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ORCIDBioinformatics, 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 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