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BMC Bioinformatics, Volume 11
Volume 11, 2010
- Shuangge Ma, Michael R. Kosorok:
Detection of gene pathways with predictive power for breast cancer prognosis. 1 - Leander Schietgat, Celine Vens, Jan Struyf, Hendrik Blockeel
, Dragi Kocev
Predicting gene function using hierarchical multi-label decision tree ensembles. 2 - Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka
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
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. 5 - Mats Ensterö, Örjan Åkerborg
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. 6 - Ben C. Stöver
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. 7 - Roberto Amato
A novel approach to simulate gene-environment interactions in complex diseases. 8 - Benjamin Georgi, Ivan Gesteira Costa
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
SKPDB: a structural database of shikimate pathway enzymes. 12 - Nysia I. George, Joanne R. Lupton, Nancy D. Turner
Evaluation of fecal mRNA reproducibility via a marginal transformed mixture modeling approach. 13 - Norman E. Davey
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
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
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
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
Assembly complexity of prokaryotic genomes using short reads. 21 - Alexander G. Churbanov, Igor Vorechovsky
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
ETE: a python Environment for Tree Exploration. 24 - Shuai Cheng Li
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
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. 27 - Shi Yu, Léon-Charles Tranchevent
Gene prioritization and clustering by multi-view text mining. 28 - Anders Jacobsen Skanderup
miRMaid: a unified programming interface for microRNA data resources. 29 - Benjamin Misselwitz
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
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
OLS Dialog: An open-source front end to the Ontology Lookup Service. 34 - Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker
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
Predicting Bevirimat resistance of HIV-1 from genotype. 37 - Juan Falgueras, Antonio J. Lara, Noé Fernández-Pozo, Francisco R. Cantón
SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. 38 - Emanuela Giombini
An automatic method for identifying surface proteins in bacteria: SLEP. 39 - Yaqiang Wang
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
Applying unmixing to gene expression data for tumor phylogeny inference. 42 - Tamir Tuller
Discovering local patterns of co - evolution: computational aspects and biological examples. 43 - Ulrike Naumann, George Luta
The curvHDR method for gating flow cytometry samples. 44 - Satwik Rajaram
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
BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. 47 - Wei-Jiun Lin, Huey-miin Hsueh
Power and sample size estimation in microarray studies. 48 - Dimitris G. Bariamis, Dimitrios K. Iakovidis
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
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
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
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
Comparison of evolutionary algorithms in gene regulatory network model inference. 59 - Mayer Alvo, Zhongzhu Liu, Andrew Williams
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
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
Haplotype allelic classes for detecting ongoing positive selection. 65 - Guimei Liu
FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium. 66 - Ronald van Eijk
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
A temporal precedence based clustering method for gene expression microarray data. 68 - Bram Slabbinck, Willem Waegeman, Peter Dawyndt
From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification. 69 - Adriano Barbosa-Silva
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
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
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. 74 - Leslie Regad
Mining protein loops using a structural alphabet and statistical exceptionality. 75 - Xue Gong, Ruihong Wu, Yuannv Zhang, Wenyuan Zhao, Lixin Cheng
Extracting consistent knowledge from highly inconsistent cancer gene data sources. 76 - Ricardo Cao
A random effect multiplicative heteroscedastic model for bacterial growth. 77 - Anne-Laure Boulesteix
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
Parameters for accurate genome alignment. 80 - Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. 81 - Hedda Høvik
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
LINNAEUS: A species name identification system for biomedical literature. 85 - Like Fokkens
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
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
Finding sRNA generative locales from high-throughput sequencing data with NiBLS. 93 - James H. Bullard, Elizabeth Purdom, Kasper D. Hansen
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
SING: Subgraph search In Non-homogeneous Graphs. 96 - Alessandro Pandini
Structural alphabets derived from attractors in conformational space. 97 - Jens Keilwagen
Unifying generative and discriminative learning principles. 98 - Brice Hoffmann
