Works matching DE "GENOMIC information retrieval"

Results: 284

Simulation study for analysis of binary responses in the presence of extreme case problems.

Published in:

Genetics Selection Evolution, 2011, v. 43, n. 11, p. 1, doi. 10.1186/1297-9686-43-41

By:

Rekaya, Romdhane;
Sapp, Robyn L.;
Hay, El H.;
Davis, Ryan;
Bertrand, Joseph K.

Publication type:

Article

Irys Extract.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 134, doi. 10.1093/bioinformatics/btx437

By:

Arielly, Rani;
Ebenstein, Yuval

Publication type:

Article

PySeqLab: an open source Python package for sequence labeling and segmentation.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3497, doi. 10.1093/bioinformatics/btx451

By:

Allam, Ahmed;
Krauthammer, Michael

Publication type:

Article

A Zoom-Focus algorithm (ZFA) to locate the optimal testing region for rare variant association tests.

Published in:

Bioinformatics, 2017, v. 33, n. 15, p. 2330, doi. 10.1093/bioinformatics/btx130

By:

Maggie Haitian Wang;
Haoyi Weng;
Rui Sun;
Jack Lee;
Wu, William Ka Kei;
Ka Chun Chong;
Benny Chung-Ying Zee

Publication type:

Article

FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications.

Published in:

Bioinformatics, 2017, v. 33, n. 10, p. 1575, doi. 10.1093/bioinformatics/btx010

By:

Petrillo, Umberto Ferraro;
Roscigno, Gianluca;
Cattaneo, Giuseppe;
Giancarlo, Raffaele

Publication type:

Article

NRGC: a novel referential genome compression algorithm.

Published in:

Bioinformatics, 2016, v. 32, n. 22, p. 3405, doi. 10.1093/bioinformatics/btw505

By:

Saha, Subrata;
Rajasekaran, Sanguthevar

Publication type:

Article

Assemblytics: a web analytics tool for the detection of variants from an assembly.

Published in:

Bioinformatics, 2016, v. 32, n. 19, p. 3021, doi. 10.1093/bioinformatics/btw369

By:

Nattestad, Maria;
Schatz, Michael C.

Publication type:

Article

KCMBT: a k-mer Counter based on Multiple Burst Trees.

Published in:

Bioinformatics, 2016, v. 32, n. 18, p. 2783, doi. 10.1093/bioinformatics/btw345

By:

Mamun, Abdullah-Al;
Pal, Soumitra;
Rajasekaran, Sanguthevar

Publication type:

Article

Pathway-based approach using hierarchical components of collapsed rare variants.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i586, doi. 10.1093/bioinformatics/btw425

By:

Sungyoung Lee;
Sungkyoung Choi;
Young Jin Kim;
Bong-Jo Kim;
Heungsun Hwang;
Taesung Park

Publication type:

Article

SoFIA: a data integration framework for annotating high-throughput datasets.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. 2590, doi. 10.1093/bioinformatics/btw302

By:

Childs, Liam Harold;
Mamlouk, Soulafa;
Brandt, Jörgen;
Sers, Christine;
Leser, Ulf

Publication type:

Article

MuCor: mutation aggregation and correlation.

Published in:

Bioinformatics, 2016, v. 32, n. 10, p. 1557, doi. 10.1093/bioinformatics/btw028

By:

Kroll, Karl W.;
Eisfeld, Ann-Katherin;
Lozanski, Gerard;
Bloomfield, Clara D.;
Byrd, John C.;
Blachly, James S.

Publication type:

Article

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 140, doi. 10.1093/bioinformatics/btu601

By:

Corpas, Manuel;
Jimenez, Rafael C.;
Bongcam-Rudloff, Erik;
Budd, Aidan;
Brazas, Michelle D.;
Fernandes, Pedro L.;
Gaeta, Bruno;
van Gelder, Celia;
Korpelainen, Eija;
Lewitter, Fran;
McGrath, Annette;
MacLean, Daniel;
Palagi, Patricia M.;
Rother, Kristian;
Taylor, Jan;
Via, Allegra;
Watson, Mick;
Schneider, Maria Victoria;
Attwood, Teresa K.

Publication type:

Article

ballaxy: web services for structural bioinformatics.

