- Meng Wang, Xiaobo Zhou, Fuhai Li, Jeremy F. Huckins
, Randall W. King, Stephen T. C. Wong:
Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy. 94-101 - Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng
, Haixu Tang, Zhiyin Xun, Rong Zeng, Predrag Radivojac:
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. 102-109
- Michal Draminski
, Alvaro Rada-Iglesias
, Stefan Enroth
, Claes Wadelius, Jacek Koronacki
, Henryk Jan Komorowski
:
Monte Carlo feature selection for supervised classification. 110-117 - Seonho Kim, Juntae Yoon, Jihoon Yang:
Kernel approaches for genic interaction extraction. 118-126
- Cedric Simillion
, Koen Janssens, Lieven Sterck
, Yves Van de Peer
:
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. 127-128
- Luke J. Harmon, Jason T. Weir, Chad D. Brock, Richard E. Glor
, Wendell Challenger:
GEIGER: investigating evolutionary radiations. 129-131
- James Long, Mitchell Roth:
Synthetic microarray data generation with RANGE and NEMO. 132-134 - Nicola Lama, Mark A. Girolami
:
vbmp: Variational Bayesian Multinomial Probit Regression for multi-class classification in R. 135-136 - Xiaojiang Xu
, Yingdong Zhao, Richard M. Simon:
Gene Set Expression Comparison kit for BRB-ArrayTools. 137-139
- Chun Li
, Mingyao Li:
GWAsimulator: a rapid whole-genome simulation program. 140-142
- Fabien Jourdan
, Rainer Breitling
, Michael P. Barrett, David R. Gilbert:
MetaNetter: inference and visualization of high-resolution metabolomic networks. 143-145
- Daniel F. Schwarz, Oliver Hädicke, Jeanette Erdmann
, Andreas Ziegler
, Daniel Bayer, Steffen Möller
:
SNPtoGO: characterizing SNPs by enriched GO terms. 146-148
- Peng Liu, J. T. Gene Hwang:
Gene expression: Quick calculation for sample size while controlling false discovery rate with application to microarray analysis. 149
Volume 24, Number 2, 15 January 2008
- Athanasia C. Tzika
, Raphaël Helaers
, Yves Van de Peer
, Michel C. Milinkovitch
:
MANTIS: a phylogenetic framework for multi-species genome comparisons. 151-157
- Jana Hertel
, Ivo L. Hofacker
, Peter F. Stadler
:
SnoReport: computational identification of snoRNAs with unknown targets. 158-164 - Xiaowo Wang
, Jin Gu
, Michael Q. Zhang, Yanda Li:
Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. 165-171 - Dean Laslett, Björn Canbäck:
ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. 172-175
- Anagha Joshi, Yves Van de Peer
, Tom Michoel
:
Analysis of a Gibbs sampler method for model-based clustering of gene expression data. 176-183 - Jaehee Kim, Haseong Kim:
Clustering of change patterns using Fourier coefficients. 184-191 - Dan Nettleton
, Justin Recknor, James M. Reecy
:
Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis. 192-201
- Changyu Shen, Zhiping Wang, Ganesh Shankar, Xiang Zhang, Lang Li:
A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. 202-208 - Simon V. Hardy
, Pierre N. Robillard:
Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways. 209-217 - Denise Scholtens, Tony Chiang, Wolfgang Huber
, Robert Gentleman:
Estimating node degree in bait-prey graphs. 218-224 - Jean-Loup Faulon
, Milind Misra, Shawn Martin, Ken Sale, Rajat Sapra:
Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. 225-233
- Hanchuan Peng, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers:
Straightening Caenorhabditis elegans images. 234-242 - Mounir Errami, Justin M. Hicks, Wayne G. Fisher, David Trusty, Jonathan D. Wren
, Tara C. Long, Harold R. Garner:
Déjà vu - A study of duplicate citations in Medline. 243-249 - Ichigaku Takigawa
, Hiroshi Mamitsuka
:
Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis. 250-257 - Giuseppe Jurman
, Stefano Merler
, Annalisa Barla
, Silvano Paoli, Antonio Galea, Cesare Furlanello
:
Algebraic stability indicators for ranked lists in molecular profiling. 258-264
- Da Yang
, Yanhui Li, Hui Xiao, Qing Liu, Min Zhang, Jing Zhu, Wencai Ma, Chen Yao, Jing Wang, Dong Wang, Zheng Guo, Baofeng Yang:
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. 265-271
- Annamária F. Ángyán, András Perczel, Sándor Pongor, Zoltán Gáspári:
Fast protein fold estimation from NMR-derived distance restraints. 272-275
- Wolfgang Raffelsberger, Yannick Krause, Luc Moulinier, David Kieffer, Anne-Laure Morand, Laurent Brino
, Olivier Poch:
RReportGenerator: automatic reports from routine statistical analysis using R. 276-278
- Christian Fuchsberger
, Mario Falchi
, Lukas Forer
, Peter P. Pramstaller:
PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees. 279-281
- Yassen Assenov, Fidel Ramírez, Sven-Eric Schelhorn, Thomas Lengauer, Mario Albrecht:
Computing topological parameters of biological networks. 282-284 - Thomas W. Evans, Colin S. Gillespie
, Darren J. Wilkinson
:
The SBML discrete stochastic models test suite. 285-286 - Peter Li
, Tom Oinn, Stian Soiland
, Douglas B. Kell
:
Automated manipulation of systems biology models using libSBML within Taverna workflows. 287-289 - Kevin Y. Yip
, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein:
An integrated system for studying residue coevolution in proteins. 290-292 - Sema Kachalo, Ranran Zhang, Eduardo D. Sontag, Réka Albert, Bhaskar DasGupta:
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks. 293-295
- Dietrich Rebholz-Schuhmann, Miguel Arregui, Sylvain Gaudan, Harald Kirsch, Antonio Jimeno-Yepes
:
Text processing through Web services: calling Whatizit. 296-298
- Unitsa Sangket, Amornrat Phongdara, Wilaiwan Chotigeat, Darran Nathan, Woo-Yeon Kim, Jong Bhak, Chumpol Ngamphiw, Sissades Tongsima
, Asif M. Khan
, Honghuang Lin
, Tin Wee Tan:
Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries. 299-301
Volume 24, Number 3, 1 February 2008
- Shuji Fujita, Hideo Iba:
Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates. 303-308
- Roger Pique-Regi
, Jordi Monso-Varona, Antonio Ortega, Robert C. Seeger, Timothy Triche, Shahab Asgharzadeh:
Sparse representation and Bayesian detection of genome copy number alterations from microarray data. 309-318
- Gabriel Moreno-Hagelsieb
, Kristen Latimer:
Choosing BLAST options for better detection of orthologs as reciprocal best hits. 319-324 - Xiaowei Wang, Issam M. El Naqa
:
Prediction of both conserved and nonconserved microRNA targets in animals. 325-332 - S. D. Dunn, Lindi M. Wahl
, Gregory B. Gloor
:
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. 333-340 - Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee:
TFBS identification based on genetic algorithm with combined representations and adaptive post-processing. 341-349 - Utz J. Pape, Sven Rahmann
, Martin Vingron:
Natural similarity measures between position frequency matrices with an application to clustering. 350-357 - Laurent Jacob, Jean-Philippe Vert
:
Efficient peptide-MHC-I binding prediction for alleles with few known binders. 358-366
- Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
Rfold: an exact algorithm for computing local base pairing probabilities. 367-373
- Fangxin Hong, Rainer Breitling
:
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. 374-382
- F. F. Vale, Pedro Encarnação
, J. M. B. Vítor:
A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case. 383-388
- Anatoly L. Mayburd, Inna Golovchikova, James L. Mulshine
:
Successful anti-cancer drug targets able to pass FDA review demonstrate the identifiable signature distinct from the signatures of random genes and initially proposed targets. 389-395 - David J. Reiss, Marc T. Facciotti, Nitin S. Baliga:
Model-based deconvolution of genome-wide DNA binding. 396-403 - Peng Wei
, Wei Pan:
Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model. 404-411
- Li Wang, Ji Zhu, Hui Zou
:
Hybrid huberized support vector machines for microarray classification and gene selection. 412-419
- Tae-Min Kim
, Yu-Chae Jung, Mun-Gan Rhyu, Myeong Ho Jung, Yeun-Jun Chung:
GEAR: genomic enrichment analysis of regional DNA copy number changes. 420-421 - Lukas A. Mueller, Adri A. Mills, Beth Skwarecki, Robert M. Buels, Naama Menda, Steven D. Tanksley:
The SGN comparative map viewer. 422-423 - Jacques Oberto:
BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence. 424-425
- Manfred J. Sippl, Markus Wiederstein
:
A note on difficult structure alignment problems. 426-427
- Daniele Masotti, Christine Nardini
, Simona Rossi, Elena Bonora
, Giovanni Romeo, Stefano Volinia
, Luca Benini
:
TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders. 428-429 - Paolo Magni
, Fulvia Ferrazzi
, Lucia Sacchi
, Riccardo Bellazzi
:
TimeClust: a clustering tool for gene expression time series. 430-432 - Rudi Alberts, Gonzalo Vera
, Ritsert C. Jansen:
affyGG: computational protocols for genetical genomics with Affymetrix arrays. 433-434
- Xiaoquan Wen
, Dan L. Nicolae
:
Association studies for untyped markers with TUNA. 435-437
- Tianming Liu, Jingxin Nie, Gang Li
, Lei Guo, Stephen T. C. Wong:
ZFIQ: a software package for zebrafish biology. 438-439
- Julia Stoyanovich, Itsik Pe'er:
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. 440-442 - J. Stuart Aitken, Yin Chen, Jonathan Bard:
OBO Explorer: an editor for open biomedical ontologies in OWL. 443-444 - Quentin Kaas
, Jan-C. Westermann, Reena Halai, Conan K. L. Wang, David J. Craik
:
ConoServer, a database for conopeptide sequences and structures. 445-446 - David Salgado
, Gregory Gimenez, François Coulier, Christophe Marcelle:
COMPARE, a multi-organism system for cross-species data comparison and transfer of information. 447-449 - Gil Alterovitz, Adnaan Jiwaji, Marco Ramoni:
Automated programming for bioinformatics algorithm deployment. 450-451
Volume 24, Number 4, 15 February 2008
- Sushama Michael
, Gilles Travé, Chenna Ramu, Claudia Chica
, Toby J. Gibson
:
Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation. 453-457 - Saraswathi Abhiman, Lakshminarayan M. Iyer, L. Aravind
:
BEN: a novel domain in chromatin factors and DNA viral proteins. 458-461
- James Robert White, Michael Roberts, James A. Yorke, Mihai Pop
:
Figaro: a novel statistical method for vector sequence removal. 462-467
- Xuehui Li, Tamer Kahveci, A. Mark Settles
:
A novel genome-scale repeat finder geared towards transposons. 468-476 - Ido Ginodi, Tal Vider-Shalit, Lea Tsaban, Yoram Louzoun
