Works matching IS 14712105 AND DT 2013 AND VI 14 AND IP 1

Results: 374

SRAdb: query and use public next-generation sequencing data from within R.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-19

By:

Yuelin Zhu;
Stephens, Robert M.;
Meltzer, Paul S.;
Davis, Sean R.

Publication type:

Article

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-18

By:

Seitzer, Phillip;
Huynh, Tu Anh;
Facciotti, Marc T.

Publication type:

Article

The taxonomic name resolution service: an online tool for automated standardization of plant names.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-16

By:

Boyle, Brad;
Hopkins, Nicole;
Zhenyuan Lu;
Raygoza Garay, Juan Antonio;
Mozzherin, Dmitry;
Rees, Tony;
Matasci, Naim;
Narro, Martha L.;
Piel, William H.;
Mckay, Sheldon J.;
Lowry, Sonya;
Freeland, Chris;
Peet, Robert K.;
Enquist, Brian J.

Publication type:

Article

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-9

By:

Klepper, Kjetil;
Drabløs, Finn

Publication type:

Article

LUD, a new protein domain associated with lactate utilization.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-341

By:

Hwang, William C.;
Bakolitsa, Constantina;
Punta, Marco;
Coggill, Penelope C.;
Bateman, Alex;
Axelrod, Herbert L.;
Rawlings, Neil D.;
Sedova, Mayya;
Peterson, Scott N.;
Eberhardt, Ruth Y.;
Aravind, L.;
Pascual, Jaime;
Godzik, Adam

Publication type:

Article

Heterodimeric protein complex identification by naïve Bayes classifiers.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-347

By:

Maruyama, Osamu

Publication type:

Article

A novel approach for protein subcellular location prediction using amino acid exposure.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-342

By:

Mer, Arvind Singh;
Andrade-Navarro, Miguel A.

Publication type:

Article

Selecting informative subsets of sparse supermatrices increases the chance to find correct trees.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-348

By:

Misof, Bernhard;
Meyer, Benjamin;
Reumont, Björn Marcus von;
Kück, Patrick;
Misof, Katharina;
Meusemann, Karen

Publication type:

Article

Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of highthroughput data.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-340

By:

Catlett, Natalie L.;
Bargnesi, Anthony J.;
Ungerer, Stephen;
Seagaran, Toby;
Ladd, William;
Elliston, Keith O.;
Pratt, Dexter

Publication type:

Article

Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-343

By:

Barghash, Ahmad;
Helms, Volkhard

Publication type:

Article

Disulfide by design 2.0: a web-based tool for disulfide engineering in proteins.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-346

By:

Craig, Douglas B.;
Dombkowski, Alan A.

Publication type:

Article

wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-345

By:

Izarzugaza, Jose M. G.;
Vazquez, Miguel;
Pozo, Angela del;
Valencia, Alfonso

Publication type:

Article

Partial inhibition and bilevel optimization in flux balance analysis.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-344

By:

Facchetti, Giuseppe;
Altafini, Claudio

Publication type:

Article

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-339

By:

Sand, Andreas;
Kristiansen, Martin;
Pedersen, Christian N. S.;
Mailund, Thomas

Publication type:

Article

MetSizeR: selecting the optimal sample size for metabolomic studies using an analysis based approach.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-338

By:

Nyamundanda, Gift;
Gormley, Isobel Claire;
Yue Fan;
Gallagher, William M.;
Brennan, Lorraine

Publication type:

Article

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-337

By:

Changjin Hong;
Clement, Nathan L.;
Clement, Spencer;
Hammoud, Saher Sue;
Carrell, Douglas T.;
Cairns, Bradley R.;
Snell, Quinn;
Clement, Mark J.;
Johnson, William Evan

Publication type:

Article

A novel phenotypic dissimilarity method for image-based high-throughput screens.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-336

By:

Xian Zhang;
Boutros, Michael

Publication type:

Article

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application).

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-335

By:

Peng Zhou;
Silverstein, Kevin A. T.;
Liangliang Gao;
Walton, Jonathan D.;
Nallu, Sumitha;
Guhlin, Joseph;
Young, Nevin D.

Publication type:

Article

Fastphylo: Fast tools for phylogenetics.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-334

By:

Khan, Mehmood Alam;
Elias, Isaac;
̈lund, Erik Sjo;
Nylander, Kristina;
Guimera, Roman Valls;
Schobesberger, Richard;
Schmitzberger, Peter;
Lagergren, Jens;
Arvestad, Lars

Publication type:

Article

Similarity maps and hierarchical clustering for annotating FT-IR spectral images.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-333

By:

Qiaoyong Zhong;
Chen Yang;
Großerüschkamp, Frederik;
Kallenbach-Thieltges, Angela;
Serocka, Peter;
Gerwert, Klaus;
Mosig, Axel

Publication type:

Article

Reconciliation-based detection of co-evolving gene families.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-332

By:

Yao-ban Chan;
Ranwez, Vincent;
Scornavacca, Celine

Publication type:

Article

YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-331

By:

Fan Zhang;
Ruoyan Chen;
Dongbing Liu;
Xiaotian Yao;
Guoqing Li;
Yabin Jin;
Chang Yu;
Yingrui Li;
Coin, Lachlan J. M.

