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BMC 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 - Elisa Cilia, Andrea Passerini
:
Automatic prediction of catalytic residues by modeling residue structural neighborhood. 115 - Daniel Wegmann
, Christoph Leuenberger, Samuel Neuenschwander
, Laurent Excoffier
:
ABCtoolbox: a versatile toolkit for approximate Bayesian computations. 116 - Aaron M. Newman
, James B. Cooper:
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. 117 - Chongle Pan
, Byung-Hoon Park, William H. McDonald
, Patricia A. Carey, Jillian F. Banfield
, Nathan Verberkmoes, Robert L. Hettich
, Nagiza F. Samatova:
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. 118 - Doug Hyatt, Gwo-Liang Chen, Philip F. LoCascio, Miriam L. Land
, Frank W. Larimer, Loren J. Hauser:
Prodigal: prokaryotic gene recognition and translation initiation site identification. 119 - Tamás Nepusz, Rajkumar Sasidharan, Alberto Paccanaro:
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. 120 - Florian Battke
, Stephan Symons, Kay Nieselt
:
Mayday - integrative analytics for expression data. 121 - Hansi Weißensteiner
, Sebastian Schönherr, Günther Specht, Florian Kronenberg
, Anita Brandstätter
:
eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. 122 - Jennifer M. Staab, Thomas M. O'Connell, Shawn M. Gomez
:
Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). 123 - Tetyana Ivanovska, Andrea Schenk
, André Homeyer
, Meihong Deng, Uta Dahmen, Olaf Dirsch, Horst K. Hahn, Lars Linsen:
A fast and robust hepatocyte quantification algorithm including vein processing. 124 - Aarti Garg, Rupinder Tewari
, Gajendra P. S. Raghava
:
KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. 125 - Martin Paluszewski, Thomas Hamelryck
:
Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks. 126 - Andrew Williams
, Errol M. Thomson
:
Effects of scanning sensitivity and multiple scan algorithms on microarray data quality. 127 - Dmitry Rykunov, András Fiser:
New statistical potential for quality assessment of protein models and a survey of energy functions. 128 - Jessica S. Reuter, David H. Mathews:
RNAstructure: software for RNA secondary structure prediction and analysis. 129 - Aakrosh Ratan, Yu Zhang, Vanessa M. Hayes
, Stephan C. Schuster, Webb Miller:
Calling SNPs without a reference sequence. 130 - Andrew S. Warren
, Jeremy S. Archuleta, Wu-chun Feng, João Carlos Setubal
:
Missing genes in the annotation of prokaryotic genomes. 131 - Hsiao Ping Lee, Tzu-Fang Sheu, Chuan Yi Tang:
A parallel and incremental algorithm for efficient unique signature discovery on DNA databases. 132 - José Afonso Guerra-Assunção
, Anton J. Enright
:
MapMi: automated mapping of microRNA loci. 133 - Yurii S. Aulchenko
, Maksim V. Struchalin, Cornelia M. van Duijn
:
ProbABEL package for genome-wide association analysis of imputed data. 134 - Haroon Naeem
, Robert Küffner, Gergely Csaba, Ralf Zimmer
:
miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. 135 - Luis Quintales
, Mar Sánchez
, Francisco Antequera
:
Analysis of DNA strand-specific differential expression with high density tiling microarrays. 136 - Louis Licamele, Lise Getoor:
Indirect two-sided relative ranking: a robust similarity measure for gene expression data. 137 - Mallika Veeramalai, David R. Gilbert, Gabriel Valiente
:
An optimized TOPS+ comparison method for enhanced TOPS models. 138 - Hunter N. B. Moseley
:
Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. 139 - Ioannis A. Maraziotis, Andrei Dragomir
, Dimitris Thanos:
Gene regulatory networks modelling using a dynamic evolutionary hybrid. 140 - Brady Olsen, Christopher J. Murakami, Matt Kaeberlein
:
YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. 141 - Kirill Kryukov, Naruya Saitou:
MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. 142 - Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang
:
MPprimer: a program for reliable multiplex PCR primer design. 143 - Martial Hue, Michael Riffle
, Jean-Philippe Vert
, William Stafford Noble:
Large-scale prediction of protein-protein interactions from structures. 144 - Bobbie-Jo M. Webb-Robertson
, Kyle G. Ratuiste, Christopher S. Oehmen:
Physicochemical property distributions for accurate and rapid pairwise protein homology detection. 145 - Michael L. Sierk
, Michael E. Smoot, Ellen J. Bass
, William R. Pearson
:
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. 146 - Teo Shu Mei
, Agus Salim
, Stefano Calza
, Ku Chee Seng, Kee Seng Chia, Yudi Pawitan:
Identification of recurrent regions of copy-number variants across multiple individuals. 147 - Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann
, Steffen Neumann
:
In silico fragmentation for computer assisted identification of metabolite mass spectra. 148 - Jens Keilwagen
, Jan Grau, Stefan Posch, Ivo Grosse:
Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis. 149 - Sigrid Rouam, Thierry Moreau, Philippe Broët
:
Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes. 150 - Pierre M. Durand
, Scott Hazelhurst
, Theresa L. Coetzer:
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function. 151 - James Robert White, Saket Navlakha, Niranjan Nagarajan
, Mohammadreza Ghodsi, Carl Kingsford, Mihai Pop
:
Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. 152 - Feng-Jie Sun, Gustavo Caetano-Anollés:
The ancient history of the structure of ribonuclease P and the early origins of Archaea. 153 - Pietro Zoppoli
, Sandro Morganella
, Michele Ceccarelli
:
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. 154 - Zong Hong Zhang
, Hwee Kuan Lee, Ivana Mihalek:
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. 155 - Marc Hulsman, Anouk Mentink, Eugene P. van Someren, Koen J. Dechering, Jan de Boer
, Marcel J. T. Reinders:
Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization. 156 - Mariana L. Neves
, José María Carazo, Alberto D. Pascual-Montano:
Moara: a Java library for extracting and normalizing gene and protein mentions. 157 - Jorn R. de Haan, Ester Piek, René C. van Schaik, Jacob de Vlieg, Susanne Bauerschmidt, Lutgarde M. C. Buydens, Ron Wehrens
:
Integrating gene expression and GO classification for PCA by preclustering. 158 - Thomas Kuhn, Egon L. Willighagen
, Achim Zielesny, Christoph Steinbeck
:
CDK-Taverna: an open workflow environment for cheminformatics. 159 - Hifzur Rahman Ansari
, Gajendra P. S. Raghava
:
Identification of NAD interacting residues in proteins. 160 - Israel T. da Silva
, Ricardo Z. N. Vêncio
, Thiago Y. K. Oliveira
, Greice A. Molfetta
, Wilson A. Silva Jr.
