Works matching IS 13674803 AND DT 2015 AND VI 31 AND IP 12

Results: 73

ISMB/ECCB 2015.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i1, doi. 10.1093/bioinformatics/btv303
Publication type:: Article

Integrative random forest for gene regulatory network inference.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i197, doi. 10.1093/bioinformatics/btv268

By:

Petralia, Francesca;
Pei Wang;
Jialiang Yang;
Zhidong Tu

Publication type:

Article

Inferring orthologous gene regulatory networks using interspecies data fusion.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i97, doi. 10.1093/bioinformatics/btv267
Publication type:: Article

Using collective expert judgements to evaluate quality measures of mass spectrometry images.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i375, doi. 10.1093/bioinformatics/btv266

By:

Palmer, Andrew;
Ovchinnikova, Ekaterina;
Thune, Mikael;
Lavigne, Regis;
Guevel, Blandine;
Dyatlov, Andrey;
Vitek, Olga;
Pineau, Charles;
Boren, Mats;
Alexandrov, Theodore

Publication type:

Article

PAGER: constructing PAGs and new PAG--PAG relationships for network biology.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i250, doi. 10.1093/bioinformatics/btv265

By:

Zongliang Yue;
Kshirsagar, Madhura M.;
Thanh Nguyen;
Suphavilai, Chayaporn;
Neylon, Michael T.;
Zhu, Liugen;
Ratliff, Timothy;
Chen, Jake Y.

Publication type:

Article

Protein (multi-)location prediction: utilizing interdependencies via a generative model.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i365, doi. 10.1093/bioinformatics/btv264

By:

Simha, Ramanuja;
Briesemeister, Sebastian;
Kohlbacher, Oliver;
Shatkay, Hagit

Publication type:

Article

Genome-wide detection of intervals of genetic heterogeneity associated with complex traits.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i240, doi. 10.1093/bioinformatics/btv263

By:

Llinares-López, Felipe;
Grimm, Dominik G.;
Bodenham, Dean A.;
Gieraths, Udo;
Sugiyama, Mahito;
Rowan, Beth;
Borgwardt, Karsten

Publication type:

Article

Misassembly detection using paired-end sequence reads and optical mapping data.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i80, doi. 10.1093/bioinformatics/btv262

By:

Muggli, Martin D.;
Puglisi, Simon J.;
Ronen, Roy;
Boucher, Christina

Publication type:

Article

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i62, doi. 10.1093/bioinformatics/btv261
Publication type:: Article

Exploiting ontology graph for predicting sparsely annotated gene function.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i357, doi. 10.1093/bioinformatics/btv260

By:

Sheng Wang;
Hyunghoon Cho;
Cheng Xiang Zhai;
Bonnie Berger;
Jian Peng

Publication type:

Article

Knowledge-driven geospatial location resolution for phylogeographic models of virus migration.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i348, doi. 10.1093/bioinformatics/btv259

By:

Weissenbacher, Davy;
Tahsin, Tasnia;
Beard, Rachel;
Figaro, Mari;
Rivera, Robert;
Scotch, Matthew;
Gonzalez, Graciela

Publication type:

Article

Gene network inference by fusing data from diverse distributions.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i230, doi. 10.1093/bioinformatics/btv258

By:

Žitnik, Marinka;
Zupan, Blaž

Publication type:

Article

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i89, doi. 10.1093/bioinformatics/btv257
Publication type:: Article

Improving compound-protein interaction prediction by building up highly credible negative samples.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i221, doi. 10.1093/bioinformatics/btv256
Publication type:: Article

FERAL: network-based classifier with application to breast cancer outcome prediction.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i311, doi. 10.1093/bioinformatics/btv255
Publication type:: Article

In silico phenotyping via co-training for improved phenotype prediction from genotype.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i303, doi. 10.1093/bioinformatics/btv254

By:

Roqueiro, Damian;
Witteveen, Menno J.;
Anttila, Verneri;
Terwindt, Gisela M.;
den Maagdenberg, Arn M. J. M. van;
Borgwardt, Karsten

Publication type:

Article

Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i293, doi. 10.1093/bioinformatics/btv253

By:

Schissler, A. Grant;
Gardeux, Vincent;
Qike Li;
Achour, Ikbel;
Haiquan Li;
Piegorsch, Walter W.;
Lussier, Yves A.