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 121, doi. 10.1093/bioinformatics/btu574

By:

Hildebrandt, Anna Katharina;
Stöckel, Daniel;
Fischer, Nina M.;
de la Garza, Luis;
Krüger, Jens;
Nickels, Stefan;
Röttig, Marc;
Schärfe, Charlotta;
Schumann, Marcel;
Thiel, Philipp;
Lenhof, Hans-Peter;
Kohlbacher, Oliver;
Hildebrandt, Andreas

Publication type:

Article

Correcting for link loss in causal network inference caused by regulator interference.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2779, doi. 10.1093/bioinformatics/btu388

By:

Wang, Ying;
Penfold, Christopher A.;
Hodgson, David A.;
Gifford, Miriam L.;
Burroughs, Nigel J.

Publication type:

Article

MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2764, doi. 10.1093/bioinformatics/btu370

By:

Daly, Rónán;
Rogers, Simon;
Wandy, Joe;
Jankevics, Andris;
Burgess, Karl E. V.;
Breitling, Rainer

Publication type:

Article

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2757, doi. 10.1093/bioinformatics/btu375

By:

Parker, Hilary S.;
Leek, Jeffrey T.;
Favorov, Alexander V.;
Considine, Michael;
Xia, Xiaoxin;
Chavan, Sameer;
Chung, Christine H.;
Fertig, Elana J.

Publication type:

Article

miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2837, doi. 10.1093/bioinformatics/btu380

By:

Lei, Jikai;
Sun, Yanni

Publication type:

Article

Literome: PubMed-scale genomic knowledge base in the cloud.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2840, doi. 10.1093/bioinformatics/btu383

By:

Poon, Hoifung;
Quirk, Chris;
DeZiel, Charlie;
Heckerman, David

Publication type:

Article

Gene set analysis: limitations in popular existing methods and proposed improvements.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2747, doi. 10.1093/bioinformatics/btu374

By:

Mishra, Pashupati;
Törönen, Petri;
Leino, Yrjö;
Holm, Liisa

Publication type:

Article

MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2826, doi. 10.1093/bioinformatics/btu377

By:

Kim, Jihoon;
Levy, Eric;
Ferbrache, Alex;
Stepanowsky, Petra;
Farcas, Claudiu;
Wang, Shuang;
Brunner, Stefan;
Bath, Tyler;
Wu, Yuan;
Ohno-Machado, Lucila

Publication type:

Article

Detecting differential protein expression in large-scale population proteomics.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2741, doi. 10.1093/bioinformatics/btu341

By:

Ryu, So Young;
Qian, Wei-Jun;
Camp, David G.;
Smith, Richard D.;
Tompkins, Ronald G.;
Davis, Ronald W.;
Xiao, Wenzhong

Publication type:

Article

Network-guided regression for detecting associations between DNA methylation and gene expression.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2693, doi. 10.1093/bioinformatics/btu361

By:

Wang, Zi;
Curry, Edward;
Montana, Giovanni

Publication type:

Article

Cloud4Psi: cloud computing for 3D protein structure similarity searching.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2822, doi. 10.1093/bioinformatics/btu389

By:

Mrozek, Dariusz;
Małysiak-Mrozek, Bożena;
Kłapciński, Artur

Publication type:

Article

NetBioV: an R package for visualizing large network data in biology and medicine.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2834, doi. 10.1093/bioinformatics/btu384

By:

Tripathi, Shailesh;
Dehmer, Matthias;
Emmert-Streib, Frank

Publication type:

Article

PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2802, doi. 10.1093/bioinformatics/btu396

By:

Zheng, Yinan;
Fei, Zhe;
Zhang, Wei;
Starren, Justin B.;
Liu, Lei;
Baccarelli, Andrea A.;
Li, Yi;
Hou, Lifang

Publication type:

Article

Improving translation initiation site and stop codon recognition by using more than two classes.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2702, doi. 10.1093/bioinformatics/btu369

By:

Pérez-Rodríguez, Javier;
Arroyo-Peña, Alexis G.;
García-Pedrajas, Nicolás

Publication type:

Article

Omega: an Overlap-graph de novo Assembler for Metagenomics.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2717, doi. 10.1093/bioinformatics/btu395

By:

Haider, Bahlul;
Ahn, Tae-Hyuk;
Bushnell, Brian;
Chai, Juanjuan;
Copeland, Alex;
Pan, Chongle

Publication type:

Article

circlize implements and enhances circular visualization in R.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2811, doi. 10.1093/bioinformatics/btu393

By:

Gu, Zuguang;
Gu, Lei;
Eils, Roland;
Schlesner, Matthias;
Brors, Benedikt

Publication type:

Article

ABRA: improved coding indel detection via assembly-based realignment.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2813, doi. 10.1093/bioinformatics/btu376

By:

Mose, Lisle E.;
Wilkerson, Matthew D.;
Hayes, D. Neil;
Perou, Charles M.;
Parker, Joel S.

Publication type:

Article

BEETL-fastq: a searchable compressed archive for DNA reads.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2796, doi. 10.1093/bioinformatics/btu387

By:

Janin, Lilian;
Schulz-Trieglaff, Ole;
Cox, Anthony J.

Publication type:

Article

SMaSH: a benchmarking toolkit for human genome variant calling.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2787, doi. 10.1093/bioinformatics/btu345

By:

Talwalkar, Ameet;
Liptrap, Jesse;
Newcomb, Julie;
Hartl, Christopher;
Terhorst, Jonathan;
Curtis, Kristal;
Bresler, Ma’ayan;
Song, Yun S.;
Jordan, Michael I.;
Patterson, David

Publication type:

Article

Lossy compression of quality scores in genomic data.

Published in:

Bioinformatics, 2014, v. 30, n. 15, p. 2130

By:

Cánovas, Rodrigo;
Moffat, Alistair;
Turpin, Andrew

Publication type:

Article

Estimating optimal window size for analysis of low-coverage next-generation sequence data.

Published in:

Bioinformatics, 2014, v. 30, n. 13, p. 1823, doi. 10.1093/bioinformatics/btu123

By:

Gusnanto, Arief;
Taylor, Charles C.;
Nafisah, Ibrahim;
Wood, Henry M.;
Rabbitts, Pamela;
Berri, Stefano

Publication type:

Article

SegAnnDB: interactive Web-based genomic segmentation.

Published in:

Bioinformatics, 2014, v. 30, n. 11, p. 1539, doi. 10.1093/bioinformatics/btu072

By:

Hocking, Toby D.;
Boeva, Valentina;
Rigaill, Guillem;
Schleiermacher, Gudrun;
Janoueix-Lerosey, Isabelle;
Delattre, Olivier;
Richer, Wilfrid;
Bourdeaut, Franck;
Suguro, Miyuki;
Seto, Masao;
Bach, Francis;
Vert, Jean-Philippe

Publication type:

Article

Supercomputing for the parallelization of whole genome analysis.

Published in:

Bioinformatics, 2014, v. 30, n. 11, p. 1508, doi. 10.1093/bioinformatics/btu071

By:

Puckelwartz, Megan J.;
Pesce, Lorenzo L.;
Nelakuditi, Viswateja;
Dellefave-Castillo, Lisa;
Golbus, Jessica R.;
Day, Sharlene M.;
Cappola, Thomas P.;
Dorn, Gerald W.;
Foster, Ian T.;
McNally, Elizabeth M.

Publication type:

Article

CGAT: computational genomics analysis toolkit.

Published in:

Bioinformatics, 2014, v. 30, n. 9, p. 1290, doi. 10.1093/bioinformatics/btt756

By:

Sims, David;
Ilott, Nicholas E.;
Sansom, Stephen N.;
Sudbery, Ian M.;
Johnson, Jethro S.;
Fawcett, Katherine A.;
Berlanga-Taylor, Antonio J.;
Luna-Valero, Sebastian;
Ponting, Chris P.;
Heger, Andreas

Publication type:

Article

PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data.

Published in:

Bioinformatics, 2014, v. 30, n. 9, p. 1302, doi. 10.1093/bioinformatics/btt774

By:

McCarthy, Michael T.;
O’Callaghan, Christopher A.

Publication type:

Article

InterProScan 5: genome-scale protein function classification.

