default search action
BMC Bioinformatics, Volume 13
Volume 13, 2012
- Rebecca F. Halperin, Phillip Stafford, Jack S. Emery, Krupa Navalkar
, Stephen A. Johnston:
GuiTope: an application for mapping random-sequence peptides to protein sequences. 1 - Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jingchu Luo, Ge Gao:
ABrowse - a customizable next-generation genome browser framework. 2 - Leonid L. Chepelev, Janna Hastings
Self-organizing ontology of biochemically relevant small molecules. 3 - Yanglan Gan, Jihong Guan, Shuigeng Zhou:
A comparison study on feature selection of DNA structural properties for promoter prediction. 4 - David Rosenkranz, Hans Zischler
proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis. 5 - Akhil Kumar
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. 6 - Bin Li, Daisuke Kihara:
Protein docking prediction using predicted protein-protein interface. 7 - Danny Challis, Jin Yu
An integrative variant analysis suite for whole exome next-generation sequencing data. 8 - Ana Brândusa Pavel, Cristian Ioan Vasile
PyElph - a software tool for gel images analysis and phylogenetics. 9 - Shannon M. Bell, Lyle D. Burgoon
MIPHENO: data normalization for high throughput metabolite analysis. 10 - Kentaro Tomii
Convergent evolution in structural elements of proteins investigated using cross profile analysis. 11 - Ruoting Yang, Bernie J. Daigle Jr., Linda R. Petzold, Francis J. Doyle III:
Core module biomarker identification with network exploration for breast cancer metastasis. 12 - Douglas Londono, Steven Buyske
TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data. 13 - Muneef Ayyash, Hashem Tamimi
Developing a powerful In Silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome. 14 - Thomas Triplet, Gregory Butler:
The EnzymeTracker: an open-source laboratory information management system for sample tracking. 15 - Ruihua Fang, Gary Schindelman, Kimberly Van Auken, Jolene Fernandes, Wen J. Chen, Xiaodong Wang, Paul Davis
Automatic categorization of diverse experimental information in the bioscience literature. 16 - Ning Kang, Erik M. van Mulligen
Training text chunkers on a silver standard corpus: can silver replace gold? 17 - Marvin Schulz, Edda Klipp, Wolfram Liebermeister
Propagating semantic information in biochemical network models. 18 - Cyrille Lepoivre, Aurélie Bergon, Fabrice Lopez, Narayanan Perumal, Catherine Nguyen, Jean Imbert
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. 19 - Gabriele Sales
graphite - a Bioconductor package to convert pathway topology to gene network. 20 - Ching-Wei Wang
Fast automatic quantitative cell replication with fluorescent live cell imaging. 21 - Monir Hajiaghayi, Anne Condon, Holger H. Hoos
Analysis of energy-based algorithms for RNA secondary structure prediction. 22 - H. Robert Frost, Alexa T. McCray:
Markov Chain Ontology Analysis (MCOA). 23 - Fangzhou Yao, Jeff Coquery, Kim-Anh Lê Cao
Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets. 24 - Hani Z. Girgis, Ivan Ovcharenko:
Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. 25 - Satish Viswanath
Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data. 26 - Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim, Changyu Shen:
Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry. 27 - Alejandro Cáceres
Identification of polymorphic inversions from genotypes. 28 - Richard J. Giuly, Maryann E. Martone
Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets. 29 - Itziar Irigoien
ICGE: an R package for detecting relevant clusters and atypical units in gene expression. 30 - Andre P. Masella, Andrea K. Bartram, Jakub Truszkowski
PANDAseq: paired-end assembler for illumina sequences. 31 - Yang Ding, William Andrew Lorenz, Jeffrey H. Chuang
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences. 32 - Matti Kankainen
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. 33 - Chris Bauer, Frank Kleinjung, Dorothea Rutishauser
PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. 34 - Leonid Chindelevitch
Assessing statistical significance in causal graphs. 35 - Cedric Laczny
miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. 36 - Bhakti Dwivedi
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. 37 - Sandra Ortega-Martorell
Non-negative matrix factorisation methods for the spectral decomposition of MRS data from human brain tumours. 38 - Paul Ashford
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. 39 - Chun-Wei Tung
PupDB: a database of pupylated proteins. 40 - Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs
Predicting protein-protein interface residues using local surface structural similarity. 41 - Konstantinos Krampis, Tim Booth, Brad Chapman