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
Word add-in for ontology recognition: semantic enrichment of scientific literature. 103 - Jakub Mieczkowski
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. 104 - Dan C. Tulpan
Free energy estimation of short DNA duplex hybridizations. 105 - Sandra Ortega-Martorell
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
Ovarian cancer classification based on dimensionality reduction for SELDI-TOF data. 109 - Kristin K. Nicodemus, James D. Malley, Carolin Strobl
The behaviour of random forest permutation-based variable importance measures under predictor correlation. 110 - Ching-Lin Hsiao, Ie-Bin Lian
Modeling expression quantitative trait loci in data combining ethnic populations. 111 - Yevhen Vainshtein
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
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
ABCtoolbox: a versatile toolkit for approximate Bayesian computations. 116 - Aaron M. Newman
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. 117 - Chongle Pan
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
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
Mayday - integrative analytics for expression data. 121 - Hansi Weißensteiner
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
A fast and robust hepatocyte quantification algorithm including vein processing. 124 - Aarti Garg, Rupinder Tewari
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
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
Calling SNPs without a reference sequence. 130 - Andrew S. Warren
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
MapMi: automated mapping of microRNA loci. 133 - Yurii S. Aulchenko
ProbABEL package for genome-wide association analysis of imputed data. 134 - Haroon Naeem
miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. 135 - Luis Quintales
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
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
Large-scale prediction of protein-protein interactions from structures. 144 - Bobbie-Jo M. Webb-Robertson
Physicochemical property distributions for accurate and rapid pairwise protein homology detection. 145 - Michael L. Sierk
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. 146 - Teo Shu Mei
Identification of recurrent regions of copy-number variants across multiple individuals. 147 - Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann
In silico fragmentation for computer assisted identification of metabolite mass spectra. 148 - Jens Keilwagen
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
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function. 151 - James Robert White, Saket Navlakha, Niranjan Nagarajan
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
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. 154 - Zong Hong Zhang
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
Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization. 156 - Mariana L. Neves
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
CDK-Taverna: an open workflow environment for cheminformatics. 159 - Hifzur Rahman Ansari
Identification of NAD interacting residues in proteins. 160 - Israel T. da Silva
ProbFAST: Probabilistic Functional Analysis System Tool. 161 - Chen Wang
Knowledge-guided gene ranking by coordinative component analysis. 162 - Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan
New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. 163 - Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew
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
Using jackknife to assess the quality of gene order phylogenies. 168 - Johann M. Kraus
A highly efficient multi-core algorithm for clustering extremely large datasets. 169 - Ken Tatebe, Ahmet Zeytun, Ruy M. Ribeiro
Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. 170 - Mehar S. Khatkar
Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates. 171 - Jonathan J. Ellis
Directionality in protein fold prediction. 172 - Hsueh-Wei Chang, Yu-Huei Cheng
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. 173 - Junfeng Xia
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. 174 - Rabie Saidi
Protein sequences classification by means of feature extraction with substitution matrices. 175 - Gregor Stiglic
Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays. 176 - Karl W. Kuschner, Dariya I. Malyarenko, William E. Cooke, Lisa H. Cazares
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
An overview of the CellML API and its implementation. 178 - Timothy L. Bailey, Mikael Bodén
The value of position-specific priors in motif discovery using MEME. 179 - Andrew S. Parker, Wei Zheng, Karl E. Griswold
Optimization algorithms for functional deimmunization of therapeutic proteins. 180 - Qi Liu, Qian Xu, Vincent Wenchen Zheng, Hong Xue
Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study. 181 - Bing Wang
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
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
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
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
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
Systematic calibration of a cell signaling network model. 202 - Pao-Yang Chen
BS Seeker: precise mapping for bisulfite sequencing. 203 - Annalisa Marsico, Andreas Henschel, Christof Winter
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. 204 - Kevin Horan, Christian R. Shelton