Published in:

Bioinformatics, 2014, v. 30, n. 9, p. 1236, doi. 10.1093/bioinformatics/btu031

By:

Jones, Philip;
Binns, David;
Chang, Hsin-Yu;
Fraser, Matthew;
Li, Weizhong;
McAnulla, Craig;
McWilliam, Hamish;
Maslen, John;
Mitchell, Alex;
Nuka, Gift;
Pesseat, Sebastien;
Quinn, Antony F.;
Sangrador-Vegas, Amaia;
Scheremetjew, Maxim;
Yong, Siew-Yit;
Lopez, Rodrigo;
Hunter, Sarah

Publication type:

Article

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.

Published in:

Bioinformatics, 2014, v. 30, n. 9, p. 1327, doi. 10.1093/bioinformatics/btt758

By:

Jensen, Paul A.;
Papin, Jason A.

Publication type:

Article

Assimilating genome-scale metabolic reconstructions with modelBorgifier.

Published in:

Bioinformatics, 2014, v. 30, n. 7, p. 1036, doi. 10.1093/bioinformatics/btt747

By:

Sauls, John T.;
Buescher, Joerg M.

Publication type:

Article

Efficient clustering of identity-by-descent between multiple individuals.

Published in:

Bioinformatics, 2014, v. 30, n. 7, p. 915, doi. 10.1093/bioinformatics/btt734

By:

Qian, Yu;
Browning, Brian L.;
Browning, Sharon R.

Publication type:

Article

Precise inference of copy number alterations in tumor samples from SNP arrays.

Published in:

Bioinformatics, 2013, v. 29, n. 23, p. 2964, doi. 10.1093/bioinformatics/btt521

By:

Chen, Gary K.;
Chang, Xiao;
Curtis, Christina;
Wang, Kai

Publication type:

Article

PLncDB: plant long non-coding RNA database.

Published in:

Bioinformatics, 2013, v. 29, n. 8, p. 1068, doi. 10.1093/bioinformatics/btt107

By:

Jin, Jingjing;
Liu, Jun;
Wang, Huan;
Wong, Limsoon;
Chua, Nam-Hai

Publication type:

Article

Measuring guide-tree dependency of inferred gaps in progressive aligners.

Published in:

Bioinformatics, 2013, v. 29, n. 8, p. 1011, doi. 10.1093/bioinformatics/btt095

By:

Capella-Gutiérrez, Salvador;
Gabaldón, Toni

Publication type:

Article

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

Published in:

Bioinformatics, 2013, v. 29, n. 6, p. 815, doi. 10.1093/bioinformatics/btt036

By:

Ganter, Mathias;
Bernard, Thomas;
Moretti, Sébastien;
Stelling, Joerg;
Pagni, Marco

Publication type:

Article

HitWalker: variant prioritization for personalized functional cancer genomics.

Published in:

Bioinformatics, 2013, v. 29, n. 4, p. 509, doi. 10.1093/bioinformatics/btt003

By:

Bottomly, Daniel;
Wilmot, Beth;
Tyner, Jeffrey W.;
Eide, Christopher A.;
Loriaux, Marc M.;
Druker, Brian J.;
McWeeney, Shannon K.

Publication type:

Article

htSeqTools: high-throughput sequencing quality control, processing and visualization in R.

Published in:

Bioinformatics, 2012, v. 28, n. 4, p. 589, doi. 10.1093/bioinformatics/btr700

By:

Planet, Evarist;
Attolini, Camille Stephan-Otto;
Reina, Oscar;
Flores, Oscar;
Rossell, David

Publication type:

Article

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

Published in:

Bioinformatics, 2011, v. 27, n. 14, p. 1894, doi. 10.1093/bioinformatics/btr314

By:

Rose, Dominic;
Hiller, Michael;
Schutt, Katharina;
Hackermüller, Jörg;
Backofen, Rolf;
Stadler, Peter F.

Publication type:

Article

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks.

Published in:

Bioinformatics, 2011, v. 27, n. 14, p. 2009, doi. 10.1093/bioinformatics/btr308

By:

Thorleifsson, Stefan Gretar;
Thiele, Ines

Publication type:

Article

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

Published in:

Bioinformatics, 2011, v. 27, n. 14, p. 1922, doi. 10.1093/bioinformatics/btr310

By:

Ge, Huanying;
Liu, Kejun;
Juan, Todd;
Fang, Fang;
Newman, Matthew;
Hoeck, Wolfgang

Publication type:

Article