:
ProbFAST: Probabilistic Functional Analysis System Tool. 161 - Chen Wang
, Jianhua Xuan, Huai Li, Yue Joseph Wang, Ming Zhan, Eric P. Hoffman
, Robert Clarke
:
Knowledge-guided gene ranking by coordinative component analysis. 162 - Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan
, Adam Kuspa
, Devika Subramanian
, Gad Shaulsky
:
New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. 163 - Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew
, Hong Yan
:
Multiconstrained gene clustering based on generalized projections. 164 - Robert C. McLeay, Timothy L. Bailey:
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. 165 - Saurin D. Jani, Gary L. Argraves, Jeremy L. Barth, W. Scott Argraves:
GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. 166 - Chi-Yuan Yu, Lih-Ching Chou, Darby Tien-Hao Chang:
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. 167 - Jian Shi, Yiwei Zhang, Haiwei Luo
, Jijun Tang:
Using jackknife to assess the quality of gene order phylogenies. 168 - Johann M. Kraus
, Hans A. Kestler
:
A highly efficient multi-core algorithm for clustering extremely large datasets. 169 - Ken Tatebe, Ahmet Zeytun, Ruy M. Ribeiro
, Robert Hoffmann, Kevin S. Harrod
, Christian V. Forst
:
Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. 170 - Mehar S. Khatkar, Matthew Hobbs, Markus Neuditschko
, Johann Sölkner
, Frank W. Nicholas
, Herman W. Raadsma:
Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates. 171 - Jonathan J. Ellis
, Fabien P. E. Huard, Charlotte M. Deane
, Sheenal Srivastava, Graham R. Wood:
Directionality in protein fold prediction. 172 - Hsueh-Wei Chang, Yu-Huei Cheng
, Li-Yeh Chuang, Cheng-Hong Yang:
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. 173 - Junfeng Xia
, Xing-Ming Zhao, Jiangning Song
, De-Shuang Huang:
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. 174 - Rabie Saidi
, Mondher Maddouri, Engelbert Mephu Nguifo
:
Protein sequences classification by means of feature extraction with substitution matrices. 175 - Gregor Stiglic
, Mateja Bajgot, Peter Kokol
:
Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays. 176 - Karl W. Kuschner, Dariya I. Malyarenko, William E. Cooke, Lisa H. Cazares
, O. John Semmes, Eugene R. Tracy:
A Bayesian network approach to feature selection in mass spectrometry data. 177 - Andrew K. Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt D. B. Halstead, Jonathan Cooper
, David P. Nickerson
, Poul M. F. Nielsen:
An overview of the CellML API and its implementation. 178 - Timothy L. Bailey, Mikael Bodén
, Tom Whitington, Philip Machanick
:
The value of position-specific priors in motif discovery using MEME. 179 - Andrew S. Parker, Wei Zheng, Karl E. Griswold
, Chris Bailey-Kellogg:
Optimization algorithms for functional deimmunization of therapeutic proteins. 180 - Qi Liu, Qian Xu, Vincent Wenchen Zheng, Hong Xue
, Zhi-Wei Cao, Qiang Yang:
Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study. 181 - Bing Wang
, Steve Valentine, Manolo Plasencia
, Sriram Raghuraman, Xiang Zhang:
Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. 182 - Megu Ohtaki, Keiko Otani, Keiko Hiyama, Naomi Kamei, Kenichi Satoh, Eiso Hiyama:
A robust method for estimating gene expression states using Affymetrix microarray probe level data. 183 - Stephanie Zierke, Jason D. Bakos:
FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods. 184 - Oliver Pelz, Moritz Gilsdorf, Michael Boutros
:
web cellHTS2: A web-application for the analysis of high-throughput screening data. 185 - Davide Sisti
, Michele Guescini
, Marco B. L. Rocchi
, Pasquale Tibollo, Mario D'Atri, Vilberto Stocchi:
Shape based kinetic outlier detection in real-time PCR. 186 - Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li
:
Artificial and natural duplicates in pyrosequencing reads of metagenomic data. 187 - Márton Münz, Rune B. Lyngsø, Jotun Hein, Philip C. Biggin
:
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. 188 - Felix Sanchez-Garcia, Uri David Akavia, Eyal Mozes, Dana Pe'er
:
JISTIC: Identification of Significant Targets in Cancer. 189 - Sanghamitra Bandyopadhyay, Malay Bhattacharyya
:
PuTmiR: A database for extracting neighboring transcription factors of human microRNAs. 190 - Charlotte Soneson
, Henrik Lilljebjörn
, Thoas Fioretos
, Magnus Fontes:
Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. 191 - Andrew J. Bordner:
Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design. 192 - Tiejun Cheng
, Zhihai Liu, Renxiao Wang
:
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction. 193 - Benedikt Zacher, Pei Fen Kuan, Achim Tresch:
Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. 194 - Tala Bakheet, Andrew J. Doig
:
Properties and identification of antibiotic drug targets. 195 - Hui-Hsien Chou:
Shared probe design and existing microarray reanalysis using PICKY. 196 - Colm Ryan
, Derek Greene
, Gerard Cagney
, Padraig Cunningham
:
Missing value imputation for epistatic MAPs. 197 - Antonio Deiana, Andrea Giansanti
:
Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets. 198 - Franziska Hoffgaard, Philipp Weil, Kay Hamacher:
BioPhysConnectoR: Connecting Sequence Information and Biophysical Models. 199 - Fuhai Li, Xiaobo Zhou, Wanting Huang, Chung-Che Chang, Stephen T. C. Wong:
Conditional random pattern model for copy number aberration detection. 200 - Olof Görnerup, Martin Nilsson Jacobi:
A model-independent approach to infer hierarchical codon substitution dynamics. 201 - Kyoung Ae Kim, Sabrina L. Spencer
, John G. Albeck, John M. Burke, Peter K. Sorger
, Suzanne Gaudet
, Do Hyun Kim:
Systematic calibration of a cell signaling network model. 202 - Pao-Yang Chen
, Shawn Cokus, Matteo Pellegrini
:
BS Seeker: precise mapping for bisulfite sequencing. 203 - Annalisa Marsico, Andreas Henschel, Christof Winter
, Anne Tuukkanen, Boris Vassilev
, Kerstin Scheubert, Michael Schroeder:
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. 204 - Kevin Horan, Christian R. Shelton
, Thomas Girke
:
Predicting conserved protein motifs with Sub-HMMs. 205 - Massimiliano Virgilio
, Thierry Backeljau, Bruno Nevado
, Marc De Meyer:
Comparative performances of DNA barcoding across insect orders. 206 - Mario Fasold, Peter F. Stadler
, Hans Binder
:
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. 207 - Mike L. Smith
, Mark J. Dunning
, Simon Tavaré, Andy G. Lynch
:
Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. 208 - Federico Plazzi
, Ronald R. Ferrucci, Marco Passamonti
:
Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. 209 - Subhadip Basu
, Dariusz Plewczynski
:
AMS 3.0: prediction of post-translational modifications. 210 - Yi Qu, Fei He, Yuchen Chen:
Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays. 211 - Sérgio Matos
, Joel Arrais
, João Maia-Rodrigues
, José Luís Oliveira
:
Concept-based query expansion for retrieving gene related publications from MEDLINE. 212 - Jan Schellenberger, Junyoung O. Park
, Tom M. Conrad, Bernhard O. Palsson:
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. 213 - Henning Redestig
, Miyako Kusano
, Atsushi Fukushima
, Fumio Matsuda, Kazuki Saito
, Masanori Arita:
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. 214 - Jaehee Jung, Gangman Yi, Serenella A. Sukno
, Michael R. Thon
:
PoGO: Prediction of Gene Ontology terms for fungal proteins. 215 - Rileen Sinha
, Thorsten Lenser, Niels Jahn, Ulrike Gausmann
, Swetlana Friedel, Karol Szafranski, Klaus Huse
, Philip Rosenstiel
, Jochen Hampe
, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer:
TassDB2 - A comprehensive database of subtle alternative splicing events. 216 - Unitsa Sangket, Surakameth Mahasirimongkol
, Wasun Chantratita, Pichaya Tandayya, Yurii S. Aulchenko
:
ParallABEL: an R library for generalized parallelization of genome-wide association studies. 217 - Stuart Collins, Michail Stamatakis
, Dionisios G. Vlachos
:
Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes. 218 - Fan Mo, Qun Mo, Yuanyuan Chen, David R. Goodlett, Leroy Hood, Gilbert S. Omenn
, Song Li, Biaoyang Lin:
WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. 219 - Andreas Prlic
, Marco A. Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T. Yukich, Peter W. Rose
, Philip E. Bourne, J. Lynn Fink
:
Integration of open access literature into the RCSB Protein Data Bank using BioLit. 220 - Alberto Risueño
, Celia Fontanillo
, Marcel E. Dinger
, Javier De Las Rivas
:
GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. 221 - Andreas Bremges, Stefanie Schirmer, Robert Giegerich:
Fine-tuning structural RNA alignments in the twilight zone. 222 - Jérôme Lane, Patrice Duroux, Marie-Paule Lefranc
:
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. 223 - Ryuichiro Nakato
, Osamu Gotoh:
Cgaln: fast and space-efficient whole-genome alignment. 224 - Denitsa Alamanova, Philip Stegmaier, Alexander E. Kel:
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. 225 - Louis-Philippe Lemieux Perreault, Gregor U. Andelfinger, Géraldine Asselin, Marie-Pierre Dubé
:
Partitioning of copy-number genotypes in pedigrees. 226 - Hailong Meng, Andrew R. Joyce, Daniel E. Adkins, Priyadarshi Basu, Yankai Jia, Guoya Li, Tapas K. Sengupta, Barbara K. Zedler, Edward Lenn Murrelle, Edwin J. C. G. van den Oord:
A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling. 227 - Luigi Cerulo
, Charles Elkan, Michele Ceccarelli
:
Learning gene regulatory networks from only positive and unlabeled data. 228 - Alain B. Tchagang, Alexander Gawronski, Hugo Bérubé, Sieu Phan, Fazel Famili, Youlian Pan
:
GOAL: A software tool for assessing biological significance of genes groups. 229 - Christian Rohde, Yingying Zhang, Richard Reinhardt
, Albert Jeltsch
:
BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. 230 - Mariusz Popenda, Marta Szachniuk
, Marek Blazewicz, Szymon Wasik
, Edmund K. Burke
, Jacek Blazewicz, Ryszard W. Adamiak:
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. 231 - Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, Masaru Tomita:
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. 232 - Jan Krumsiek, Sebastian Pölsterl
, Dominik M. Wittmann, Fabian J. Theis
:
Odefy -- From discrete to continuous models. 233 - Johannes M. Freudenberg
, Siva Sivaganesan, Michael Wagner
, Mario Medvedovic:
A semi-parametric Bayesian model for unsupervised differential co-expression analysis. 234 - Toshihide Hara, Keiko Sato, Masanori Ohya:
MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues. 235 - Nobuyuki Uchikoga, Takatsugu Hirokawa:
Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. 236 - Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson
, Hervé Pagès, Simon M. Lin, David S. Lapointe, Michael R. Green:
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. 237 - Daniel Rios, William M. McLaren
, Yuan Chen, Ewan Birney
, Arne Stabenau, Paul Flicek
, Fiona Cunningham
:
A database and API for variation, dense genotyping and resequencing data. 238 - Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard
, James A. Smith
, Stephen J. Trevanion
:
Using caching and optimization techniques to improve performance of the Ensembl website. 239 - Jessica Severin, Kathryn Beal, Albert J. Vilella
, Stephen Fitzgerald, Michael Schuster
, Leo Gordon, Abel Ureta-Vidal, Paul Flicek
, Javier Herrero
:
eHive: An Artificial Intelligence workflow system for genomic analysis. 240 - Chi Kin Chow, Hai Long Zhu, Jessica Lacy, Winston Patrick Kuo:
Error margin analysis for feature gene extraction. 241 - Drew H. Bryant, Mark Moll
, Brian Y. Chen, Viacheslav Fofanov, Lydia E. Kavraki
:
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. 242 - Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder
, Mark B. Gerstein:
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. 243 - Qian Liu, Jinyan Li:
Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective. 244 - Henrik Bengtsson
, Pierre Neuvial
, Terence P. Speed:
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. 245 - Hong-Xuan Zhang, John Goutsias:
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems. 246 - Huaien Luo, Juntao Li, Majid Eshaghi, Jianhua Liu, R. Krishna Murthy Karuturi:
Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data. 247 - Pekka Ruusuvuori, Tarmo Äijö
, Sharif Chowdhury, Cecilia Garmendia-Torres, Jyrki Selinummi, Mirko Birbaumer, Aimée M. Dudley
, Lucas Pelkmans
, Olli Yli-Harja
:
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. 248 - Isana Veksler-Lublinsky
, Yonat Shemer-Avni, Klara Kedem, Michal Ziv-Ukelson:
Gene bi-targeting by viral and human miRNAs. 249 - Qi Liu, Juan Cui, Qiang Yang, Ying Xu:
In-silico prediction of blood-secretory human proteins using a ranking algorithm. 250 - Florian Teichert, Jonas Minning, Ugo Bastolla
, Markus Porto:
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH. 251 - Donald M. Gray, Carla W. Gray, Byong-Hoon Yoo, Tzu-Fang Lou:
Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data. 252 - Inna Chervoneva, Yanyan Li, Stephanie Schulz, Sean Croker, Chantell Wilson, Scott A. Waldman
, Terry Hyslop:
Selection of optimal reference genes for normalization in quantitative RT-PCR. 253 - Maciej Paszkowski-Rogacz, Mikolaj Slabicki, M. Teresa Pisabarro
, Frank Buchholz
:
PhenoFam-gene set enrichment analysis through protein structural information. 254 - Bin Chen, Xiao Dong, Dazhi Jiao, Huijun Wang, Qian Zhu
, Ying Ding
, David J. Wild:
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. 255 - Edon Sung, Sangsoo Kim, Whanchul Shin:
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. 256 - Stephen F. Madden
, Susan B. Carpenter, Ian B. Jeffery
, Harry Björkbacka
, Katherine A. Fitzgerald, Luke A. O'Neill
, Desmond G. Higgins:
Detecting microRNA activity from gene expression data. 257 - Retraction: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase. 258
- Dennis P. Wall, Parul Kudtarkar
, Vincent A. Fusaro, Rimma Pivovarov
, Prasad Patil, Peter J. Tonellato:
Cloud computing for comparative genomics. 259 - Andrew N. Tolopko, John P. Sullivan, Sean D. Erickson, David Wrobel, Su L. Chiang, Katrina Rudnicki, Stewart Rudnicki, Jennifer Nale, Laura M. Selfors
, Dara Greenhouse, Jeremy Muhlich
, Caroline E. Shamu:
Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities. 260 - Jingming Ma, Carrie Dykes, Tao Wu, Yangxin Huang, Lisa M. Demeter, Hulin Wu:
vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments. 261 - Tomás Norambuena
, Francisco Melo
:
The Protein-DNA Interface database. 262 - Michael Riffle
, Trisha N. Davis
:
The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. 263 - Arnald Alonso, Antonio Julià
, Raül Tortosa, Cristina Canaleta, Juan D. Cañete
, Javier Ballina, Alejandro Balsa, Jesús Tornero, Sara Marsal
:
CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays. 264 - Troy Hawkins, Meghana Chitale, Daisuke Kihara:
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. 265 - Jason W. H. Wong, Alexander B. Schwahn, Kevin M. Downard
:
FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data. 266 - Guofeng Meng, Axel Mosig
, Martin Vingron:
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. 267 - Miguel Arenas
, Mateus Patricio
, David Posada
, Gabriel Valiente
:
Characterization of phylogenetic networks with NetTest. 268 - Joachim M. De Schrijver, Kim De Leeneer
, Steve Lefever, Nick Sabbe, Filip Pattyn
, Filip Van Nieuwerburgh
, Paul Coucke
, Dieter Deforce
, Jo Vandesompele
, Sofie Bekaert, Jan Hellemans, Wim Van Criekinge
:
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. 269 - Marta Blangiardo, Alberto Cassese
, Sylvia Richardson
:
sdef: an R package to synthesize lists of significant features in related experiments. 270 - Shuangge Ma, Mingyu Shi, Yang Li, Danhui Yi, Ben-Chang Shia:
Incorporating gene co-expression network in identification of cancer prognosis markers. 271 - Xin He, Moushumi Sen Sarma, Xu Ling, Brant W. Chee
, Chengxiang Zhai, Bruce R. Schatz:
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. 272 - Ashis Kumer Biswas
, Nasimul Noman
, Abdur Rahman Sikder:
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. 273 - Benjamin Schmid
, Johannes E. Schindelin, Albert Cardona, Mark Longair, Martin Heisenberg:
A high-level 3D visualization API for Java and ImageJ. 274 - Erdogan Taskesen
, Renee Beekman
, Jeroen de Ridder
, Bas J. Wouters, Justine K. Peeters, Ivo P. Touw, Marcel J. T. Reinders, Ruud Delwel:
HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data. 275 - Birte Hellwig, Jan G. Hengstler
, Marcus Schmidt, Mathias C. Gehrmann, Wiebke Schormann, Jörg Rahnenführer
:
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. 276 - Gad Abraham
, Adam Kowalczyk, Sherene Loi
, Izhak Haviv, Justin Zobel:
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. 277 - Hong Cui
:
Semantic annotation of morphological descriptions: an overall strategy. 278 - Tung T. Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis:
Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver. 279 - Matthew E. Ritchie, Matthew S. Forrest
, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panagiotis Deloukas, Simon Tavaré:
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. 280 - John R. Stevens, Jason L. Bell, Kenneth I. Aston
, Kenneth L. White:
A comparison of probe-level and probeset models for small-sample gene expression data. 281 - Martin Eklund, Ola Spjuth
, Jarl E. S. Wikberg:
An eScience-Bayes strategy for analyzing omics data. 282 - Jose M. Duarte
, Rajagopal Sathyapriya
, Henning Stehr, Ioannis Filippis, Michael Lappe:
Optimal contact definition for reconstruction of Contact Maps. 283 - Steven N. Steinway
, Ruth Dannenfelser
, Christopher D. Laucius, James E. Hayes, Sudhir Nayak:
JCoDA: a tool for detecting evolutionary selection. 284 - Qianqian Zhu, Jeffrey C. Miecznikowski, Marc S. Halfon:
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. 285 - Mainak Guharoy
, Pinak Chakrabarti:
Conserved residue clusters at protein-protein interfaces and their use in binding site identification. 286 - Conor Lawless
, Darren J. Wilkinson
, Alexander Young, Stephen G. Addinall, David A. Lydall:
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. 287 - Reedik Mägi
, Andrew P. Morris:
GWAMA: software for genome-wide association meta-analysis. 288 - Lars Vogt
:
Spatio-structural granularity of biological material entities. 289 - Jing Wang, Xianxiao Zhou, Jing Zhu, Chenggui Zhou, Zheng Guo:
Revealing and avoiding bias in semantic similarity scores for protein pairs. 290 - Hans Binder
, Knut Krohn, Conrad J. Burden
:
Washing scaling of GeneChip microarray expression. 291 - Martin Sturm, Michael Hackenberg