Predicting conserved protein motifs with Sub-HMMs. 205 - Massimiliano Virgilio
Comparative performances of DNA barcoding across insect orders. 206 - Mario Fasold, Peter F. Stadler
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. 207 - Mike L. Smith
Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. 208 - Federico Plazzi
Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies. 209 - Subhadip Basu
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
Concept-based query expansion for retrieving gene related publications from MEDLINE. 212 - Jan Schellenberger, Junyoung O. Park
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. 213 - Henning Redestig
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. 214 - Jaehee Jung, Gangman Yi, Serenella A. Sukno
PoGO: Prediction of Gene Ontology terms for fungal proteins. 215 - Rileen Sinha
TassDB2 - A comprehensive database of subtle alternative splicing events. 216 - Unitsa Sangket, Surakameth Mahasirimongkol
ParallABEL: an R library for generalized parallelization of genome-wide association studies. 217 - Stuart Collins, Michail Stamatakis
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
WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. 219 - Andreas Prlic
Integration of open access literature into the RCSB Protein Data Bank using BioLit. 220 - Alberto Risueño
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
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
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
BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. 230 - Mariusz Popenda, Marta Szachniuk
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
Odefy -- From discrete to continuous models. 233 - Johannes M. Freudenberg
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
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. 237 - Daniel Rios, William M. McLaren
A database and API for variation, dense genotyping and resequencing data. 238 - Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard
Using caching and optimization techniques to improve performance of the Ensembl website. 239 - Jessica Severin, Kathryn Beal, Albert J. Vilella
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
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
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
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
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. 248 - Isana Veksler-Lublinsky
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
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
Selection of optimal reference genes for normalization in quantitative RT-PCR. 253 - Maciej Paszkowski-Rogacz
PhenoFam-gene set enrichment analysis through protein structural information. 254 - Bin Chen, Xiao Dong, Dazhi Jiao, Huijun Wang, Qian Zhu
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
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
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
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
The Protein-DNA Interface database. 262 - Michael Riffle
The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images. 263 - Arnald Alonso, Antonio Julià
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
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. 267 - Miguel Arenas
Characterization of phylogenetic networks with NetTest. 268 - Joachim M. De Schrijver, Kim De Leeneer
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. 269 - Marta Blangiardo, Alberto Cassese
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
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. 272 - Ashis Kumer Biswas
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. 273 - Benjamin Schmid
A high-level 3D visualization API for Java and ImageJ. 274 - Erdogan Taskesen
HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data. 275 - Birte Hellwig, Jan G. Hengstler
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. 276 - Gad Abraham
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
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. 280 - John R. Stevens, Jason L. Bell, Kenneth I. Aston
A comparison of probe-level and probeset models for small-sample gene expression data. 281 - Martin Eklund, Ola Spjuth
An eScience-Bayes strategy for analyzing omics data. 282 - Jose M. Duarte
Optimal contact definition for reconstruction of Contact Maps. 283 - Steven N. Steinway
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
Conserved residue clusters at protein-protein interfaces and their use in binding site identification. 286 - Conor Lawless
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. 287 - Reedik Mägi
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
Washing scaling of GeneChip microarray expression. 291 - Martin Sturm, Michael Hackenberg
TargetSpy: a supervised machine learning approach for microRNA target prediction. 292 - Lei Chen
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. 293 - Javier Tamames
EnvMine: A text-mining system for the automatic extraction of contextual information. 294 - Rashi Gupta, Dario Greco
Bayesian integrated modeling of expression data: a case study on RhoG. 295 - Donghwan Lee
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
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
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
Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base. 302 - Changhoon Kim, Jodi Basner
Detecting internally symmetric protein structures. 303 - Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A. Albert
Scaffold filling, contig fusion and comparative gene order inference. 304 - Leandro A. Loss, Anguraj Sadanandam
Prediction of epigenetically regulated genes in breast cancer cell lines. 305 - Tim Harder, Wouter Boomsma
Beyond rotamers: a generative, probabilistic model of side chains in proteins. 306 - Gerd Gruenert, Bashar Ibrahim
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
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
L2-norm multiple kernel learning and its application to biomedical data fusion. 309 - Kieran Alden
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. 310 - Stephen J. Goodswen
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
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
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. 316 - Amber L. Hartman
WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences. 317 - Lukas Forer
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
Pripper: prediction of caspase cleavage sites from whole proteomes. 320 - Paola M. V. Rancoita
An integrated Bayesian analysis of LOH and copy number data. 321 - Emidio Capriotti
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. 322 - Patrick Happel
A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from topographical data obtained by scanning probe microscopy. 323 - Sophie S. Abby
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
PPLook: an automated data mining tool for protein-protein interaction. 326 - Svetlana Kirillova, Silvio C. E. Tosatto
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
Computing and visually analyzing mutual information in molecular co-evolution. 330 - Ilari Scheinin, Jose A. Ferreira, Sakari Knuutila, Gerrit Meijer
CGHpower: exploring sample size calculations for chromosomal copy number experiments. 331 - Hiroshi Mori
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
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. 335 - Marc Bruckskotten, Mario Looso
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
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
A high-throughput pipeline for the design of real-time PCR signatures. 340 - Robert Schmieder, Yan Wei Lim, Forest Rohwer
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. 341 - Xiaoqin Xia
TabSQL: a MySQL tool to facilitate mapping user data to public databases. 342 - Zhuhong You
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. 343 - Benjamin Chain
Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays. 344 - Adel Dayarian, Todd P. Michael
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
Metamotifs - a generative model for building families of nucleotide position weight matrices. 348 - Yichuan Liu
Modular composition predicts kinase/substrate interactions. 349 - Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita:
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. 350 - Martin Klammer, Klaus Godl, Andreas Tebbe, Christoph Schaab
Identifying differentially regulated subnetworks from phosphoproteomic data. 351 - Albert Solernou, Juan Fernández-Recio
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. 352 - John C. Dittmar
ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data. 353 - Omar J. Jabado, Sean Conlan
Nonparametric methods for the analysis of single-color pathogen microarrays. 354 - Marc Bailly-Bechet
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
Interaction prediction and classification of PDZ domains. 357 - Wolfgang Hankeln, Pier Luigi Buttigieg
MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. 358 - David S. Huen
On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence. 359 - Kris Laukens
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. 360 - Alexander E. Pozhitkov
Scanner calibration revisited. 361 - Lars Carlsson, Ola Spjuth
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
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
Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. 366 - Renaud Gaujoux, Cathal Seoighe:
A flexible R package for nonnegative matrix factorization. 367 - Yuna Blum
A factor model to analyze heterogeneity in gene expression. 368 - Zhaohui S. Qin
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. 369 - Jian Tian
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
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
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. 377 - Petr Novák
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. 378 - Raphaël Helaers
MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics. 379 - Roger Pique-Regi
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
Integration and visualization of systems biology data in context of the genome. 382 - Giovanni Capone, Giuseppe Novello, Candida Fasano
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
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
Efficiency clustering for low-density microarrays and its application to QPCR. 386 - Jonas S. Almeida, Helena F. Deus
S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. 387 - Fredrik Johansson, Hiroyuki Toh:
A comparative study of conservation and variation scores. 388 - Joel Arrais
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. 389 - Uri Weingart, Erez Persi, Uri Gophna