:
Precise score for the prediction of peptides cleaved by the proteasome. 477-483 - Sumedha Gunewardena, Zhaolei Zhang:
A hybrid model for robust detection of transcription factor binding sites. 484-491 - Walter Pirovano
, K. Anton Feenstra
, Jaap Heringa:
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. 492-497 - Rotem Rubinstein
, András Fiser:
Predicting disulfide bond connectivity in proteins by correlated mutations analysis. 498-504 - Yu-Chieh Liao
, Min-Shi Lee, Chin-Yu Ko, Chao A. Hsiung:
Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus. 505-512
- Arlo Z. Randall, Jianlin Cheng
, Michael J. Sweredoski, Pierre Baldi:
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. 513-520 - Konrad Hinsen
:
Structural flexibility in proteins: impact of the crystal environment. 521-528
- Jeffrey S. Morris, Brittan N. Clark, Howard B. Gutstein:
Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. 529-536 - Jelle J. Goeman
, Ulrich Mansmann:
Multiple testing on the directed acyclic graph of gene ontology. 537-544
- Debayan Datta
, Hongyu Zhao
:
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. 545-552 - Hao Xiong, Yoonsuck Choe:
Structural systems identification of genetic regulatory networks. 553-560 - Vasyl Pihur, Somnath Datta, Susmita Datta:
Reconstruction of genetic association networks from microarray data: a partial least squares approach. 561-568
- Yuntao Qian, Robert F. Murphy:
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. 569-576
- Niranjan Nagarajan
, Uri Keich
:
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. 577-578
- Yuri R. Bendaña, Ian H. Holmes
:
Colorstock, SScolor, Ratón: RNA alignment visualization tools. 579-580
- Johan A. A. Nylander, James C. Wilgenbusch
, Dan L. Warren
, David L. Swofford
:
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. 581-583
- Dominik Gront
, Andrzej Kolinski
:
Utility library for structural bioinformatics. 584-585 - Liam J. McGuffin
:
The ModFOLD server for the quality assessment of protein structural models. 586-587
- Priit Adler, Jüri Reimand
, Jürgen Jänes, Raivo Kolde
, Hedi Peterson
, Jaak Vilo
:
KEGGanim: pathway animations for high-throughput data. 588-590 - Sebastian Böcker
, Zsuzsanna Lipták
, Marcel Martin
, Anton Pervukhin, Henner Sudek:
DECOMP - from interpreting Mass Spectrometry peaks to solving the Money Changing Problem. 591-593
- Maxim Kalaev, Michael E. Smoot, Trey Ideker
, Roded Sharan:
NetworkBLAST: comparative analysis of protein networks. 594-596
Volume 24, Number 5, 1 March 2008
- Qian Liu, Aaron J. Mackey
, David S. Roos
, Fernando C. N. Pereira:
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction. 597-605 - Onur Sakarya, Kenneth S. Kosik, Todd H. Oakley
:
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. 606-612
- J. D. Fischer, Christian E. Mayer, Johannes Söding
:
Prediction of protein functional residues from sequence by probability density estimation. 613-620 - Igor V. Tetko
, Igor V. Rodchenkov, Mathias C. Walter
, Thomas Rattei
, Hans-Werner Mewes
:
Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information. 621-628 - Leping Li
, Robert L. Bass, Yu Liang:
fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control. 629-636 - Mario Stanke, Mark Diekhans
, Robert Baertsch
, David Haussler:
Using native and syntenically mapped cDNA alignments to improve de novo gene finding. 637-644
- Arun Siddharth Konagurthu, Peter J. Stuckey
, Arthur M. Lesk
:
Structural search and retrieval using a tableau representation of protein folding patterns. 645-651 - Julie Bernauer
, Ranjit Prasad Bahadur, Francis Rodier, Joël Janin, Anne Poupon:
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. 652-658 - Changjun Chen, Yi Xiao:
Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories. 659-665
- Yinglei Lai:
Genome-wide co-expression based prediction of differential expressions. 666-673 - Jainab Khatun, Eric Hamlett
, Morgan C. Giddings:
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. 674-681 - Laurent Bréhélin, Olivier Gascuel, Olivier Martin:
Using repeated measurements to validate hierarchical gene clusters. 682-688
- Ramazan Saeed, Charlotte M. Deane
:
An assessment of the uses of homologous interactions. 689-695 - Nicolas Thierry-Mieg
, Gilles Bailly
:
Interpool: interpreting smart-pooling results. 696-703 - Andreas Kremling, Katja Bettenbrock, Ernst Dieter Gilles:
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. 704-710
- Simon Gog, Martin Bader, Enno Ohlebusch:
GENESIS: genome evolution scenarios. 711-712
- Ruiqiang Li, Yingrui Li, Karsten Kristiansen
, Jun Wang
:
SOAP: short oligonucleotide alignment program. 713-714
- Stephen A. Smith
, Casey W. Dunn
:
Phyutility: a phyloinformatics tool for trees, alignments and molecular data. 715-716 - Jonathan D. Moore
, Robin G. Allaby:
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism. 717-718
- Peter Langfelder, Bin Zhang, Steve Horvath:
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. 719-720
- Jian Yang
, Chengcheng Hu, Han Hu
, Rongdong Yu, Zhen Xia, Xiuzi Ye, Jun Zhu:
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. 721-723 - Mario Falchi
, Christian Fuchsberger
:
Jenti: an efficient tool for mining complex inbred genealogies. 724-726
- Martijn J. Schuemie
, Jan A. Kors:
Jane: suggesting journals, finding experts. 727-728 - Giorgio Valentini
, Nicolò Cesa-Bianchi:
HCGene: a software tool to support the hierarchical classification of genes. 729-731 - Alexander Lüdemann, Katrin Strassburg, Alexander Erban, Joachim Kopka
:
TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments. 732-737
- Sorin Draghici
, Adi L. Tarca, Longfei Yu, Stephen Ethier, Roberto Romero:
KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours. 738-740
Volume 24, Number 6, 15 March 2008
- Scott Grandison, Richard J. Morris
:
Biological pathway kinetic rate constants are scale-invariant. 741-743
- Jeong-Hyeon Choi, Sun Kim, Haixu Tang, Justen Andrews, Don G. Gilbert, John Colbourne
:
A machine-learning approach to combined evidence validation of genome assemblies. 744-750 - Robin Andersson
, Carl E. G. Bruder, Arkadiusz Piotrowski
, Uwe Menzel, Helena Nord, Johanna Sandgren
, Torgeir R. Hvidsten
, Teresita Diaz de Ståhl
, Jan P. Dumanski
, Henryk Jan Komorowski
:
A segmental maximum a posteriori approach to genome-wide copy number profiling. 751-758 - Henrik Bengtsson
, Rafael A. Irizarry, Benilton S. Carvalho
, Terence P. Speed:
Estimation and assessment of raw copy numbers at the single locus level. 759-767 - Guillem Rigaill, Philippe Hupé
, Anna Almeida
, Philippe La Rosa, Jean-Philippe Meyniel
, Charles Decraene, Emmanuel Barillot
:
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays. 768-774
- Nanjiang Shu
, Tuping Zhou, Sven Hovmöller:
Prediction of zinc-binding sites in proteins from sequence. 775-782 - Anuj R. Shah, Christopher S. Oehmen, Bobbie-Jo M. Webb-Robertson
:
SVM-HUSTLE - an iterative semi-supervised machine learning approach for pairwise protein remote homology detection. 783-790 - Tak Wah Lam
, Wing-Kin Sung
, Siu-Lung Tam, Chi-Kwong Wong, Siu-Ming Yiu:
Compressed indexing and local alignment of DNA. 791-797 - Mark N. Wass
, Michael J. E. Sternberg
:
ConFunc - functional annotation in the twilight zone. 798-806 - Andreas Biegert, Johannes Söding
:
De novo identification of highly diverged protein repeats by probabilistic consistency. 807-814 - Bruce R. Southey
, Jonathan V. Sweedler
, Sandra L. Rodriguez-Zas
:
Prediction of neuropeptide cleavage sites in insects. 815-825
- Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller
:
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. 826-832
- Vladislav Vyshemirsky, Mark A. Girolami
:
Bayesian ranking of biochemical system models. 833-839 - Julio Saez-Rodriguez
, Arthur Goldsipe, Jeremy Muhlich
, Leonidas G. Alexopoulos
, Bjorn Millard, Douglas A. Lauffenburger, Peter K. Sorger
:
Flexible informatics for linking experimental data to mathematical models via DataRail. 840-847 - Henning Schmidt, Mads F. Madsen, Sune Danø, Gunnar Cedersund:
Complexity reduction of biochemical rate expressions. 848-854
- Frank M. Graziano, Samira Y. Kettoola, Judy M. Munshower, Jack T. Stapleton
, George Towfic:
Effect of spatial distribution of T-Cells and HIV load on HIV progression. 855-860
- Gavin C. Conant
, Kenneth H. Wolfe
:
GenomeVx: simple web-based creation of editable circular chromosome maps. 861-862 - Gipsi Lima-Mendez
, Jacques van Helden
, Ariane Toussaint, Raphaël Leplae:
Prophinder: a computational tool for prophage prediction in prokaryotic genomes. 863-865
- Bram Slabbinck, Peter Dawyndt
, M. Martens, Paul De Vos, Bernard De Baets
:
TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers. 866-867
- Mark Derthick:
Interactive visualization software for exploring phylogenetic trees and clades. 868-869
- Manfred J. Sippl, Stefan J. Suhrer, Markus Gruber, Markus Wiederstein
:
A discrete view on fold space. 870-871 - Manfred J. Sippl:
On distance and similarity in fold space. 872-873
- Yongsung Joo, James G. Booth, Younghwan Namkoong, George Casella:
Model-based Bayesian clustering (MBBC). 874-875
- Andrei Yu. Zinovyev
, Eric Viara, Laurence Calzone
, Emmanuel Barillot
:
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 876-877 - Deepayan Sarkar
, Nolwenn Le Meur
, Robert Gentleman:
Using flowViz to visualize flow cytometry data. 878-879 - Benjamin J. Bornstein, Sarah M. Keating
, Akiya Jouraku
, Michael Hucka
:
LibSBML: an API Library for SBML. 880-881
- HyungJun Cho
, Yang-jin Kim, Hee Jung Jung, Sang-Won Lee
, Jae Won Lee:
OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data. 882-884
- Erick Antezana
, Mikel Egaña
, Bernard De Baets
, Martin Kuiper
, Vladimir Mironov:
ONTO-PERL: An API for supporting the development and analysis of bio-ontologies. 885-887
Volume 24, Number 7, 1 April 2008
- Hyunju Lee
, Sek Won Kong
, Peter J. Park
:
Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. 889-896
- Ketil Malde:
The effect of sequence quality on sequence alignment. 897-900 - Ian M. Overton
, Gianandrea Padovani, Mark A. Girolami