, David Langenberger
, Dmitrij Frishman:
TargetSpy: a supervised machine learning approach for microRNA target prediction. 292 - Lei Chen
, Kai-Yan Feng, Yu-Dong Cai
, Kuo-Chen Chou, Hai-Peng Li
:
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. 293 - Javier Tamames
, Victor de Lorenzo
:
EnvMine: A text-mining system for the automatic extraction of contextual information. 294 - Rashi Gupta, Dario Greco
, Petri Auvinen, Elja Arjas:
Bayesian integrated modeling of expression data: a case study on RhoG. 295 - Donghwan Lee
, Woojoo Lee, Youngjo Lee, Yudi Pawitan:
Super-sparse principal component analyses for high-throughput genomic data. 296 - Irina Ostrovnaya, Gouri Nanjangud, Adam B. Olshen:
A classification model for distinguishing copy number variants from cancer-related alterations. 297 - Zhong-Ru Xie
, Ming-Jing Hwang:
An interaction-motif-based scoring function for protein-ligand docking. 298 - Raghunandan M. Kainkaryam, Angela Bruex, Anna C. Gilbert, John Schiefelbein, Peter J. Woolf:
poolMC: Smart pooling of mRNA samples in microarray experiments. 299 - Assaf Gottlieb, Roy Varshavsky, Michal Linial
, David Horn
:
UFFizi: a generic platform for ranking informative features. 300 - Jagat Singh Chauhan, Nitish K. Mishra, Gajendra P. S. Raghava
:
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information. 301 - Jiye Ai, Barry Smith
, Wong T. David:
Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base. 302 - Changhoon Kim, Jodi Basner, Byungkook Lee:
Detecting internally symmetric protein structures. 303 - Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A. Albert
, Steve Rounsley, David Sankoff:
Scaffold filling, contig fusion and comparative gene order inference. 304 - Leandro A. Loss, Anguraj Sadanandam
, Steffen Durinck, Shivani Nautiya, Diane Flaucher, Victoria E. H. Carlton, Martin Moorhead, Yontao Lu, Joe W. Gray, Malek Faham, Paul T. Spellman, Bahram Parvin:
Prediction of epigenetically regulated genes in breast cancer cell lines. 305 - Tim Harder, Wouter Boomsma
, Martin Paluszewski, Jes Frellsen
, Kristoffer E. Johansson
, Thomas Hamelryck
:
Beyond rotamers: a generative, probabilistic model of side chains in proteins. 306 - Gerd Gruenert, Bashar Ibrahim
, Thorsten Lenser, Maiko Lohel, Thomas Hinze
, Peter Dittrich:
Rule-based spatial modeling with diffusing, geometrically constrained molecules. 307 - Shih Chi Peng, David Shan-Hill Wong, Kai Che Tung, Yan Yu Chen, Chun Cheih Chao
, Chien Hua Peng, Yung-Jen Chuang
, Chuan Yi Tang:
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation. 308 - Shi Yu, Tillmann Falck, Anneleen Daemen, Léon-Charles Tranchevent
, Johan A. K. Suykens
, Bart De Moor, Yves Moreau
:
L2-norm multiple kernel learning and its application to biomedical data fusion. 309 - Kieran Alden
, Stella Veretnik, Philip E. Bourne:
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. 310 - Stephen J. Goodswen
, Cedric Gondro
, Nathan S. Watson-Haigh
, Haja N. Kadarmideen
:
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. 311 - Paul D. Thomas
:
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. 312 - Boris Sobolev
, Dmitry Filimonov
, Alexey Lagunin
, Alexey V. Zakharov, Olga Koborova, Alexander E. Kel, Vladimir Poroikov
:
Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. 313 - Osamu Komori, Shinto Eguchi
:
A boosting method for maximizing the partial area under the ROC curve. 314 - Pietro Hiram Guzzi, Mario Cannataro
:
mu-CS: An extension of the TM4 platform to manage Affymetrix binary data. 315 - Eelke van der Horst, Julio E. Peironcely, Adriaan P. IJzerman
, Margot W. Beukers, Jonathan Robert Lane
, Herman W. T. van Vlijmen, Michael T. M. Emmerich
, Yasushi Okuno, Andreas Bender:
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. 316 - Amber L. Hartman
, Sean Riddle, Timothy M. McPhillips, Bertram Ludäscher, Jonathan A. Eisen
:
WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences. 317 - Lukas Forer
, Sebastian Schönherr, Hansi Weißensteiner
, Florian Haider, Thomas Kluckner, Christian Gieger
, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg
, Anita Kloss-Brandstätter
:
CONAN: copy number variation analysis software for genome-wide association studies. 318 - Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards
:
Accessing the SEED genome databases via Web services API: tools for programmers. 319 - Mirva Piippo, Niina Lietzén, Olli Nevalainen, Jussi Salmi
, Tuula A. Nyman
:
Pripper: prediction of caspase cleavage sites from whole proteomes. 320 - Paola M. V. Rancoita
, Marcus Hutter
, Francesco Bertoni
, Ivo Kwee:
An integrated Bayesian analysis of LOH and copy number data. 321 - Emidio Capriotti
, Marc A. Martí-Renom
:
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. 322 - Patrick Happel
, Kerstin Moller, Ralf Kunz, Irmgard D. Dietzel
:
A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy. 323 - Sophie S. Abby
, Eric Tannier, Manolo Gouy, Vincent Daubin
:
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. 324 - Zhanchao Li, Xuan Zhou, Zong Dai, Xiaoyong Zou:
Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm. 325 - Shao-Wu Zhang, Yao-Jun Li, Li C. Xia
, Quan Pan:
PPLook: an automated data mining tool for protein-protein interaction. 326 - Svetlana Kirillova, Silvio C. E. Tosatto
, Oliviero Carugo:
FRASS: the web-server for RNA structural comparison. 327 - Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin R. Schiller
:
MimoSA: a system for minimotif annotation. 328 - Ivo D. Shterev, Sin-Ho Jung, Stephen L. George, Kouros Owzar:
permGPU: Using graphics processing units in RNA microarray association studies. 329 - Sebastian Bremm, Tobias Schreck
, Patrick Boba, Stephanie Held, Kay Hamacher:
Computing and visually analyzing mutual information in molecular co-evolution. 330 - Ilari Scheinin, Jose A. Ferreira, Sakari Knuutila, Gerrit Meijer
, Mark A. van de Wiel
, Bauke Ylstra
:
CGHpower: exploring sample size calculations for chromosomal copy number experiments. 331 - Hiroshi Mori
, Fumito Maruyama
, Ken Kurokawa:
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. 332 - Kristoffer Illergård, Simone Callegari, Arne Elofsson
:
MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane. 333 - Chun-Chi Chou, M. Rajasekaran, Chinpan Chen:
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking. 334 - Kaname Kojima, Masao Nagasaki
, Satoru Miyano
:
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. 335 - Marc Bruckskotten, Mario Looso
, Franz Cemic
, Anne Konzer, Jürgen Hemberger, Markus Kruger, Thomas Braun
:
PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms. 336 - Cunlu Zou, Christophe Ladroue, Shuixia Guo, Jianfeng Feng
:
Identifying interactions in the time and frequency domains in local and global networks - A Granger Causality Approach. 337 - Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu, Kun Zhang:
svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification. 338 - Maris Lapins
, Jarl E. S. Wikberg:
Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques. 339 - Ravi Vijaya Satya, Kamal Kumar
, Nela Zavaljevski, Jaques Reifman:
A high-throughput pipeline for the design of real-time PCR signatures. 340 - Robert Schmieder, Yan Wei Lim, Forest Rohwer
, Robert A. Edwards
:
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. 341 - Xiaoqin Xia
, Michael McClelland
, Yipeng Wang:
TabSQL: a MySQL tool to facilitate mapping user data to public databases. 342 - Zhuhong You
, Zheng Yin
, Kyungsook Han, De-Shuang Huang, Xiaobo Zhou:
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. 343 - Benjamin Chain
, Helen Bowen, John Hammond
, Wilfried Posch
, Jane Rasaiyaah, Jhen Tsang, Mahdad Noursadeghi
:
Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays. 344 - Adel Dayarian, Todd P. Michael
, Anirvan M. Sengupta:
SOPRA: Scaffolding algorithm for paired reads via statistical optimization. 345 - Liqun Xi, Yvonne Fondufe-Mittendorf, Lei Xia, Jared Flatow, Jonathan Widom, Ji-Ping Wang:
Predicting nucleosome positioning using a duration Hidden Markov Model. 346 - Nils Homer, Stanley F. Nelson, Barry Merriman:
Local alignment of generalized k-base encoded DNA sequence. 347 - Matias Piipari
, Thomas A. Down, Tim J. P. Hubbard:
Metamotifs - a generative model for building families of nucleotide position weight matrices. 348 - Yichuan Liu
, Aydin Tözeren:
Modular composition predicts kinase/substrate interactions. 349 - Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita:
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. 350 - Martin Klammer, Klaus Godl, Andreas Tebbe, Christoph Schaab
:
Identifying differentially regulated subnetworks from phosphoproteomic data. 351 - Albert Solernou, Juan Fernández-Recio
:
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. 352 - John C. Dittmar
, Robert J. D. Reid, Rodney Rothstein
:
ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data. 353 - Omar J. Jabado, Sean Conlan
, Phenix-Lan Quan, Jeffrey Hui, Gustavo F. Palacios
, Mady Hornig
, Thomas Briese, W. Ian Lipkin
:
Nonparametric methods for the analysis of single-color pathogen microarrays. 354 - Marc Bailly-Bechet
, Alfredo Braunstein
, Andrea Pagnani
, Martin Weigt
, Riccardo Zecchina
:
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. 355 - High-Seng Chai, Terry M. Therneau, Kent R. Bailey, Jean-Pierre A. Kocher:
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. 356 - Sibel Kalyoncu
, Ozlem Keskin, Attila Gürsoy
:
Interaction prediction and classification of PDZ domains. 357 - Wolfgang Hankeln, Pier Luigi Buttigieg
, Dennis Fink, Renzo Kottmann, Pelin Yilmaz
, Frank Oliver Glöckner:
MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. 358 - David S. Huen
, Steven Russell
:
On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence. 359 - Kris Laukens
, Jens Hollunder
, Thanh Hai Dang, Geert De Jaeger
, Martin Kuiper
, Erwin Witters, Alain Verschoren, Koenraad Van Leemput:
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. 360 - Alexander E. Pozhitkov
:
Scanner calibration revisited. 361 - Lars Carlsson, Ola Spjuth
, Samuel E. Adams
, Robert C. Glen, Scott Boyer:
Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse. 362 - Martin Mechelke, Michael Habeck
:
Robust probabilistic superposition and comparison of protein structures. 363 - Pooja Jain
, Jonathan D. Hirst
:
Automatic structure classification of small proteins using random forest. 364 - Ratna R. Thangudu, Manoj Tyagi, Benjamin A. Shoemaker, Stephen H. Bryant, Anna R. Panchenko, Thomas Madej:
Knowledge-based annotation of small molecule binding sites in proteins. 365 - Denis C. Bauer
, Fabian A. Buske, Timothy L. Bailey:
Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. 366 - Renaud Gaujoux, Cathal Seoighe:
A flexible R package for nonnegative matrix factorization. 367 - Yuna Blum
, Guillaume Le Mignon, Sandrine Lagarrigue
, David Causeur:
A factor model to analyze heterogeneity in gene expression. 368 - Zhaohui S. Qin
, Jianjun Yu, Jincheng Shen, Christopher A. Maher, Ming Hu
, Shanker Kalyana-Sundaram
, Jindan Yu, Arul M. Chinnaiyan:
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. 369 - Jian Tian
, Ningfeng Wu, Xiaoyu Chu, Yunliu Fan:
Predicting changes in protein thermostability brought about by single- or multi-site mutations. 370 - David-Olivier D. Azulay, Hendrik Neubert, Mireia Fernández Ocaña:
Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL isoelectric focussing. 371 - Jo A. Helmuth, Grégory Paul, Ivo F. Sbalzarini
:
Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. 372 - Yoshitaka Kimori, Norio Baba, Nobuhiro Morone
:
Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images. 373 - Vladimir Potapov
, Mati Cohen, Yuval Inbar, Gideon Schreiber:
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. 374 - Stephanie Heinen, Bernhard Thielen, Dietmar Schomburg
:
KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes. 375 - Adam J. Carroll, Murray R. Badger, A. Harvey Millar
:
The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets. 376 - David B. Burdick, Christopher C. Cavnor, Jeremy Handcock, Sarah A. Killcoyne
, Jake Lin
, Bruz Marzolf, Stephen A. Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich, John Boyle
:
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. 377 - Petr Novák
, Pavel Neumann
, Jirí Macas
:
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. 378 - Raphaël Helaers
, Michel C. Milinkovitch
:
MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics. 379 - Roger Pique-Regi
, Alejandro Cáceres
, Juan R. González
:
R-Gada: a fast and flexible pipeline for copy number analysis in association studies. 380 - Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang
:
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. 381 - J. Christopher Bare
, Tie Koide
, David J. Reiss, Dan Tenenbaum, Nitin S. Baliga:
Integration and visualization of systems biology data in context of the genome. 382 - Giovanni Capone, Giuseppe Novello, Candida Fasano
, Brett Trost
, Mikelis G. Bickis, Anthony J. Kusalik, Darja Kanduc
:
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. 383 - Adam F. Allred, Guang Wu, Tuya Wulan, Kael F. Fischer
, Michael R. Holbrook, Robert B. Tesh, David Wang:
VIPR: A probabilistic algorithm for analysis of microbial detection microarrays. 384 - Fabien Corblin, Eric Fanchon, Laurent Trilling:
Applications of a formal approach to decipher discrete genetic networks. 385 - Eric F. Lock, Ryan Ziemiecki
, J. S. Marron, Dirk P. Dittmer
:
Efficiency clustering for low-density microarrays and its application to QPCR. 386 - Jonas S. Almeida, Helena F. Deus
, Wolfgang Maass
:
S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. 387 - Fredrik Johansson, Hiroyuki Toh:
A comparative study of conservation and variation scores. 388 - Joel Arrais
, João Fernandes, João E. Pereira, José Luís Oliveira
:
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. 389 - Uri Weingart, Erez Persi, Uri Gophna
, David Horn
:
Deriving enzymatic and taxonomic signatures of metagenomes from short read data. 390 - Insuk Sohn, Kouros Owzar, Stephen L. George, Sujong Kim, Sin-Ho Jung:
Robust test method for time-course microarray experiments. 391 - Lina Chen
, Hong Wang, Liangcai Zhang, Wan Li
, Qian Wang, Yukui Shang, Yuehan He, Weiming He, Xu Li, Jingxie Tai, Xia Li:
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks. 392 - Tong Hao, Hongwu Ma, Xue-Ming Zhao, Igor Goryanin
:
Compartmentalization of the Edinburgh Human Metabolic Network. 393 - Stacey J. Winham
, Andrew J. Slater, Alison A. Motsinger-Reif
:
A comparison of internal validation techniques for multifactor dimensionality reduction. 394 - Tomás Pluskal
, Sandra Castillo
, Alejandro Villar-Briones
, Matej Oresic
:
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. 395 - Xiaojiang Xu
, Stephen Hoang, Marty W. Mayo, Stefan Bekiranov:
Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. 396 - Shaoqiang Zhang
, Shan Li, Phuc T. Pham, Zhengchang Su:
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. 397 - Yoji Nakamura, Tomoyoshi Komiyama
, Motoki Furue, Takashi Gojobori, Yasuto Akiyama:
CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies. 398 - Shouyong Peng, Mitzi I. Kuroda, Peter J. Park
:
Quantized correlation coefficient for measuring reproducibility of ChIP-chip data. 399 - Amit Zeisel, Amnon Amir, Wolfgang J. Köstler, Eytan Domany:
Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes. 400 - Jean-Marie Cornuet, Virgine Ravigné
, Arnaud Estoup:
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). 401 - Peng Chen, Jinyan Li:
Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. 402 - Habil Zare
, Parisa Shooshtari, Arvind Gupta, Ryan Remy Brinkman
:
Data reduction for spectral clustering to analyze high throughput flow cytometry data. 403 - Joshua Colvin, Michael I. Monine, Ryan N. Gutenkunst, William S. Hlavacek
, Daniel D. Von Hoff, Richard G. Posner:
RuleMonkey: software for stochastic simulation of rule-based models. 404 - Philip Wenig, Juergen Odermatt:
OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data. 405 - Eduardo Corel
, Florian Pitschi, Ivan Laprevotte, Gilles Grasseau, Gilles Didier
, Claudine Devauchelle:
MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences. 406 - Petros Kountouris
, Jonathan D. Hirst
:
Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures. 407 - Anna Campain
, Yee Hwa Yang
:
Comparison study of microarray meta-analysis methods. 408 - Kristof Theys, Koen Deforche, Gertjan Beheydt, Yves Moreau
, Kristel Van Laethem
, Philippe Lemey, Ricardo Camacho
, Soo-Yon Rhee
, Robert W. Shafer, Eric Van Wijngaerden, Anne-Mieke Vandamme
:
Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. 409 - Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso
, Guillermo López-Campos
, Guillermo de la Calle
, Diana de la Iglesia, David Pérez-Rey, José Crespo, Fernando Martín-Sánchez
, Victor Maojo:
A method for automatically extracting infectious disease-related primers and probes from the literature. 410 - Chia-Ying Cheng, Yuh-Jyh Hu:
Extracting the abstraction pyramid from complex networks. 411 - Junbai Wang:
The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data. 412 - Anil Aswani
, Soile V. E. Keränen, James Brown, Charless C. Fowlkes
, David W. Knowles, Mark D. Biggin, Peter J. Bickel, Claire J. Tomlin:
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data. 413 - Suresh Kumar Poovathingal
, Rudiyanto Gunawan
:
Global parameter estimation methods for stochastic biochemical systems. 414 - Mali Salmon-Divon
, Heidi Dvinge
, Kairi Tammoja
, Paul Bertone
:
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci. 415 - Lorenzo Beretta, Alessandro Santaniello, Piet L. C. M. van Riel, Marieke J. H. Coenen
, Raffaella Scorza:
Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-censored data. 416 - Tina Koestler, Arndt von Haeseler, Ingo Ebersberger:
FACT: Functional annotation transfer between proteins with similar feature architectures. 417 - Catalina O. Tudor, Carl J. Schmidt
, K. Vijay-Shanker:
eGIFT: Mining Gene Information from the Literature. 418 - Ming Lu, Bing Shi, Juan Wang, Qun Cao, Qinghua Cui:
TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs. 419 - Zhen-Ling Peng
, Jianyi Yang
, Xin Chen:
An improved classification of G-protein-coupled receptors using sequence-derived features. 420 - Wei-Chung Cheng
, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen
, Wun-Yi Shu, Yun-Shien Lee, Tzu-Hao Wang, Ji-Hong Hong, Chia-Yang Li
, Ian C. Hsu:
Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. 421 - Thomas J. Hardcastle
, Krystyna A. Kelly:
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. 422 - Ron Henkel
, Lukas Endler
, André Peters, Nicolas Le Novère, Dagmar Waltemath:
Ranked retrieval of Computational Biology models. 423 - Ernst Althaus, Stefan Canzar
, Carsten Ehrler, Mark R. Emmett
, Andreas Karrenbauer
, Alan G. Marshall, Anke Meyer-Bäse
, Jeremiah D. Tipton, Huimin Zhang:
Computing H/D-Exchange rates of single residues from data of proteolytic fragments. 424 - Xiaoqi Cui, Tong Wang, Huann-Sheng Chen
, Victor Busov, Hairong Wei:
TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base. 425 - Dana Weekes, S. Sri Krishna, Constantina Bakolitsa
, Ian A. Wilson, Adam Godzik
, John C. Wooley:
TOPSAN: a collaborative annotation environment for structural genomics. 426 - Susmita Datta, Vasyl Pihur, Somnath Datta:
An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data. 427 - Aydin Albayrak, Hasan H. Otu
, Osman Ugur Sezerman
:
Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets. 428 - Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff-Borg, Thomas Hamelryck
:
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. 429 - Steven N. Evans, Valerie Hower, Lior Pachter
:
Coverage statistics for sequence census methods. 430 - L. Steven Johnson, Sean R. Eddy
, Elon Portugaly:
Hidden Markov model speed heuristic and iterative HMM search procedure. 431 - Tae-Min Kim, Lovelace J. Luquette, Ruibin Xi
, Peter J. Park
:
rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data. 432 - Ming Zhang, Yudong Zhang, Li Liu, Lijuan Yu, Shirley Tsang, Jing Tan, Wenhua Yao, Manjit S. Kang
, Yongqiang An, Xingming Fan:
Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. 433 - Ji Woong Kim, Yongju Ahn, Kichan Lee, Sung-Hee Park, Sangsoo Kim:
A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis. 434 - Olivier Friard
, Angela Re
, Daniela Taverna
, Michele De Bortoli
, Davide Corà
:
CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. 435 - Hua Xu, Michael A. Freitas
:
A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra. 436 - Ali Al-Shahib, Raju Misra, Nadia Ahmod, Min Fang, Haroun Shah, Saheer Gharbia:
Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics. 437 - Diego H. Milone
, Georgina Stegmayer
, Laura Kamenetzky, Mariana G. Lopez
, Je Min Lee
, James J. Giovannoni, Fernando Carrari:
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. 438 - Gong-Hua Li
, Jing-Fei Huang:
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation. 439 - Tianwei Yu
:
An exploratory data analysis method to reveal modular latent structures in high-throughput data. 440 - Robert Hoehndorf
, Anika Oellrich, Michel Dumontier
, Janet Kelso
, Dietrich Rebholz-Schuhmann, Heinrich Herre:
Relations as patterns: bridging the gap between OBO and OWL. 441 - Bo Peng
, Christopher I. Amos:
Forward-time simulation of realistic samples for genome-wide association studies. 442 - Pekka Marttinen
, Jukka Corander:
Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. 443 - Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng:
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. 444 - Florian Pitschi, Claudine Devauchelle, Eduardo Corel
:
Automatic detection of anchor points for multiple sequence alignment. 445 - Alex D. Stivala
, Peter J. Stuckey, Anthony Wirth
:
Fast and accurate protein substructure searching with simulated annealing and GPUs. 446 - Yu Guo, Armin Graber, Robert N. McBurney, Raji Balasubramanian:
Sample size and statistical power considerations in high-dimensionality data settings: a comparative study of classification algorithms. 447 - Leo C. McHugh, Jonathan W. Arthur:
Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. 448 - Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong
:
Consistency, comprehensiveness, and compatibility of pathway databases. 449 - Maarten van Iterson, Judith M. Boer, Renée X. de Menezes:
Filtering, FDR and power. 450 - Shiliang Wang, Jaideep P. Sundaram, David Spiro:
VIGOR, an annotation program for small viral genomes. 451 - Stuart G. Baker:
Simple and flexible classification of gene expression microarrays via Swirls and Ripples. 452 - Ioannis K. Valavanis, Stavroula G. Mougiakakou, Keith A. Grimaldi
, Konstantina S. Nikita
:
A multifactorial analysis of obesity as CVD risk factor: Use of neural network based methods in a nutrigenetics context. 453 - Elissa J. Cosgrove, Timothy S. Gardner, Eric D. Kolaczyk:
On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference. 454 - David A. Nix, Tonya L. Di Sera, Brian K. Dalley, Brett A. Milash, Robert M. Cundick, Kevin S. Quinn, Samir J. Courdy:
Next generation tools for genomic data generation, distribution, and visualization. 455 - Lisbeth Carstensen, Albin Sandelin
, Ole Winther
, Niels Richard Hansen
:
Multivariate Hawkes process models of the occurrence of regulatory elements. 456 - Sergey Koren
, Jason R. Miller
, Brian Walenz, Granger G. Sutton:
An algorithm for automated closure during assembly. 457 - Nophar Geifman
, Alon Monsonego, Eitan Rubin
:
The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems. 458 - Martin T. Swain, Johannes J. Mandel, Werner Dubitzky:
Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks. 459 - Daniela Nitsch, Joana P. Gonçalves
, Fabian Ojeda, Bart De Moor, Yves Moreau
:
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. 460 - Chad Laing
, Cody Buchanan, Eduardo N. Taboada
, Yongxiang Zhang, Andrew Kropinski
, Andre Villegas, James E. Thomas, Victor P. J. Gannon:
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. 461 - P. Andrew Nevarez, Christopher M. DeBoever
, Benjamin J. Freeland, Marissa A. Quitt, Eliot C. Bush:
Context dependent substitution biases vary within the human genome. 462 - Fran Supek, Kristian Vlahovicek
:
Correction: Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. 463 - Gayathri Jayaraman, Rahul Siddharthan:
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model. 464 - Wayne Wenzhong Xu, Clay J. Carter:
Parallel multiplicity and error discovery rate (EDR) in microarray experiments. 465 - Minlu Zhang, Long J. Lu:
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. 466 - Taeho Kim, Hyun Joo:
ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment. 467 - Lina Hultin Rosenberg, Bo Franzén, Gert Auer
, Janne Lehtiö
, Jenny Forshed:
Multivariate meta-analysis of proteomics data from human prostate and colon tumours. 468 - Ming Jia, Suh-Yeon Choi, Dirk Reiners, Eve Syrkin Wurtele
, Julie A. Dickerson
:
MetNetGE: interactive views of biological networks and ontologies. 469 - William P. Kelly, Michael P. H. Stumpf:
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. 470 - Amol Carl Shetty
, Prashanth Athri, Kajari Mondal, Vanessa L. Horner, Karyn Meltz Steinberg
, Viren Patel, Tamara Caspary
, David J. Cutler, Michael E. Zwick:
SeqAnt: A web service to rapidly identify and annotate DNA sequence variations. 471 - Steffen Uebe, Francesca Pasutto, Mandy Krumbiegel, Denny Schanze, Arif B. Ekici
, André Reis
:
GPFrontend and GPGraphics: graphical analysis tools for genetic association studies. 472 - Khader Shameer
, Lalima L. Madan
, Shivamurthy Veeranna, Balasubramanian Gopal, Ramanathan Sowdhamini:
PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. 473 - Sébastien Tempel, Christine Rousseau, Fariza Tahi, Jacques Nicolas:
ModuleOrganizer: detecting modules in families of transposable elements. 474 - Miha Stajdohar, Minca Mramor, Blaz Zupan
, Janez Demsar:
FragViz: visualization of fragmented networks. 475 - Hui Liu, Dong Yue, Yidong Chen, Shou-Jiang Gao
, Yufei Huang:
Improving performance of mammalian microRNA target prediction. 476 - Fan Shi, Christopher Leckie
, Geoff MacIntyre
, Izhak Haviv, Alex Boussioutas
, Adam Kowalczyk:
A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer. 477 - Sébastien Terrat
, Eric Peyretaillade, Olivier Gonçalves
, Eric Dugat-Bony
, Fabrice Gravelat, Anne Moné, Corinne Biderre-Petit, Delphine Boucher
, Julien Troquet
, Pierre Peyret
:
Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development. 478 - Carmen M. Diez-Rivero, Esther M. Lafuente
, Pedro A. Reche
:
Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome. 479 - Yu-Shen Liu, Qi Li, Guo-Qin Zheng, Karthik Ramani, William Benjamin:
Using diffusion distances for flexible molecular shape comparison. 480 - Thomas Lingner, Stefanie Mühlhausen
, Toni Gabaldón
, Cédric Notredame
, Peter Meinicke:
Predicting phenotypic traits of prokaryotes from protein domain frequencies. 481 - Andrew J. Bordner, Hans D. Mittelmann:
MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. 482 - Noor B. Dawany, Aydin Tözeren:
Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. 483 - Andrés F. Flórez
, Daeui Park
, Jong Bhak, Byoung-Chul Kim, Allan Kuchinsky, John H. Morris
, Jairo Espinosa, Carlos Muskus:
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. 484 - Murray P. Cox
, Daniel A. Peterson
, Patrick J. Biggs
:
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. 485 - Lianbo Yu, Rebecca W. Doerge:
A semi-nonparametric mixture model for selecting functionally consistent proteins. 486 - Alex Aussem, André Tchernof
, Sergio Rodrigues de Morais, Sophie Rome
:
Analysis of lifestyle and metabolic predictors of visceral obesity with Bayesian Networks. 487 - Paola Bertolazzi, Concettina Guerra, Giampaolo Liuzzi
:
A global optimization algorithm for protein surface alignment. 488 - Steinn Gudmundsson, Ines Thiele
:
Computationally efficient flux variability analysis. 489 - Youting Sun, Jianqiu Zhang, Ulisses M. Braga-Neto, Edward R. Dougherty:
BPDA - A Bayesian peptide detection algorithm for mass spectrometry. 490 - Peter Raasch, Ulf Schmitz
, Nadja Patenge, Julio Vera
, Bernd Kreikemeyer
, Olaf Wolkenhauer
:
Non-coding RNA detection methods combined to improve usability, reproducibility and precision. 491 - K. Bretonnel Cohen, Helen L. Johnson, Karin Verspoor
, Christophe Roeder, Lawrence Hunter
:
The structural and content aspects of abstracts versus bodies of full text journal articles are different. 492 - Luciana Ferrer, Joseph M. Dale, Peter D. Karp
:
A systematic study of genome context methods: calibration, normalization and combination. 493 - Majid Masso
, Iosif I. Vaisman
:
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage. 494 - Chen-Hsiang Yeang:
An integrated analysis of molecular aberrations in NCI-60 cell lines. 495 - Harriet J. Muncey
, Rebecca Jones, Maria De Iorio
, Timothy M. D. Ebbels
:
MetAssimulo: Simulation of Realistic NMR Metabolic Profiles. 496 - Bruno M. Tesson, Rainer Breitling
, Ritsert C. Jansen:
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. 497 - Melissa J. Davis
, Muhammad Shoaib B. Sehgal, Mark A. Ragan
:
Automatic, context-specific generation of Gene Ontology slims. 498 - Melissa J. Morine, Jolene McMonagle, Sinead Toomey, Clare M. Reynolds
, Aidan P. Moloney, Isobel Claire Gormley
, Peadar Ó Gaora
, Helen M. Roche
:
Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome. 499 - Ilenia Giangreco
, Orazio Nicolotti
, Angelo Carotti, Francesco De Carlo, Gianfranco Gargano, Roberto Bellotti
:
Analysis of X-ray Structures of Matrix Metalloproteinases via Chaotic Map Clustering. 500 - Limin Li, Xiaobo Zhou, Wai-Ki Ching, Ping Wang:
Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60 cell lines. 501 - István P. Sugár, Stuart C. Sealfon
:
Misty Mountain clustering: application to fast unsupervised flow cytometry gating. 502 - Eva Freyhult, Mattias Landfors, Jenny Önskog, Torgeir R. Hvidsten
, Patrik Rydén
:
Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering. 503 - Sriganesh Srihari
, Kang Ning
, Hon Wai Leong:
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. 504 - Kang Ning
, Hoong Kee Ng, Sriganesh Srihari
, Hon Wai Leong, Alexey I. Nesvizhskii
:
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. 505 - James Gurtowski, Anthony Cancio, Hardik Shah, Chaya Levovitz, Ajish George, Robert Homann, Ravi Sachidanandam:
Geoseq: a tool for dissecting deep-sequencing datasets. 506 - Shirley Hui, Gary D. Bader
:
Proteome scanning to predict PDZ domain interactions using support vector machines. 507 - GongXin Yu:
GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing. 508 - Cheng-Hong Yang, Yu-Huei Cheng
, Li-Yeh Chuang, Hsueh-Wei Chang
:
Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm. 509 - Fabrice Berger, Bertrand De Meulder, Anthoula Gaigneaux, Sophie Depiereux, Eric Bareke
, Michael Pierre, Benoît De Hertogh, Mauro Delorenzi, Eric Depiereux:
Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets. 510 - Linh M. Tran, Daniel R. Hyduke, James C. Liao
:
Trimming of mammalian transcriptional networks using network component analysis. 511 - Vincent A. Emanuele II, Brian M. Gurbaxani:
Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data. 512 - Long H. Do
, Francisco F. Esteves
, Harvey J. Karten, Ethan Bier:
Booly: a new data integration platform. 513 - Kenny Daily
, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi:
Data structures and compression algorithms for high-throughput sequencing technologies. 514 - Tung T. Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis:
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures. 515 - Rudi Alberts, Klaus Schughart
:
QTLminer: identifying genes regulating quantitative traits. 516 - Isabel A. Nepomuceno-Chamorro
, Jesús S. Aguilar-Ruiz
, José C. Riquelme:
Inferring gene regression networks with model trees. 517 - Nicola Barbarini, Paolo Magni
:
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies. 518 - Nicholus Bhattacharjee, Parbati Biswas
:
Statistical analysis and molecular dynamics simulations of ambivalent alpha -helices. 519 - Yong Li
, Lili Liu, Xi Bai, Hua Cai, Wei Ji, Dianjing Guo, Yanming Zhu:
Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks. 520 - Jongkwang Kim, Kai Tan
:
Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity. 521 - Mara L. Hartsperger, Florian Blöchl, Volker Stümpflen, Fabian J. Theis
:
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. 522 - Rok Blagus, Lara Lusa
:
Class prediction for high-dimensional class-imbalanced data. 523 - Pengyi Yang
, Joshua Wing Kei Ho
, Albert Y. Zomaya
, Bing Bing Zhou
:
A genetic ensemble approach for gene-gene interaction identification. 524 - Isaak Y. Tecle, Naama Menda, Robert M. Buels, Esther van der Knaap
, Lukas A. Mueller:
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. 525 - Andrew K. Rider, Geoffrey Siwo, Nitesh V. Chawla
, Michael T. Ferdig, Scott J. Emrich
:
A statistical approach to finding overlooked genetic associations. 526 - Robert Lawrence, Aaron G. Day-Williams, Katherine S. Elliott, Andrew P. Morris, Eleftheria Zeggini
:
CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies. 527 - Eric Bareke
, Michael Pierre, Anthoula Gaigneaux, Bertrand De Meulder, Sophie Depiereux, Naji Habra, Eric Depiereux:
PathEx: a novel multi factors based datasets selector web tool. 528 - Ross K. Shepherd, Theo H. E. Meuwissen, John A. Woolliams:
Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers. 529 - Jennifer I. Deegan, Emily C. Dimmer, Christopher J. Mungall
:
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. 530 - Andreas Hildebrandt
, Anna Katharina Dehof, Alexander Rurainski, Andreas Bertsch, Marcel Schumann
, Nora C. Toussaint
, Andreas Moll, Daniel Stöckel, Stefan Nickels, Sabine C. Mueller
, Hans-Peter Lenhof, Oliver Kohlbacher
:
BALL - biochemical algorithms library 1.3. 531 - Elena E. Giorgi, Bob Funkhouser, Gayathri Athreya, Alan S. Perelson, Bette T. Korber
, Tanmoy Bhattacharya
:
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model. 532 - Shandar Ahmad
, Yumlembam Hemjit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita
, Kenji Mizuguchi
:
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. 533 - Joel Hedlund
, Hans Jörnvall, Bengt Persson
:
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. 534 - Jérôme Gracy, Laurent Chiche:
Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots. 535 - Shu-An Chen, Tzong-Yi Lee, Yu-Yen Ou
:
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. 536 - Alvaro J. González, Li Liao:
Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. 537 - Frederick A. Matsen IV, Robin B. Kodner, E. Virginia Armbrust:
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. 538 - Zhengdong D. Zhang, Mark B. Gerstein:
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. 539 - Meric A. Ovacik, Siddharth Sukumaran, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis:
Circadian signatures in rat liver: from gene expression to pathways. 540 - Eric Bareke
, Michael Pierre, Anthoula Gaigneaux, Bertrand De Meulder, Sophie Depiereux, Fabrice Berger, Naji Habra, Eric Depiereux:
Correction: PathEx: A novel multi factors based datasets selector web tool. 541 - Wei Tan, Ravi K. Madduri
, Aleksandra Nenadic, Stian Soiland-Reyes
, Dinanath Sulakhe, Ian T. Foster, Carole A. Goble
:
caGrid Workflow Toolkit: A Taverna based workflow tool for cancer Grid. 542 - Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, Jonathan E. Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R. Regan, Elizabeth Dahlborg, Mathew J. Goodwin, Fengli Fu, Daniel F. Voytas
, J. Keith Joung, Drena Dobbs
:
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. 543 - David R. Kelley, Steven L. Salzberg
:
Clustering metagenomic sequences with interpolated Markov models. 544 - Fang Bai
, Xiaofeng Liu, Jiabo Li, Haoyun Zhang, Hualiang Jiang, Xicheng Wang, Honglin Li:
Bioactive Conformational Generation of Small Molecules: A Comparative Analysis between Force-Field and Multiple Empirical Criteria Based Methods. 545 - Greg Finak
, Juan-Manuel Perez, Andrew Weng, Raphael Gottardo
:
Optimizing Transformations for Automated, High Throughput Analysis of Flow Cytometry Data. 546 - W. Garrett Jenkinson, Xiaogang Zhong, John Goutsias:
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems. 547 - Hanka Venselaar
, Tim A. H. te Beek, Remko K. P. Kuipers, Maarten L. Hekkelman
, Gert Vriend:
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. 548 - Lianyi Han
, Tugba O. Suzek
, Yanli Wang, Steve H. Bryant:
The Text-mining based PubChem Bioassay neighboring analysis. 549 - Liya Wang
, Lincoln D. Stein:
Localizing triplet periodicity in DNA and cDNA sequences. 550 - Fernando García-Alcalde, Armando Blanco, Adrian J. Shepherd
:
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. 551 - Bo Chen, Minhua Chen, John W. Paisley, Aimee K. Zaas, Christopher W. Woods, Geoffrey S. Ginsburg, Alfred O. Hero III, Joseph E. Lucas, David B. Dunson, Lawrence Carin