Publication type:

Article

Agalma: an automated phylogenomics workflow.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-330

By:

Dunn, Casey W.;
Howison, Mark;
Zapata, Felipe

Publication type:

Article

Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-329

By:

Jamal, Salma;
Scaria, Vinod

Publication type:

Article

A novel cell nuclei segmentation method for 3D C. elegans embryonic time-lapse images.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-328

By:

Long Chen;
Leanne Lai Hang Chan;
Zhongying Zhao;
Hong Yan

Publication type:

Article

Filling out the structural map of the NTF2-like superfamily.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-327

By:

Eberhardt, Ruth Y.;
Chang, Yuanyuan;
Bateman, Alex;
Murzin, Alexey G.;
Axelrod, Herbert L.;
Hwang, William C.;
Aravind, L.

Publication type:

Article

snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-326

By:

Al-Shahib, Ali;
Underwood, Anthony

Publication type:

Article

Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-325

By:

Christensen, Kris A.;
Brunelli, Joseph P.;
Lambert, Matthew J.;
DeKoning, Jenefer;
Phillips, Ruth B.;
Thorgaard, Gary H.

Publication type:

Article

SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-324

By:

Martins, Wellington S.;
Carmo, Welton C.;
Longo, Humberto J.;
Rosa, Thierson C.;
Rangel, Thiago F.

Publication type:

Article

CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-323

By:

Hee-Jin Lee;
Sang-Hyung Shim;
Mi-Ryoung Song;
Hyunju Lee;
Park, Jong C.

Publication type:

Article

3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-322

By:

Qi Wang;
Biao Tang;
Lifu Song;
Biao Ren;
Qun Liang;
Feng Xie;
Ying Zhuo;
Xueting Liu;
Lixin Zhan

Publication type:

Article

PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-321

By:

Dai, Xinbin;
Sinharoy, Senjuti;
Udvardi, Michael;
Zhao, Patrick Xuechun

Publication type:

Article

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-320

By:

Sturgill, David;
Malone, John H.;
Sun, Xia;
Smith, Harold E.;
Rabinow, Leonard;
Samson, Marie-Laure;
Oliver, Brian

Publication type:

Article

Benchmark for multi-cellular segmentation of bright field microscopy images.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-319

By:

Zaritsky, Assaf;
Manor, Nathan;
Wolf, Lior;
Ben-Jacob, Eshel;
Tsarfaty, Ilan

Publication type:

Article

Comparison and improvement of algorithms for computing minimal cut sets.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-318

By:

Jungreuthmayer, Christian;
Nair, Govind;
Klamt, Steffen;
Zanghellini, Jürgen

Publication type:

Article

Automated analysis of phylogenetic clusters.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-317

By:

Ragonnet-Cronin, Manon;
Hodcroft, Emma;
Hué, Stéphane;
Fearnhill, Esther;
Delpech, Valerie;
Brown, Andrew J.;
Lycett, Samantha

Publication type:

Article

DCE@urLAB: a dynamic contrast-enhanced MRI pharmacokinetic analysis tool for preclinical data.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-316

By:

Ortuño, Juan E.;
Ledesma-Carbayo, María J.;
SimÕes, Rui V.;
Candiota, Ana P.;
Arús, Carles;
Santos, Andrés

Publication type:

Article

A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-315

By:

Goodswen, Stephen J.;
Kennedy, Paul J.;
Ellis, John T.

Publication type:

Article

Identification of properties important to protein aggregation using feature selection.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-314

By:

Yaping Fang;
Shan Gao;
David Tai;
Russell Middaugh, C.;
Jianwen Fang

Publication type:

Article

Compact representation of k-mer de Bruijn graphs for genome read assembly.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-313

By:

Rødland, Einar Andreas

Publication type:

Article

A scalable, knowledge-based analysis framework for genetic association studies.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-312

By:

Baurley, James W.;
Conti, David V.

Publication type:

Article

Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-311

By:

Pantazis, Yannis;
Katsoulakis, Markos A.;
Vlachos, Dionisios G.

Publication type:

Article

A method to identify differential expression profiles of time-course gene data with Fourier transformation.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-310

By:

Jaehee Kim;
Ogden, Robert Todd;
Haseong Kim

Publication type:

Article

High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-309

By:

Hoban, Sean M.;
Mezzavilla, Massimo;
Gaggiotti, Oscar E.;
Benazzo, Andrea;
van Oosterhout, Cock;
Bertorelle, Giorgio

Publication type:

Article

Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-308

By:

Pau, Gregoire;
Walter, Thomas;
Neumann, Beate;
Heriche, Jean-Karim;
Ellenberg, Jan;
Huber, Wolfgang

Publication type:

Article

Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-307

By:

Ghaffari, Noushin;
Youse, Mohammadmahdi R.;
Johnson, Charles D.;
Ivanov, Ivan;
Dougherty, Edward R.

Publication type:

Article

Jimena: efficient computing and system state identification for genetic regulatory networks.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-306

By:

Karl, Stefan;
Dandekar, Thomas

Publication type:

Article

cudaMap: a GPU accelerated program for gene expression connectivity mapping.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-305

By:

McArt, Darragh G.;
Bankhead, Peter;
Dunne, Philip D.;
Salto-Tellez, Manuel;
Hamilton, Peter;
Shu-Dong Zhang

Publication type:

Article

Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-304

By:

Jhih-Siang Lai;
Cheng-Wei Cheng;
Allan Lo;
Ting-Yi Sung;
Wen-Lian Hsu

Publication type:

Article

A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-303

By:

DeJesus, Michael A.;
Ioerger, Thomas R.

Publication type:

Article