Works matching IS 13674803 AND DT 2019 AND VI 35 AND IP 18

Results: 58

3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3512, doi. 10.1093/bioinformatics/btz118

By:

Segura, Joan;
Sanchez-Garcia, Ruben;
Sorzano, C O S;
Carazo, J M

Publication type:

Article

Biological sequence modeling with convolutional kernel networks.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3294, doi. 10.1093/bioinformatics/btz094

By:

Chen, Dexiong;
Jacob, Laurent;
Mairal, Julien

Publication type:

Article

Temporal network alignment via GoT-WAVE.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3527, doi. 10.1093/bioinformatics/btz119

By:

Aparício, David;
Ribeiro, Pedro;
Milenković, Tijana;
Silva, Fernando

Publication type:

Article

BioKEEN: a library for learning and evaluating biological knowledge graph embeddings.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3538, doi. 10.1093/bioinformatics/btz117

By:

Ali, Mehdi;
Hoyt, Charles Tapley;
Domingo-Fernández, Daniel;
Lehmann, Jens;
Jabeen, Hajira

Publication type:

Article

NFPws: a web server for delineating broadly neutralizing antibody specificities from serum HIV-1 neutralization data.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3502, doi. 10.1093/bioinformatics/btz097

By:

Raju, Nagarajan;
Setliff, Ian;
Georgiev, Ivelin S

Publication type:

Article

Using local alignment to enhance single-cell bisulfite sequencing data efficiency.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3273, doi. 10.1093/bioinformatics/btz125

By:

Wu, Peng;
Gao, Yan;
Guo, Weilong;
Zhu, Ping

Publication type:

Article

Protein model quality assessment using 3D oriented convolutional neural networks.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3313, doi. 10.1093/bioinformatics/btz122

By:

Pagès, Guillaume;
Charmettant, Benoit;
Grudinin, Sergei

Publication type:

Article

RiboD: a comprehensive database for prokaryotic riboswitches.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3541, doi. 10.1093/bioinformatics/btz093

By:

Mukherjee, Sumit;
Mandal, Sukhen Das;
Gupta, Nikita;
Drory-Retwitzer, Matan;
Barash, Danny;
Sengupta, Supratim

Publication type:

Article

Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3441, doi. 10.1093/bioinformatics/btz114

By:

Ma, Jing;
Karnovsky, Alla;
Afshinnia, Farsad;
Wigginton, Janis;
Rader, Daniel J;
Natarajan, Loki;
Sharma, Kumar;
Porter, Anna C;
Rahman, Mahboob;
He, Jiang;
Hamm, Lee;
Shafi, Tariq;
Gipson, Debbie;
Gadegbeku, Crystal;
Feldman, Harold;
Michailidis, George;
Pennathur, Subramaniam

Publication type:

Article

Explore, edit and leverage genomic annotations using Python GTF toolkit.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3487, doi. 10.1093/bioinformatics/btz116

By:

Lopez, F;
Charbonnier, G;
Kermezli, Y;
Belhocine, M;
Ferré, Q;
Zweig, N;
Aribi, M;
Gonzalez, A;
Spicuglia, S;
Puthier, D

Publication type:

Article

Finding enzyme cofactors in Protein Data Bank.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3510, doi. 10.1093/bioinformatics/btz115

By:

Mukhopadhyay, Abhik;
Borkakoti, Neera;
Pravda, Lukáš;
Tyzack, Jonathan D;
Thornton, Janet M;
Velankar, Sameer

Publication type:

Article

Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3468, doi. 10.1093/bioinformatics/btz113

By:

Khater, Ismail M;
Meng, Fanrui;
Nabi, Ivan Robert;
Hamarneh, Ghassan

Publication type:

Article

SUBSTRA: Supervised Bayesian Patient Stratification.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3263, doi. 10.1093/bioinformatics/btz112

By:

Khakabimamaghani, Sahand;
Kelkar, Yogeshwar D;
Grande, Bruno M;
Morin, Ryan D;
Ester, Martin;
Ziemek, Daniel

Publication type:

Article

DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3329, doi. 10.1093/bioinformatics/btz111

By:

Karimi, Mostafa;
Wu, Di;
Wang, Zhangyang;
Shen, Yang

Publication type:

Article

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE).

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3508, doi. 10.1093/bioinformatics/btz107

By:

Senapathi, Tharindu;
Bray, Simon;
Barnett, Christopher B;
Grüning, Björn;
Naidoo, Kevin J

Publication type:

Article

ST-Steiner: a spatio-temporal gene discovery algorithm.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3433, doi. 10.1093/bioinformatics/btz110

By:

Norman, Utku;
Cicek, A Ercument

Publication type:

Article

rMETL: sensitive mobile element insertion detection with long read realignment.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3484, doi. 10.1093/bioinformatics/btz106

By:

Jiang, Tao;
Liu, Bo;
Li, Junyi;
Wang, Yadong

Publication type:

Article

Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3421, doi. 10.1093/bioinformatics/btz105

By:

Muldoon, Joseph J;
Yu, Jessica S;
Fassia, Mohammad-Kasim;
Bagheri, Neda

Publication type:

Article

Comparison of six breast cancer classifiers using qPCR.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3412, doi. 10.1093/bioinformatics/btz103

By:

Berchtold, Evi;
Vetter, Martina;
Gündert, Melanie;
Csaba, Gergely;
Fathke, Christine;
Ulbrich, Susanne E;
Thomssen, Christoph;
Zimmer, Ralf;
Kantelhardt, Eva J

Publication type:

Article

eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3505, doi. 10.1093/bioinformatics/btz104

By:

Orellana, Laura;
Gustavsson, Johan;
Bergh, Cathrine;
Yoluk, Ozge;
Lindahl, Erik

Publication type:

Article

refineD: improved protein structure refinement using machine learning based restrained relaxation.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3320, doi. 10.1093/bioinformatics/btz101

By:

Bhattacharya, Debswapna

Publication type:

Article

Miso: an R package for multiple isotope labeling assisted metabolomics data analysis.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3524, doi. 10.1093/bioinformatics/btz092

By:

Dong, Yonghui;
Feldberg, Liron;
Aharoni, Asaph

Publication type:

Article

KOnezumi: a web application for automating gene disruption strategies to generate knockout mice.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3479, doi. 10.1093/bioinformatics/btz090

By:

Kuno, Akihiro;
Mizuno, Seiya;
Takahashi, Satoru

Publication type:

Article

Bacterial Feature Finder (BaFF)—a system for extracting features overrepresented in sets of prokaryotic organisms.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3482, doi. 10.1093/bioinformatics/btz099

By:

López-Ibáñez, Javier;
Martín, Laura T;
Chagoyen, Mónica;
Pazos, Florencio

Publication type:

Article

Compositional data network analysis via lasso penalized D-trace loss.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3404, doi. 10.1093/bioinformatics/btz098

By:

Yuan, Huili;
He, Shun;
Deng, Minghua

Publication type:

Article

How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3372, doi. 10.1093/bioinformatics/btz089

By:

Froussios, Kimon;
Schurch, Nick J;
Mackinnon, Katarzyna;
Gierliński, Marek;
Duc, Céline;
Simpson, Gordon G;
Barton, Geoffrey J

Publication type:

Article

mCSEA: detecting subtle differentially methylated regions.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3257, doi. 10.1093/bioinformatics/btz096

By:

Martorell-Marugán, Jordi;
González-Rumayor, Víctor;
Carmona-Sáez, Pedro

Publication type:

Article

Gsmodutils: a python based framework for test-driven genome scale metabolic model development.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3397, doi. 10.1093/bioinformatics/btz088

By:

Gilbert, James;
Pearcy, Nicole;
Norman, Rupert;
Millat, Thomas;
Winzer, Klaus;
King, John;
Hodgman, Charlie;
Minton, Nigel;
Twycross, Jamie

Publication type:

Article

G4Hunter web application: a web server for G-quadruplex prediction.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3493, doi. 10.1093/bioinformatics/btz087

By:

Brázda, Václav;
Kolomazník, Jan;
Lýsek, Jiří;
Bartas, Martin;
Fojta, Miroslav;
Šťastný, Jiří;
Mergny, Jean-Louis

Publication type:

Article

IGLOSS: iterative gapless local similarity search.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3491, doi. 10.1093/bioinformatics/btz086

By:

Rabar, Braslav;
Zagorščak, Maja;
Ristov, Strahil;
Rosenzweig, Martin;
Goldstein, Pavle

Publication type:

Article

Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3489, doi. 10.1093/bioinformatics/btz085

By:

Lima, Diogo B;
Silva, André R F;
Dupré, Mathieu;
Santos, Marlon D M;
Clasen, Milan A;
Kurt, Louise U;
Aquino, Priscila F;
Barbosa, Valmir C;
Carvalho, Paulo C;
Chamot-Rooke, Julia

Publication type:

Article

Multispectral tracing in densely labeled mouse brain with nTracer.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3544, doi. 10.1093/bioinformatics/btz084

By:

Roossien, Douglas H;
Sadis, Benjamin V;
Yan, Yan;
Webb, John M;
Min, Lia Y;
Dizaji, Aslan S;
Bogart, Luke J;
Mazuski, Cristina;
Huth, Robert S;
Stecher, Johanna S;
Akula, Sriakhila;
Shen, Fred;
Li, Ye;
Xiao, Tingxin;
Vandenbrink, Madeleine;
Lichtman, Jeff W;
Hensch, Takao K;
Herzog, Erik D;
Cai, Dawen

Publication type:

Article

Structured crowdsourcing enables convolutional segmentation of histology images.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3461, doi. 10.1093/bioinformatics/btz083

By:

Amgad, Mohamed;
Elfandy, Habiba;
Hussein, Hagar;
Atteya, Lamees A;
Elsebaie, Mai A T;
Elnasr, Lamia S Abo;
Sakr, Rokia A;
Salem, Hazem S E;
Ismail, Ahmed F;
Saad, Anas M;
Ahmed, Joumana;
Elsebaie, Maha A T;
Rahman, Mustafijur;
Ruhban, Inas A;
Elgazar, Nada M;
Alagha, Yahya;
Osman, Mohamed H;
Alhusseiny, Ahmed M;
Khalaf, Mariam M;
Younes, Abo-Alela F

Publication type:

Article

SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3496, doi. 10.1093/bioinformatics/btz081

By:

Kundu, Soumya;
Bansal, Mukul S

Publication type:

Article

ChimeraUGEM: unsupervised gene expression modeling in any given organism.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3365, doi. 10.1093/bioinformatics/btz080

By:

Diament, Alon;
Weiner, Iddo;
Shahar, Noam;
Landman, Shira;
Feldman, Yael;
Atar, Shimshi;
Avitan, Meital;
Schweitzer, Shira;
Yacoby, Iftach;
Tuller, Tamir

Publication type:

Article

Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3217, doi. 10.1093/bioinformatics/btz071

By:

Wren, Jonathan D;
Valencia, Alfonso;
Kelso, Janet

Publication type:

Article

Finding de novo methylated DNA motifs.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3287, doi. 10.1093/bioinformatics/btz079

By:

Ngo, Vu;
Wang, Mengchi;
Wang, Wei

Publication type:

Article

Gag-protease coevolution shapes the outcome of lopinavir-inclusive treatment regimens in chronically infected HIV-1 subtype C patients.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3219, doi. 10.1093/bioinformatics/btz076

By:

Marie, V;
Gordon, M

Publication type:

Article

GLAD: GLycan Array Dashboard, a visual analytics tool for glycan microarrays.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3536, doi. 10.1093/bioinformatics/btz075

By:

Mehta, Akul Y;
Cummings, Richard D

Publication type:

Article

ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3514, doi. 10.1093/bioinformatics/btz073

By:

Dong, Danyue;
Tian, Yuan;
Zheng, Shijie C;
Teschendorff, Andrew E

Publication type:

Article

Assembly Graph Browser: interactive visualization of assembly graphs.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3476, doi. 10.1093/bioinformatics/btz072

By:

Mikheenko, Alla;
Kolmogorov, Mikhail

Publication type:

Article

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3517, doi. 10.1093/bioinformatics/btz078

By:

Papadopoulos, Nikolaos;
Gonzalo, Parra R;
Söding, Johannes

Publication type:

Article

PMC text mining subset in BioC: about three million full-text articles and growing.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3533, doi. 10.1093/bioinformatics/btz070

By:

Comeau, Donald C;
Wei, Chih-Hsuan;
Doğan, Rezarta Islamaj;
Lu, Zhiyong

Publication type:

Article

Aligning optical maps to de Bruijn graphs.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3250, doi. 10.1093/bioinformatics/btz069

By:

Mukherjee, Kingshuk;
Alipanahi, Bahar;
Kahveci, Tamer;
Salmela, Leena;
Boucher, Christina

Publication type:

Article

Rapid alignment-free phylogenetic identification of metagenomic sequences.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3303, doi. 10.1093/bioinformatics/btz068

By:

Linard, Benjamin;
Swenson, Krister;
Pardi, Fabio

Publication type:

Article

DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3240, doi. 10.1093/bioinformatics/btz067

By:

Yang, Yang;
Walker, Timothy M;
Walker, A Sarah;
Wilson, Daniel J;
Peto, Timothy E A;
Crook, Derrick W;
Shamout, Farah;
Consortium, CRyPTIC;
Zhu, Tingting;
Clifton, David A

Publication type:

Article

Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3357, doi. 10.1093/bioinformatics/btz066

By:

Weishaupt, Holger;
Johansson, Patrik;
Sundström, Anders;
Lubovac-Pilav, Zelmina;
Olsson, Björn;
Nelander, Sven;
Swartling, Fredrik J

Publication type:

Article

A unified approach for sparse dynamical system inference from temporal measurements.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3387, doi. 10.1093/bioinformatics/btz065

By:

Pantazis, Yannis;
Tsamardinos, Ioannis

Publication type:

Article

Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3232, doi. 10.1093/bioinformatics/btz064

By:

Mehdi, Tahmid F;
Singh, Gurdeep;
Mitchell, Jennifer A;
Moses, Alan M

Publication type:

Article

Modeling cell proliferation in human acute myeloid leukemia xenografts.

Published in:

Bioinformatics, 2019, v. 35, n. 18, p. 3378, doi. 10.1093/bioinformatics/btz063

By:

Nobile, Marco S;
Vlachou, Thalia;
Spolaor, Simone;
Bossi, Daniela;
Cazzaniga, Paolo;
Lanfrancone, Luisa;
Mauri, Giancarlo;
Pelicci, Pier Giuseppe;
Besozzi, Daniela

Publication type:

Article