Publication type:

Article

cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i151, doi. 10.1093/bioinformatics/btv252

By:

Oliwa, Tomasz;
Yang Shen

Publication type:

Article

Deconvolving molecular signatures of interactions between microbial colonies.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i142, doi. 10.1093/bioinformatics/btv251

By:

Harn, Y.-C.;
Powers, M. J.;
Shank, E. A.;
Jojic, V.

Publication type:

Article

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i284, doi. 10.1093/bioinformatics/btv247
Publication type:: Article

Robust reconstruction of gene expression profiles from reporter gene data using linear inversion.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i71, doi. 10.1093/bioinformatics/btv246

By:

Zulkower, Valentin;
Page, Michel;
Ropers, Delphine;
Geiselmann, Johannes;
Hidde de Jong

Publication type:

Article

Phenome-driven disease genetics prediction toward drug discovery.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i276, doi. 10.1093/bioinformatics/btv245

By:

Yang Chen;
Guo-Qiang Zhang;
Rong Xu;
Li Li

Publication type:

Article

Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i268, doi. 10.1093/bioinformatics/btv244

By:

Speicher, Nora K.;
Pfeifer, Nico

Publication type:

Article

Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i214, doi. 10.1093/bioinformatics/btv243

By:

Childs, Dorothee;
Grimbs, Sergio;
Selbig, Joachim

Publication type:

Article

Finding optimal interaction interface alignments between biological complexes.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i133, doi. 10.1093/bioinformatics/btv242

By:

Xuefeng Cui;
Naveed, Hammad;
Xin Gao

Publication type:

Article

Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i124, doi. 10.1093/bioinformatics/btv241
Publication type:: Article

Identification of causal genes for complex traits.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i206, doi. 10.1093/bioinformatics/btv240

By:

Hormozdiari, Farhad;
Kichaev, Gleb;
Wen-Yun Yang;
Pasaniuc, Bogdan;
Eskin, Eleazar

Publication type:

Article

Inferring parental genomic ancestries using pooled semi-Markov processes.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i190, doi. 10.1093/bioinformatics/btv239

By:

Zou, James Y.;
Halperin, Eran;
Burchard, Esteban;
Sankararaman, Sriram

Publication type:

Article

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i53, doi. 10.1093/bioinformatics/btv238

By:

Safonova, Yana;
Bonissone, Stefano;
Kurpilyansky, Eugene;
Starostina, Ekaterina;
Lapidus, Alla;
Stinson, Jeremy;
DePalatis, Laura;
Sandoval, Wendy;
Lill, Jennie;
Pevzner, Pavel A.

Publication type:

Article

MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i339, doi. 10.1093/bioinformatics/btv237

By:

Ke Liu;
Shengwen Peng;
Junqiu Wu;
Chengxiang Zhai;
Hiroshi Mamitsuka;
Shanfeng Zhu

Publication type:

Article

MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i106, doi. 10.1093/bioinformatics/btv236
Publication type:: Article

Large-scale model quality assessment for improving protein tertiary structure prediction.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i116, doi. 10.1093/bioinformatics/btv235

By:

Renzhi Cao;
Bhattacharya, Debswapna;
Adhikari, Badri;
Jilong Li;
Jianlin Cheng

Publication type:

Article

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i44, doi. 10.1093/bioinformatics/btv234

By:

Mirarab, Siavash;
Warnow, Tandy

Publication type:

Article

Inferring models of multiscale copy number evolution for single-tumor phylogenetics.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i258, doi. 10.1093/bioinformatics/btv233

By:

Chowdhury, Salim Akhter;
Gertz, E. Michael;
Wangsa, Darawalee;
Heselmeyer-Haddad, Kerstin;
Ried, Thomas;
Schäffer, Alejandro A.;
Schwartz, Russell

Publication type:

Article

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i27, doi. 10.1093/bioinformatics/btv232

