Works matching IS 13674803 AND DT 2020 AND VI 36 AND IP 6

Results: 64

Discovery of disease- and drug-specific pathways through community structures of a literature network.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1881, doi. 10.1093/bioinformatics/btz857

By:

Pham, Minh;
Wilson, Stephen;
Govindarajan, Harikumar;
Lin, Chih-Hsu;
Lichtarge, Olivier

Publication type:

Article

SPDI: data model for variants and applications at NCBI.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1902, doi. 10.1093/bioinformatics/btz856

By:

Holmes, J Bradley;
Moyer, Eric;
Phan, Lon;
Maglott, Donna;
Kattman, Brandi

Publication type:

Article

Improved linking of motifs to their TFs using domain information.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1655, doi. 10.1093/bioinformatics/btz855

By:

Baumgarten, Nina;
Schmidt, Florian;
Schulz, Marcel H

Publication type:

Article

RaNA-Seq: interactive RNA-Seq analysis from FASTQ files to functional analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1955, doi. 10.1093/bioinformatics/btz854

By:

Prieto, Carlos;
Barrios, David

Publication type:

Article

Cross-lingual semantic annotation of biomedical literature: experiments in Spanish and English.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1872, doi. 10.1093/bioinformatics/btz853

By:

Perez, Naiara;
Accuosto, Pablo;
Bravo, Àlex;
Cuadros, Montse;
Martínez-Garcia, Eva;
Saggion, Horacio;
Rigau, German

Publication type:

Article

Priors for genotyping polyploids.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1795, doi. 10.1093/bioinformatics/btz852

By:

Gerard, David;
Ferrão, Luís Felipe Ventorim

Publication type:

Article

Somatic selection distinguishes oncogenes and tumor suppressor genes.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1712, doi. 10.1093/bioinformatics/btz851

By:

Chandrashekar, Pramod;
Ahmadinejad, Navid;
Wang, Junwen;
Sekulic, Aleksandar;
Egan, Jan B;
Asmann, Yan W;
Kumar, Sudhir;
Maley, Carlo;
Liu, Li

Publication type:

Article

DigestiFlow: from BCL to FASTQ with ease.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1983, doi. 10.1093/bioinformatics/btz850

By:

Holtgrewe, Manuel;
Messerschmidt, Clemens;
Nieminen, Mikko;
Beule, Dieter

Publication type:

Article

MILES: a Java tool to extract node-specific enriched subgraphs in biomolecular networks.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1978, doi. 10.1093/bioinformatics/btz849

By:

Moris, Pieter;
Bui-Thi, Danh;
Laukens, Kris;
Meysman, Pieter

Publication type:

Article

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1925, doi. 10.1093/bioinformatics/btz848

By:

Chaumeil, Pierre-Alain;
Mussig, Aaron J;
Hugenholtz, Philip;
Parks, Donovan H

Publication type:

Article

Differentiating isoform functions with collaborative matrix factorization.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1864, doi. 10.1093/bioinformatics/btz847

By:

Wang, Keyao;
Wang, Jun;
Domeniconi, Carlotta;
Zhang, Xiangliang;
Yu, Guoxian

Publication type:

Article

Mining single-cell time-series datasets with Time Course Inspector.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1968, doi. 10.1093/bioinformatics/btz846

By:

Dobrzyński, Maciej;
Jacques, Marc-Antoine;
Pertz, Olivier

Publication type:

Article

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1731, doi. 10.1093/bioinformatics/btz845

By:

Smakaj, Erand;
Babrak, Lmar;
Ohlin, Mats;
Shugay, Mikhail;
Briney, Bryan;
Tosoni, Deniz;
Galli, Christopher;
Grobelsek, Vendi;
D'Angelo, Igor;
Olson, Branden;
Reddy, Sai;
Greiff, Victor;
Trück, Johannes;
Marquez, Susanna;
Lees, William;
Miho, Enkelejda

Publication type:

Article

Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1908, doi. 10.1093/bioinformatics/btz844

By:

Xu, Ying-Ying;
Shen, Hong-Bin;
Murphy, Robert F

Publication type:

Article

An integrative approach for fine-mapping chromatin interactions.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1704, doi. 10.1093/bioinformatics/btz843

By:

Jaroszewicz, Artur;
Ernst, Jason

Publication type:

Article

NCutYX: a package for clustering analysis of multilayer omics data.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1976, doi. 10.1093/bioinformatics/btz842

By:

Hidalgo, Sebastian J Teran;
Wu, Mengyun;
Ma, Shuangge

Publication type:

Article

HypercubeME: two hundred million combinatorially complete datasets from a single experiment.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1960, doi. 10.1093/bioinformatics/btz841

By:

Esteban, Laura A;
Lonishin, Lyubov R;
Bobrovskiy, Daniil M;
Leleytner, Gregory;
Bogatyreva, Natalya S;
Kondrashov, Fyodor A;
Ivankov, Dmitry N

Publication type:

Article

Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1668, doi. 10.1093/bioinformatics/btz840

By:

Tarlachkov, Sergey V;
Shevchuk, Taras V;
Montero-Calasanz, Maria del Carmen;
Starodumova, Irina P

Publication type:

Article

Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1923, doi. 10.1093/bioinformatics/btz839

By:

Jiang, Yu;
Zhang, Hongmei;
Andrews, Shan V;
Arshad, Hasan;
Ewart, Susan;
Holloway, John W;
Fallin, M Daniele;
Bakulski, Kelly M;
Karmaus, Wilfried

Publication type:

Article

Estimating chain length for time delays in dynamical systems using profile likelihood.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1848, doi. 10.1093/bioinformatics/btz838

By:

Hauber, Adrian L;
Engesser, Raphael;
Vanlier, Joep;
Timmer, Jens

Publication type:

Article

Differential privacy under dependent tuples—the case of genomic privacy.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1696, doi. 10.1093/bioinformatics/btz837

By:

Almadhoun, Nour;
Ayday, Erman;
Ulusoy, Özgür

Publication type:

Article

DiNGO: standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1981, doi. 10.1093/bioinformatics/btz836

By:

Davidović, Radoslav;
Perovic, Vladimir;
Gemovic, Branislava;
Veljkovic, Nevena

Publication type:

Article

The Cytoscape BioGateway App: explorative network building from an RDF store.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1966, doi. 10.1093/bioinformatics/btz835

By:

Holmås, Stian;
Puig, Rafel Riudavets;
Acencio, Marcio Luis;
Mironov, Vladimir;
Kuiper, Martin

Publication type:

Article

DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1952, doi. 10.1093/bioinformatics/btz834

By:

Carlucci, Matthew;
Kriščiūnas, Algimantas;
Li, Haohan;
Gibas, Povilas;
Koncevičius, Karolis;
Petronis, Art;
Oh, Gabriel

Publication type:

Article

EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1950, doi. 10.1093/bioinformatics/btz833

By:

Zheng, Shijie C;
Breeze, Charles E;
Beck, Stephan;
Dong, Danyue;
Zhu, Tianyu;
Ma, Liangxiao;
Ye, Wei;
Zhang, Guoqing;
Teschendorff, Andrew E

Publication type:

Article

On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1986, doi. 10.1093/bioinformatics/btz832

By:

Ponce-de-León, Miguel;
Apaolaza, Iñigo;
Valencia, Alfonso;
Planes, Francisco J

Publication type:

Article

BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1689, doi. 10.1093/bioinformatics/btz831

By:

Hukku, Abhay;
Quick, Corbin;
Luca, Francesca;
Pique-Regi, Roger;
Wen, Xiaoquan

Publication type:

Article

scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1948, doi. 10.1093/bioinformatics/btz830

By:

Cai, James J

Publication type:

Article

ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein–protein complexes upon mutation using functional classification.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1725, doi. 10.1093/bioinformatics/btz829

By:

Jemimah, Sherlyn;
Sekijima, Masakazu;
Gromiha, M Michael

Publication type:

Article

QMEANDisCo—distance constraints applied on model quality estimation.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1765, doi. 10.1093/bioinformatics/btz828

By:

Studer, Gabriel;
Rempfer, Christine;
Waterhouse, Andrew M;
Gumienny, Rafal;
Haas, Juergen;
Schwede, Torsten

Publication type:

Article

SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1963, doi. 10.1093/bioinformatics/btz827

By:

Ravichandran, Srikanth;
Hartmann, András;
Sol, Antonio del

Publication type:

Article

MDiNE: a model to estimate differential co-occurrence networks in microbiome studies.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1840, doi. 10.1093/bioinformatics/btz824

By:

McGregor, Kevin;
Labbe, Aurélie;
Greenwood, Celia M T

Publication type:

Article

Improved dropClust R package with integrative analysis support for scRNA-seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1946, doi. 10.1093/bioinformatics/btz823

By:

Sinha, Debajyoti;
Sinha, Pradyumn;
Saha, Ritwik;
Bandyopadhyay, Sanghamitra;
Sengupta, Debarka

Publication type:

Article

Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1785, doi. 10.1093/bioinformatics/btz822

By:

Li, Jun;
Lu, Qing;
Wen, Yalu

Publication type:

Article

RNASeq_similarity_matrix: visually identify sample mix-ups in RNASeq data using a 'genomic' sequence similarity matrix.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1940, doi. 10.1093/bioinformatics/btz821

By:

Kist, Nicolaas C;
Power, Robert A;
Skelton, Andrew;
Seegobin, Seth D;
Verbelen, Moira;
Bonde, Bushan;
Malki, Karim

Publication type:

Article

WPMIAS: Whole-degradome-based Plant MicroRNA–target Interaction Analysis Server.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1937, doi. 10.1093/bioinformatics/btz820

By:

Fei, Yuhan;
Mao, Yiyang;
Shen, Chengji;
Wang, Rui;
Zhang, Hongsheng;
Huang, Ji

Publication type:

Article

DrawGlycan-SNFG and gpAnnotate: rendering glycans and annotating glycopeptide mass spectra.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1942, doi. 10.1093/bioinformatics/btz819

By:

Cheng, Kai;
Pawlowski, Gabrielle;
Yu, Xinheng;
Zhou, Yusen;
Neelamegham, Sriram

Publication type:

Article

Generalized Born radii computation using linear models and neural networks.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1757, doi. 10.1093/bioinformatics/btz818

By:

Mahmoud, Saida Saad Mohamed;
Esposito, Gennaro;
Serra, Giuseppe;
Fogolari, Federico

Publication type:

Article

Enzyme annotation in UniProtKB using Rhea.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1896, doi. 10.1093/bioinformatics/btz817

By:

Morgat, Anne;
Lombardot, Thierry;
Coudert, Elisabeth;
Axelsen, Kristian;
Neto, Teresa Batista;
Gehant, Sebastien;
Bansal, Parit;
Bolleman, Jerven;
Gasteiger, Elisabeth;
Castro, Edouard de;
Baratin, Delphine;
Pozzato, Monica;
Xenarios, Ioannis;
Poux, Sylvain;
Redaschi, Nicole;
Bridge, Alan;
Consortium, The UniProt

Publication type:

Article

The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1750, doi. 10.1093/bioinformatics/btz816

By:

Chonofsky, Mark;
Oliveira, Saulo H P de;
Krawczyk, Konrad;
Deane, Charlotte M

Publication type:

Article

PRODIGY: personalized prioritization of driver genes.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1831, doi. 10.1093/bioinformatics/btz815

By:

Dinstag, Gal;
Shamir, Ron

Publication type:

Article

Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1681, doi. 10.1093/bioinformatics/btz814

By:

Southgate, Joel A;
Bull, Matthew J;
Brown, Clare M;
Watkins, Joanne;
Corden, Sally;
Southgate, Benjamin;
Moore, Catherine;
Connor, Thomas R

Publication type:

Article

Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1823, doi. 10.1093/bioinformatics/btz813

By:

Ong, Wai Kit;
Midford, Peter E;
Karp, Peter D

Publication type:

Article

YY1 is a cis-regulator in the organoid models of high mammographic density.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1663, doi. 10.1093/bioinformatics/btz812

By:

Cheng, Qingsu;
Khoshdeli, Mina;
Ferguson, Bradley S;
Jabbari, Kosar;
Zang, Chongzhi;
Parvin, Bahram

Publication type:

Article

CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long non-coding RNAs.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1673, doi. 10.1093/bioinformatics/btz811

By:

Bergadà-Pijuan, Judith;
Pulido-Quetglas, Carlos;
Vancura, Adrienne;
Johnson, Rory

Publication type:

Article

OLOGRAM: determining significance of total overlap length between genomic regions sets.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1920, doi. 10.1093/bioinformatics/btz810

By:

Ferré, Q;
Charbonnier, G;
Sadouni, N;
Lopez, F;
Kermezli, Y;
Spicuglia, S;
Capponi, C;
Ghattas, B;
Puthier, D

Publication type:

Article

Network-based multi-task learning models for biomarker selection and cancer outcome prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1814, doi. 10.1093/bioinformatics/btz809

By:

Wang, Zhibo;
He, Zhezhi;
Shah, Milan;
Zhang, Teng;
Fan, Deliang;
Zhang, Wei

Publication type:

Article

HiCBricks: building blocks for efficient handling of large Hi-C datasets.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1917, doi. 10.1093/bioinformatics/btz808

By:

Pal, Koustav;
Tagliaferri, Ilario;
Livi, Carmen Maria;
Ferrari, Francesco

Publication type:

Article

GenCLiP 3: mining human genes' functions and regulatory networks from PubMed based on co-occurrences and natural language processing.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1973, doi. 10.1093/bioinformatics/btz807

By:

Wang, Jia-Hong;
Zhao, Ling-Feng;
Wang, Hua-Feng;
Wen, Yue-Ting;
Jiang, Kui-Kui;
Mao, Xiang-Ming;
Zhou, Zi-Ying;
Yao, Kai-Tai;
Geng, Qing-Shan;
Guo, Dan;
Huang, Zhong-Xi

Publication type:

Article

Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1933, doi. 10.1093/bioinformatics/btz806

By:

Zhong, Xiangfu;
Pla, Albert;
Rayner, Simon

Publication type:

Article