Google
Google Scholar
MS Academic
CiteSeerX
CORE
Semantic ScholarBMC 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 - 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, 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 - 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 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, J. 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 - 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 - 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 - 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 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 Dewhirst, Mariano A. Garcia-Blanco, James L. Pearson:
SplicerAV: a tool for mining microarray expression data for changes in RNA processing. 108 - Kai-Lin Tang, Tong-Hua Li, Wen-Wei 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 - 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 - 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 - 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 - 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 Dube:
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 - 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 - Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra, Abhijit Datta:
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 - 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 - 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 - Jing Wang, Xianxiao Zhou, Jing Zhu, Chenggui Zhou, Zheng Guo:
Revealing and avoiding bias in semantic similarity scores for protein pairs. 290 - 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 - 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 - 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 Charlie 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 - 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 - 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 - 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 - 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 - Habil Zare, Parisa Shooshtari, Arvind Gupta, Ryan R. 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 - 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 - 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 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, Andre 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 - 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 - 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 - 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, R. 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 - Youting Sun, Jianqiu Zhang, Ulisses 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 - 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 - 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 - Pengyi Yang, Joshua W. K. 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 III, 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 - 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 William 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 - 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, Simin He:
Speeding up tandem mass spectrometry-based database searching by longest common prefix. 577 - Miguel A. Anton, 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 - 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
maintained by 
at 
at 
last updated on 2018-07-12 22:03 CEST by the dblp team
data released under the ODC-BY 1.0 license
see also: Terms of Use | Privacy Policy | Imprint