Deriving enzymatic and taxonomic signatures of metagenomes from short read data. 390 - Insuk Sohn, Kouros Owzar, Stephen L. George, Sujong Kim
Robust test method for time-course microarray experiments. 391 - Lina Chen
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
A comparison of internal validation techniques for multifactor dimensionality reduction. 394 - Tomás Pluskal
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. 395 - Xiaojiang Xu
Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. 396 - Shaoqiang Zhang
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. 397 - Yoji Nakamura, Tomoyoshi Komiyama
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
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). 401 - Peng Chen, Jinyan Li:
Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. 402 - Habil Zare
Data reduction for spectral clustering to analyze high throughput flow cytometry data. 403 - Joshua Colvin, Michael I. Monine, Ryan N. Gutenkunst, William S. Hlavacek
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
MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences. 406 - Petros Kountouris
Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures. 407 - Anna Campain
Comparison study of microarray meta-analysis methods. 408 - Kristof Theys, Koen Deforche, Gertjan Beheydt, Yves Moreau
Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. 409 - Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso
A method for automatically extracting infectious disease-related primers and probes from the literature. 410 - Chia-Ying Cheng, Yuh-Jyh Hu:
Extracting the abstraction pyramid from complex networks. 411 - Junbai Wang:
The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data. 412 - Anil Aswani
Nonparametric identification of regulatory interactions from spatial and temporal gene expression data. 413 - Suresh Kumar Poovathingal
Global parameter estimation methods for stochastic biochemical systems. 414 - Mali Salmon-Divon
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
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
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
An improved classification of G-protein-coupled receptors using sequence-derived features. 420 - Wei-Chung Cheng
Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. 421 - Thomas J. Hardcastle
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. 422 - Ron Henkel
Ranked retrieval of Computational Biology models. 423 - Ernst Althaus, Stefan Canzar
Computing H/D-Exchange rates of single residues from data of proteolytic fragments. 424 - Xiaoqi Cui, Tong Wang, Huann-Sheng Chen
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
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
Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets. 428 - Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff-Borg, Thomas Hamelryck
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. 429 - Steven N. Evans, Valerie Hower, Lior Pachter
Coverage statistics for sequence census methods. 430 - L. Steven Johnson, Sean R. Eddy
Hidden Markov model speed heuristic and iterative HMM search procedure. 431 - Tae-Min Kim
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
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
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
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. 438 - Gong-Hua Li
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
Relations as patterns: bridging the gap between OBO and OWL. 441 - Bo Peng
Forward-time simulation of realistic samples for genome-wide association studies. 442 - Pekka Marttinen
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
Fast and accurate protein substructure searching with simulated annealing and GPUs. 446 - Yu Guo, Armin Graber, Robert N. McBurney, Raji Balasubramanian:
Sample size and statistical power considerations in high-dimensionality data settings: a comparative study of classification algorithms. 447 - Leo C. McHugh, Jonathan W. Arthur:
Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. 448 - Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong
Consistency, comprehensiveness, and compatibility of pathway databases. 449 - Maarten van Iterson, Judith M. Boer, Renée X. de Menezes:
Filtering, FDR and power. 450 - Shiliang Wang, Jaideep P. Sundaram, David Spiro:
VIGOR, an annotation program for small viral genomes. 451 - Stuart G. Baker:
Simple and flexible classification of gene expression microarrays via Swirls and Ripples. 452 - Ioannis K. Valavanis, Stavroula G. Mougiakakou, Keith A. Grimaldi
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
Multivariate Hawkes process models of the occurrence of regulatory elements. 456 - Sergey Koren
An algorithm for automated closure during assembly. 457 - Nophar Geifman
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
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. 460 - Chad Laing
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
Context dependent substitution biases vary within the human genome. 462 - Fran Supek, Kristian Vlahovicek
Correction: Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. 463 - Gayathri Jayaraman, Rahul Siddharthan:
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model. 464 - Wayne Wenzhong Xu, Clay J. Carter:
Parallel multiplicity and error discovery rate (EDR) in microarray experiments. 465 - Minlu Zhang, Long J. Lu:
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. 466 - Taeho Kim, Hyun Joo:
ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment. 467 - Lina Hultin Rosenberg, Bo Franzén, Gert Auer
Multivariate meta-analysis of proteomics data from human prostate and colon tumours. 468 - Ming Jia, Suh-Yeon Choi, Dirk Reiners, Eve Syrkin Wurtele
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
SeqAnt: A web service to rapidly identify and annotate DNA sequence variations. 471 - Steffen Uebe, Francesca Pasutto, Mandy Krumbiegel, Denny Schanze, Arif B. Ekici
GPFrontend and GPGraphics: graphical analysis tools for genetic association studies. 472 - Khader Shameer
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
FragViz: visualization of fragmented networks. 475 - Hui Liu, Dong Yue, Yidong Chen, Shou-Jiang Gao
Improving performance of mammalian microRNA target prediction. 476 - Fan Shi, Christopher Leckie
A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer. 477 - Sébastien Terrat
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
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
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
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. 484 - Murray P. Cox
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. 485 - Lianbo Yu, Rebecca W. Doerge:
A semi-nonparametric mixture model for selecting functionally consistent proteins. 486 - Alex Aussem, André Tchernof
Analysis of lifestyle and metabolic predictors of visceral obesity with Bayesian Networks. 487 - Paola Bertolazzi, Concettina Guerra, Giampaolo Liuzzi
A global optimization algorithm for protein surface alignment. 488 - Steinn Gudmundsson, Ines Thiele
Computationally efficient flux variability analysis. 489 - Youting Sun, Jianqiu Zhang, Ulisses M. Braga-Neto, Edward R. Dougherty:
BPDA - A Bayesian peptide detection algorithm for mass spectrometry. 490 - Peter Raasch, Ulf Schmitz
Non-coding RNA detection methods combined to improve usability, reproducibility and precision. 491 - K. Bretonnel Cohen, Helen L. Johnson, Karin Verspoor
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
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage. 494 - Chen-Hsiang Yeang:
An integrated analysis of molecular aberrations in NCI-60 cell lines. 495 - Harriet J. Muncey
MetAssimulo: Simulation of Realistic NMR Metabolic Profiles. 496 - Bruno M. Tesson, Rainer Breitling
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. 497 - Melissa J. Davis
Automatic, context-specific generation of Gene Ontology slims. 498 - Melissa J. Morine, Jolene McMonagle, Sinead Toomey
Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome. 499 - Ilenia Giangreco
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
Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering. 503 - Sriganesh Srihari
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. 504 - Kang Ning
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
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
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
Booly: a new data integration platform. 513 - Kenny Daily
Data structures and compression algorithms for high-throughput sequencing technologies. 514 - Tung T. Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis:
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures. 515 - Rudi Alberts, Klaus Schughart
QTLminer: identifying genes regulating quantitative traits. 516 - Isabel A. Nepomuceno-Chamorro
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
Statistical analysis and molecular dynamics simulations of ambivalent alpha -helices. 519 - Yong Li
Comparative study of discretization methods of microarray data for inferring transcriptional regulatory networks. 520 - Jongkwang Kim, Kai Tan
Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity. 521 - Mara L. Hartsperger, Florian Blöchl, Volker Stümpflen, Fabian J. Theis
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. 522 - Rok Blagus, Lara Lusa
Class prediction for high-dimensional class-imbalanced data. 523 - Pengyi Yang
A genetic ensemble approach for gene-gene interaction identification. 524 - Isaak Y. Tecle, Naama Menda, Robert M. Buels, Esther van der Knaap
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. 525 - Andrew K. Rider, Geoffrey Siwo, Nitesh V. Chawla
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
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
BALL - biochemical algorithms library 1.3. 531 - Elena E. Giorgi, Bob Funkhouser, Gayathri Athreya, Alan S. Perelson, Bette T. Korber
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model. 532 - Shandar Ahmad
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. 533 - Joel Hedlund
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. 534 - Jérôme Gracy, Laurent Chiche:
Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots. 535 - Shu-An Chen, Tzong-Yi Lee, Yu-Yen Ou
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. 536 - Alvaro J. González, Li Liao:
Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. 537 - Frederick A. Matsen IV, Robin B. Kodner, E. Virginia Armbrust:
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. 538 - Zhengdong D. Zhang, Mark B. Gerstein:
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. 539 - Meric A. Ovacik, Siddharth Sukumaran, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis:
