Works matching DE "BIOLOGICAL databases"

Results: 1009

Implementing distinct spatial proteogenomic technologies: opportunities, challenges, and key considerations.

Published in:

Clinical & Experimental Immunology, 2024, v. 218, n. 2, p. 151, doi. 10.1093/cei/uxae077

By:

Verstappe, Bram;
Scott, Charlotte L

Publication type:

Article

Gaussian processes for time series with lead–lag effects with applications to biology data.

Published in:

Biometrics, 2025, v. 81, n. 1, p. 1, doi. 10.1093/biomtc/ujae156

By:

Mu, Wancen;
Chen, Jiawen;
Davis, Eric S;
Reed, Kathleen;
Phanstiel, Douglas;
Love, Michael I;
Li, Didong

Publication type:

Article

Cover Image.

Published in:: Ecology, 2025, v. 106, n. 5, p. 1, doi. 10.1002/ecy.4344
Publication type:: Article

Towards unified quality verification of synthetic count data with countsimQC.

Published in:

Bioinformatics, 2018, v. 34, n. 4, p. 691, doi. 10.1093/bioinformatics/btx631

By:

Soneson, Charlotte;
Robinson, Mark D

Publication type:

Article

On patterns and re-use in bioinformatics databases.

Published in:

Bioinformatics, 2017, v. 33, n. 17, p. 2731, doi. 10.1093/bioinformatics/btx310

By:

Bell, Michael J.;
Lord, Phillip

Publication type:

Article

Neuro-symbolic representation learning on biological knowledge graphs.

Published in:

Bioinformatics, 2017, v. 33, n. 17, p. 2723, doi. 10.1093/bioinformatics/btx275

By:

Alshahrani, Mona;
Khan, Mohammad Asif;
Hoehndorf, Robert;
Maddouri, Omar;
Kinjo, Akira R.;
Queralt-Rosinach, Nùria

Publication type:

Article

Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data.

Published in:

Bioinformatics, 2017, v. 33, n. 15, p. 2421, doi. 10.1093/bioinformatics/btx147

By:

Pontikos, Nikolas;
Jing Yu;
Moghul, Ismail;
Withington, Lucy;
Blanco-Kelly, Fiona;
Vulliamy, Tom;
Wong, Tsz Lun Ernest;
Murphy, Cian;
Cipriani, Valentina;
Fiorentino, Alessia;
Arno, Gavin;
Greene, Daniel;
Jacobsen, Julius O. B.;
Clark, Tristan;
Gregory, David S.;
Nemeth, Andrea M.;
Halford, Stephanie;
Inglehearn, Chris F.;
Downes, Susan;
Black, Graeme C.

Publication type:

Article

DextMP: deep dive into text for predicting moonlighting proteins.

Published in:

Bioinformatics, 2017, v. 33, n. 14, p. i83, doi. 10.1093/bioinformatics/btx231

By:

Khan, Ishita K.;
Bhuiyan, Mansurul;
Kihara, Daisuke

Publication type:

Article

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 1096, doi. 10.1093/bioinformatics/btw731

By:

Balaur, Irina;
Mazein, Alexander;
Saqi, Mansoor;
Lysenko, Artem;
Rawlings, Christopher J.;
Auffray, Charles

Publication type:

Article

Network-based analysis of omics data: the LEAN method.

Published in:

Bioinformatics, 2017, v. 33, n. 5, p. 701, doi. 10.1093/bioinformatics/btw676

By:

Gwinner, Frederik;
Boulday, Gwénola;
Vandiedonck, Claire;
Arnould, Minh;
Cardoso, Cécile;
Nikolayeva, Iryna;
Guitart-Pla, Oriol;
Denis, Cécile V.;
Christophe, Olivier D.;
Beghain, Johann;
Tournier-Lasserve, Elisabeth;
Schwikowski, Benno

Publication type:

Article

Imputing gene expression to maximize platform compatibility.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 522, doi. 10.1093/bioinformatics/btw664

By:

Weizhuang Zhou;
Lichy Han;
Altman, Russ B.

Publication type:

Article

CloudPhylo: a fast and scalable tool for phylogeny reconstruction.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 438, doi. 10.1093/bioinformatics/btw645

By:

Xingjian Xu;
Zhaohua Ji;
Zhang Zhang

Publication type:

Article

simPATHy: a new method for simulating data from perturbed biological PATHways.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 456, doi. 10.1093/bioinformatics/btw642

By:

Salviato, Elisa;
Djordjilović, Vera;
Chiogna, Monica;
Romualdi, Chiara

Publication type:

Article

CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 464, doi. 10.1093/bioinformatics/btw640

By:

Russo, Daniel P.;
Kim, Marlene T.;
Wenyi Wang;
Pinolini, Daniel;
Shende, Sunil;
Strickland, Judy;
Hartung, Thomas;
Hao Zhu

Publication type:

Article

densityCut: an efficient and versatile topological approach for automatic clustering of biological data.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. 2567, doi. 10.1093/bioinformatics/btw227

By:

Ding, Jiarui;
Shah, Sohrab;
Condon, Anne

Publication type:

Article

TnT: a set of libraries for visualizing trees and track-based annotations for the web.

Published in:

Bioinformatics, 2016, v. 32, n. 16, p. 2524, doi. 10.1093/bioinformatics/btw210

By:

Pignatelli, Miguel

Publication type:

Article

LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations.

Published in:

Bioinformatics, 2016, v. 32, n. 6, p. 949, doi. 10.1093/bioinformatics/btv690

By:

Dadaev, Tokhir;
Leongamornlert, Daniel A.;
Saunders, Edward J.;
Eeles, Rosalind;
Kote-Jarai, Zsofia

Publication type:

Article

Cell line name recognition in support of the identification of synthetic lethality in cancer from text.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 276, doi. 10.1093/bioinformatics/btv570

By:

Kaewphan, Suwisa;
Van Landeghem, Sofie;
Ohta, Tomoko;
Van de Peer, Yves;
Ginter, Filip;
Pyysalo, Sampo

Publication type:

Article

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 301, doi. 10.1093/bioinformatics/btv553

By:

Hodor, Paul;
Chawla, Amandeep;
Clark, Andrew;
Neal, Lauren

Publication type:

Article

Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 195, doi. 10.1093/bioinformatics/btv569

By:

Hardcastle, Thomas J.

Publication type:

Article

GLASS: a comprehensive database for experimentally-validated GPCR-ligand associations associations.

Published in:

Bioinformatics, 2015, v. 31, n. 18, p. 3035, doi. 10.1093/bioinformatics/btv302

By:

Chan, Wallace K. B.;
Hongjiu Zhang;
Jianyi Yang;
Brender, Jeffrey R.;
Junguk Hur;
Özgür, Arzucan;
Yang Zhang

Publication type:

Article

SpeeDB: fast structural protein searches.

Published in:

Bioinformatics, 2015, v. 31, n. 18, p. 3027, doi. 10.1093/bioinformatics/btv274

By:

Robillard, David E.;
Mpangase, Phelelani T.;
Hazelhurst, Scott;
Dehne, Frank

Publication type:

Article

mirPub: a database for searching microRNA publications.

Published in:

2015

By:

Vergoulis, Thanasis;
Kanellos, Ilias;
Kostoulas, Nikos;
Georgakilas, Georgios;
Sellis, Timos;
Hatzigeorgiou, Artemis;
Dalamagas, Theodore

Publication type:

Product Review

Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model.

Published in:

Bioinformatics, 2015, v. 31, n. 8, p. 1243, doi. 10.1093/bioinformatics/btu799

By:

Tsoi, Lam C.;
Elder, James T.;
Abecasis, Goncalo R.

Publication type:

Article

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.

Published in:

Bioinformatics, 2015, v. 31, n. 6, p. 926, doi. 10.1093/bioinformatics/btu739

By:

Suzek, Baris E.;
Yuqi Wang;
Hongzhan Huang;
McGarvey, Peter B.;
Wu, Cathy H.

Publication type:

Article

Mass spectrometry-based protein identification with accurate statistical significance assignment.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 699, doi. 10.1093/bioinformatics/btu717

By:

Alves, Gelio;
Yu, Yi-Kuo

Publication type:

Article

iDoComp: a compression scheme for assembled genomes.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 626, doi. 10.1093/bioinformatics/btu698

By:

Ochoa, Idoia;
Hernaez, Mikel;
Weissman, Tsachy

Publication type:

Article

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 770, doi. 10.1093/bioinformatics/btu719

By:

Renaud, Gabriel;
Stenzel, Udo;
Maricic, Tomislav;
Wiebe, Victor;
Kelso, Janet

Publication type:

Article

MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC–MS metabolomic datasets.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 788, doi. 10.1093/bioinformatics/btu705

By:

Edmands, William M. B.;
Barupal, Dinesh K.;
Scalbert, Augustin

Publication type:

Article

Measuring the wisdom of the crowds in network-based gene function inference.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 745, doi. 10.1093/bioinformatics/btu715

By:

Verleyen, W.;
Ballouz, S.;
Gillis, J.

Publication type:

Article

PPDMs—a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.

Published in:

Bioinformatics, 2015, v. 31, n. 5, p. 776, doi. 10.1093/bioinformatics/btu711

By:

Kruger, Felix A.;
Gaulton, Anna;
Nowotka, Michal;
Overington, John P.

Publication type:

Article

WhopGenome: high-speed access to whole-genome variation and sequence data in R.

Published in:

Bioinformatics, 2015, v. 31, n. 3, p. 413, doi. 10.1093/bioinformatics/btu636

By:

Wittelsbürger, Ulrich;
Pfeifer, Bastian;
Lercher, Martin J.

Publication type:

Article

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.

Published in:

2015

By:

Verspoor, Karin;
Shatkay, Hagit;
Hirschman, Lynette;
Blaschke, Christian;
Valencia, Alfonso

Publication type:

Proceeding

Limbform: a functional ontology-based database of limb regeneration experiments.

Published in:

Bioinformatics, 2014, v. 30, n. 24, p. 3598, doi. 10.1093/bioinformatics/btu582

By:

Lobo, Daniel;
Feldman, Erica B.;
Shah, Michelle;
Malone, Taylor J.;
Levin, Michael

Publication type:

Article

Polytomy refinement for the correction of dubious duplications in gene trees.

Published in:

Bioinformatics, 2014, v. 30, n. 17, p. i519, doi. 10.1093/bioinformatics/btu463

By:

Lafond, Manuel;
Chauve, Cedric;
Dondi, Riccardo;
El-Mabrouk, Nadia

Publication type:

Article

ASTRAL: genome-scale coalescent-based species tree estimation.

Published in:

Bioinformatics, 2014, v. 30, n. 17, p. i541, doi. 10.1093/bioinformatics/btu462

By:

Mirarab, S.;
Reaz, R.;
Bayzid, Md. S.;
Zimmermann, T.;
Swenson, M. S.;
Warnow, T.

Publication type:

Article

Ceiba: scalable visualization of phylogenies and 2D/3D image collections.

Published in:

2014

By:

Sanderson, Michael J.

Publication type:

Product Review

SIBIS: a Bayesian model for inconsistent protein sequence estimation.

Published in:

2014

By:

Khenoussi, Walyd;
Vanhoutrève, Renaud;
Poch, Olivier;
Thompson, Julie D.

Publication type:

Product Review

GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype.

Published in:

2014

By:

Ryu, Daeun;
Cho, SeongBeom;
Kim, Hun;
Lee, Sanghyuk;
Kim, Wankyu

Publication type:

Product Review

fastGapFill: efficient gap filling in metabolic networks.

Published in:

Bioinformatics, 2014, v. 30, n. 17, p. 2529, doi. 10.1093/bioinformatics/btu321

By:

Thiele, Ines;
Vlassis, Nikos;
Fleming, Ronan M. T.

Publication type:

Article

GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms.

Published in:

2014

By:

Guney, Emre;
Garcia-Garcia, Javier;
Oliva, Baldo

Publication type:

Product Review

Functional association networks as priors for gene regulatory network inference.

Published in:

2014

By:

Studham, Matthew E.;
Tjärnberg, Andreas;
Nordling, Torbjörn E.M.;
Nelander, Sven;
Sonnhammer, Erik L. L.

Publication type:

Product Review

BiPACE 2D—graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry.

Published in:

Bioinformatics, 2014, v. 30, n. 7, p. 988, doi. 10.1093/bioinformatics/btt738

By:

Hoffmann, Nils;
Wilhelm, Mathias;
Doebbe, Anja;
Niehaus, Karsten;
Stoye, Jens

Publication type:

Article

Don't use a cannon to kill the … miRNA mosquito.

Published in:

Bioinformatics, 2014, v. 30, n. 7, p. 1047, doi. 10.1093/bioinformatics/btu100

By:

Karathanasis, Nestoras;
Tsamardinos, Ioannis;
Poirazi, Panayiota

Publication type:

Article

Further Steps in TANGO: improved taxonomic assignment in metagenomics.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 17, doi. 10.1093/bioinformatics/btt256

By:

Alonso-Alemany, Daniel;
Barré, Aurélien;
Beretta, Stefano;
Bonizzoni, Paola;
Nikolski, Macha;
Valiente, Gabriel

Publication type:

Article

Pattern search in BioPAX models.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 139, doi. 10.1093/bioinformatics/btt539

By:

Babur, Özgün;
Aksoy, Bülent Arman;
Rodchenkov, Igor;
Sümer, Selçuk Onur;
Sander, Chris;
Demir, Emek

Publication type:

Article

MSPrep—Summarization, normalization and diagnostics for processing of mass spectrometry–based metabolomic data.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 133, doi. 10.1093/bioinformatics/btt589

By:

Hughes, Grant;
Cruickshank-Quinn, Charmion;
Reisdorph, Richard;
Lutz, Sharon;
Petrache, Irina;
Reisdorph, Nichole;
Bowler, Russell;
Kechris, Katerina

Publication type:

Article

MFCompress: a compression tool for FASTA and multi-FASTA data.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 117, doi. 10.1093/bioinformatics/btt594

By:

Pinho, Armando J.;
Pratas, Diogo

Publication type:

Article

A C library for retrieving specific reactions from the BioModels database.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 129, doi. 10.1093/bioinformatics/btt567

By:

Neal, M. L.;
Galdzicki, M.;
Gallimore, J. T.;
Sauro, H. M.

Publication type:

Article

Sequence alignment visualization in HTML5 without Java.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 121, doi. 10.1093/bioinformatics/btt614

By:

Gille, Christoph;
Birgit, Weyand;
Gille, Andreas

Publication type:

Article