, Geoffrey J. Barton
:
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. 901-907 - Kai Ye
, Gert Vriend, Adriaan P. IJzerman
:
Tracing evolutionary pressure. 908-915
- Michael Stout, Jaume Bacardit
, Jonathan D. Hirst
, Natalio Krasnogor
:
Prediction of recursive convex hull class assignments for protein residues. 916-923 - Sitao Wu, Yang Zhang
:
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. 924-931
- Osamu Hirose
, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones
, Cristin G. Print
, Satoru Miyano
:
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. 932-942 - Yuan Ji, Yiling Lu, Gordon B. Mills:
Bayesian models based on test statistics for multiple hypothesis testing problems. 943-949 - Andrew W. Dowsey
, Michael J. Dunn, Guang-Zhong Yang:
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline. 950-957 - Joshua N. Sampson, Steven G. Self:
Identifying trait clusters by linkage profiles: application in genetical genomics. 958-964
- Yu Zhang:
Tree-guided Bayesian inference of population structures. 965-971 - Shu-Yi Su, David J. Balding
, Lachlan J. M. Coin
:
Disease association tests by inferring ancestral haplotypes using a hidden markov model. 972-978
- Bing Zhang, Byung-Hoon Park, Tatiana V. Karpinets, Nagiza F. Samatova:
From pull-down data to protein interaction networks and complexes with biological relevance. 979-986 - Yung-Keun Kwon, Kwang-Hyun Cho:
Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics. 987-994
- Juby Jacob, Marcel Jentsch, Dennis Kostka, Stefan Bentink, Rainer Spang
:
Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs. 995-1001
- Norio Kobayashi, Tetsuro Toyoda:
Statistical search on the Semantic Web. 1002-1010
- Qing Xiong
, Yuhui Qiu, Weikuan Gu:
PGMapper: a web-based tool linking phenotype to genes. 1011-1013 - Weil R. Lai, Vidhu Choudhary, Peter J. Park
:
CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. 1014-1015
- David He
, John Parkinson
:
SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences. 1016-1017
- Liam J. Revell, Alexis S. Harrison:
PCCA: a program for phylogenetic canonical correlation analysis. 1018-1020
- Anoop M. Mayampurath, Navdeep Jaitly, Samuel O. Purvine
, Matthew E. Monroe, Kenneth J. Auberry, Joshua N. Adkins, Richard D. Smith
:
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. 1021-1023
- Jongsun Park
, Jaejin Park, Suwang Jang, Seryun Kim, Sunghyung Kong, Jaeyoung Choi
, Kyohun Ahn, Juhyeon Kim, Seungmin Lee, Sunggon Kim, Bongsoo Park, Kyongyong Jung, Soonok Kim, Seogchan Kang
, Yong-Hwan Lee:
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. 1024-1025 - Bongshin Lee, Kristy Brown
, Yetrib Hathout, Jinwook Seo:
GOTreePlus: an interactive gene ontology browser. 1026-1028
- Radhakrishnan Nagarajan, Meenakshi Upreti:
Comment on causality and pathway search in microarray time series experiment. 1029-1032 - Nitai D. Mukhopadhyay, Snigdhansu Chatterjee
:
Reply to "Comment on causality and pathway search in microarray time series experiment". 1033
Volume 24, Number 8, 15 April 2008
- Gennady Denisov, Brian Walenz, Aaron L. Halpern, Jason R. Miller
, Nelson Axelrod, Samuel Levy, Granger G. Sutton:
Consensus generation and variant detection by Celera Assembler. 1035-1040 - Jan Mrázek, Shaohua Xie, Xiangxue Guo, Anuj Srivastava:
AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes. 1041-1048
- Yossef Kliger, Eyal Gofer, Assaf Wool, Amir Toporik, Avihay Apatoff, Moshe Olshansky
:
Predicting proteolytic sites in extracellular proteins: only halfway there. 1049-1055
- Jin Xu, Xinping Cui:
Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays. 1056-1062 - Matthias E. Futschik
, Hanspeter Herzel:
Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. 1063-1069 - Peicheng Du, Gustavo Stolovitzky, Peter Horvatovich
, Rainer Bischoff
, Jihyeon Lim, Frank Suits
:
A noise model for mass spectrometry based proteomics. 1070-1077
- Guido Sanguinetti
, Josselin Noirel, Phillip C. Wright
:
MMG: a probabilistic tool to identify submodules of metabolic pathways. 1078-1084 - Pang-Kai Liu, Feng-Sheng Wang:
Inference of biochemical network models in S-system using multiobjective optimization approach. 1085-1092 - Desmond J. Higham, Marija Rasajski
, Natasa Przulj
:
Fitting a geometric graph to a protein-protein interaction network. 1093-1099
- Tony Chiang, Nianhua Li, Sandra E. Orchard
, Samuel Kerrien
, Henning Hermjakob
, Robert Gentleman, Wolfgang Huber
:
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. 1100-1101 - James A. Morris, Simon A. Gayther, Ian J. Jacobs
, Christopher Jones:
A suite of Perl modules for handling microarray data. 1102-1103
- Wolfgang Rieping, Michael Nilges
, Michael Habeck
:
ISD: a software package for Bayesian NMR structure calculation. 1104-1105
- Julie A. Douglas, Conner I. Sandefur:
PedMine - a simulated annealing algorithm to identify maximally unrelated individuals in population isolates. 1106-1108
- Gang Liu, Sriram Neelamegham
:
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks. 1109-1111 - David P. Nickerson
, Alberto Corrias
, Martin L. Buist:
Reference descriptions of cellular electrophysiology models. 1112-1114
- Arek Gladki
, Pawel Siedlecki
, Szymon Kaczanowski, Piotr Zielenkiewicz
:
e-LiSe - an online tool for finding needles in the "(Medline) haystack". 1115-1117
- Anders Lanzén
, Tom Oinn:
The Taverna Interaction Service: enabling manual interaction in workflows. 1118-1120
Volume 24, Number 9, 1 May 2008
- Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang
:
W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. 1121-1128 - Haiquan Li
, Xinbin Dai, Xuechun Zhao:
A nearest neighbor approach for automated transporter prediction and categorization from protein sequences. 1129-1136
- Victor I. Lesk, Michael J. E. Sternberg
:
3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. 1137-1144 - Aleksandar Poleksic
, Mark A. Fienup:
Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms. 1145-1153
- Andrey A. Shabalin
, Håkon Tjelmeland, Cheng Fan, Charles M. Perou
, Andrew B. Nobel:
Merging two gene-expression studies via cross-platform normalization. 1154-1160 - Reid F. Thompson
, Mark Reimers, Batbayar Khulan
, Mathieu Gissot
, Todd A. Richmond, Quan Chen, Xin Zheng, Kami Kim
, John M. Greally
:
An analytical pipeline for genomic representations used for cytosine methylation studies. 1161-1167 - Meaza Demissie, Barbara Mascialino
, Stefano Calza
, Yudi Pawitan:
Unequal group variances in microarray data analyses. 1168-1174
- Caiyan Li, Hongzhe Li:
Network-constrained regularization and variable selection for analysis of genomic data. 1175-1182 - Cheng-Long Chuang, Chih-Hung Jen, Chung-Ming Chen, Grace S. Shieh:
A pattern recognition approach to infer time-lagged genetic interactions. 1183-1190 - Bayu Jayawardhana
, Douglas B. Kell
, Magnus Rattray
:
Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo. 1191-1197
- Yuanyuan Xiao, Mark R. Segal:
Biological sequence classification utilizing positive and unlabeled data. 1198-1205
- Christian X. Weichenberger
, Piotr Byzia, Manfred J. Sippl:
Visualization of unfavorable interactions in protein folds. 1206-1207
- Federico Abascal, Pedro Carmona-Saez
, José María Carazo, Alberto D. Pascual-Montano:
ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. 1208-1209
- Angeline M. Loh, Steven Wiltshire, Jon Emery
, Kim W. Carter
, Lyle J. Palmer
:
Celestial3D: a novel method for 3D visualization of familial data. 1210-1211
- Rodrigo Santamaría
, Roberto Therón
, Luis Quintales
:
BicOverlapper: A tool for bicluster visualization. 1212-1213
- Matthew P. Campbell
, Louise Royle, Catherine M. Radcliffe, Raymond A. Dwek, Pauline M. Rudd:
GlycoBase and autoGU: tools for HPLC-based glycan analysis. 1214-1216 - Xiang Xu, Jinyu Wu, Jian Xiao
, Yi Tan, Qiyu Bao, Fangqing Zhao
, Xiaokun Li:
PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families. 1217-1220 - Hajo N. Krabbenhöft
, Steffen Möller
, Daniel Bayer:
Integrating ARC grid middleware with Taverna workflows. 1221-1222
- Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, Paul Horton:
CellMontage: Similar Expression Profile Search Server. 1223
Volume 24, Number 10, 15 May 2008
- Roger Higdon, Gerald van Belle, Eugene Kolker:
A note on the false discovery rate and inconsistent comparisons between experiments. 1225-1228
- Niranjan Nagarajan
, Timothy D. Read
, Mihai Pop
:
Scaffolding and validation of bacterial genome assemblies using optical restriction maps. 1229-1235
- Rahul Satija, Lior Pachter
, Jotun Hein:
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. 1236-1242 - Ying Liu, Eran Eyal, Ivet Bahar:
Analysis of correlated mutations in HIV-1 protease using spectral clustering. 1243-1250 - Pawel Szczesny
, Andrei N. Lupas:
Domain annotation of trimeric autotransporter adhesins - daTAA. 1251-1256
- Orland R. Gonzalez, Ralf Zimmer
:
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. 1257-1263
- Theodoros Damoulas, Mark A. Girolami
:
Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection. 1264-1270 - Yungki Park
, Volkhard Helms
:
Prediction of the translocon-mediated membrane insertion free energies of protein sequences. 1271-1277
- Naoaki Ono
, Shingo Suzuki, Chikara Furusawa
, Tomoharu Agata, Akiko Kashiwagi, Hiroshi Shimizu, Tetsuya Yomo:
An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. 1278-1285
- Jongrae Kim
, Declan G. Bates, Ian Postlethwaite, Pat Heslop-Harrison
, Kwang-Hyun Cho:
Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data. 1286-1292
- Zengyou He
, Can Yang
, Weichuan Yu
:
Peak bagging for peptide mass fingerprinting. 1293-1299
- Tiziana Castrignanò, Mattia D'Antonio, Anna Anselmo
, Danilo Carrabino, A. D'Onorio De Meo, Anna Maria D'Erchia
, Flavio Licciulli
, Marina Mangiulli, Flavio Mignone, Giulio Pavesi
, Ernesto Picardi
, Alberto Riva
, Raffaella Rizzi
, Paola Bonizzoni
, Graziano Pesole
:
ASPicDB: A database resource for alternative splicing analysis. 1300-1304
- István Albert
, Shinichiro Wachi, Cizhong Jiang, B. Franklin Pugh:
GeneTrack - a genomic data processing and visualization framework. 1305-1306
- Richard J. Edwards
, Norman E. Davey