Circadian signatures in rat liver: from gene expression to pathways. 540 - Eric Bareke
Correction: PathEx: A novel multi factors based datasets selector web tool. 541 - Wei Tan, Ravi K. Madduri
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
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
Bioactive Conformational Generation of Small Molecules: A Comparative Analysis between Force-Field and Multiple Empirical Criteria Based Methods. 545 - Greg Finak
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
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. 548 - Lianyi Han
The Text-mining based PubChem Bioassay neighboring analysis. 549 - Liya Wang
Localizing triplet periodicity in DNA and cDNA sequences. 550 - Fernando García-Alcalde
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. 551 - Bo Chen, Minhua Chen, John W. Paisley, Aimee K. Zaas, Christopher W. Woods, Geoffrey S. Ginsburg, Alfred O. Hero III, Joseph E. Lucas, David B. Dunson, Lawrence Carin
Bayesian Inference of the Number of Factors in Gene-Expression Analysis: Application to Human Virus Challenge Studies. 552 - Federico M. Giorgi
Algorithm-driven Artifacts in median polish summarization of Microarray data. 553 - Jacques Oberto:
FITBAR: a web tool for the robust prediction of prokaryotic regulons. 554 - Mark Moll
The LabelHash Algorithm for Substructure Matching. 555 - Martin Sill
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
Leukocyte Nucleus Segmentation and Nucleus Lobe Counting. 558 - Tianwei Yu
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
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs. 560 - Carsten Henneges, Pavel Laskov, Endang Darmawan
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
Empirical Bayes Analysis of Sequencing-based Transcriptional Profiling without Replicates. 564 - Francis C. Weng, Chien-Hao Su, Ming-Tsung Hsu
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency. 565 - Federica Viti
Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study. 566 - Christoph Bartenhagen, Hans-Ulrich Klein
Comparative study of unsupervised dimension reduction techniques for the visualization of microarray gene expression data. 567 - Peng Wang
Peptide binding predictions for HLA DR, DP and DQ molecules. 568 - Antonio Jimeno-Yepes
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
Probabilistic Principal Component Analysis for Metabolomic Data. 571 - Cristian Coarfa, Fuli Yu, Christopher A. Miller, Zuozhou Chen, R. Alan Harris
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
DeltaProt: a software toolbox for comparative genomics. 573 - Ruchi Chaudhary, Mukul S. Bansal
iGTP: A software package for large-scale gene tree parsimony analysis. 574 - Patricia Francis-Lyon, Shengyin Gu, Joel Hass, Nina Amenta, Patrice Koehl
Sampling the conformation of protein surface residues for flexible protein docking. 575 - Reuben Thomas, Luis de la Torre, Xiaoqing Chang, Sanjay Mehrotra:
Validation and characterization of DNA microarray gene expression data distribution and associated moments. 576 - Chen Zhou, Hao Chi, Leheng Wang, You Li, Yan-Jie Wu, Yan Fu, Ruixiang Sun, Si-Min He:
Speeding up tandem mass spectrometry-based database searching by longest common prefix. 577 - Miguel Ángel Antón
Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays. 578 - Ari Löytynoja
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. 579 - Anthony Santella, Zhuo Du
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
Systematic integration of experimental data and models in systems biology. 582 - Matthias Kohl
Preprocessing of gene expression data by optimally robust estimators. 583 - Zeev Frenkel, Etienne Paux
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
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. 585 - Michiaki Hamada
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. 586 - Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A. Kibbe
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. 587 - Sidahmed Benabderrahmane
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
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
Haplotype association analyses in resources of mixed structure using Monte Carlo testing. 592 - Maurizio Cardelli
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
Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers. 594 - Keith A. Jolley
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
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. 597 - Angela C. M. Luyf, Barbera D. C. van Schaik
Initial steps towards a production platform for DNA sequence analysis on the grid. 598 - Minh Duc Cao
A genome alignment algorithm based on compression. 599 - Kristian Holm, Espen Melum
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
A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences. 601 - Clark D. Jeffries, Diana O. Perkins
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
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
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
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
BiologicalNetworks 2.0 - an integrative view of genome biology data. 610 - Mark Doderer, Kihoon Yoon, Kay A. Robbins:
SIDEKICK: Genomic data driven analysis and decision-making framework. 611 - Takaya Saito
A two-step site and mRNA-level model for predicting microRNA targets. 612
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