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. 42 - Zhang Zhang
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. 43 - Jianguo Liu, Xianjiang Kang:
Grading amino acid properties increased accuracies of single point mutation on protein stability prediction. 44 - Maria Secrier
Arena3D: visualizing time-driven phenotypic differences in biological systems. 45 - Chia-Ling Huang, John Lamb, Leonid Chindelevitch
Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. 46 - John P. Archer
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. 47 - Pierre Peterlongo
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. 48 - Yanglan Gan, Jihong Guan, Shuigeng Zhou, Weixiong Zhang
Structural features based genome-wide characterization and prediction of nucleosome organization. 49 - Tudor Groza
The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain. 50 - Zhenhua Li
Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. 51 - Xingbin Wang, Yan Lin, Chi Song, Etienne Sibille, George C. Tseng:
Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder. 52 - Benjamin A. Logsdon, Gabriel E. Hoffman, Jason G. Mezey:
Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control. 53 - Alain B. Tchagang, Sieu Phan, Fazel Famili, Heather Shearer, Pierre R. Fobert, Yi Huang
Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm. 54 - Jan-Oliver Janda, Markus Busch
CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure. 55 - Michael Dannemann, Michael Lachmann, Anna Lorenc
'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences. 56 - Abdelhalim Larhlimi
F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks. 57 - John Boyle
Methods for visual mining of genomic and proteomic data atlases. 58 - Joanna Zhuang, Martin Widschwendter
A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform. 59 - Neetika Nath
Is EC class predictable from reaction mechanism? 60 - Luna De Ferrari
EnzML: multi-label prediction of enzyme classes using InterPro signatures. 61 - Adam Hilterbrand, Joseph Saelens, Catherine Putonti
CBDB: The codon bias database. 62 - Teerasak E.-komon, Richard J. Burchmore
Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation. 63 - Ilya Plyusnin
Comprehensive comparison of graph based multiple protein sequence alignment strategies. 64 - Jianlin Cheng
The MULTICOM toolbox for protein structure prediction. 65 - Yejun Wang, He Huang, Ming-an Sun
T3DB: an integrated database for bacterial type III secretion system. 66 - Nicolas Terrapon
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. 67 - Bernie J. Daigle Jr., Min K. Roh
Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. 68 - Yupeng Cun
Prognostic gene signatures for patient stratification in breast cancer - accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. 69 - Xian-Wen Ren, Yong Wang, Jiguang Wang
A unified computational model for revealing and predicting subtle subtypes of cancers. 70 - Duojiao Wu, Catherine M. Rice, Xiangdong Wang:
Cancer bioinformatics: A new approach to systems clinical medicine. 71 - Masao Ueki, Gen Tamiya
Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis. 72 - Axel Skarman, Mohammad Shariati
A Bayesian variable selection procedure to rank overlapping gene sets. 73 - Joseph E. Lucas, J. Will Thompson, Laura G. Dubois, Jeanette McCarthy, Hans Tillmann, Alexander Thompson, Norah Shire, Ron Hendrickson, Francisco Dieguez, Phyllis Goldman, Kathleen Schwarz, Keyur Patel, John McHutchison, M. Arthur Moseley:
Metaprotein expression modeling for label-free quantitative proteomics. 74 - Tianlei Xu, Ruixin Zhu
Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis. 75 - Thomas Hladish
EpiFire: An open source C++ library and application for contact network epidemiology. 76 - Mohamed Abouelhoda
Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support. 77 - James W. J. Anderson, Paula Tataru
Evolving stochastic context-free grammars for RNA secondary structure prediction. 78 - Xueping Yu, Anders Wallqvist
Inferring high-confidence human protein-protein interactions. 79 - Wessel N. van Wieringen
Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses. 80 - Sonja Zehetmayer
False discovery rate control in two-stage designs. 81 - Giorgio Gonnella
Readjoiner: a fast and memory efficient string graph-based sequence assembler. 82 - Eric Audemard
Detecting long tandem duplications in genomic sequences. 83 - Douglas B. Craig, Sujatha Kannan
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny. 84 - Felix Dreher, Thomas Kreitler, Christopher Hardt
DIPSBC - data integration platform for systems biology collaborations. 85 - Eugene Andres Houseman