, Denis C. Shields:
CompariMotif: quick and easy comparisons of sequence motifs. 1307-1309
- Janosch Hennig
, Klaus D. M. Hennig, Maria Sunnerhagen:
MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins. 1310-1312 - Marco Vassura, Luciano Margara
, Pietro di Lena
, Filippo Medri, Piero Fariselli
, Rita Casadio:
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. 1313-1315
- Alistair M. Chalk
, Erik L. L. Sonnhammer
:
siRNA specificity searching incorporating mismatch tolerance data. 1316-1317
- Sushmita Roy, Margaret Werner-Washburne
, Terran Lane:
A system for generating transcription regulatory networks with combinatorial control of transcription. 1318-1320
- Samuel Patient, Daniela Wieser, Michael Kleen, Ernst Kretschmann, Maria Jesus Martin
, Rolf Apweiler
:
UniProtJAPI: a remote API for accessing UniProt data. 1321-1322
- Qing Xiong, Yuhui Qiu, Weikuan Gu:
PGMapper: a web-based tool linking phenotype to genes. 1323
Volume 24, Number 11, 1 June 2008
- Sridhar Hannenhalli:
Eukaryotic transcription factor binding sites - modeling and integrative search methods. 1325-1331
- Daniel Dalevi, Niklas Eriksen:
Expected gene-order distances and model selection in bacteria. 1332-1338 - Marianne M. Lee, Michael K. Chan
, Ralf Bundschuh
:
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. 1339-1343
- Takashi Ishida
, Kengo Kinoshita:
Prediction of disordered regions in proteins based on the meta approach. 1344-1348
- Chunqi Chang
, Zhi Ding
, Yeung Sam Hung, Peter Chin Wan Fung:
Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data. 1349-1358 - Anindya Bhattacharya, Rajat K. De:
Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. 1359-1366 - Haiyun Wang
, Qi Wang, Xia Li, Bairong Shen
, Min Ding, Ziyin Shen:
Towards patterns tree of gene coexpression in eukaryotic species. 1367-1373
- Daniele Santoni
, Marco Pedicini
, Filippo Castiglione
:
Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. 1374-1380
- Jonathan D. Wren
:
URL decay in MEDLINE - a 4-year follow-up study. 1381-1385
- Michael Hackenberg
, Rune Matthiesen
:
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists. 1386-1393
- William Ritchie, François-Xavier Théodule, Daniel Gautheret
:
Mireval: a web tool for simple microRNA prediction in genome sequences. 1394-1396
- Claus Lundegaard, Ole Lund
, Morten Nielsen
:
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. 1397-1398 - Frédéric Schütz
, Mauro Delorenzi:
MAMOT: hidden Markov modeling tool. 1399-1400
- Lixiao Wang, Uwe H. Sauer:
OnD-CRF: predicting order and disorder in proteins conditional random fields. 1401-1402
- Thibaut Jombart:
adegenet: a R package for the multivariate analysis of genetic markers. 1403-1405 - Gilles Guillot
, Filipe Santos, Arnaud Estoup:
Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. 1406-1407 - Bo Peng
, Christopher I. Amos:
Forward-time simulations of non-random mating populations using simuPOP. 1408-1409
- Jung-Jae Kim
, Piotr Pezik, Dietrich Rebholz-Schuhmann:
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline. 1410-1412 - Soyang Ha, Young-Ju Seo, Min-Seok Kwon, Byung-Ha Chang, Cheol Kyu Han, Jeong Hyeok Yoon:
IDMap: facilitating the detection of potential leads with therapeutic targets. 1413-1415 - Andreas Quandt, Patricia Hernandez, Alexandre Masselot, Céline Hernandez
, Sergio Maffioletti, Cesare Pautasso, Ron D. Appel, Frédérique Lisacek:
swissPIT: a novel approach for pipelined analysis of mass spectrometry data. 1416-1417
- Jonathan L. Lustgarten, Chad Kimmel, Henrik Ryberg
, William R. Hogan
:
EPO-KB: a searchable knowledge base of biomarker to protein links. 1418-1419
Volume 24, Number 12, 15 June 2008
- Jacob A. Tennessen
:
Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence. 1421-1425
- Rainer Malik, Erich A. Nigg
, Roman Körner
:
Comparative conservation analysis of the human mitotic phosphoproteome. 1426-1432
- Kaname Kojima, Masao Nagasaki
, Satoru Miyano
:
Fast grid layout algorithm for biological networks with sweep calculation. 1433-1441 - Yong Li, Pankaj Agarwal
, Dilip Rajagopalan:
A global pathway crosstalk network. 1442-1447
- Michael Bada, Lawrence Hunter
:
Identification of OBO nonalignments and its implications for OBO enrichment. 1448-1455
- Michael Y. Tolstorukov, Vidhu Choudhary, Wilma K. Olson, Victor Zhurkin, Peter J. Park
:
nuScore: a web-interface for nucleosome positioning predictions. 1456-1458
- Michael J. Sweredoski, Pierre Baldi:
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. 1459-1460
- Korbinian Strimmer
:
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. 1461-1462
- Andreas Weidemann, Stefan Richter, Matthias Stein
, Sven Sahle, Ralph Gauges, Razif R. Gabdoulline
, Irina Surovtsova
, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca C. Wade
, Ursula Kummer:
SYCAMORE - a systems biology computational analysis and modeling research environment. 1463-1464 - Maital Ashkenazi, Gary D. Bader
, Allan Kuchinsky, Menachem Moshelion, David J. States:
Cytoscape ESP: simple search of complex biological networks. 1465-1466 - Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer
:
jSquid: a Java applet for graphical on-line network exploration. 1467-1468
- Gábor E. Tusnády, Lajos Kalmár
, Hédi Hegyi, Peter Tompa, István Simon
:
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. 1469-1470 - Margarita C. Theodoropoulou, Pantelis G. Bagos
, Ioannis C. Spyropoulos, Stavros J. Hamodrakas:
gpDB: a database of GPCRs, G-proteins, effectors and their interactions. 1471-1472
Volume 24, Number 13, 1 July 2008
Sequence Analysis
- John A. Capra, Mona Singh
:
Characterization and prediction of residues determining protein functional specificity. 1473-1480
- Gabriel Cardona
, Mercè Llabrés
, Francesc Rosselló
, Gabriel Valiente
:
A distance metric for a class of tree-sibling phylogenetic networks. 1481-1488
- Jiangning Song
, Hao Tan, Kazuhiro Takemoto
, Tatsuya Akutsu
:
HSEpred: predict half-sphere exposure from protein sequences. 1489-1497
- István A. Bogdán, Jenny Rivers, Robert J. Beynon
, Daniel Coca:
High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting. 1498-1502
- Bobbie-Jo M. Webb-Robertson
, William R. Cannon
, Christopher S. Oehmen, Anuj R. Shah, Vidhya Gurumoorthi, Mary S. Lipton, Katrina M. Waters
:
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. 1503-1509 - Mattia Zampieri, Nicola Soranzo, Claudio Altafini:
Discerning static and causal interactions in genome-wide reverse engineering problems. 1510-1515 - Junil Kim
, Tae-Geon Kim, Sung Hoon Jung, Jeong-Rae Kim
, Taesung Park, Pat Heslop-Harrison
, Kwang-Hyun Cho:
Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity. 1516-1522
- Makio Tamura, Patrik D'haeseleer
:
Microbial genotype-phenotype mapping by class association rule mining. 1523-1529
- Kay Prüfer, Udo Stenzel, Michael Dannemann, Richard E. Green, Michael Lachmann, Janet Kelso
:
PatMaN: rapid alignment of short sequences to large databases. 1530-1531 - Michiel Van Bel
, Yvan Saeys
, Yves Van de Peer
:
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA. 1532-1533 - Igor B. Kuznetsov:
ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences. 1534-1535 - Anne-Laure Abraham, Eduardo P. C. Rocha
, Joël Pothier
:
Swelfe: a detector of internal repeats in sequences and structures. 1536-1537
- Miklós Csürös:
Malin: maximum likelihood analysis of intron evolution in eukaryotes. 1538-1539 - André Wehe, Mukul S. Bansal
, J. Gordon Burleigh, Oliver Eulenstein:
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. 1540-1541
- Scott Hazelhurst
, Winston Hide
, Zsuzsanna Lipták
, Ramon Nogueira, Richard Starfield:
An overview of the wcd EST clustering tool. 1542-1546 - Pan Du, Warren A. Kibbe
, Simon M. Lin:
lumi: a pipeline for processing Illumina microarray. 1547-1548 - Christian Ritz
, Andrej-Nikolai Spiess:
qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis. 1549-1551
- Samuel Neuenschwander
, Frédéric Hospital
, Frédéric Guillaume
, Jérôme Goudet:
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. 1552-1553
- Jason M. Gilmore, Deanna L. Auberry, Julia L. Sharp, Amanda M. White, Kevin K. Anderson
, Don Simone Daly:
A Bayesian estimator of protein-protein association probabilities. 1554-1555
- Ashoka D. Polpitiya, Wei-Jun Qian
, Navdeep Jaitly, Vladislav A. Petyuk
, Joshua N. Adkins, David G. Camp II, Gordon A. Anderson, Richard D. Smith
:
DAnTE: a statistical tool for quantitative analysis of -omics data. 1556-1558 - Curtis Huttenhower
, Mark Schroeder, Maria D. Chikina, Olga G. Troyanskaya
:
The Sleipnir library for computational functional genomics. 1559-1561
- Lixiao Wang, Uwe H. Sauer:
OnD-CRF: prediciting order and disorder in proteins conditional random fields. 1562
Volume 24, Number 14, 15 July 2008
- Andrew B. Conley, Jittima Piriyapongsa, I. King Jordan:
Retroviral promoters in the human genome. 1563-1567
- Christian Martin, Naryttza N. Diaz, Jörg Ontrup, Tim W. Nattkemper
:
Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. 1568-1574
- Christopher S. Miller
, David Eisenberg:
Using inferred residue contacts to distinguish between correct and incorrect protein models. 1575-1582
- Huaizhen Qin, Tao Feng, Scott A. Harding, Chung-Jui Tsai
, Shuanglin Zhang:
An efficient method to identify differentially expressed genes in microarray experiments. 1583-1589 - Kosaku Shinoda
, Masaru Tomita, Yasushi Ishihama:
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. 1590-1595
- Kristin L. Ayers
, Kenneth Lange:
Penalized estimation of haplotype frequencies. 1596-1602 - Sophia S. F. Lee, Lei Sun, Rafal Kustra, Shelley B. Bull:
EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis. 1603-1610
- Florian Centler
, Christoph Kaleta
, Pietro Speroni di Fenizio
, Peter Dittrich:
Computing chemical organizations in biological networks. 1611-1618 - Jiguo Cao
, Hongyu Zhao
:
Estimating dynamic models for gene regulation networks. 1619-1624 - Magali Michaut
, Samuel Kerrien
, Luisa Montecchi-Palazzi, Franck Chauvat
, Corinne Cassier-Chauvat
, Jean-Christophe Aude
, Pierre Legrain, Henning Hermjakob
:
InteroPORC: automated inference of highly conserved protein interaction networks. 1625-1631
