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ORCIDBMC Bioinformatics, Volume 11
Volume 11, 2010
- Shuangge Ma, Michael R. Kosorok:
Detection of gene pathways with predictive power for breast cancer prognosis. 1 - Leander Schietgat, Celine Vens, Jan Struyf, Hendrik Blockeel
, Dragi Kocev, Saso Dzeroski:
Predicting gene function using hierarchical multi-label decision tree ensembles. 2 - Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant:
State of the art: refinement of multiple sequence alignments. 3 - Karel Zimmermann, Jean-François Gibrat:
Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors. 4 - Martijn P. van Iersel, Alexander R. Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo:
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. 5 - Mats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S. Furey, Marie Öhman, Jens Lagergren:
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. 6 - Ben C. Stöver, Kai F. Müller:
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. 7 - Roberto Amato, Michele Pinelli, Daniel D'Andrea, Gennaro Miele, Mario Nicodemi, Giancarlo Raiconi, Sergio Cocozza:
A novel approach to simulate gene-environment interactions in complex diseases. 8 - Benjamin Georgi, Ivan Gesteira Costa, Alexander Schliep:
PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data. 9 - Guanqun Shi, Liqing Zhang, Tao Jiang:
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. 10 - Jingjing Ye, Adam Pavlícek, Elizabeth A. Lunney, Paul A. Rejto, Chi-Hse Teng:
Statistical method on nonrandom clustering with application to somatic mutations in cancer. 11 - Helen A. Arcuri, Geraldo F. D. Zafalon, Evandro A. Marucci, Carlos E. Bonalumi, Nelson José Freitas da Silveira, José Marcio Machado, Walter F. de Azevedo Jr., Mário S. Palma:
SKPDB: a structural database of shikimate pathway enzymes. 12 - Nysia I. George, Joanne R. Lupton, Nancy D. Turner, Robert S. Chapkin, Laurie A. Davidson, Naisyin Wang:
Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach. 13 - Norman E. Davey, Richard J. Edwards, Denis C. Shields:
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. 14 - Joseph M. Dale, Liviu Popescu, Peter D. Karp:
Machine learning methods for metabolic pathway prediction. 15 - Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk, Armita Sheari:
A pairwise residue contact area-based mean force potential for discrimination of native protein structure. 16 - Benoît De Hertogh, Bertrand De Meulder, Fabrice Berger, Michael Pierre, Eric Bareke, Anthoula Gaigneaux, Eric Depiereux:
A benchmark for statistical microarray data analysis that preserves actual biological and technical variance. 17 - David Edwards, Gabriel C. G. de Abreu, Rodrigo Labouriau:
Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests. 18 - Esteban Czwan, Benedikt Brors, David Kipling:
Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets. 19 - Michael Scharfe, Rainer Pielot, Falk Schreiber:
Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets. 20 - Carl Kingsford, Michael C. Schatz, Mihai Pop:
Assembly complexity of prokaryotic genomes using short reads. 21 - Alexander G. Churbanov, Igor Vorechovsky, Chindo Hicks:
A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements. 22 - Thomas K. Wolfgruber, Gernot G. Presting:
JunctionViewer: customizable annotation software for repeat-rich genomic regions. 23 - Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón:
ETE: a python Environment for Tree Exploration. 24 - Shuai Cheng Li, Yen Kaow Ng:
Calibur: a tool for clustering large numbers of protein decoys. 25 - Yu-Qing Qiu, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen:
Detecting disease associated modules and prioritizing active genes based on high throughput data. 26 - Dirk Repsilber, Sabine Kern, Anna Telaar, Gerhard Walzl, Gillian F. Black, Joachim Selbig, Shreemanta K. Parida, Stefan H. E. Kaufmann, Marc Jacobsen:
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. 27 - Shi Yu, Léon-Charles Tranchevent, Bart De Moor, Yves Moreau:
Gene prioritization and clustering by multi-view text mining. 28 - Anders Jacobsen Skanderup, Anders Krogh, Sakari Kauppinen, Morten Lindow:
miRMaid: a unified programming interface for microRNA data resources. 29 - Benjamin Misselwitz, Gerhard Strittmatter, Balamurugan Periaswamy, Markus C. Schlumberger, Samuel Rout, Péter Horváth, Karol Kozak, Wolf-Dietrich Hardt:
Enhanced CellClassifier: a multi-class classification tool for microscopy images. 30 - Sheng He, Juan Mei, Guiyang Shi, Zhengxiang Wang, Weijiang Li:
LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB. 31 - Seyed Yahya Anvar, Peter A. C. 't Hoen, Allan Tucker:
The identification of informative genes from multiple datasets with increasing complexity. 32 - Lance E. Palmer, Mathäus Dejori, Randall A. Bolanos, Daniel P. Fasulo:
Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction. 33 - Harald Barsnes, Richard G. Côté, Ingvar Eidhammer, Lennart Martens:
OLS Dialog: An open-source front end to the Ontology Lookup Service. 34 - Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, David P. Kreil:
Hybridization thermodynamics of NimbleGen Microarrays. 35 - Junbai Wang, Tianhai Tian:
Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53. 36 - Dominik Heider, Jens Verheyen, Daniel Hoffmann:
Predicting Bevirimat resistance of HIV-1 from genotype. 37 - Juan Falgueras, Antonio J. Lara, Noé Fernández-Pozo, Francisco R. Cantón, Guillermo Pérez-Trabado, M. Gonzalo Claros:
SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. 38 - Emanuela Giombini, Massimiliano Orsini, Danilo Carrabino, Anna Tramontano:
An automatic method for identifying surface proteins in bacteria: SLEP. 39 - Yaqiang Wang, Zhonghua Yu, Yongguang Jiang, Kaikuo Xu, Xia Chen:
Automatic symptom name normalization in clinical records of traditional Chinese medicine. 40 - Andrew J. Bordner, Hans D. Mittelmann:
Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. 41 - Russell Schwartz, Stanley Shackney:
Applying unmixing to gene expression data for tumor phylogeny inference. 42 - Tamir Tuller, Yifat Felder, Martin Kupiec:
Discovering local patterns of co - evolution: computational aspects and biological examples. 43 - Ulrike Naumann, George Luta, Matthew P. Wand:
The curvHDR method for gating flow cytometry samples. 44 - Satwik Rajaram, Yoshi Oono:
NeatMap - non-clustering heat map alternatives in R. 45 - Svetlana Bulashevska, Alla Bulashevska, Roland Eils:
Bayesian statistical modelling of human protein interaction network incorporating protein disorder information. 46 - Bing Xiong, Jie Wu, David L. Burk, Mengzhu Xue, Hualiang Jiang, Jingkang Shen:
BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. 47 - Wei-Jiun Lin, Huey-miin Hsueh, James J. Chen:
Power and sample size estimation in microarray studies. 48 - Dimitris G. Bariamis, Dimitrios K. Iakovidis, Dimitris Maroulis:
M3G: Maximum Margin Microarray Gridding. 49 - Taeho Hwang, Choong-Hyun Sun, Taegyun Yun, Gwan-Su Yi:
FiGS: a filter-based gene selection workbench for microarray data. 50 - Mickaël Krzeminski, Karine Loth, Rolf Boelens, Alexandre M. J. J. Bonvin:
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes. 51 - Jeremy D. Selengut, Douglas B. Rusch, Daniel H. Haft:
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. 52 - Yu-Chao Wang, Chung-Yu Lan, Wen-Ping Hsieh, Luis A. Murillo, Nina Agabian, Bor-Sen Chen:
Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. 53 - Jaebum Kim, Saurabh Sinha:
Towards realistic benchmarks for multiple alignments of non-coding sequences. 54 - Byron C. Wallace, Thomas A. Trikalinos, Joseph Lau, Carla E. Brodley, Christopher H. Schmid:
Semi-automated screening of biomedical citations for systematic reviews. 55 - Javier García-García, Emre Guney, Ramon Aragues, Joan Planas-Iglesias, Baldo Oliva:
Biana: a software framework for compiling biological interactions and analyzing networks. 56 - Pankaj Khurana, Rajesh S. Gokhale, Debasisa Mohanty:
Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles. 57 - Benjamin A. Logsdon, Gabriel E. Hoffman, Jason G. Mezey:
A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis. 58 - Alina Sîrbu, Heather J. Ruskin, Martin Crane:
Comparison of evolutionary algorithms in gene regulatory network model inference. 59 - Mayer Alvo, Zhongzhu Liu, Andrew Williams, Carole L. Yauk:
Testing for mean and correlation changes in microarray experiments: an application for pathway analysis. 60 - Xianming Wu, Songfeng Wu, Dong Li, Jiyang Zhang, Lin Hou, Jie Ma, Wanlin Liu, Daming Ren, Yunping Zhu, Fuchu He:
Computational identification of rare codons of Escherichia coli based on codon pairs preference. 61 - Yunqi Li, C. Russell Middaugh, Jianwen Fang:
A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants. 62 - Corey M. Yanofsky, David R. Bickel:
Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing. 63 - Evgeniy V. Petrotchenko, Christoph H. Borchers:
ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. 64 - Julie Hussin, Philippe Nadeau, Jean-François Lefebvre, Damian Labuda:
Haplotype allelic classes for detecting ongoing positive selection. 65 - Guimei Liu, Yue Wang, Limsoon Wong:
FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium. 66 - Ronald van Eijk, Paul H. C. Eilers, Remco Natté, Anne-Marie Cleton-Jansen, Hans Morreau, Tom van Wezel, Jan Oosting:
MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification. 67 - Ritesh Krishna, Chang-Tsun Li, Vicky Buchanan-Wollaston:
A temporal precedence based clustering method for gene expression microarray data. 68 - Bram Slabbinck, Willem Waegeman, Peter Dawyndt, Paul De Vos, Bernard De Baets:
From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification. 69 - Adriano Barbosa-Silva, Theodoros G. Soldatos, Ivan L. F. Magalhães, Georgios A. Pavlopoulos, Jean-Fred Fontaine, Miguel A. Andrade-Navarro, Reinhard Schneider, José Miguel Ortega:
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships. 70 - Ivaylo Ilinkin, Jieping Ye, Ravi Janardan:
Multiple structure alignment and consensus identification for proteins. 71 - Russell L. Zaretzki, Michael A. Gilchrist, William M. Briggs, Artin Armagan:
Bias correction and Bayesian analysis of aggregate counts in SAGE libraries. 72 - Mark J. Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini:
BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets. 73 - Xiaowu Gai, Juan C. Perin, Kevin Murphy, Ryan O'Hara, Monica D'arcy, Adam Wenocur, Hongbo M. Xie, Eric F. Rappaport, Tamim H. Shaikh, Peter S. White:
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. 74 - Leslie Regad, Juliette Martin, Grégory Nuel, Anne-Claude Camproux:
Mining protein loops using a structural alphabet and statistical exceptionality. 75 - Xue Gong, Ruihong Wu, Yuannv Zhang, Wenyuan Zhao, Lixin Cheng, Yunyan Gu, Lin Zhang, Jing Wang, Jing Zhu, Zheng Guo:
Extracting consistent knowledge from highly inconsistent cancer gene data sources. 76 - Ricardo Cao, Mario Francisco-Fernández, Emiliano J. Quinto:
A random effect multiplicative heteroscedastic model for bacterial growth. 77 - Anne-Laure Boulesteix, Torsten Hothorn:
Testing the additional predictive value of high-dimensional molecular data. 78 - Maria Pamela C. David, Gisela P. Concepcion, Eduardo A. Padlan:
Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies. 79 - Martin C. Frith, Michiaki Hamada, Paul Horton:
Parameters for accurate genome alignment. 80 - Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson, Dabing Zhang:
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. 81 - Hedda Høvik, Tsute Chen:
Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. 82 - Aliah Hazmah Hawari, Zeti-Azura Mohamed-Hussein:
Simulation of a Petri net-based Model of the Terpenoid Biosynthesis Pathway. 83 - Zafer Aydin, John I. Murray, Robert H. Waterston, William Stafford Noble:
Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo. 84 - Martin Gerner, Goran Nenadic, Casey M. Bergman:
LINNAEUS: A species name identification system for biomedical literature. 85 - Like Fokkens, Sandra M. C. Botelho, Jos Boekhorst, Berend Snel:
Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. 86 - Alexander Lachmann, Avi Ma'ayan:
Lists2Networks: Integrated analysis of gene/protein lists. 87 - Yi-Ruen Lin, Hsin-Yuan Wei, Tsung-Lin Tsai, Thy-Hou Lin:
HDAPD: a web tool for searching the disease-associated protein structures. 88 - Mindaugas Margelevicius, Ceslovas Venclovas:
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. 89 - Kirsten Roomp, Iris Antes, Thomas Lengauer:
Predicting MHC class I epitopes in large datasets. 90 - Alexander Martin, Maria Elena Ochagavía, Laya C. Rabasa, Jamilet Miranda, Jorge Fernandez-de-Cossío, Ricardo Bringas:
BisoGenet: a new tool for gene network building, visualization and analysis. 91 - Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan:
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. 92 - Daniel MacLean, Vincent Moulton, David J. Studholme:
Finding sRNA generative locales from high-throughput sequencing data with NiBLS. 93 - James H. Bullard, Elizabeth Purdom, Kasper D. Hansen, Sandrine Dudoit:
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. 94 - Ryan Gill, Somnath Datta, Susmita Datta:
A statistical framework for differential network analysis from microarray data. 95 - Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dennis E. Shasha:
SING: Subgraph search In Non-homogeneous Graphs. 96 - Alessandro Pandini, Arianna Fornili, Jens Kleinjung:
Structural alphabets derived from attractors in conformational space. 97 - Jens Keilwagen, Jan Grau, Stefan Posch, Marc Strickert, Ivo Grosse:
Unifying generative and discriminative learning principles. 98 - Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe Vert, Véronique Stoven:
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. 99 - Stacy Duncan, Ruchita Sirkanungo, Leslie Miller, Gregory J. Phillips:
DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data. 100 - Quoc-Chinh Bui, Breanndán Ó Nualláin, Charles A. Boucher, Peter M. A. Sloot:
Extracting causal relations on HIV drug resistance from literature. 101 - Chih-Hsien Cheng, Chung-Han Yang, Hsien-Tai Chiu, Chin Lung Lu:
Reconstructing genome trees of prokaryotes using overlapping genes. 102 - J. Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex D. Wade, Oscar Naim, Greg B. Quinn, Philip E. Bourne:
Word add-in for ontology recognition: semantic enrichment of scientific literature. 103 - Jakub Mieczkowski, Magdalena E. Tyburczy, Michal Dabrowski, Piotr Pokarowski:
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. 104 - Dan C. Tulpan, Mirela Andronescu, Serge Léger:
Free energy estimation of short DNA duplex hybridizations. 105 - Sandra Ortega-Martorell, Iván Olier, Margarida Julià-Sapé, Carles Arús:
SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system. 106 - Seonho Kim, Juntae Yoon, Jihoon Yang, Seog Park:
Walk-weighted subsequence kernels for protein-protein interaction extraction. 107 - Timothy J. Robinson, Michaela A. Dinan, Mark W. Dewhirst, Mariano A. Garcia-Blanco, James L. Pearson:
SplicerAV: a tool for mining microarray expression data for changes in RNA processing. 108 - Kailin Tang, Tong-Hua Li, Wenwei Xiong, Kai Chen:
Ovarian cancer classification based on dimensionality reduction for SELDI-TOF data. 109 - Kristin K. Nicodemus, James D. Malley, Carolin Strobl, Andreas Ziegler:
The behaviour of random forest permutation-based variable importance measures under predictor correlation. 110 - Ching-Lin Hsiao, Ie-Bin Lian, Ai-Ru Hsieh, Cathy S. J. Fann:
Modeling expression quantitative trait loci in data combining ethnic populations. 111 - Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W. Hentze, Thomas Dandekar, Martina U. Muckenthaler:
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. 112 - Eisuke Chikayama, Atsushi Kurotani, Takanori Tanaka, Takashi Yabuki, Satoshi Miyazaki, Shigeyuki Yokoyama, Yutaka Kuroda:
Mathematical model for empirically optimizing large scale production of soluble protein domains. 113 - Weilong Hao:
OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs. 114