DNA methylation arrays as surrogate measures of cell mixture distribution. 86 - Alexandre P. Francisco
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. 87 - Gad Abraham
SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction. 88 - Rasna R. Walia
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. 89 - Antoni Miró, Carlos Pozo
Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems. 90 - Jacek Blazewicz
GeVaDSs - decision support system for novel Genetic Vaccine development process. 91 - Adam L. Bazinet, Michael P. Cummings:
A comparative evaluation of sequence classification programs. 92 - Sunisa Chatsurachai, Chikara Furusawa
An in silico platform for the design of heterologous pathways in nonnative metabolite production. 93 - Steven M. Hill
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. 94 - Yu-Shen Liu, Meng Wang, Jean-Claude Paul, Karthik Ramani:
3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison. 95 - Zanoni Dias, Ulisses Dias
SIS: a program to generate draft genome sequence scaffolds for prokaryotes. 96 - Tahir Mehmood
Exploration of multivariate analysis in microbial coding sequence modeling. 97 - Weiliang Shi, Grace Wahba, Rafael A. Irizarry, Héctor Corrada Bravo
The partitioned LASSO-patternsearch algorithm with application to gene expression data. 98 - Dinesh K. Barupal
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. 99 - Dandi Qiao, Wai-Ki Yip, Christoph Lange:
Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data. 100 - Marine Dumousseau, Nicolas Rodriguez
MELTING, a flexible platform to predict the melting temperatures of nucleic acids. 101 - Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda:
Workflows for microarray data processing in the Kepler environment. 102 - András Bodor, István Csabai
rCUR: an R package for CUR matrix decomposition. 103 - Niall J. Haslam
Profile-based short linear protein motif discovery. 104 - Paul Shealy, Homayoun Valafar
Multiple structure alignment with msTALI. 105 - Kalai Vanii
Natural product-likeness score revisited: an open-source, open-data implementation. 106 - Lei Yuan, Alexander Woodard, Shuiwang Ji
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval. 107 - Makoto Miwa, Paul Thompson, John McNaught, Douglas B. Kell
Extracting semantically enriched events from biomedical literature. 108 - Min Li, Xuehong Wu
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. 109 - Thomas Laubach, Arndt von Haeseler, Martin J. Lercher
TreeSnatcher plus: capturing phylogenetic trees from images. 110 - Lukasz Pawel Kozlowski
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. 111 - Suleiman A. Khan, Ali Faisal
Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. 112 - Ye Deng
Molecular ecological network analyses. 113 - Tobias Petri, Evi Berchtold
Detection and correction of probe-level artefacts on microarrays. 114 - Sean O'Callaghan
PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. 115 - Steven Vercruysse
OLSVis: an animated, interactive visual browser for bio-ontologies. 116 - Peter W. Collingridge, Steven Kelly
MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. 117 - Ya-Nan Zhang, Dong-Jun Yu, Shu-Sen Li, Yong-Xian Fan, Yan Huang, Hong-Bin Shen:
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features. 118 - Lauri Eronen, Hannu Toivonen
Biomine: predicting links between biological entities using network models of heterogeneous databases. 119 - Ann-Kristin Petersen, Jan Krumsiek, Brigitte Wägele, Fabian J. Theis
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. 120 - Shu-Yi Su, Jay Kasberger, Sergio Baranzini
Detection of identity by descent using next-generation whole genome sequencing data. 121 - Zsolt L. Husz, Nicholas Burton, Bill Hill, Nestor Milyaev, Richard A. Baldock
Web tools for large-scale 3D biological images and atlases. 122 - Fenglou Mao, David Williams
Quartet decomposition server: a platform for analyzing phylogenetic trees. 123 - Laura J. Anzaldi, Daniel Muñoz-Fernández, Ivan Erill
BioWord: a sequence manipulation suite for Microsoft Word. 124 - Andrea Aguirre, Bernd Wollenweber, Ursula K. Frei, Thomas Lübberstedt
PollenCALC: Software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species. 125 - Keqin Liu, Zhi-Ping Liu, Jin-Kao Hao
Identifying dysregulated pathways in cancers from pathway interaction networks. 126 - Leila Kalankesh, Robert Stevens, Andy Brass
The language of gene ontology: a Zipf's law analysis. 127 - Jean-Eudes J. Dazard
ROCS: A reproducibility index and confidence score for interaction proteomics. 128 - Adam M. Szalkowski:
Fast and robust multiple sequence alignment with phylogeny-aware gap placement. 129 - Juan R. Gonzalez, Carlos Abellan, Juan J. Abellán
Bayesian model to detect phenotype-specific genes for copy number data. 130 - Xuan Vinh Nguyen, Madhu Chetty
Gene regulatory network modeling via global optimization of high-order dynamic Bayesian network. 131 - Michele Pinelli
Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2. 132 - Julien Pelé, Jean-Michel Bécu, Hervé Abdi
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling. 133 - Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. 134 - Mohammad Hossain Mollah, M. Haque Mollah, Hirohisa Kishino:
β-empirical Bayes inference and model diagnosis of microarray data. 135 - Adi L. Tarca, Sorin Draghici
Down-weighting overlapping genes improves gene set analysis. 136 - Steven H. Wu
A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels. 137 - Alfred Kick, Martin Bönsch, Michael Mertig:
EGNAS: an exhaustive DNA sequence design algorithm. 138 - Muskan Kukreja, Stephen A. Johnston, Phillip Stafford:
Comparative study of classification algorithms for immunosignaturing data. 139 - Ming Wen, Yang Shen, Suhua Shi, Tian Tang:
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. 140 - Andreas Wilke, Travis Harrison, Jared Wilkening, Dawn Field, Elizabeth M. Glass, Nikos Kyrpides
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. 141 - Dhriti Sengupta
Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization. 142 - Chenggang Yu, Valmik Desai, Li Cheng, Jaques Reifman:
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. 143 - Andrew F. Neuwald, Christopher J. Lanczycki, Aron Marchler-Bauer
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. 144 - Tim Massingham, Nick Goldman
Error-correcting properties of the SOLiD Exact Call Chemistry. 145 - Wenjuan Cui
Identifying mutation regions for closely related individuals without a known pedigree. 146 - Carina Silva-Fortes
Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups. 147 - Gaston H. Gonnet:
Surprising results on phylogenetic tree building methods based on molecular sequences. 148 - Richard Howey, Heather J. Cordell
PREMIM and EMIM: tools for estimation of maternal, imprinting and interaction effects using multinomial modelling. 149 - Jeffrey T. Leek
A statistical approach to selecting and confirming validation targets in -omics experiments. 150 - Amin Zia
Towards a theoretical understanding of false positives in DNA motif finding. 151 - Frank Emmert-Streib
Detecting sequence dependent transcriptional pauses from RNA and protein number time series. 152 - Joanna M. Kasprzak, Anna Czerwoniec, Janusz M. Bujnicki:
Molecular evolution of dihydrouridine synthases. 153 - Aaron L. Sarver, Jesse Erdman, Timothy K. Starr
TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data. 154 - Zhi-Zhong Chen, Lusheng Wang
A fast tool for minimum hybridization networks. 155 - Ruth Dannenfelser
Genes2FANs: connecting genes through functional association networks. 156 - Jhih-rong Lin, Ananda Mondal
Minimalist ensemble algorithms for genome-wide protein localization prediction. 157 - Fei Guo, Shuai Cheng Li
Protein-protein binding site identification by enumerating the configurations. 158 - Anika Scheid, Markus E. Nebel:
Evaluating the Effect of Disturbed Ensemble Distributions on SCFG Based Statistical Sampling of RNA Secondary Structures. 159 - Xiaohu Shen, Haris Vikalo:
ParticleCall: A particle filter for base calling in next-generation sequencing systems. 160 - Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A. Baumgartner Jr., K. Bretonnel Cohen, Karin Verspoor
Concept annotation in the CRAFT corpus. 161 - José Carlos Almeida Santos, Houssam Nassif, David Page, Stephen H. Muggleton, Michael J. E. Sternberg
Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study. 162 - Maíra R. Rodrigues, Wagner C. S. Magalhães, Moara Machado, Eduardo Tarazona-Santos
A graph-based approach for designing extensible pipelines. 163 - Stacey J. Winham
SNP interaction detection with Random Forests in high-dimensional genetic data. 164 - Sony Malhotra, Ramanathan Sowdhamini:
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. 165 - Georgiy Golovko
Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation. 166 - David Edwards, Lei Wang, Peter Sørensen:
Network-enabled gene expression analysis. 167 - Rui Song
Integrative prescreening in analysis of multiple cancer genomic studies. 168 - Timothy Nugent, David T. Jones:
Detecting pore-lining regions in transmembrane protein sequences. 169 - Berat Z. Haznedaroglu
Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms. 170 - Marek Schikora, Balram Neupane, Satish Madhogaria, Wolfgang Koch, Daniel Cremers