- Ludger Evers, Claudia-Martina Messow
:
Sparse kernel methods for high-dimensional survival data. 1632-1638
- James Thurmond
, Hyejin Yoon, Carla Kuiken, Karina Yusim, Simon Perkins, James Theiler, Tanmoy Bhattacharya
, Bette T. Korber
, Will Fischer
:
Web-based design and evaluation of T-cell vaccine candidates. 1639-1640
- Gregory E. Jordan
, William H. Piel:
PhyloWidget: web-based visualizations for the tree of life. 1641-1642
- Carlos Morcillo-Suarez, Josep Alegre, Ricardo Sangros, Elodie Gazave
, Rafael de Cid
, Roger Milne, Jorge Amigo
, Anna Ferrer-Admetlla, Andrés Moreno-Estrada
, Michelle Gardner
, Ferran Casals, Anna Pérez-Lezaun, David Comas
, Elena Bosch
, Francesc Calafell
, Jaume Bertranpetit
, Arcadi Navarro
:
SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data. 1643-1644 - Mamoru Kato, Yusuke Nakamura, Tatsuhiko Tsunoda
:
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data. 1645-1646
- Ahmet Sacan, Hakan Ferhatosmanoglu, Huseyin Coskun:
CellTrack: an open-source software for cell tracking and motility analysis. 1647-1649
- Sebastian Bauer, Steffen Grossmann, Martin Vingron, Peter N. Robinson
:
Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration. 1650-1651
- Mark R. Segal:
On E-values for tandem MS scoring schemes. 1652-1653
- Jainab Khatun, Morgan C. Giddings:
In response to "On E-value for tandem MS scoring schemes". 1654
Volume 24, Number 15, 1 August 2008
- Shuo Jiao, Shunpu Zhang:
On correcting the overestimation of the permutation-based false discovery rate estimator. 1655-1661
- Håkan Viklund, Arne Elofsson
:
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. 1662-1668 - Kyoung-Jae Won
, Albin Sandelin
, Troels Torben Marstrand
, Anders Krogh
:
Modeling promoter grammars with evolving hidden Markov models. 1669-1675 - Tiago José P. Sobreira, Arthur Gruber
:
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data. 1676-1680 - Kristoffer Forslund
, Erik L. L. Sonnhammer
:
Predicting protein function from domain content. 1681-1687
- Reinhard Schachtner, Dominik Lutter
, P. Knollmüller, Ana Maria Tomé
, Fabian J. Theis
, Gerd Schmitz, Martin Stetter, Pedro Gómez Vilda, Elmar Wolfgang Lang:
Knowledge-based gene expression classification via matrix factorization. 1688-1697 - Anne-Laure Boulesteix
, Christine Porzelius, Martin Daumer:
Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value. 1698-1706 - E. Purdom, Ken M. Simpson, Mark D. Robinson
, J. G. Conboy, A. V. Lapuk, Terence P. Speed:
FIRMA: a method for detection of alternative splicing from exon array data. 1707-1714
- Francesco Pappalardo
, Salvatore Musumeci, Santo Motta
:
Modeling immune system control of atherogenesis. 1715-1721
- Derek Greene
, Gerard Cagney
, Nevan J. Krogan, Padraig Cunningham
:
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. 1722-1728
- Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew N. Bainbridge, Steven J. M. Jones
:
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. 1729-1730
- Josep Ramón Goñi, Carlos Fenollosa, Alberto Pérez
, David Torrents
, Modesto Orozco
:
DNAlive: a tool for the physical analysis of DNA at the genomic scale. 1731-1732 - Yiqun Cao, Anna Charisi, Li-Chang Cheng, Tao Jiang
, Thomas Girke
:
ChemmineR: a compound mining framework for R. 1733-1734
- Carl Murie, Robert Nadon:
A correction for estimating error when using the Local Pooled Error Statistical Test. 1735-1736
- Meizhuo Zhang, Rui Feng, Xiang Chen
, Buqu Hu, Heping Zhang
:
LOT: a tool for linkage analysis of ordinal traits for pedigree data. 1737-1739
- Marzio Pennisi
, Roberto Catanuto, Francesco Pappalardo
, Santo Motta
:
Optimal vaccination schedules using simulated annealing. 1740-1742
- Johannes Goll, Seesandra V. Rajagopala, Shen C. Shiau, Hank Wu, Brian T. Lamb, Peter Uetz
:
MPIDB: the microbial protein interaction database. 1743-1744
Volume 24, Number 16, 15 August 2008
Discovery Note: Genome Analysis
- Meng Li, Hyun-il Henry Paik, Curtis Balch, Yoosung Kim, Lang Li, Tim Hui-Ming Huang, Kenneth P. Nephew, Sun Kim:
Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. 1745-1748
- Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai
, Pan-Chyr Yang
, Paul S. Meltzer, Eric Y. Chuang, Yidong Chen:
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. 1749-1756 - Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala
, Alejandro A. Schäffer:
Database indexing for production MegaBLAST searches. 1757-1764
- Duncan P. Brown:
Efficient functional clustering of protein sequences using the Dirichlet process. 1765-1771 - Lee Aaron Newberg:
Memory-efficient dynamic programming backtrace and pairwise local sequence alignment. 1772-1778 - Aalt D. J. van Dijk, D. Bosch, Cajo J. F. ter Braak
, A. R. van der Krol, Roeland C. H. J. van Ham:
Predicting sub-Golgi localization of type II membrane proteins. 1779-1786 - Ali Torkamani, Nicholas J. Schork
:
Predicting functional regulatory polymorphisms. 1787-1792 - Daniel J. Rigden
, Michael Y. Galperin
:
Sequence analysis of GerM and SpoVS, uncharacterized bacterial "sporulation" proteins with widespread phylogenetic distribution. 1793-1797
- Liam J. McGuffin
:
Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. 1798-1804
- Scott F. Saccone, Nancy L. Saccone, Gary E. Swan, Pamela A. F. Madden, Alison M. Goate
, John P. Rice, Laura J. Bierut:
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. 1805-1811
- Jung Hun Oh
, Young Bun Kim, Prem Gurnani, Kevin P. Rosenblatt, Jean X. Gao:
Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data. 1812-1818
- Yungki Park
, Volkhard Helms
:
MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon. 1819-1820
- Brian W. Lambert, Joseph D. Terwilliger, Kenneth M. Weiss:
ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth. 1821-1822
- Olivier Filangi
, Yoann Beausse, Anthony Assi, Ludovic Legrand
, Jean-Marc Larré, Véronique Martin, Olivier Collin
, Christophe Caron, Hugues Leroy, David Allouche:
BioMAJ: a flexible framework for databanks synchronization and processing. 1823-1825
Volume 24, Number 17, 1 September 2008
- Hanchuan Peng:
Bioimage informatics: a new area of engineering biology. 1827-1836
- Gyan Prakash Srivastava, Juyuan Guo, Huidong Shi
, Dong Xu:
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. 1837-1842 - Jie Wu, Douglas H. Sieglaff, Joshua Gervin, Xiaohui S. Xie:
Discovering regulatory motifs in the Plasmodium genome using comparative genomics. 1843-1849
- Jiajian Liu, Gary D. Stormo:
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. 1850-1857 - James Lara, Robert M. Wohlhueter, Zoya Dimitrova, Yuri Khudyakov:
Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein. 1858-1864
- David W. Ritchie
, Dima Kozakov
, Sandor Vajda:
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. 1865-1873
- Huai Li, Ming Zhan:
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data. 1874-1880 - Shuiwang Ji
, Liang Sun, Rong Jin, Sudhir Kumar
, Jieping Ye:
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. 1881-1888 - Blaise Hanczar, Edward R. Dougherty:
Classification with reject option in gene expression data. 1889-1895
- Nils Homer, Waibhav Tembe, Szabolcs Szelinger, Margot Redman, Dietrich A. Stephan, John V. Pearson
, Stanley F. Nelson, David W. Craig:
Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies. 1896-1902
- Mario A. Marchisio, Jörg Stelling:
Computational design of synthetic gene circuits with composable parts. 1903-1910 - Heng Lian, William A. Thompson, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble, Charles E. Lawrence:
Automated mapping of large-scale chromatin structure in ENCODE. 1911-1916 - Abhishek Garg, Alessandro Di Cara, Ioannis Xenarios
, Luis Mendoza
, Giovanni De Micheli:
Synchronous versus asynchronous modeling of gene regulatory networks. 1917-1925 - Yung-Keun Kwon, Kwang-Hyun Cho:
Coherent coupling of feedback loops: a design principle of cell signaling networks. 1926-1932 - Vladislav Vyshemirsky, Mark A. Girolami
:
BioBayes: A software package for Bayesian inference in systems biology. 1933-1934
- Theodosios Theodosiou
, Nikos Darzentas, Lefteris Angelis, Christos A. Ouzounis
:
PuReD-MCL: a graph-based PubMed document clustering methodology. 1935-1941 - Han Zhang
, Hsin-Chou Yang
, Yaning Yang:
PoooL: an efficient method for estimating haplotype frequencies from large DNA pools. 1942-1948
- Art F. Y. Poon, Fraser I. Lewis
, Simon D. W. Frost, Sergei L. Kosakovsky Pond:
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. 1949-1950
- Shantanu Sharma
, Feng Ding
, Nikolay V. Dokholyan
:
iFoldRNA: three-dimensional RNA structure prediction and folding. 1951-1952 - Paolo Marcatili
, Alessandra Rosi, Anna Tramontano:
PIGS: automatic prediction of antibody structures. 1953-1954 - Martin Prokop, Jan Adam, Zdenek Kríz, Michaela Wimmerová
, Jaroslav Koca
:
TRITON: a graphical tool for ligand-binding protein engineering. 1955-1956
- Tae-Min Kim
, Seon-Hee Yim, Yong-Bok Jeong, Yu-Chae Jung, Yeun-Jun Chung:
PathCluster: a framework for gene set-based hierarchical clustering. 1957-1958 - Eoghan D. Harrington
, Peer Bork
:
Sircah: a tool for the detection and visualization of alternative transcripts. 1959-1960
- Dominik Heider
, Daniel Kessler, Angelika Barnekow:
Watermarking sexually reproducing diploid organisms. 1961-1962
- Frank T. Bergmann
, Herbert M. Sauro
:
Comparing simulation results of SBML capable simulators. 1963-1965 - Garrett M. Dancik
, Karin S. Dorman
:
mlegp: statistical analysis for computer models of biological systems using R. 1966-1967
- Songhua Xu, Jamie P. McCusker
, Michael Krauthammer
:
Yale Image Finder (YIF): a new search engine for retrieving biomedical images. 1968-1970
- Jung-Wei Fan, Carol Friedman:
Semantic reclassification of the UMLS concepts. 1971-1973
Volume 24, Number 18, 15 September 2008
- Krishna R. Kalari
, Thomas L. Casavant, Todd E. Scheetz
:
A knowledge-based approach to predict intragenic deletions or duplications. 1975-1979 - Matthew N. Davies, Andrew Secker, Alex Alves Freitas
, Edward Clark, Jonathan Timmis
, Darren R. Flower:
Optimizing amino acid groupings for GPCR classification. 1980-1986 - Dariusz Przybylski, Burkhard Rost