:
Bayesian Inference of the Number of Factors in Gene-Expression Analysis: Application to Human Virus Challenge Studies. 552 - Federico M. Giorgi
, Anthony M. Bolger, Marc Lohse, Björn Usadel
:
Algorithm-driven Artifacts in median polish summarization of Microarray data. 553 - Jacques Oberto:
FITBAR: a web tool for the robust prediction of prokaryotic regulons. 554 - Mark Moll
, Drew H. Bryant, Lydia E. Kavraki
:
The LabelHash Algorithm for Substructure Matching. 555 - Martin Sill
, Christoph Schröder
, Jörg D. Hoheisel, Axel Benner, Manuela Zucknick
:
Assessment and optimisation of normalisation methods for dual-colour antibody microarrays. 556 - Jessica L. Larson, Guo-Cheng Yuan:
Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. 557 - Yung-Kuan Chan
, Meng-Hsiun Tsai, Der-Chen Huang, Zong-Han Zheng, Kun-Ding Hung:
Leukocyte Nucleus Segmentation and Nucleus Lobe Counting. 558 - Tianwei Yu
, Hesen Peng:
Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture model and statistical model selection. 559 - Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh, Matthew Vaughn
, Vishal Thapar:
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs. 560 - Carsten Henneges, Pavel Laskov, Endang Darmawan
, Juergen Backhaus, Bernd Kammerer, Andreas Zell:
A factorization method for the classification of infrared spectra. 561 - Shobhit Jain, Gary D. Bader
:
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology. 562 - Yao Qing Shen, Gertraud Burger:
TESTLoc: protein subcellular localization prediction from EST data. 563 - Zhijin Wu
, Bethany D. Jenkins, Tatiana A. Rynearson, Sonya T. Dyhrman, Mak A. Saito, Melissa Mercier, LeAnn P. Whitney:
Empirical Bayes Analysis of Sequencing-based Transcriptional Profiling without Replicates. 564 - Francis C. Weng, Chien-Hao Su, Ming-Tsung Hsu
, Tse-Yi Wang, Huai-Kuang Tsai
, Daryi Wang:
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency. 565 - Federica Viti
, Ivan Merelli
, Mieke Timmermans, Michael den Bakker, Francesco Beltrame, Peter Riegman
, Luciano Milanesi
:
Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study. 566 - Christoph Bartenhagen, Hans-Ulrich Klein
, Christian Ruckert, Xiaoyi Jiang
, Martin Dugas:
Comparative study of unsupervised dimension reduction techniques for the visualization of microarray gene expression data. 567 - Peng Wang
, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund
, Morten Nielsen
, Björn Peters:
Peptide binding predictions for HLA DR, DP and DQ molecules. 568 - Antonio Jimeno-Yepes
, Alan R. Aronson:
Knowledge-based biomedical word sense disambiguation: comparison of approaches. 569 - Adrienn Szabó, Ádám Novák, István Miklós, Jotun Hein:
Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment. 570 - Gift Nyamundanda, Lorraine Brennan
, Isobel Claire Gormley
:
Probabilistic Principal Component Analysis for Metabolomic Data. 571 - Cristian Coarfa, Fuli Yu, Christopher A. Miller, Zuozhou Chen, R. Alan Harris
, Aleksandar Milosavljevic:
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. 572 - Steinar Thorvaldsen
, Tor Flå, Nils Willassen:
DeltaProt: a software toolbox for comparative genomics. 573 - Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein:
iGTP: A software package for large-scale gene tree parsimony analysis. 574 - Patricia Francis-Lyon, Shengyin Gu, Joel Hass, Nina Amenta, Patrice Koehl
:
Sampling the conformation of protein surface residues for flexible protein docking. 575 - Reuben Thomas, Luis de la Torre, Xiaoqing Chang, Sanjay Mehrotra:
Validation and characterization of DNA microarray gene expression data distribution and associated moments. 576 - Chen Zhou, Hao Chi, Leheng Wang, You Li, Yan-Jie Wu, Yan Fu, Ruixiang Sun, Si-Min He:
Speeding up tandem mass spectrometry-based database searching by longest common prefix. 577 - Miguel Ángel Antón
, Ander Aramburu, Angel Rubio
:
Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays. 578 - Ari Löytynoja
, Nick Goldman
:
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. 579 - Anthony Santella, Zhuo Du
, Sonja Nowotschin, Anna-Katerina Hadjantonakis
, Zhirong Bao
:
A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. 580 - Alexander Pérez-Ruiz, Margarida Julià-Sapé, Guillem Mercadal, Iván Olier, Carles Majós, Carles Arús:
The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses. 581 - Peter Li
, Joseph O. Dada
, Daniel Jameson
, Irena Spasic, Neil Swainston, Kathleen Carroll
, Warwick B. Dunn
, Farid Khan, Naglis Malys
, Hanan L. Messiha, Evangelos Simeonidis
, Dieter Weichart, Catherine Winder, Jill Wishart, David S. Broomhead, Carole A. Goble
, Simon J. Gaskell, Douglas B. Kell
, Hans V. Westerhoff
, Pedro Mendes
, Norman W. Paton
:
Systematic integration of experimental data and models in systems biology. 582 - Matthias Kohl
, Hans-Peter Deigner:
Preprocessing of gene expression data by optimally robust estimators. 583 - Zeev Frenkel, Etienne Paux
, David I. Mester, Catherine Feuillet, Abraham B. Korol:
LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. 584 - Andreas Kowarsch, Florian Blöchl, Sebastian Bohl, Maria Saile, Norbert Gretz, Ursula Klingmüller
, Fabian J. Theis
:
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. 585 - Michiaki Hamada
, Kengo Sato
, Kiyoshi Asai:
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. 586 - Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A. Kibbe
, Lifang Hou, Simon M. Lin:
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. 587 - Sidahmed Benabderrahmane
, Malika Smaïl-Tabbone, Olivier Poch, Amedeo Napoli, Marie-Dominique Devignes
:
IntelliGO: a new vector-based semantic similarity measure including annotation origin. 588 - Constantin Bannert, A. Welfle, C. aus dem Spring, Dietmar Schomburg
:
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation. 589 - T. Ian Simpson
, J. Douglas Armstrong
, Andrew P. Jarman
:
Merged consensus clustering to assess and improve class discovery with microarray data. 590 - Morten Källberg, Hui Lu
:
An improved machine learning protocol for the identification of correct Sequest search results. 591 - Ryan Abo, Jathine Wong, Alun Thomas
, Nicola J. Camp:
Haplotype association analyses in resources of mixed structure using Monte Carlo testing. 592 - Maurizio Cardelli
, Matteo Nicoli, Armando Bazzani
, Claudio Franceschi:
Application of Wavelet Packet Transform to detect genetic polymorphisms by the analysis of inter-Alu PCR patterns. 593 - Mohammed Dakna, Keith Harris, Alexandros Kalousis, Sebastien Carpentier
, Walter Kolch
, Joost P. Schanstra
, Marion Haubitz, Antonia Vlahou
, Harald Mischak
, Mark A. Girolami
:
Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers. 594 - Keith A. Jolley
, Martin C. J. Maiden
:
BIGSdb: Scalable analysis of bacterial genome variation at the population level. 595 - Gürkan Bebek, Vishal N. Patel, Mark R. Chance:
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling. 596 - Enrico Glaab
, Anaïs Baudot
, Natalio Krasnogor, Alfonso Valencia:
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. 597 - Angela C. M. Luyf, Barbera D. C. van Schaik
, Michel de Vries, Frank Baas
, Antoine H. C. van Kampen, Sílvia D. Olabarriaga:
Initial steps towards a production platform for DNA sequence analysis on the grid. 598 - Minh Duc Cao
, Trevor I. Dix, Lloyd Allison
:
A genome alignment algorithm based on compression. 599 - Kristian Holm, Espen Melum
, Andre Franke, Tom H. Karlsen:
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels. 600 - David J. Russell, Samuel F. Way, Andrew K. Benson
, Khalid Sayood:
A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences. 601 - Clark D. Jeffries, Diana O. Perkins
, Xiaojun Guan:
Gene processing control loops suggested by sequencing, splicing, and RNA folding. 602 - Jesse M. Engreitz, Alexander A. Morgan, Joel Dudley, Rong Chen, Rahul Thathoo, Russ B. Altman, Atul J. Butte:
Content-based microarray search using differential expression profiles. 603 - Miriam R. Kantorovitz, Zoi Rapti
, Vladimir Gelev
, Anny Usheva:
Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites. 604 - Laure Sambourg, Nicolas Thierry-Mieg
:
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. 605 - Zhenqiu Liu, Dechang Chen, Ming Tan, Feng Jiang, Ronald B. Gartenhaus:
Kernel based methods for accelerated failure time model with ultra-high dimensional data. 606 - Xiaoliang Sun, Yong Zou
, Victoria J. Nikiforova, Jürgen Kurths, Dirk Walther
:
The complexity of gene expression dynamics revealed by permutation entropy. 607 - Daren Lee, Seth Ruffins, Queenie Ng, Nikhil Sane, Steve Anderson, Arthur W. Toga:
MBAT: A scalable informatics system for unifying digital atlasing workflows. 608 - Vipin Singh
, Rakesh K. Mishra
:
RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes. 609 - Sergey Kozhenkov, Yulia Dubinina, Mayya Sedova
, Amarnath Gupta, Julia V. Ponomarenko
, Michael Baitaluk:
BiologicalNetworks 2.0 - an integrative view of genome biology data. 610 - Mark Doderer, Kihoon Yoon, Kay A. Robbins:
SIDEKICK: Genomic data driven analysis and decision-making framework. 611 - Takaya Saito
, Pål Sætrom
:
A two-step site and mRNA-level model for predicting microRNA targets. 612
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