An image classification approach to analyze the suppression of plant immunity by the human pathogen Salmonella Typhimurium. 171 - Jan Czarnecki, Irene Nobeli
A text-mining system for extracting metabolic reactions from full-text articles. 172 - Maria U. Johansson, Vincent Zoete, Olivier Michielin
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. 173 - Dan Wei, Qingshan Jiang, Yanjie Wei, Shengrui Wang:
A novel hierarchical clustering algorithm for gene sequences. 174 - Olivier Sallou
Seqcrawler: biological data indexing and browsing platform. 175 - Karl Kornacker, Morten Rye, Tony Håndstad, Finn Drabløs
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. 176 - Wenge Guo
Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data. 177 - Shu-Lin Wang, Xueling Li
Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification. 178 - Jonathan M. Keith
A Bayesian method for comparing and combining binary classifiers in the absence of a gold standard. 179 - Anália Lourenço
Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. 180 - Mark K. Transtrum
Optimal experiment selection for parameter estimation in biological differential equation models. 181 - Chao Wu, Jun Zhu, Xuegong Zhang:
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. 182 - William L. Trimble
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. 183 - Amanda M. Maia, João H. M. da Silva, André L. Mencalha
Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants. 184 - Xin Victoria Wang, Natalie Blades, Jie Ding, Razvan Sultana, Giovanni Parmigiani:
Estimation of sequencing error rates in short reads. 185 - Jun Gao, Dongsheng Che, Vincent Wenchen Zheng, Ruixin Zhu
Integrated QSAR study for inhibitors of hedgehog signal pathway against multiple cell lines: a collaborative filtering method. 186 - Daniel S. Standage
ParsEval: parallel comparison and analysis of gene structure annotations. 187 - Daniel Carbajo
A resource for benchmarking the usefulness of protein structure models. 188 - Henry C. Lin, Steve Goldstein, Lee Mendelowitz, Shiguo Zhou, Joshua L. Wetzel
AGORA: Assembly Guided by Optical Restriction Alignment. 189 - Kashi Vishwanath Revanna, Daniel Munro
A web-based multi-genome synteny viewer for customized data. 190 - Parminder Kaur, Daniela Schlatzer, Kenneth Cooke, Mark R. Chance:
Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis. 191 - David Mosén-Ansorena, Ana M. Aransay
Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data. 192 - Nathan L. Tintle
Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data. 193 - Linda Dib, Alessandra Carbone
CLAG: an unsupervised non hierarchical clustering algorithm handling biological data. 194 - Mohamed F. Ghalwash
Early classification of multivariate temporal observations by extraction of interpretable shapelets. 195 - Nikolaos Alachiotis
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. 196 - Dan Jacobson, Guy Emerton:
GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network. 197 - Junsu Ko, Hahnbeom Park
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions. 198 - Kun Liang, Sündüz Keles:
Normalization of ChIP-seq data with control. 199 - Sebastian Schönherr, Lukas Forer
Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds. 200 - Saroja K. Weeratunga
SDAR: a practical tool for graphical analysis of two-dimensional data. 201 - Igor V. Deyneko, Siegfried Weiss, Sara Leschner:
An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters. 202 - Gary Cobbs:
Stepwise kinetic equilibrium models of quantitative polymerase chain reaction. 203 - Ross E. Curtis, Jing Xiang, Ankur P. Parikh, Peter Kinnaird, Eric P. Xing:
Enabling dynamic network analysis through visualization in TVNViewer. 204 - Zhongyang Zhang, Kenneth Lange, Chiara Sabatti:
Reconstructing DNA copy number by joint segmentation of multiple sequences. 205 - Ivan Borozan
CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes. 206 - Karin Verspoor
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. 207 - Aaron T. L. Lun, Jason W. H. Wong, Kevin M. Downard
FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry. 208 - Eric Talevich
Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. 209 - David C. Haws, Peter Huggins, Eric M. O'Neill, David W. Weisrock
A support vector machine based test for incongruence between sets of trees in tree space. 210 - Lakshmi M. Akella, Catherine N. Norton, Holly Miller
NetiNeti: discovery of scientific names from text using machine learning methods. 211 - Dingfeng Wu, Qi Huang, Yida Zhang
Screening of selective histone deacetylase inhibitors by proteochemometric modeling. 212 - Blazej Ruszczycki