:
Powerful fusion: PSI-BLAST and consensus sequences. 1987-1993
- Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen
, Wen Gao:
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. 1994-2001 - Majid Masso
, Iosif I. Vaisman
:
Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. 2002-2009
- Dhammika Amaratunga, Javier Cabrera, Yung-Seop Lee:
Enriched random forests. 2010-2014 - Liang Chen, Tiejun Tong
, Hongyu Zhao
:
Considering dependence among genes and markers for false discovery control in eQTL mapping. 2015-2022 - TaeHyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu
, Jean-Pierre A. Kocher, Dennis A. Wigle, Vipin Kumar, Rui Kuang:
Robust and efficient identification of biomarkers by classifying features on graphs. 2023-2029
- Ioanna Tachmazidou, Toby Andrew
, Claudio J. Verzilli, Michael R. Johnson, Maria De Iorio
:
Bayesian survival analysis in genetic association studies. 2030-2036
- Thomas Maiwald, Jens Timmer:
Dynamical modeling and multi-experiment fitting with PottersWheel. 2037-2043 - Markus W. Covert
, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr
:
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. 2044-2050 - Viviane Galvão, José Garcia Vivas Miranda
, Ricardo Ribeiro-dos-Santos:
Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation. 2051-2056 - Min Zhang, Chen Yao, Zheng Guo, Jinfeng Zou, Lin Zhang, Hui Xiao, Dong Wang, Da Yang
, Xue Gong, Jing Zhu, Yanhui Li, Xia Li:
Apparently low reproducibility of true differential expression discoveries in microarray studies. 2057-2063 - Mudassar Iqbal
, Alex Alves Freitas
, Colin G. Johnson
, Massimo Vergassola
:
Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data. 2064-2070 - Marco Grzegorczyk, Dirk Husmeier
, Kieron D. Edwards
, Peter Ghazal
, Andrew J. Millar
:
Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. 2071-2078
- Kathrin Fenner, Junfeng Gao, Stefan Kramer, Lynda B. M. Ellis, Lawrence P. Wackett:
Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction. 2079-2085 - Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky
, W. John Wilbur:
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. 2086-2093
- Marco Lippi
, Andrea Passerini
, Marco Punta
, Burkhard Rost
, Paolo Frasconi:
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. 2094-2095 - Richard C. G. Holland
, Thomas A. Down, Matthew R. Pocock, Andreas Prlic
, David S. Huen
, Keith James, Sylvain Foisy, Andreas Dräger
, Andy Yates
, Michael L. Heuer, Mark J. Schreiber:
BioJava: an open-source framework for bioinformatics. 2096-2097
- Campbell O. Webb
, David D. Ackerly
, Steven W. Kembel
:
Phylocom: software for the analysis of phylogenetic community structure and trait evolution. 2098-2100
- Romain Gautier
, Dominique Douguet, Bruno Antonny
, Guillaume Drin
:
HELIQUEST: a web server to screen sequences with specific alpha-helical properties. 2101-2102
- William D. Nelson, Kert Viele, Bert C. Lynn
:
An integrated approach for automating validation of extracted ion chromatographic peaks. 2103-2104
- Ryan Abo, Stacey Knight
, Jathine Wong, Angela Cox
, Nicola J. Camp:
hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework. 2105-2107
- Torsten Blum, Oliver Kohlbacher
:
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. 2108-2109 - Hector Ramos, P. Shannon, Ruedi Aebersold:
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. 2110-2111 - Robert Kincaid
, Allan Kuchinsky, Michael L. Creech:
VistaClara: an expression browser plug-in for Cytoscape. 2112-2114 - Jan Krumsiek, Caroline C. Friedel
, Ralf Zimmer
:
ProCope - protein complex prediction and evaluation. 2115-2116 - Bing Xiong
, Ke Liu, Jie Wu, David L. Burk, Hualiang Jiang, Jingkang Shen:
DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks. 2117-2118
- Rafael C. Jiménez
, Antony F. Quinn
, Alexander García Castro, Alberto Labarga
, Kieran O'Neill
, Fernando Martinez, Gustavo A. Salazar
, Henning Hermjakob
:
Dasty2, an Ajax protein DAS client. 2119-2121 - Catherine M. Lloyd, James R. Lawson
, Peter J. Hunter
, Poul M. F. Nielsen
:
The CellML Model Repository. 2122-2123
- Miguel Pignatelli, Gabriel Aparício, Ignacio Blanquer, Vicente Hernández, Andrés Moya
, Javier Tamames
:
Metagenomics reveals our incomplete knowledge of global diversity. 2124-2125
Volume 24, Number 19, 1 October 2008
- Jonathan D. Wren
, Alex Bateman
:
Databases, data tombs and dust in the wind. 2127-2128
- Alejandro Cruz-Marcelo, Rudy Guerra, Marina Vannucci, Yiting Li, Ching C. Lau, Tsz-Kwong Man
:
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data. 2129-2136 - Holger Fröhlich
, Mark Fellmann, Holger Sültmann
, Annemarie Poustka, Tim Beißbarth:
Predicting pathway membership via domain signatures. 2137-2142 - Chandra Erdman, John W. Emerson:
A fast Bayesian change point analysis for the segmentation of microarray data. 2143-2148 - Laurent Jacob, Jean-Philippe Vert
:
Protein-ligand interaction prediction: an improved chemogenomics approach. 2149-2156
- Martin Peifer
, John E. Karro, H. H. von Grünberg:
Is there an acceleration of the CpG transition rate during the mammalian radiation? 2157-2164 - Virpi Ahola, Tero Aittokallio
, Mauno Vihinen
, Esa Uusipaikka:
Model-based prediction of sequence alignment quality. 2165-2171 - Karl Frank, Manfred J. Sippl:
High-performance signal peptide prediction based on sequence alignment techniques. 2172-2176
- Andrew D. Fernandes, William R. Atchley:
Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative. 2177-2183
- Michael Hirsch, Michael Habeck
:
Mixture models for protein structure ensembles. 2184-2192
- Jianhua Hu:
Cancer outlier detection based on likelihood ratio test. 2193-2199 - Benjamin Haibe-Kains
, Christine Desmedt
, Christos P. Sotiriou, Gianluca Bontempi
:
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? 2200-2208
- Eleni Giannoulatou
, Christopher Yau
, Stefano Colella
, Jiannis Ragoussis
, Christopher C. Holmes
:
GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population. 2209-2214 - Zhihong Ding, Thomas Mailund
, Yun S. Song:
Efficient whole-genome association mapping using local phylogenies for unphased genotype data. 2215-2221 - Gilles Guillot
:
Inference of structure in subdivided populations at low levels of genetic differentiation - the correlated allele frequencies model revisited. 2222-2228
- Marco Terzer, Jörg Stelling:
Large-scale computation of elementary flux modes with bit pattern trees. 2229-2235 - Diogo A. R. S. Latino, Qing-You Zhang, João Aires-de-Sousa
:
Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps. 2236-2244 - Albert Gevorgyan, Mark G. Poolman, David A. Fell
:
Detection of stoichiometric inconsistencies in biomolecular models. 2245-2251
- Simon Moxon
, Frank Schwach
, Tamas Dalmay
, Daniel MacLean
, David J. Studholme
, Vincent Moulton
:
A toolkit for analysing large-scale plant small RNA datasets. 2252-2253
- Wencheng Li, Bo Yang, Shaoguang Liang, Yonghua Wang, Chris Whiteley, Yicheng Cao, Xiaoning Wang:
BLogo: a tool for visualization of bias in biological sequences. 2254-2255 - Patrick Ng, Uri Keich
:
GIMSAN: a Gibbs motif finder with significance analysis. 2256-2257
- Doroteya K. Staykova
, Jonas Fredriksson, Martin Billeter:
PRODECOMPv3: decompositions of NMR projections for protein backbone and side-chain assignments and structural studies. 2258-2259
- Lin S. Chen, John D. Storey
:
Eigen-R2 for dissecting variation in high-dimensional studies. 2260-2262 - Ananyo Choudhury
, Ansuman Lahiri
:
Arabidopsis thaliana regulatory element analyzer. 2263-2264
- Faruck Morcos
, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre:
Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. 2265-2266
- Anastasia Alexandridou, George T. Tsangaris
, Konstantinos N. Vougas, Konstantina S. Nikita
, George M. Spyrou:
Peptide Finder: mapping measured molecular masses to peptides and proteins. 2267-2269
- Tiago L. Moda, Leonardo G. Torres, Alexandre E. Carrara, Adriano D. Andricopulo:
PK/DB: database for pharmacokinetic properties and predictive in silico ADME models. 2270-2271 - Gabriel F. Berriz, Frederick P. Roth
:
The Synergizer service for translating gene, protein and other biological identifiers. 2272-2273
- Sofia Wichert
, Konstantinos Fokianos
, Korbinian Strimmer:
Identifying periodically expressed transcripts in microarray time series data. 2274 - Kristoffer Forslund, Erik L. L. Sonnhammer
:
Predicting protein function from domain content. 2275
- Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai
, Pan-Chyr Yang
, Paul S. Meltzer, Eric Y. Chuang, Yidong Chen:
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. 2276
Volume 24, Number 20, 15 October 2008
- Antonina Andreeva
, Henning Tidow
:
A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes. 2277-2280
- Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L. Malmberg
, Liming Cai:
Fast and accurate search for non-coding RNA pseudoknot structures in genomes. 2281-2287
- Edward Wijaya, Siu-Ming Yiu, Ngo Thanh Son, Kanagasabai Rajaraman
, Wing-Kin Sung
:
MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders. 2288-2295 - Qi Dai, Yanchun Yang, Tian-Ming Wang:
Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. 2296-2302 - François Fauteux
, Mathieu Blanchette, Martina V. Stromvik
:
Seeder: discriminative seeding DNA motif discovery. 2303-2307 - K. C. Dukka Bahadur, Dennis R. Livesay:
Improving position-specific predictions of protein functional sites using phylogenetic motifs. 2308-2316
- Si Quang Le
, Olivier Gascuel, Nicolas Lartillot:
Empirical profile mixture models for phylogenetic reconstruction. 2317-2323
- Vinay Pulim, Bonnie Berger, Jadwiga R. Bienkowska:
Optimal contact map alignment of protein-protein interfaces. 2324-2328 - Tuo Zhang, Hua Zhang, Ke Chen
, Shiyi Shen, Jishou Ruan, Lukasz A. Kurgan
:
Accurate sequence-based prediction of catalytic residues. 2329-2338 - Ryan M. Bannen
, Vanitha Suresh, George N. Phillips Jr., Stephen J. Wright, Julie C. Mitchell:
Optimal design of thermally stable proteins. 2339-2343
- Han Xu, Chia-Lin Wei, Feng Lin, Wing-Kin Sung
:
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. 2344-2349
- Iuliana Ionita-Laza, Nan M. Laird, Benjamin A. Raby, Scott T. Weiss, Christoph Lange:
On the frequency of copy number variants. 2350-2355 - Meijuan Li, Cavan Reilly, Timothy Hanson:
A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations. 2356-2362
- Jaroslaw Smieja
, Mohammad Jamaluddin, Allan R. Brasier
, Marek Kimmel:
Model-based analysis of interferon-beta induced signaling pathway. 2363-2369 - Juan Cui, Qi Liu, David Puett, Ying Xu:
Computational prediction of human proteins that can be secreted into the bloodstream. 2370-2375 - Shuye Pu, Karen Ronen, James Vlasblom, Jack Greenblatt, Shoshana J. Wodak
:
Local coherence in genetic interaction patterns reveals prevalent functional versatility. 2376-2383 - Kristen A. Wieghaus, Erwin P. Gianchandani, Mikell A. Paige, Milton L. Brown, Edward A. Botchwey, Jason A. Papin
:
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule. 2384-2390
- Jasmina Bogojeska, Adrian Alexa, André Altmann
, Thomas Lengauer, Jörg Rahnenführer
:
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. 2391-2392
- Anika Jöcker, Fabian Hoffmann, Andreas Groscurth, Heiko Schoof
:
Protein function prediction and annotation in an integrated environment powered by web services (AFAWE). 2393-2394 - Hui Jiang
, Wing Hung Wong:
SeqMap: mapping massive amount of oligonucleotides to the genome. 2395-2396 - Yana Bromberg
, Guy Yachdav, Burkhard Rost
:
SNAP predicts effect of mutations on protein function. 2397-2398
- Thasso Griebel, Malte Brinkmeyer, Sebastian Böcker
:
EPoS: a modular software framework for phylogenetic analysis. 2399-2400 - Matthias Wolf
, Benjamin Ruderisch, Thomas Dandekar
, Jörg Schultz, Tobias Müller:
ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. 2401-2402 - Ádám Novák, István Miklós, Rune B. Lyngsø, Jotun Hein:
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. 2403-2404
- Wuming Gong, Yongliang Ren, Haiyan Zhou, Yejun Wang, Shuli Kang, Tongbin Li:
siDRM: an effective and generally applicable online siRNA design tool. 2405-2406
- Jérôme Wojcik, Karl Forner:
ExactFDR: exact computation of false discovery rate estimate in case-control association studies. 2407-2408
- Jing Zhang, Tao Ma, Yanda Li, Shao Li
:
dbNEI2.0: building multilayer network for drug-NEI-disease. 2409-2411 - Siyuan Zheng
, Jia Sheng, Chuan Wang, Xiaojing Wang, Yao Yu, Yun Li
, Alex Michie, Jianliang Dai, Yang Zhong, Pei Hao
, Lei Liu, Yixue Li:
MPSQ: a web tool for protein-state searching. 2412-2413 - Chaka Tang, Josephine F. Reyes
, Fabio Luciani
, Andrew R. Francis
, Mark M. Tanaka:
spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex. 2414-2415 - Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei
, Lu Xie
, Yangyong Zhu, Yixue Li:
ITFP: an integrated platform of mammalian transcription factors. 2416-2417 - Jason Persampieri, Deborah I. Ritter, Daniel Lees, Jessica Lehoczky, Qiang Li, Su Guo, Jeffrey H. Chuang
:
cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. 2418-2419
- Yang Xie:
Comments on "On correcting the overestimation of the permutation-based false discovery rate estimator". 2420
- Vladislav Vyshemirsky, Mark A. Girolami
:
Bayesian ranking of biochemical system models. 2421
Volume 24, Number 21, 1 November 2008
- Robson Francisco de Souza
, Vivek Anantharaman
, Sandro José de Souza, L. Aravind
, Frederico J. Gueiros-Filho
:
AMIN domains have a predicted role in localization of diverse periplasmic protein complexes. 2423-2426 - Fanny Jadeau, Emmanuelle Bechet
, Alain J. Cozzone, Gilbert Deléage
, Christophe Grangeasse
, Christophe Combet
:
Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature. 2427-2430
- Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li:
ZOOM! Zillions of oligos mapped. 2431-2437 - Osamu Gotoh:
Direct mapping and alignment of protein sequences onto genomic sequence. 2438-2444 - Sriram Sankararaman, Kimmen Sjölander:
INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification. 2445-2452
- Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin
, Kevin Karplus:
PREDICT-2ND: a tool for generalized protein local structure prediction. 2453-2459 - Mirabela Rusu
, Stefan Birmanns, Willy Wriggers
:
Biomolecular pleiomorphism probed by spatial interpolation of coarse models. 2460-2466
- Chang-Tsun Li
, Yinyin Yuan
, Roland Wilson:
An unsupervised conditional random fields approach for clustering gene expression time series. 2467-2473 - Xi Chen, Lily Wang, Jonathan D. Smith
, Bing Zhang:
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. 2474-2481 - Elissa J. Cosgrove, Yingchun Zhou, Timothy S. Gardner, Eric D. Kolaczyk:
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. 2482-2490 - Antonio Reverter, Eva K. F. Chan:
Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. 2491-2497
- Zachary A. Szpiech, Mattias Jakobsson
, Noah A. Rosenberg
:
ADZE: a rarefaction approach for counting alleles private to combinations of populations. 2498-2504
- Gautam Goel, I-Chun Chou, Eberhard O. Voit:
System estimation from metabolic time-series data. 2505-2511
- Alona Fyshe
, Yifeng Liu, Duane Szafron, Russell Greiner, Paul Lu:
Improving subcellular localization prediction using text classification and the gene ontology. 2512-2517 - Justin Klekota, Frederick P. Roth
:
Chemical substructures that enrich for biological activity. 2518-2525
- Brendan Elliott, Mustafa Kirac
, Ali Cakmak
, Gökhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Özsoyoglu, Z. Meral Özsoyoglu:
PathCase: pathways database system. 2526-2533
- Darren Kessner, Matt Chambers, Robert Burke, David B. Agus
, Parag Mallick
:
ProteoWizard: open source software for rapid proteomics tools development. 2534-2536 - Alan P. Boyle
, Justin Guinney
, Gregory E. Crawford, Terrence S. Furey:
F-Seq: a feature density estimator for high-throughput sequence tags. 2537-2538
- Salvador Ramírez-Flandes
, Osvaldo Ulloa
:
Bosque: integrated phylogenetic analysis software. 2539-2541 - Liang Liu:
BEST: Bayesian estimation of species trees under the coalescent model. 2542-2543
- Denis C. Bauer
, Timothy L. Bailey:
STREAM: Static Thermodynamic REgulAtory Model of transcription. 2544-2545
- Dorothea Emig, Melissa S. Cline, Thomas Lengauer, Mario Albrecht:
Integrating expression data with domain interaction networks. 2546-2548 - Holger Fröhlich
, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang
, Florian Markowetz:
Analyzing gene perturbation screens with nested effects models in R and bioconductor. 2549-2550 - Anthony D. Hill, Jonathan R. Tomshine
, Emma M. B. Weeding, Vassilios Sotiropoulos, Yiannis N. Kaznessis
:
SynBioSS: the synthetic biology modeling suite. 2551-2553 - Guillermo Rodrigo
, Javier Carrera, Kristala Jones Prather, Alfonso Jaramillo
:
DESHARKY: automatic design of metabolic pathways for optimal cell growth. 2554-2556 - Tian Xia, Julie A. Dickerson:
OmicsViz: Cytoscape plug-in for visualizing omics data across species. 2557-2558
- Yoshimasa Tsuruoka
, Jun'ichi Tsujii, Sophia Ananiadou:
FACTA: a text search engine for finding associated biomedical concepts. 2559-2560
- Mehdi Pirooznia
, Tanwir Habib
, Edward J. Perkins, Youping Deng:
GOfetcher: a database with complex searching facility for gene ontology. 2561-2563 - C. Nelson Hayes, Diego Diez
, Nicolas Joannin, Wataru Honda, Minoru Kanehisa, Mats Wahlgren, Craig E. Wheelock, Susumu Goto:
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. 2564-2565
- Harald Binder
, Martin Schumacher:
Comment on "network-constrained regularization and variable selection for analysis of genomic data". 2566-2568
- Caiyan Li, Hongzhe Li:
In Response to Comment on "Network-constrained regularization and variable selection for analysis of genomic data". 2569
Volume 24, Number 22, 15 November 2008
- Christina Beargie, Tsunglin Liu, Mark Corriveau, Ha Youn Lee, Jonatha Gott, Ralf Bundschuh
:
Genome annotation in the presence of insertional RNA editing. 2571-2578
- Aurélien Mazurie
, Danail Bonchev, Benno Schwikowski
, Gregory A. Buck:
Phylogenetic distances are encoded in networks of interacting pathways. 2579-2585
- Assaf P. Oron, Zhen Jiang, Robert Gentleman:
Gene set enrichment analysis using linear models and diagnostics. 2586-2591
- Ryo Yoshida, Masao Nagasaki
, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
, Tomoyuki Higuchi:
Bayesian learning of biological pathways on genomic data assimilation. 2592-2601 - Katrin Sameith
, Philipp Antczak
, Elliot Marston, Nil Turan, Dieter Maier, Tanja Stankovic
, Francesco Falciani:
Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage. 2602-2607 - Ta-tsen Soong, Kazimierz O. Wrzeszczynski, Burkhard Rost
:
Physical protein-protein interactions predicted from microarrays. 2608-2614 - Luis F. de Figueiredo
, Stefan Schuster, Christoph Kaleta
, David A. Fell
:
Can sugars be produced from fatty acids? A test case for pathway analysis tools. 2615-2621
- Seesandra V. Rajagopala, Johannes Goll, N. D. Deve Gowda, Kumar C. Sunil, Björn Titz
, Arnab Mukherjee
, Sharmila S. Mary, Naresh Raviswaran, Chetan S. Poojari
, Srinivas Ramachandra
, Svetlana Shtivelband, Stephen M. Blazie
, Julia Hofmann, Peter Uetz
:
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. 2622-2627
- Craig E. Jones, Julian Schwerdt, Tessa Arwen Bretag, Ute Baumann, Alfred L. Brown
:
GOSLING: a rule-based protein annotator using BLAST and GO. 2628-2629
- Martin Madera:
Profile Comparer: a program for scoring and aligning profile hidden Markov models. 2630-2631
- Francesco Sirocco, Silvio C. E. Tosatto
:
TESE: generating specific protein structure test set ensembles. 2632-2633 - Shiyong Liu
, Ying Gao, Ilya A. Vakser:
DOCKGROUND protein-protein docking decoy set. 2634-2635
- Edi Prifti
, Jean-Daniel Zucker
, Karine Clément, Corneliu Henegar
:
FunNet: an integrative tool for exploring transcriptional interactions. 2636-2638 - Xin Zhou, Zhen Su:
tCal: transcriptional probability calculator using thermodynamic model. 2639-2640
- Daehee Hwang, Ning Zhang, Hookeun Lee
, Eugene Yi, Hui Zhang, Inyoul Y. Lee, Leroy Hood, Ruedi Aebersold:
MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. 2641-2642
- Ricardo Martínez, Nicolas Pasquier, Claude Pasquier
:
GenMiner: mining non-redundant association rules from integrated gene expression data and annotations. 2643-2644
- Samone Khouangsathiene, Carlo Pearson, Summer Street, Betsy Ferguson, Christopher Dubay:
MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms. 2645-2646 - Khalid Belhajjame, Andrew R. Jones
, Norman W. Paton
:
A toolkit for capturing and sharing FuGE experiments. 2647-2649
- Holger Fröhlich
, Mark Fellmann, Holger Sültmann
, Annemarie Poustka, Tim Beißbarth:
Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. 2650-2656
- Hakim Tafer
, Ivo L. Hofacker
:
RNAplex: a fast tool for RNA-RNA interaction search. 2657-2663
Volume 24, Number 23, December 2008
- Yan Lin, George C. Tseng, Soo Yeon Cheong, Lora J. H. Bean, Stephanie L. Sherman, Eleanor Feingold
:
Smarter clustering methods for SNP genotype calling. 2665-2671 - Tim J. Carver, Matthew Berriman
, Adrian Tivey, Chinmay Patel, Ulrike Böhme
, Bart Barrell, Julian Parkhill
, Marie-Adèle Rajandream:
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. 2672-2676
- Robert K. Bradley
, Lior Pachter
, Ian H. Holmes
:
Specific alignment of structured RNA: stochastic grammars and sequence annealing. 2677-2683 - Lucie N. Hutchins, Sean M. Murphy, Priyam Singh, Joel H. Graber
:
Position-dependent motif characterization using non-negative matrix factorization. 2684-2690 - Ching-Tai Chen
, Ei-Wen Yang
, Hung-Ju Hsu, Yi-Kun Sun, Wen-Lian Hsu, An-Suei Yang
:
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. 2691-2697
- Mallika Veeramalai, David R. Gilbert:
A novel method for comparing topological models of protein structures enhanced with ligand information. 2698-2705
- Elmer Andrés Fernández, María R. Girotti, Juan A. López del Olmo, Andrea S. Llera
, Osvaldo L. Podhajcer
, Rodolfo J. C. Cantet
, Mónica Balzarini
:
Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study. 2706-2712
- Jean-Marie Cornuet, Filipe Santos, Mark A. Beaumont
, Christian P. Robert
, Jean-Michel Marin
, David J. Balding
, Thomas Guillemaud
, Arnaud Estoup:
Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. 2713-2719 - YuZhong Zhao, Yun Xu, ZhiHao Wang, Hong Zhang, Guoliang Chen:
A better block partition and ligation strategy for individual haplotyping. 2720-2725
- Heiko Neuweger, Stefan P. Albaum, Michael Dondrup
, Marcus Persicke
, Tony Watt, Karsten Niehaus, Jens Stoye
, Alexander Goesmann
:
MeltDB: a software platform for the analysis and integration of metabolomics experiment data. 2726-2732 - Fergal P. Casey, Gerard Cagney
, Nevan J. Krogan, Denis C. Shields:
Optimal stepwise experimental design for pairwise functional interaction studies. 2733-2739 - Gang Liu, Dhananjay D. Marathe
, Khushi L. Matta, Sriram Neelamegham
:
Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands. 2740-2747 - Eugenio Cinquemani, Andreas Milias-Argeitis
, Sean Summers, John Lygeros:
Stochastic dynamics of genetic networks: modelling and parameter identification. 2748-2754 - Jiri Jablonsky, Petr Susila, Dusan Lazar
:
Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting. 2755-2759
- Sirarat Sarntivijai
, Alexander S. Ade, Brian D. Athey
, David J. States:
A bioinformatics analysis of the cell line nomenclature. 2760-2766 - Gabrielle A. Reeves
, Karen Eilbeck, Michele Magrane
, Claire O'Donovan
, Luisa Montecchi-Palazzi, Midori A. Harris
, Sandra E. Orchard
, Rafael C. Jiménez
, Andreas Prlic
, Tim J. P. Hubbard, Henning Hermjakob
, Janet M. Thornton
:
The Protein Feature Ontology: a tool for the unification of protein feature annotations. 2767-2772
- Peng-An Chen, Hsiao-Fei Liu, Kun-Mao Chao
:
CNVDetector: locating copy number variations using array CGH data. 2773-2775
- Brian D. Ondov, Anjana Varadarajan, Karla D. Passalacqua
, Nicholas H. Bergman:
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. 2776-2777
- Thorhildur Juliusdottir, Fredrik Pettersson, Richard R. Copley:
POPE - a tool to aid high-throughput phylogenetic analysis. 2778-2779
- Liisa Holm
, S. Kääriäinen, Päivi Rosenström, A. Schenkel:
Searching protein structure databases with DaliLite v.3. 2780-2781 - Michaël Heymann, David Paramelle
, Gilles Subra
, Eric Forest, Jean Martinez, Christophe Geourjon, Gilbert Deléage
:
MSX-3D: a tool to validate 3D protein models using mass spectrometry. 2782-2783
- Marit Holden, Shiwei Deng, Leszek Wojnowski, Bettina Kulle
:
GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. 2784-2785 - Ryan D. Hernandez:
A flexible forward simulator for populations subject to selection and demography. 2786-2787 - Roby Joehanes, James C. Nelson:
QGene 4.0, an extensible Java QTL-analysis platform. 2788-2789 - Anna Ramírez-Soriano, Francesc Calafell
:
FABSIM: a software for generating FST distributions with various ascertainment biases. 2790-2791
- Josselin Noirel, Guido Sanguinetti
, Phillip C. Wright
:
Identifying differentially expressed subnetworks with MMG. 2792-2793 - Tom S. Price
, Julie E. Baggs, Anne M. Curtis
, Garret A. FitzGerald, John B. Hogenesch:
WAVECLOCK: wavelet analysis of circadian oscillation. 2794-2795
- John T. Prince
, Edward M. Marcotte
:
mspire: mass spectrometry proteomics in Ruby. 2796-2797 - Yuelin Zhu, Sean R. Davis
, Robert M. Stephens, Paul S. Meltzer, Yidong Chen:
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. 2798-2800
- Dihui Lu, Richard Z. Liu, Victoria Izumi, David A. Fenstermacher, Eric B. Haura, John M. Koomen, Steven Eschrich
:
IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry. 2801-2802 - Geoffrey L. Winsor
, Bhavjinder Khaira, Thea Van Rossum
, Raymond Lo, Matthew D. Whiteside, Fiona S. L. Brinkman
:
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. 2803-2804
- Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre:
Addendum. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. 2805
Volume 24, Number 24, December 2008
- Christophe Pichon, Brice Felden:
Small RNA gene identification and mRNA target predictions in bacteria. 2807-2813
- Alexander E. Vinogradov:
Modularity of cellular networks shows general center-periphery polarization. 2814-2817
- Jason R. Miller
, Arthur L. Delcher, Sergey Koren
, Eli Venter, Brian Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark M. Mobarry, Granger G. Sutton:
Aggressive assembly of pyrosequencing reads with mates. 2818-2824 - Yu Zhang:
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays. 2825-2831 - Jhonny R. Demey
, José L. Vicente-Villardón
, M. P. Galindo-Villardón
, Asia Yusely Zambrano:
Identifying molecular markers associated with classification of genotypes by External Logistic Biplots. 2832-2838
- Paolo Ribeca, Emanuele Raineri:
Faster exact Markovian probability functions for motif occurrences: a DFA-only approach. 2839-2848 - Anke Busch, Andreas S. Richter
, Rolf Backofen:
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. 2849-2856 - Thanh Hai Dang, Koenraad Van Leemput, Alain Verschoren, Kris Laukens
:
Prediction of kinase-specific phosphorylation sites using conditional random fields. 2857-2864
- Andrew J. Bordner:
Predicting small ligand binding sites in proteins using backbone structure. 2865-2871 - Ahmet Sacan, Ismail Hakki Toroslu
, Hakan Ferhatosmanoglu:
Integrated search and alignment of protein structures. 2872-2879
- Ronglai Shen, Jeremy M. G. Taylor, Debashis Ghosh:
Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model. 2880-2886 - Karen Kapur
, Hui Jiang
, Yi Xing, Wing Hung Wong:
Cross-hybridization modeling on Affymetrix exon arrays. 2887-2893
- Simon Rogers
, Mark A. Girolami
, Walter Kolch
, Katrina M. Waters
, Tao Liu
, Brian Thrall, H. Steven Wiley
:
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. 2894-2900 - Bärbel Finkenstädt, Elizabeth A. Heron
, Michal Komorowski, Kieron D. Edwards, Sanyi Tang, Claire V. Harper
, Julian R. E. Davis
, Michael R. H. White
, Andrew J. Millar
, David A. Rand
:
Reconstruction of transcriptional dynamics from gene reporter data using differential equations. 2901-2907
- Melanie Osl, Stephan Dreiseitl, Bernhard Pfeifer
, Klaus Weinberger
, Helmut Klocker, Georg Bartsch, Georg Schäfer, Bernhard Tilg, Armin Graber, Christian Baumgartner
:
A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry. 2908-2914
- Robert T. Morris, Timothy R. O'Connor, John J. Wyrick:
Osiris: an integrated promoter database for Oryza sativa L.. 2915-2917 - Matteo Cesaroni, Davide Cittaro
, Alessandro Brozzi, Pier Giuseppe Pelicci
, Lucilla Luzi
:
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data. 2918-2920 - Jonathan M. Cairns
, Mark J. Dunning
, Matthew E. Ritchie
, Roslin Russell, Andy G. Lynch
:
BASH: a tool for managing BeadArray spatial artefacts. 2921-2922
- Jun Kong, Fei Zhu, Jim Stalker, David J. Adams:
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes. 2923-2925 - Leming Zhou
, Ingrid Mihai, Liliana Florea:
Effective cluster-based seed design for cross-species sequence comparisons. 2926-2927 - Håkan Viklund, Andreas Bernsel, Marcin J. Skwark
, Arne Elofsson
:
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. 2928-2929 - Vinhthuy Phan, Nicholas A. Furlotte:
Motif Tool Manager: a web-based framework for motif discovery. 2930-2931
- Jeffrey C. Oliver:
AUGIST: inferring species trees while accommodating gene tree uncertainty. 2932-2933
- Hui Kian Ho, Michael J. Kuiper, Kotagiri Ramamohanarao
:
PConPy - a Python module for generating 2D protein maps. 2934-2935
- Matthew J. Jobin, Joanna L. Mountain:
REJECTOR: software for population history inference from genetic data via a rejection algorithm. 2936-2937 - Andrew D. Johnson, Robert E. Handsaker, Sara L. Pulit
, Marcia M. Nizzari, Christopher J. O'Donnell, Paul I. W. de Bakker:
SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. 2938-2939
- Nigel Collier
, Son Doan
, Ai Kawazoe, Reiko Matsuda Goodwin, Mike Conway, Yoshio Tateno, Hung Quoc Ngo, Dinh Dien, Asanee Kawtrakul, Koichi Takeuchi, Mika Shigematsu, Kiyosu Taniguchi:
BioCaster: detecting public health rumors with a Web-based text mining system. 2940-2941
- Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala
, Alejandro A. Schäffer:
Database indexing for production MegaBLAST searches. 2942

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