default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBMC Bioinformatics, Volume 11
Volume 11, 2010
- Shuangge Ma, Michael R. Kosorok:
Detection of gene pathways with predictive power for breast cancer prognosis. 1 - Leander Schietgat, Celine Vens, Jan Struyf, Hendrik Blockeel
, Dragi Kocev, Saso Dzeroski:
Predicting gene function using hierarchical multi-label decision tree ensembles. 2 - Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant:
State of the art: refinement of multiple sequence alignments. 3 - Karel Zimmermann, Jean-François Gibrat:
Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors. 4 - Martijn P. van Iersel, Alexander R. Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R. Conklin, Chris T. A. Evelo:
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. 5 - Mats Ensterö, Örjan Åkerborg, Daniel Lundin, Bei Wang, Terrence S. Furey, Marie Öhman, Jens Lagergren:
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. 6 - Ben C. Stöver, Kai F. Müller:
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. 7 - Roberto Amato, Michele Pinelli, Daniel D'Andrea, Gennaro Miele, Mario Nicodemi, Giancarlo Raiconi, Sergio Cocozza:
A novel approach to simulate gene-environment interactions in complex diseases. 8 - Benjamin Georgi, Ivan Gesteira Costa, Alexander Schliep:
PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data. 9 - Guanqun Shi, Liqing Zhang, Tao Jiang:
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. 10 - Jingjing Ye, Adam Pavlícek, Elizabeth A. Lunney, Paul A. Rejto, Chi-Hse Teng:
Statistical method on nonrandom clustering with application to somatic mutations in cancer. 11 - Helen A. Arcuri, Geraldo F. D. Zafalon, Evandro A. Marucci, Carlos E. Bonalumi, Nelson José Freitas da Silveira, José Marcio Machado, Walter F. de Azevedo Jr., Mário S. Palma:
SKPDB: a structural database of shikimate pathway enzymes. 12 - Nysia I. George, Joanne R. Lupton, Nancy D. Turner, Robert S. Chapkin, Laurie A. Davidson, Naisyin Wang:
Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach. 13 - Norman E. Davey, Richard J. Edwards, Denis C. Shields:
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. 14 - Joseph M. Dale, Liviu Popescu, Peter D. Karp:
Machine learning methods for metabolic pathway prediction. 15 - Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk, Armita Sheari:
A pairwise residue contact area-based mean force potential for discrimination of native protein structure. 16 - Benoît De Hertogh, Bertrand De Meulder, Fabrice Berger, Michael Pierre, Eric Bareke, Anthoula Gaigneaux, Eric Depiereux:
A benchmark for statistical microarray data analysis that preserves actual biological and technical variance. 17 - David Edwards, Gabriel C. G. de Abreu, Rodrigo Labouriau:
Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests. 18 - Esteban Czwan, Benedikt Brors, David Kipling:
Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets. 19 - Michael Scharfe, Rainer Pielot, Falk Schreiber:
Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets. 20 - Carl Kingsford, Michael C. Schatz, Mihai Pop:
Assembly complexity of prokaryotic genomes using short reads. 21 - Alexander G. Churbanov, Igor Vorechovsky, Chindo Hicks:
A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements. 22 - Thomas K. Wolfgruber, Gernot G. Presting:
JunctionViewer: customizable annotation software for repeat-rich genomic regions. 23 - Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón:
ETE: a python Environment for Tree Exploration. 24 - Shuai Cheng Li, Yen Kaow Ng:
Calibur: a tool for clustering large numbers of protein decoys. 25 - Yu-Qing Qiu, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen:
Detecting disease associated modules and prioritizing active genes based on high throughput data. 26 - Dirk Repsilber, Sabine Kern, Anna Telaar, Gerhard Walzl, Gillian F. Black, Joachim Selbig, Shreemanta K. Parida, Stefan H. E. Kaufmann, Marc Jacobsen:
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. 27 - Shi Yu, Léon-Charles Tranchevent, Bart De Moor, Yves Moreau:
Gene prioritization and clustering by multi-view text mining. 28 - Anders Jacobsen Skanderup, Anders Krogh, Sakari Kauppinen, Morten Lindow:
miRMaid: a unified programming interface for microRNA data resources. 29 - Benjamin Misselwitz, Gerhard Strittmatter, Balamurugan Periaswamy, Markus C. Schlumberger, Samuel Rout, Péter Horváth, Karol Kozak, Wolf-Dietrich Hardt:
Enhanced CellClassifier: a multi-class classification tool for microscopy images. 30 - Sheng He, Juan Mei, Guiyang Shi, Zhengxiang Wang, Weijiang Li:
LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB. 31 - Seyed Yahya Anvar, Peter A. C. 't Hoen, Allan Tucker:
The identification of informative genes from multiple datasets with increasing complexity. 32 - Lance E. Palmer, Mathäus Dejori, Randall A. Bolanos, Daniel P. Fasulo:
Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction. 33 - Harald Barsnes, Richard G. Côté, Ingvar Eidhammer, Lennart Martens:
OLS Dialog: An open-source front end to the Ontology Lookup Service. 34 - Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, David P. Kreil:
Hybridization thermodynamics of NimbleGen Microarrays. 35 - Junbai Wang, Tianhai Tian:
Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53. 36 - Dominik Heider, Jens Verheyen, Daniel Hoffmann:
Predicting Bevirimat resistance of HIV-1 from genotype. 37 - Juan Falgueras, Antonio J. Lara, Noé Fernández-Pozo, Francisco R. Cantón, Guillermo Pérez-Trabado, M. Gonzalo Claros:
SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. 38 - Emanuela Giombini, Massimiliano Orsini, Danilo Carrabino, Anna Tramontano:
An automatic method for identifying surface proteins in bacteria: SLEP. 39 - Yaqiang Wang, Zhonghua Yu, Yongguang Jiang, Kaikuo Xu, Xia Chen:
Automatic symptom name normalization in clinical records of traditional Chinese medicine. 40 - Andrew J. Bordner, Hans D. Mittelmann:
Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. 41 - Russell Schwartz, Stanley Shackney:
Applying unmixing to gene expression data for tumor phylogeny inference. 42 - Tamir Tuller, Yifat Felder, Martin Kupiec:
Discovering local patterns of co - evolution: computational aspects and biological examples. 43 - Ulrike Naumann, George Luta, Matthew P. Wand:
The curvHDR method for gating flow cytometry samples. 44 - Satwik Rajaram, Yoshi Oono:
NeatMap - non-clustering heat map alternatives in R. 45 - Svetlana Bulashevska, Alla Bulashevska, Roland Eils:
Bayesian statistical modelling of human protein interaction network incorporating protein disorder information. 46 - Bing Xiong, Jie Wu, David L. Burk, Mengzhu Xue, Hualiang Jiang, Jingkang Shen:
BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. 47 - Wei-Jiun Lin, Huey-miin Hsueh, James J. Chen:
Power and sample size estimation in microarray studies. 48 - Dimitris G. Bariamis, Dimitrios K. Iakovidis, Dimitris Maroulis:
M3G: Maximum Margin Microarray Gridding. 49 - Taeho Hwang, Choong-Hyun Sun, Taegyun Yun, Gwan-Su Yi:
FiGS: a filter-based gene selection workbench for microarray data. 50 - Mickaël Krzeminski, Karine Loth, Rolf Boelens, Alexandre M. J. J. Bonvin:
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes. 51 - Jeremy D. Selengut, Douglas B. Rusch, Daniel H. Haft:
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. 52 - Yu-Chao Wang, Chung-Yu Lan, Wen-Ping Hsieh, Luis A. Murillo, Nina Agabian, Bor-Sen Chen:
Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. 53 - Jaebum Kim, Saurabh Sinha:
Towards realistic benchmarks for multiple alignments of non-coding sequences. 54 - Byron C. Wallace, Thomas A. Trikalinos, Joseph Lau, Carla E. Brodley, Christopher H. Schmid:
Semi-automated screening of biomedical citations for systematic reviews. 55 - Javier García-García, Emre Guney, Ramon Aragues, Joan Planas-Iglesias, Baldo Oliva:
Biana: a software framework for compiling biological interactions and analyzing networks. 56 - Pankaj Khurana, Rajesh S. Gokhale, Debasisa Mohanty:
Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles. 57 - Benjamin A. Logsdon, Gabriel E. Hoffman, Jason G. Mezey:
A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis. 58 - Alina Sîrbu, Heather J. Ruskin, Martin Crane:
Comparison of evolutionary algorithms in gene regulatory network model inference. 59 - Mayer Alvo, Zhongzhu Liu, Andrew Williams, Carole L. Yauk:
Testing for mean and correlation changes in microarray experiments: an application for pathway analysis. 60 - Xianming Wu, Songfeng Wu, Dong Li, Jiyang Zhang, Lin Hou, Jie Ma, Wanlin Liu, Daming Ren, Yunping Zhu, Fuchu He:
Computational identification of rare codons of Escherichia coli based on codon pairs preference. 61 - Yunqi Li, C. Russell Middaugh, Jianwen Fang:
A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants. 62 - Corey M. Yanofsky, David R. Bickel:
Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing. 63 - Evgeniy V. Petrotchenko, Christoph H. Borchers:
ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite. 64 - Julie Hussin, Philippe Nadeau, Jean-François Lefebvre, Damian Labuda:
Haplotype allelic classes for detecting ongoing positive selection. 65 - Guimei Liu, Yue Wang, Limsoon Wong:
FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium. 66 - Ronald van Eijk, Paul H. C. Eilers, Remco Natté, Anne-Marie Cleton-Jansen, Hans Morreau, Tom van Wezel, Jan Oosting:
MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification. 67 - Ritesh Krishna, Chang-Tsun Li, Vicky Buchanan-Wollaston:
A temporal precedence based clustering method for gene expression microarray data. 68 - Bram Slabbinck, Willem Waegeman, Peter Dawyndt, Paul De Vos, Bernard De Baets:
From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification. 69 - Adriano Barbosa-Silva, Theodoros G. Soldatos, Ivan L. F. Magalhães, Georgios A. Pavlopoulos, Jean-Fred Fontaine, Miguel A. Andrade-Navarro, Reinhard Schneider, José Miguel Ortega:
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships. 70 - Ivaylo Ilinkin, Jieping Ye, Ravi Janardan:
Multiple structure alignment and consensus identification for proteins. 71 - Russell L. Zaretzki, Michael A. Gilchrist, William M. Briggs, Artin Armagan:
Bias correction and Bayesian analysis of aggregate counts in SAGE libraries. 72 - Mark J. Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini:
BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets. 73 - Xiaowu Gai, Juan C. Perin, Kevin Murphy, Ryan O'Hara, Monica D'arcy, Adam Wenocur, Hongbo M. Xie, Eric F. Rappaport, Tamim H. Shaikh, Peter S. White:
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. 74 - Leslie Regad, Juliette Martin, Grégory Nuel, Anne-Claude Camproux:
Mining protein loops using a structural alphabet and statistical exceptionality. 75 - Xue Gong, Ruihong Wu, Yuannv Zhang, Wenyuan Zhao, Lixin Cheng, Yunyan Gu, Lin Zhang, Jing Wang, Jing Zhu, Zheng Guo:
Extracting consistent knowledge from highly inconsistent cancer gene data sources. 76 - Ricardo Cao, Mario Francisco-Fernández, Emiliano J. Quinto:
A random effect multiplicative heteroscedastic model for bacterial growth. 77 - Anne-Laure Boulesteix, Torsten Hothorn:
Testing the additional predictive value of high-dimensional molecular data. 78 - Maria Pamela C. David, Gisela P. Concepcion, Eduardo A. Padlan:
Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies. 79 - Martin C. Frith, Michiaki Hamada, Paul Horton:
Parameters for accurate genome alignment. 80 - Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson, Dabing Zhang:
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. 81 - Hedda Høvik, Tsute Chen:
Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. 82 - Aliah Hazmah Hawari, Zeti-Azura Mohamed-Hussein:
Simulation of a Petri net-based Model of the Terpenoid Biosynthesis Pathway. 83 - Zafer Aydin, John I. Murray, Robert H. Waterston, William Stafford Noble:
Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo. 84 - Martin Gerner, Goran Nenadic, Casey M. Bergman:
LINNAEUS: A species name identification system for biomedical literature. 85 - Like Fokkens, Sandra M. C. Botelho, Jos Boekhorst, Berend Snel:
Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. 86 - Alexander Lachmann, Avi Ma'ayan:
Lists2Networks: Integrated analysis of gene/protein lists. 87 - Yi-Ruen Lin, Hsin-Yuan Wei, Tsung-Lin Tsai, Thy-Hou Lin:
HDAPD: a web tool for searching the disease-associated protein structures. 88 - Mindaugas Margelevicius, Ceslovas Venclovas:
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. 89 - Kirsten Roomp, Iris Antes, Thomas Lengauer:
Predicting MHC class I epitopes in large datasets. 90 - Alexander Martin, Maria Elena Ochagavía, Laya C. Rabasa, Jamilet Miranda, Jorge Fernandez-de-Cossío, Ricardo Bringas:
BisoGenet: a new tool for gene network building, visualization and analysis. 91 - Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan:
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. 92 - Daniel MacLean, Vincent Moulton, David J. Studholme:
Finding sRNA generative locales from high-throughput sequencing data with NiBLS. 93 - James H. Bullard, Elizabeth Purdom, Kasper D. Hansen, Sandrine Dudoit:
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. 94 - Ryan Gill, Somnath Datta, Susmita Datta:
A statistical framework for differential network analysis from microarray data. 95 - Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dennis E. Shasha:
SING: Subgraph search In Non-homogeneous Graphs. 96 - Alessandro Pandini, Arianna Fornili, Jens Kleinjung:
Structural alphabets derived from attractors in conformational space. 97 - Jens Keilwagen, Jan Grau, Stefan Posch, Marc Strickert, Ivo Grosse:
Unifying generative and discriminative learning principles. 98 - Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe Vert, Véronique Stoven:
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. 99 - Stacy Duncan, Ruchita Sirkanungo, Leslie Miller, Gregory J. Phillips:
DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data. 100 - Quoc-Chinh Bui, Breanndán Ó Nualláin, Charles A. Boucher, Peter M. A. Sloot:
Extracting causal relations on HIV drug resistance from literature. 101 - Chih-Hsien Cheng, Chung-Han Yang, Hsien-Tai Chiu, Chin Lung Lu:
Reconstructing genome trees of prokaryotes using overlapping genes. 102 - J. Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex D. Wade, Oscar Naim, Greg B. Quinn, Philip E. Bourne:
Word add-in for ontology recognition: semantic enrichment of scientific literature. 103 - Jakub Mieczkowski, Magdalena E. Tyburczy, Michal Dabrowski, Piotr Pokarowski:
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. 104 - Dan C. Tulpan, Mirela Andronescu, Serge Léger:
Free energy estimation of short DNA duplex hybridizations. 105 - Sandra Ortega-Martorell, Iván Olier, Margarida Julià-Sapé, Carles Arús:
SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system. 106 - Seonho Kim, Juntae Yoon, Jihoon Yang, Seog Park:
Walk-weighted subsequence kernels for protein-protein interaction extraction. 107 - Timothy J. Robinson, Michaela A. Dinan, Mark W. Dewhirst, Mariano A. Garcia-Blanco, James L. Pearson:
SplicerAV: a tool for mining microarray expression data for changes in RNA processing. 108 - Kailin Tang, Tong-Hua Li, Wenwei Xiong, Kai Chen:
Ovarian cancer classification based on dimensionality reduction for SELDI-TOF data. 109 - Kristin K. Nicodemus, James D. Malley, Carolin Strobl, Andreas Ziegler:
The behaviour of random forest permutation-based variable importance measures under predictor correlation. 110 - Ching-Lin Hsiao, Ie-Bin Lian, Ai-Ru Hsieh, Cathy S. J. Fann:
Modeling expression quantitative trait loci in data combining ethnic populations. 111 - Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W. Hentze, Thomas Dandekar, Martina U. Muckenthaler:
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. 112 - Eisuke Chikayama, Atsushi Kurotani, Takanori Tanaka, Takashi Yabuki, Satoshi Miyazaki, Shigeyuki Yokoyama, Yutaka Kuroda:
Mathematical model for empirically optimizing large scale production of soluble protein domains. 113 - Weilong Hao:
OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs. 114 - Elisa Cilia, Andrea Passerini:
Automatic prediction of catalytic residues by modeling residue structural neighborhood. 115 - Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander, Laurent Excoffier:
ABCtoolbox: a versatile toolkit for approximate Bayesian computations. 116 - Aaron M. Newman, James B. Cooper:
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. 117 - Chongle Pan, Byung-Hoon Park, William H. McDonald, Patricia A. Carey, Jillian F. Banfield, Nathan Verberkmoes, Robert L. Hettich, Nagiza F. Samatova:
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. 118 - Doug Hyatt, Gwo-Liang Chen, Philip F. LoCascio, Miriam L. Land, Frank W. Larimer, Loren J. Hauser:
Prodigal: prokaryotic gene recognition and translation initiation site identification. 119 - Tamás Nepusz, Rajkumar Sasidharan, Alberto Paccanaro:
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. 120 - Florian Battke, Stephan Symons, Kay Nieselt:
Mayday - integrative analytics for expression data. 121 - Hansi Weißensteiner, Sebastian Schönherr, Günther Specht, Florian Kronenberg, Anita Brandstätter:
eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. 122 - Jennifer M. Staab, Thomas M. O'Connell, Shawn M. Gomez:
Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). 123 - Tetyana Ivanovska, Andrea Schenk, André Homeyer, Meihong Deng, Uta Dahmen, Olaf Dirsch, Horst K. Hahn, Lars Linsen:
A fast and robust hepatocyte quantification algorithm including vein processing. 124 - Aarti Garg, Rupinder Tewari, Gajendra P. S. Raghava:
KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. 125 - Martin Paluszewski, Thomas Hamelryck:
Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks. 126 - Andrew Williams, Errol M. Thomson:
Effects of scanning sensitivity and multiple scan algorithms on microarray data quality. 127 - Dmitry Rykunov, András Fiser:
New statistical potential for quality assessment of protein models and a survey of energy functions. 128 - Jessica S. Reuter, David H. Mathews:
RNAstructure: software for RNA secondary structure prediction and analysis. 129 - Aakrosh Ratan, Yu Zhang, Vanessa M. Hayes, Stephan C. Schuster, Webb Miller:
Calling SNPs without a reference sequence. 130 - Andrew S. Warren, Jeremy S. Archuleta, Wu-chun Feng, João Carlos Setubal:
Missing genes in the annotation of prokaryotic genomes. 131 - Hsiao Ping Lee, Tzu-Fang Sheu, Chuan Yi Tang:
A parallel and incremental algorithm for efficient unique signature discovery on DNA databases. 132 - José Afonso Guerra-Assunção, Anton J. Enright:
MapMi: automated mapping of microRNA loci. 133 - Yurii S. Aulchenko, Maksim V. Struchalin, Cornelia M. van Duijn:
ProbABEL package for genome-wide association analysis of imputed data. 134 - Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer:
miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. 135 - Luis Quintales, Mar Sánchez, Francisco Antequera:
Analysis of DNA strand-specific differential expression with high density tiling microarrays. 136 - Louis Licamele, Lise Getoor:
Indirect two-sided relative ranking: a robust similarity measure for gene expression data. 137 - Mallika Veeramalai, David R. Gilbert, Gabriel Valiente:
An optimized TOPS+ comparison method for enhanced TOPS models. 138 - Hunter N. B. Moseley:
Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. 139 - Ioannis A. Maraziotis, Andrei Dragomir, Dimitris Thanos:
Gene regulatory networks modelling using a dynamic evolutionary hybrid. 140 - Brady Olsen, Christopher J. Murakami, Matt Kaeberlein:
YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. 141 - Kirill Kryukov, Naruya Saitou:
MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. 142 - Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang:
MPprimer: a program for reliable multiplex PCR primer design. 143 - Martial Hue, Michael Riffle, Jean-Philippe Vert, William Stafford Noble:
Large-scale prediction of protein-protein interactions from structures. 144 - Bobbie-Jo M. Webb-Robertson, Kyle G. Ratuiste, Christopher S. Oehmen:
Physicochemical property distributions for accurate and rapid pairwise protein homology detection. 145 - Michael L. Sierk, Michael E. Smoot, Ellen J. Bass, William R. Pearson:
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. 146 - Teo Shu Mei, Agus Salim, Stefano Calza, Ku Chee Seng, Kee Seng Chia, Yudi Pawitan:
Identification of recurrent regions of copy-number variants across multiple individuals. 147 - Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann, Steffen Neumann:
In silico fragmentation for computer assisted identification of metabolite mass spectra. 148 - Jens Keilwagen, Jan Grau, Stefan Posch, Ivo Grosse:
Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis. 149 - Sigrid Rouam, Thierry Moreau, Philippe Broët:
Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes. 150 - Pierre M. Durand, Scott Hazelhurst, Theresa L. Coetzer:
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function. 151 - James Robert White, Saket Navlakha, Niranjan Nagarajan, Mohammadreza Ghodsi, Carl Kingsford, Mihai Pop:
Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. 152 - Feng-Jie Sun, Gustavo Caetano-Anollés:
The ancient history of the structure of ribonuclease P and the early origins of Archaea. 153 - Pietro Zoppoli, Sandro Morganella, Michele Ceccarelli:
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. 154 - Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek:
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. 155 - Marc Hulsman, Anouk Mentink, Eugene P. van Someren, Koen J. Dechering, Jan de Boer, Marcel J. T. Reinders:
Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization. 156 - Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano:
Moara: a Java library for extracting and normalizing gene and protein mentions. 157 - Jorn R. de Haan, Ester Piek, René C. van Schaik, Jacob de Vlieg, Susanne Bauerschmidt, Lutgarde M. C. Buydens, Ron Wehrens:
Integrating gene expression and GO classification for PCA by preclustering. 158 - Thomas Kuhn, Egon L. Willighagen, Achim Zielesny, Christoph Steinbeck:
CDK-Taverna: an open workflow environment for cheminformatics. 159 - Hifzur Rahman Ansari, Gajendra P. S. Raghava:
Identification of NAD interacting residues in proteins. 160 - Israel T. da Silva, Ricardo Z. N. Vêncio, Thiago Y. K. Oliveira, Greice A. Molfetta, Wilson A. Silva Jr.:
ProbFAST: Probabilistic Functional Analysis System Tool. 161 - Chen Wang, Jianhua Xuan, Huai Li, Yue Joseph Wang, Ming Zhan, Eric P. Hoffman, Robert Clarke:
Knowledge-guided gene ranking by coordinative component analysis. 162 - Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan, Adam Kuspa, Devika Subramanian, Gad Shaulsky:
New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. 163 - Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew, Hong Yan:
Multiconstrained gene clustering based on generalized projections. 164 - Robert C. McLeay, Timothy L. Bailey:
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. 165 - Saurin D. Jani, Gary L. Argraves, Jeremy L. Barth, W. Scott Argraves:
GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. 166 - Chi-Yuan Yu, Lih-Ching Chou, Darby Tien-Hao Chang:
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. 167 - Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang:
Using jackknife to assess the quality of gene order phylogenies. 168 - Johann M. Kraus, Hans A. Kestler:
A highly efficient multi-core algorithm for clustering extremely large datasets. 169 - Ken Tatebe, Ahmet Zeytun, Ruy M. Ribeiro, Robert Hoffmann, Kevin S. Harrod, Christian V. Forst:
Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. 170 - Mehar S. Khatkar, Matthew Hobbs, Markus Neuditschko, Johann Sölkner, Frank W. Nicholas, Herman W. Raadsma:
Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates. 171 - Jonathan J. Ellis, Fabien P. E. Huard, Charlotte M. Deane, Sheenal Srivastava, Graham R. Wood:
Directionality in protein fold prediction. 172 - Hsueh-Wei Chang, Yu-Huei Cheng, Li-Yeh Chuang, Cheng-Hong Yang:
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. 173 - Junfeng Xia, Xing-Ming Zhao, Jiangning Song, De-Shuang Huang:
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. 174 - Rabie Saidi, Mondher Maddouri, Engelbert Mephu Nguifo:
Protein sequences classification by means of feature extraction with substitution matrices. 175 - Gregor Stiglic, Mateja Bajgot, Peter Kokol:
Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays. 176 - Karl W. Kuschner, Dariya I. Malyarenko, William E. Cooke, Lisa H. Cazares, O. John Semmes, Eugene R. Tracy:
A Bayesian network approach to feature selection in mass spectrometry data. 177 - Andrew K. Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt D. B. Halstead, Jonathan Cooper, David P. Nickerson, Poul M. F. Nielsen:
An overview of the CellML API and its implementation. 178 - Timothy L. Bailey, Mikael Bodén, Tom Whitington, Philip Machanick:
The value of position-specific priors in motif discovery using MEME. 179 - Andrew S. Parker, Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg:
Optimization algorithms for functional deimmunization of therapeutic proteins. 180 - Qi Liu, Qian Xu, Vincent Wenchen Zheng, Hong Xue, Zhi-Wei Cao, Qiang Yang:
Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study. 181 - Bing Wang, Steve Valentine, Manolo Plasencia, Sriram Raghuraman, Xiang Zhang:
Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry. 182 - Megu Ohtaki, Keiko Otani, Keiko Hiyama, Naomi Kamei, Kenichi Satoh, Eiso Hiyama:
A robust method for estimating gene expression states using Affymetrix microarray probe level data. 183 - Stephanie Zierke, Jason D. Bakos:
FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods. 184 - Oliver Pelz, Moritz Gilsdorf, Michael Boutros:
web cellHTS2: A web-application for the analysis of high-throughput screening data. 185 - Davide Sisti, Michele Guescini, Marco B. L. Rocchi, Pasquale Tibollo, Mario D'Atri, Vilberto Stocchi:
Shape based kinetic outlier detection in real-time PCR. 186 - Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li:
Artificial and natural duplicates in pyrosequencing reads of metagenomic data. 187 - Márton Münz, Rune B. Lyngsø, Jotun Hein, Philip C. Biggin:
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. 188 - Felix Sanchez-Garcia, Uri David Akavia, Eyal Mozes, Dana Pe'er:
JISTIC: Identification of Significant Targets in Cancer. 189 - Sanghamitra Bandyopadhyay, Malay Bhattacharyya:
PuTmiR: A database for extracting neighboring transcription factors of human microRNAs. 190 - Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos, Magnus Fontes:
Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. 191 - Andrew J. Bordner:
Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design. 192 - Tiejun Cheng, Zhihai Liu, Renxiao Wang:
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction. 193 - Benedikt Zacher, Pei Fen Kuan, Achim Tresch:
Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. 194 - Tala Bakheet, Andrew J. Doig:
Properties and identification of antibiotic drug targets. 195 - Hui-Hsien Chou:
Shared probe design and existing microarray reanalysis using PICKY. 196 - Colm J. Ryan, Derek Greene, Gerard Cagney, Padraig Cunningham:
Missing value imputation for epistatic MAPs. 197 - Antonio Deiana, Andrea Giansanti:
Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets. 198 - Franziska Hoffgaard, Philipp Weil, Kay Hamacher:
BioPhysConnectoR: Connecting Sequence Information and Biophysical Models. 199 - Fuhai Li, Xiaobo Zhou, Wanting Huang, Chung-Che Chang, Stephen T. C. Wong:
Conditional random pattern model for copy number aberration detection. 200 - Olof Görnerup, Martin Nilsson Jacobi:
A model-independent approach to infer hierarchical codon substitution dynamics. 201 - Kyoung Ae Kim, Sabrina L. Spencer, John G. Albeck, John M. Burke, Peter K. Sorger, Suzanne Gaudet, Do Hyun Kim:
Systematic calibration of a cell signaling network model. 202 - Pao-Yang Chen, Shawn Cokus, Matteo Pellegrini:
BS Seeker: precise mapping for bisulfite sequencing. 203 - Annalisa Marsico, Andreas Henschel, Christof Winter, Anne Tuukkanen, Boris Vassilev, Kerstin Scheubert, Michael Schroeder:
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. 204 - Kevin Horan, Christian R. Shelton, Thomas Girke:
Predicting conserved protein motifs with Sub-HMMs. 205 - Massimiliano Virgilio, Thierry Backeljau, Bruno Nevado, Marc De Meyer:
Comparative performances of DNA barcoding across insect orders. 206 - Mario Fasold, Peter F. Stadler, Hans Binder:
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. 207 - Mike L. Smith, Mark J. Dunning, Simon Tavaré, Andy G. Lynch:
Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. 208 - Federico Plazzi, Ronald R. Ferrucci, Marco Passamonti:
Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. 209 - Subhadip Basu, Dariusz Plewczynski:
AMS 3.0: prediction of post-translational modifications. 210 - Yi Qu, Fei He, Yuchen Chen:
Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays. 211 - Sérgio Matos, Joel Arrais, João Maia-Rodrigues, José Luís Oliveira:
Concept-based query expansion for retrieving gene related publications from MEDLINE. 212 - Jan Schellenberger, Junyoung O. Park, Tom M. Conrad, Bernhard O. Palsson:
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. 213 - Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, Masanori Arita:
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. 214 - Jaehee Jung, Gangman Yi, Serenella A. Sukno, Michael R. Thon:
PoGO: Prediction of Gene Ontology terms for fungal proteins. 215 - Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer:
TassDB2 - A comprehensive database of subtle alternative splicing events. 216 - Unitsa Sangket, Surakameth Mahasirimongkol, Wasun Chantratita, Pichaya Tandayya, Yurii S. Aulchenko:
ParallABEL: an R library for generalized parallelization of genome-wide association studies. 217 - Stuart Collins, Michail Stamatakis, Dionisios G. Vlachos:
Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes. 218 - Fan Mo, Qun Mo, Yuanyuan Chen, David R. Goodlett, Leroy Hood, Gilbert S. Omenn, Song Li, Biaoyang Lin:
WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. 219 - Andreas Prlic, Marco A. Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T. Yukich, Peter W. Rose, Philip E. Bourne, J. Lynn Fink:
Integration of open access literature into the RCSB Protein Data Bank using BioLit. 220 - Alberto Risueño, Celia Fontanillo, Marcel E. Dinger, Javier De Las Rivas:
GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. 221 - Andreas Bremges, Stefanie Schirmer, Robert Giegerich:
Fine-tuning structural RNA alignments in the twilight zone. 222 - Jérôme Lane, Patrice Duroux, Marie-Paule Lefranc:
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. 223 - Ryuichiro Nakato, Osamu Gotoh:
Cgaln: fast and space-efficient whole-genome alignment. 224 - Denitsa Alamanova, Philip Stegmaier, Alexander E. Kel:
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. 225 - Louis-Philippe Lemieux Perreault, Gregor U. Andelfinger, Géraldine Asselin, Marie-Pierre Dubé:
Partitioning of copy-number genotypes in pedigrees. 226 - Hailong Meng, Andrew R. Joyce, Daniel E. Adkins, Priyadarshi Basu, Yankai Jia, Guoya Li, Tapas K. Sengupta, Barbara K. Zedler, Edward Lenn Murrelle, Edwin J. C. G. van den Oord:
A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling. 227 - Luigi Cerulo, Charles Elkan, Michele Ceccarelli:
Learning gene regulatory networks from only positive and unlabeled data. 228 - Alain B. Tchagang, Alexander Gawronski, Hugo Bérubé, Sieu Phan, Fazel Famili, Youlian Pan:
GOAL: A software tool for assessing biological significance of genes groups. 229 - Christian Rohde, Yingying Zhang, Richard Reinhardt, Albert Jeltsch:
BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. 230 - Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K. Burke, Jacek Blazewicz, Ryszard W. Adamiak:
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. 231 - Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, Masaru Tomita:
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. 232 - Jan Krumsiek, Sebastian Pölsterl, Dominik M. Wittmann, Fabian J. Theis:
Odefy -- From discrete to continuous models. 233 - Johannes M. Freudenberg, Siva Sivaganesan, Michael Wagner, Mario Medvedovic:
A semi-parametric Bayesian model for unsupervised differential co-expression analysis. 234 - Toshihide Hara, Keiko Sato, Masanori Ohya:
MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues. 235 - Nobuyuki Uchikoga, Takatsugu Hirokawa:
Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes. 236 - Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon M. Lin, David S. Lapointe, Michael R. Green:
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. 237 - Daniel Rios, William M. McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham:
A database and API for variation, dense genotyping and resequencing data. 238 - Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James A. Smith, Stephen J. Trevanion:
Using caching and optimization techniques to improve performance of the Ensembl website. 239 - Jessica Severin, Kathryn Beal, Albert J. Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero:
eHive: An Artificial Intelligence workflow system for genomic analysis. 240 - Chi Kin Chow, Hai Long Zhu, Jessica Lacy, Winston Patrick Kuo:
Error margin analysis for feature gene extraction. 241 - Drew H. Bryant, Mark Moll, Brian Y. Chen, Viacheslav Fofanov, Lydia E. Kavraki:
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. 242 - Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder, Mark B. Gerstein:
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. 243 - Qian Liu, Jinyan Li:
Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective. 244 - Henrik Bengtsson, Pierre Neuvial, Terence P. Speed:
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. 245 - Hong-Xuan Zhang, John Goutsias:
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems. 246 - Huaien Luo, Juntao Li, Majid Eshaghi, Jianhua Liu, R. Krishna Murthy Karuturi:
Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data. 247 - Pekka Ruusuvuori, Tarmo Äijö, Sharif Chowdhury, Cecilia Garmendia-Torres, Jyrki Selinummi, Mirko Birbaumer, Aimée M. Dudley, Lucas Pelkmans, Olli Yli-Harja:
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. 248 - Isana Veksler-Lublinsky, Yonat Shemer-Avni, Klara Kedem, Michal Ziv-Ukelson:
Gene bi-targeting by viral and human miRNAs. 249 - Qi Liu, Juan Cui, Qiang Yang, Ying Xu:
In-silico prediction of blood-secretory human proteins using a ranking algorithm. 250 - Florian Teichert, Jonas Minning, Ugo Bastolla, Markus Porto:
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH. 251 - Donald M. Gray, Carla W. Gray, Byong-Hoon Yoo, Tzu-Fang Lou:
Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data. 252 - Inna Chervoneva, Yanyan Li, Stephanie Schulz, Sean Croker, Chantell Wilson, Scott A. Waldman, Terry Hyslop:
Selection of optimal reference genes for normalization in quantitative RT-PCR. 253 - Maciej Paszkowski-Rogacz, Mikolaj Slabicki, M. Teresa Pisabarro, Frank Buchholz:
PhenoFam-gene set enrichment analysis through protein structural information. 254 - Bin Chen, Xiao Dong, Dazhi Jiao, Huijun Wang, Qian Zhu, Ying Ding, David J. Wild:
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. 255 - Edon Sung, Sangsoo Kim, Whanchul Shin:
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. 256 - Stephen F. Madden, Susan B. Carpenter, Ian B. Jeffery, Harry Björkbacka, Katherine A. Fitzgerald, Luke A. O'Neill, Desmond G. Higgins:
Detecting microRNA activity from gene expression data. 257 - Retraction: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase. 258
- Dennis P. Wall, Parul Kudtarkar, Vincent A. Fusaro, Rimma Pivovarov, Prasad Patil, Peter J. Tonellato:
Cloud computing for comparative genomics. 259 - Andrew N. Tolopko, John P. Sullivan, Sean D. Erickson, David Wrobel, Su L. Chiang, Katrina Rudnicki, Stewart Rudnicki, Jennifer Nale, Laura M. Selfors, Dara Greenhouse, Jeremy Muhlich, Caroline E. Shamu:
Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities. 260 - Jingming Ma, Carrie Dykes, Tao Wu, Yangxin Huang, Lisa M. Demeter, Hulin Wu:
vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments. 261 - Tomás Norambuena, Francisco Melo:
The Protein-DNA Interface database. 262 - Michael Riffle, Trisha N. Davis:
The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. 263 - Arnald Alonso, Antonio Julià, Raül Tortosa, Cristina Canaleta, Juan D. Cañete, Javier Ballina, Alejandro Balsa, Jesús Tornero, Sara Marsal:
CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays. 264 - Troy Hawkins, Meghana Chitale, Daisuke Kihara:
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. 265 - Jason W. H. Wong, Alexander B. Schwahn, Kevin M. Downard:
FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data. 266 - Guofeng Meng, Axel Mosig, Martin Vingron:
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. 267 - Miguel Arenas, Mateus Patricio, David Posada, Gabriel Valiente:
Characterization of phylogenetic networks with NetTest. 268 - Joachim M. De Schrijver, Kim De Leeneer, Steve Lefever, Nick Sabbe, Filip Pattyn, Filip Van Nieuwerburgh, Paul Coucke, Dieter Deforce, Jo Vandesompele, Sofie Bekaert, Jan Hellemans, Wim Van Criekinge:
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. 269 - Marta Blangiardo, Alberto Cassese, Sylvia Richardson:
sdef: an R package to synthesize lists of significant features in related experiments. 270 - Shuangge Ma, Mingyu Shi, Yang Li, Danhui Yi, Ben-Chang Shia:
Incorporating gene co-expression network in identification of cancer prognosis markers. 271 - Xin He, Moushumi Sen Sarma, Xu Ling, Brant W. Chee, Chengxiang Zhai, Bruce R. Schatz:
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. 272 - Ashis Kumer Biswas, Nasimul Noman, Abdur Rahman Sikder:
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. 273 - Benjamin Schmid, Johannes E. Schindelin, Albert Cardona, Mark Longair, Martin Heisenberg:
A high-level 3D visualization API for Java and ImageJ. 274 - Erdogan Taskesen, Renee Beekman, Jeroen de Ridder, Bas J. Wouters, Justine K. Peeters, Ivo P. Touw, Marcel J. T. Reinders, Ruud Delwel:
HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data. 275 - Birte Hellwig, Jan G. Hengstler, Marcus Schmidt, Mathias C. Gehrmann, Wiebke Schormann, Jörg Rahnenführer:
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. 276 - Gad Abraham, Adam Kowalczyk, Sherene Loi, Izhak Haviv, Justin Zobel:
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. 277 - Hong Cui:
Semantic annotation of morphological descriptions: an overall strategy. 278 - Tung T. Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis:
Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver. 279 - Matthew E. Ritchie, Matthew S. Forrest, Antigone S. Dimas, Caroline Daelemans, Emmanouil T. Dermitzakis, Panagiotis Deloukas, Simon Tavaré:
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. 280 - John R. Stevens, Jason L. Bell, Kenneth I. Aston, Kenneth L. White:
A comparison of probe-level and probeset models for small-sample gene expression data. 281 - Martin Eklund, Ola Spjuth, Jarl E. S. Wikberg:
An eScience-Bayes strategy for analyzing omics data. 282 - Jose M. Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis, Michael Lappe:
Optimal contact definition for reconstruction of Contact Maps. 283 - Steven N. Steinway, Ruth Dannenfelser, Christopher D. Laucius, James E. Hayes, Sudhir Nayak:
JCoDA: a tool for detecting evolutionary selection. 284 - Qianqian Zhu, Jeffrey C. Miecznikowski, Marc S. Halfon:
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. 285 - Mainak Guharoy, Pinak Chakrabarti:
Conserved residue clusters at protein-protein interfaces and their use in binding site identification. 286 - Conor Lawless, Darren J. Wilkinson, Alexander Young, Stephen G. Addinall, David A. Lydall:
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. 287 - Reedik Mägi, Andrew P. Morris:
GWAMA: software for genome-wide association meta-analysis. 288 - Lars Vogt:
Spatio-structural granularity of biological material entities. 289 - Jing Wang, Xianxiao Zhou, Jing Zhu, Chenggui Zhou, Zheng Guo:
Revealing and avoiding bias in semantic similarity scores for protein pairs. 290 - Hans Binder, Knut Krohn, Conrad J. Burden:
Washing scaling of GeneChip microarray expression. 291 - Martin Sturm, Michael Hackenberg, David Langenberger, Dmitrij Frishman:
TargetSpy: a supervised machine learning approach for microRNA target prediction. 292 - Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou, Hai-Peng Li:
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. 293 - Javier Tamames, Victor de Lorenzo:
EnvMine: A text-mining system for the automatic extraction of contextual information. 294 - Rashi Gupta, Dario Greco, Petri Auvinen, Elja Arjas:
Bayesian integrated modeling of expression data: a case study on RhoG. 295 - Donghwan Lee, Woojoo Lee, Youngjo Lee, Yudi Pawitan:
Super-sparse principal component analyses for high-throughput genomic data. 296 - Irina Ostrovnaya, Gouri Nanjangud, Adam B. Olshen:
A classification model for distinguishing copy number variants from cancer-related alterations. 297 - Zhong-Ru Xie, Ming-Jing Hwang:
An interaction-motif-based scoring function for protein-ligand docking. 298 - Raghunandan M. Kainkaryam, Angela Bruex, Anna C. Gilbert, John Schiefelbein, Peter J. Woolf:
poolMC: Smart pooling of mRNA samples in microarray experiments. 299 - Assaf Gottlieb, Roy Varshavsky, Michal Linial, David Horn:
UFFizi: a generic platform for ranking informative features. 300 - Jagat Singh Chauhan, Nitish K. Mishra, Gajendra P. S. Raghava:
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information. 301 - Jiye Ai, Barry Smith, Wong T. David:
Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base. 302 - Changhoon Kim, Jodi Basner, Byungkook Lee:
Detecting internally symmetric protein structures. 303 - Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A. Albert, Steve Rounsley, David Sankoff:
Scaffold filling, contig fusion and comparative gene order inference. 304 - Leandro A. Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiya, Diane Flaucher, Victoria E. H. Carlton, Martin Moorhead, Yontao Lu, Joe W. Gray, Malek Faham, Paul T. Spellman, Bahram Parvin:
Prediction of epigenetically regulated genes in breast cancer cell lines. 305 - Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Johansson, Thomas Hamelryck:
Beyond rotamers: a generative, probabilistic model of side chains in proteins. 306 - Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Maiko Lohel, Thomas Hinze, Peter Dittrich:
Rule-based spatial modeling with diffusing, geometrically constrained molecules. 307 - Shih Chi Peng, David Shan-Hill Wong, Kai Che Tung, Yan Yu Chen, Chun Cheih Chao, Chien Hua Peng, Yung-Jen Chuang, Chuan Yi Tang:
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation. 308 - Shi Yu, Tillmann Falck, Anneleen Daemen, Léon-Charles Tranchevent, Johan A. K. Suykens, Bart De Moor, Yves Moreau:
L2-norm multiple kernel learning and its application to biomedical data fusion. 309 - Kieran Alden, Stella Veretnik, Philip E. Bourne:
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. 310 - Stephen J. Goodswen, Cedric Gondro, Nathan S. Watson-Haigh, Haja N. Kadarmideen:
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. 311 - Paul D. Thomas:
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. 312 - Boris Sobolev, Dmitry Filimonov, Alexey Lagunin, Alexey V. Zakharov, Olga Koborova, Alexander E. Kel, Vladimir Poroikov:
Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. 313 - Osamu Komori, Shinto Eguchi:
A boosting method for maximizing the partial area under the ROC curve. 314 - Pietro Hiram Guzzi, Mario Cannataro:
mu-CS: An extension of the TM4 platform to manage Affymetrix binary data. 315 - Eelke van der Horst, Julio E. Peironcely, Adriaan P. IJzerman, Margot W. Beukers, Jonathan Robert Lane, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Yasushi Okuno, Andreas Bender:
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. 316 - Amber L. Hartman, Sean Riddle, Timothy M. McPhillips, Bertram Ludäscher, Jonathan A. Eisen:
WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences. 317 - Lukas Forer, Sebastian Schönherr, Hansi Weißensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg, Anita Kloss-Brandstätter:
CONAN: copy number variation analysis software for genome-wide association studies. 318 - Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards:
Accessing the SEED genome databases via Web services API: tools for programmers. 319 - Mirva Piippo, Niina Lietzén, Olli Nevalainen, Jussi Salmi, Tuula A. Nyman:
Pripper: prediction of caspase cleavage sites from whole proteomes. 320 - Paola M. V. Rancoita, Marcus Hutter, Francesco Bertoni, Ivo Kwee:
An integrated Bayesian analysis of LOH and copy number data. 321 - Emidio Capriotti, Marc A. Martí-Renom:
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. 322 - Patrick Happel, Kerstin Moller, Ralf Kunz, Irmgard D. Dietzel:
A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy. 323 - Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent Daubin:
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. 324 - Zhanchao Li, Xuan Zhou, Zong Dai, Xiaoyong Zou:
Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm. 325 - Shao-Wu Zhang, Yao-Jun Li, Li C. Xia, Quan Pan:
PPLook: an automated data mining tool for protein-protein interaction. 326 - Svetlana Kirillova, Silvio C. E. Tosatto, Oliviero Carugo:
FRASS: the web-server for RNA structural comparison. 327 - Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin R. Schiller:
MimoSA: a system for minimotif annotation. 328 - Ivo D. Shterev, Sin-Ho Jung, Stephen L. George, Kouros Owzar:
permGPU: Using graphics processing units in RNA microarray association studies. 329 - Sebastian Bremm, Tobias Schreck, Patrick Boba, Stephanie Held, Kay Hamacher:
Computing and visually analyzing mutual information in molecular co-evolution. 330 - Ilari Scheinin, Jose A. Ferreira, Sakari Knuutila, Gerrit Meijer, Mark A. van de Wiel,