Sampling issues in quantitative analysis of dendritic spines morphology. 213 - Nils Hoffmann
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. 214 - Chih Lee, Chun-Hsi Huang:
Searching for transcription factor binding sites in vector spaces. 215 - Anna M. Kedzierska, Marta Casanellas
GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees. 216 - André Queiroz de Andrade
Process attributes in bio-ontologies. 217 - Xiaoqiang Sun, Le Zhang
Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: Incorporating EGFR signaling pathway and angiogenesis. 218 - Paul A. Wilkinson, Mark O. Winfield
CerealsDB 2.0: an integrated resource for plant breeders and scientists. 219 - Daniel Turner, RyangGuk Kim, Jun-tao Guo:
TFinDit: transcription factor-DNA interaction data depository. 220 - Christopher R. Cabanski
ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. 221 - Victor Segura
Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray. 222 - Arno Meiler, Claudia Klinger, Michael Kaufmann:
ANCAC: amino acid, nucleotide, and codon analysis of COGs - a tool for sequence bias analysis in microbial orthologs. 223 - Arjun Ray
Improved model quality assessment using ProQ2. 224 - Mehmet Gültas
Coupled Mutation Finder: A new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations. 225 - Andrey Alexeyenko
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. 226 - Andrew T. Magis
The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules. 227 - Piotr Setny, Ranjit Bahadur, Martin Zacharias:
Protein-DNA docking with a coarse-grained force field. 228 - Fahim Mohammad, Robert M. Flight
AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities. 229 - Fredrik Lysholm:
Highly improved homopolymer aware nucleotide-protein alignments with 454 data. 230 - Christian Meesters
Quick, "Imputation-free" meta-analysis with proxy-SNPs. 231 - William J. Cukierski, Kaustav Nandy, Prabhakar R. Gudla, Karen J. Meaburn
Ranked retrieval of segmented nuclei for objective assessment of cancer gene repositioning. 232 - Guillaume Santini, Henry Soldano
Automatic classification of protein structures relying on similarities between alignments. 233 - Kristof De Beuf, Peter Pipelers, Megan Andriankaja, Olivier Thas
Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling. 234 - Elin Teppa
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. 235 - Tatsiana Kirys, Anatoly M. Ruvinsky, Alexander V. Tuzikov
Correlation analysis of the side-chains conformational distribution in bound and unbound proteins. 236 - Estelle Proux-Wéra
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach. 237 - Mark Chaisson, Glenn Tesler:
Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application. 238 - Emanuele Raineri, Luca Ferretti
SNP calling by sequencing pooled samples. 239 - Hiroyuki Mishima
The Ruby UCSC API: accessing the UCSC genome database using Ruby. 240 - Geet Duggal, Carl Kingsford:
Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. 241 - Bogumil Konopka, Jean-Christophe Nebel
Quality assessment of protein model-structures based on structural and functional similarities. 242 - Suzanne M. Paley, Mario Latendresse, Peter D. Karp
Regulatory network operations in the Pathway Tools software. 243 - Cristina Baciu, Kevin J. Thompson
The LO-BaFL method and ALS microarray expression analysis. 244 - Daniel Shabtai, Guri Giaever, Corey Nislow
An algorithm for chemical genomic profiling that minimizes batch effects: Bucket evaluations. 245 - Sébastien Tempel, Nicolas Pollet
ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. 246 - Hongseok Tae, Dong-Sung Ryu, Suhas Sureshchandra, Jeong-Hyeon Choi:
ESTclean: A Cleaning Tool for Next-Gen Transcriptome Shotgun Sequencing. 247 - Roeland E. Voorrips, Chris A. Maliepaard:
The simulation of meiosis in diploid and tetraploid organisms using various genetic models. 248 - Warren A. Cheung
Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). 249 - Günhan Gülsoy, Nirmalya Bandyopadhyay, Tamer Kahveci:
HIDEN: Hierarchical decomposition of regulatory networks. 250 - Katrin Kolczyk, Regina Samaga, Holger Conzelmann, Sebastian Mirschel, Carsten Conradi:
The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. 251 - Greg Finak
QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data. 252 - Danielle G. Lemay
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. 253 - Myles Byrne
VarioML framework for comprehensive variation data representation and exchange. 254 - Veli Mäkinen
Normalized N50 assembly metric using gap-restricted co-linear chaining. 255 - Avinash Ramu
A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. 256 - Susanta Tewari