By:

Numanagić, Ibrahim;
Malikić, Salem;
Pratt, Victoria M.;
Skaar, Todd C.;
Flockhart, David A.;
Sahinalp, S. Cenk

Publication type:

Article

Reconstructing 16S rRNA genes in metagenomic data.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i35, doi. 10.1093/bioinformatics/btv231

By:

Cheng Yuan;
Jikai Lei;
Cole, James;
Yanni Sun

Publication type:

Article

Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i181, doi. 10.1093/bioinformatics/btv230

By:

Park, Danny S.;
Brown, Brielin;
Eng, Celeste;
Huntsman, Scott;
Hu, Donglei;
Torgerson, Dara G.;
Burchard, Esteban G.;
Zaitlen, Noah

Publication type:

Article

Comparing genomes with rearrangements and segmental duplications.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i329, doi. 10.1093/bioinformatics/btv229

By:

Shao, Mingfu;
Moret, Bernard M. E.

Publication type:

Article

A hierarchical Bayesian model for flexible module discovery in three-way time-series data.

Published in:: Bioinformatics, 2015, v. 31, n. 12, p. i17, doi. 10.1093/bioinformatics/btv228
Publication type:: Article

Exploring the structure and function of temporal networks with dynamic graphlets.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i171, doi. 10.1093/bioinformatics/btv227

By:

Hulovatyy, Y.;
Chen, H.;
Milenkovic, T.

Publication type:

Article

De novo meta-assembly of ultra-deep sequencing data.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i9, doi. 10.1093/bioinformatics/btv226

By:

Mirebrahim, Hamid;
Close, Timothy J.;
Lonardi, Stefano

Publication type:

Article

A generic methodological framework for studying single cell motility in high-throughput time-lapse data.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i320, doi. 10.1093/bioinformatics/btv225

By:

Sebag, Alice Schoenauer;
Plancade, Sandra;
Raulet-Tomkiewicz, Céline;
Barouki, Robert;
Vert, Jean-Philippe;
Walter, Thomas

Publication type:

Article

Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i161, doi. 10.1093/bioinformatics/btv224

By:

Yoshihiro Yamanishi;
Yasuo Tabei;
Masaaki Kotera

Publication type:

Article

Message from ISCB: Outstanding contributions to ISCB award.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 2059, doi. 10.1093/bioinformatics/btv206

By:

Fogg, Christiana N.;
Kovats, Diane E.

Publication type:

Article

The GPMDB REST interface.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 2056, doi. 10.1093/bioinformatics/btv107

By:

Fenyö, David;
Beavis, Ronald C.

Publication type:

Article

Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 1929, doi. 10.1093/bioinformatics/btv103

By:

Wenzhi Mao;
Kaya, Cihan;
Dutta, Anindita;
Horovitz, Amnon;
Bahar, Ivet

Publication type:

Article

Extending P450 site-of-metabolism models with region-resolution data.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 1966, doi. 10.1093/bioinformatics/btv100

By:

Zaretzki, Jed M.;
Browning, Michael R.;
Hughes, Tyler B.;
Swamidass, S. Joshua

Publication type:

Article

TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 2049, doi. 10.1093/bioinformatics/btv099

By:

Xian Liu;
Yuan Gao;
Jianlong Peng;
Yuan Xu;
YulanWang;
Nannan Zhou;
Jing Xing;
Xiaomin Luo;
Hualiang Jiang;
Mingyue Zheng

Publication type:

Article

Sambamba: fast processing of NGS alignment formats.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 2032, doi. 10.1093/bioinformatics/btv098

By:

Tarasov, Artem;
Vilella, Albert J.;
Cuppen, Edwin;
Nijman, Isaac J.;
Prins, Pjotr

Publication type:

Article

Characterizing spatial distributions of astrocytes in the mammalian retina.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 2024, doi. 10.1093/bioinformatics/btv097

By:

Jammalamadaka, Aruna;
Suwannatat, Panuakdet;
Fisher, Steven K.;
Manjunath, B. S.;
Hollerer, Tobias;
Luna, Gabriel

Publication type:

Article