Software: an open-source and scalable framework for exact calculations in coalescent theory. 257 - Pietro Hiram Guzzi, Giuseppe Agapito
DMET-Analyzer: automatic analysis of Affymetrix DMET Data. 258 - Noah M. Daniels, Shilpa Nadimpalli
Formatt: Correcting Protein Multiple Structural Alignments by Incorporating Sequence Alignment. 259 - Rune B. Lyngsø, James W. J. Anderson, Elena Sizikova, Amarendra Badugu, Tomas Hyland, Jotun Hein:
Frnakenstein: multiple target inverse RNA folding. 260 - Vijay Garla, Cynthia Brandt:
Semantic similarity in the biomedical domain: an evaluation across knowledge sources. 261 - Atanas Kamburov
Cluster-based assessment of protein-protein interaction confidence. 262 - Cheng-Hua Wang, Ri-Bo Huang, Bingfang He, Qishi Du:
Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis. 263 - Thomas J. Sharpton
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. 264 - Tudor Groza
Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods. 265 - Lena Scheubert, Mitja Lustrek, Rainer Schmidt, Dirk Repsilber, Georg Fuellen
Tissue-based Alzheimer gene expression markers - comparison of multiple machine learning approaches and investigation of redundancy in small biomarker sets. 266 - Yves Sucaet, Yi Wang, Jie Li, Eve Syrkin Wurtele
MetNet Online: a novel integrated resource for plant systems biology. 267 - David L. Price, Michael D. Casler:
Simple regression models as a threshold for selecting AFLP loci with reduced error rates. 268 - Shanker Kalyana-Sundaram
Gene Fusion Markup Language: a prototype for exchanging gene fusion data. 269 - Argiris Sakellariou, Despina Sanoudou
Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data. 270 - Hua Li
dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. 271 - Héctor Corrada Bravo
Gene expression anti-profiles as a basis for accurate universal cancer signatures. 272 - Alejandro Panjkovich
Exploiting protein flexibility to predict the location of allosteric sites. 273 - Zhong Wang, Zuoheng Wang, Jianxin Wang, Yihan Sui, Jian Zhang
A quantitative genetic and epigenetic model of complex traits. 274 - William J. R. Longabaugh:
Combing the hairball with BioFabric: a new approach for visualization of large networks. 275 - Darya Filippova, Aashish Gadani, Carl Kingsford:
Coral: an integrated suite of visualizations for comparing clusterings. 276 - Tae Young Yang:
Simple binary segmentation frameworks for identifying variation in DNA copy number. 277 - Saheli Datta, Abel Rodríguez
Bayesian Semiparametric Regression Models to Characterize Molecular Evolution. 278 - Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. 279 - Ying Li, Ming Duan, Yanchun Liang:
Multi-scale RNA comparison based on RNA triple vector curve representation. 280 - Dragan Bonaki, Maximilian R. Odenbrett, Anton Wijs
Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors. 281 - Scott Doyle, Michael D. Feldman, Natalie Shih, John Tomaszewski, Anant Madabhushi
Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer. 282 - Michael J. Rosen
Denoising PCR-amplified metagenome data. 283 - Verena Zuber
A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies. 284 - Zaheer-ul-Haq
Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities. 285 - Howard J. Feldman:
Identifying structural domains of proteins using clustering. 286 - James L. Kitchen, Jonathan D. Moore
MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling. 287 - Gorka Prieto
PAnalyzer: A software tool for protein inference in shotgun proteomics. 288 - Marcin Pawlowski, Janusz M. Bujnicki:
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement. 289 - Shibiao Wan
mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines. 290 - Martin Slawski, Rene Hussong, Andreas Tholey
Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching. 291 - Chao Yuan, Hao Chen, Daisuke Kihara:
Effective inter-residue contact definitions for accurate protein fold recognition. 292 - Andrés Varón, Ward C. Wheeler:
The tree alignment problem. 293 - Antonio Mora
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. 294 - C. Hart Poskar, Jan Huege, Christian Krach, Mathias Franke, Yair Shachar-Hill
iMS2Flux - a high-throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis. 295 - Daniel Wüstner
Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation. 296 - Brendan A. Veeneman, Matthew K. Iyer, Arul M. Chinnaiyan:
Oculus: faster sequence alignment by streaming read compression. 297 - Hongyan Zhang, Haiyan Wang, Zhijun Dai, Ming-shun Chen, Zheming Yuan:
Improving accuracy for cancer classification with a new algorithm for genes selection. 298 - Dong Seon Kim, Yoonsoo Hahn
Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence. 299 - Kui Wang, Shu-Kay Ng
Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects. 300 - Leonardo Arbiza, Elaine Zhong, Alon Keinan:
NRE: A tool for exploring neutral loci in the human genome. 301 - Anita Sarkar
PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides. 302 - Kristof De Beuf, Joachim M. De Schrijver, Olivier Thas
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. 303 - Ngan L. T. Nguyen, Jin-Dong Kim, Makoto Miwa, Takuya Matsuzaki, Junichi Tsujii:
Improving protein coreference resolution by simple semantic classification. 304 - Jiantao Wu, Krzysztof R. Grzeda, Chip Stewart, Fabian Grubert, Alexander E. Urban, Michael P. Snyder
Copy Number Variation detection from 1000 Genomes project exon capture sequencing data. 305 - Dong Seon Kim, Yoonsoo Hahn
Gains of ubiquitylation sites in highly conserved proteins in the human lineage. 306 - Jingyan Wang, Halima Bensmail, Xin Gao
Multiple graph regularized protein domain ranking. 307 - Sean McIlwain, Michael Mathews, Michael Bereman, Edwin W. Rubel, Michael J. MacCoss, William Stafford Noble:
Estimating relative abundances of proteins from shotgun proteomics data. 308 - Daniela M. Resende
An assessment on epitope prediction methods for protozoa genomes. 309 - Rodrigo C. Barros
Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data. 310 - Susan C. Tilton
Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools. 311 - Herman De Beukelaer
Core Hunter II: Fast core subset selection based on multiple genetic diversity measures using Mixed Replica Search. 312 - Thammakorn Saethang, Osamu Hirose
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. 313 - Gregory Cipriano, George N. Phillips Jr., Michael Gleicher:
Local functional descriptors for surface comparison based binding prediction. 314 - Enis Afgan, Brad Chapman
CloudMan as a platform for tool, data, and analysis distribution. 315 - Alessandro Bria
TeraStitcher - A Tool for Fast Automatic 3D-Stitching of Teravoxel-Sized Microscopy Images. 316 - Phillip Seitzer, Elizabeth G. Wilbanks
A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs. 317 - Faiyaz Al Zamal, Derek Ruths:
On the Contributions of Topological Features to Transcriptional Regulatory Network Robustness. 318 - Shengwen Wang, Daniel Dvorkin, Yang Da:
SNPEVG: a graphical tool for GWAS graphing with mouse clicks. 319 - Shicheng Wu, Yawen Xu, Zeny Z. Feng, Xiaojian Yang, Xiaogang Wang, Xin Gao:
Multiple-platform data integration method with application to combined analysis of microarray and proteomic data. 320 - Eithon Cadag, Peter Tarczy-Hornoch
Learning virulent proteins from integrated query networks. 321 - Isana Veksler-Lublinsky
Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV). 322 - Yang Du
Flexible and efficient genome tiling design with penalized uniqueness score. 323 - Steven Lewis, Attila Csordas, Sarah A. Killcoyne
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. 324 - Benoit Liquet
A novel approach for biomarker selection and theintegration of repeated measures experiments from two assays. 325 - Oliver P. Günther
A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers. 326 - Tahir Mehmood
Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression. 327 - Lin Song, Peter Langfelder, Steve Horvath
Comparison of co-expression measures: mutual information, correlation, and model based indices. 328 - Sandra Plancade, Yves Rozenholc
Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays. 329 - Robert B. Scharpf, Terri H. Beaty, Holger Schwender, Samuel G. Younkin
Fast detection of de novo copy number variants from SNP arrays for case-parent trios. 330 - Lei Sun, Zhihua Zhang, Timothy L. Bailey, Andrew C. Perkins
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. 331 - Gaihua Zhang, Yijing Zhang
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana. 332 - Michal J. Pietal
RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. 333 - Jose M. Duarte
Protein interface classification by evolutionary analysis. 334 - Jonatan Taminau, Stijn Meganck, Cosmin Lazar, David Steenhoff, Alain Coletta, Colin Molter, Robin Duque, Virginie de Schaetzen, David Y. Weiss Solís, Hugues Bersini, Ann Nowé:
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages. 335 - Melissa Pronold, Marzieh Vali, Roger Pique-Regi
Copy number variation signature to predict human ancestry. 336 - Hua Tan, Jing Fan, Jiguang Bao, Jennifer G. Dy, Xiaobo Zhou:
A Computational model for compressed sensing RNAi cellular screening. 337
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-12-27 21:27 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by: