Works matching IS 13674803 AND DT 2019 AND VI 35 AND IP 24

Results: 66

MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5397, doi. 10.1093/bioinformatics/btz696

By:

Ma, Anjun;
Sun, Minxuan;
McDermaid, Adam;
Liu, Bingqiang;
Ma, Qin

Publication type:

Article

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5382, doi. 10.1093/bioinformatics/btz604

By:

Morton, Kenneth;
Wang, Patrick;
Bizon, Chris;
Cox, Steven;
Balhoff, James;
Kebede, Yaphet;
Fecho, Karamarie;
Tropsha, Alexander

Publication type:

Article

BLANT—fast graphlet sampling tool.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5363, doi. 10.1093/bioinformatics/btz603

By:

Maharaj, Sridevi;
Tracy, Brennan;
Hayes, Wayne B

Publication type:

Article

VariantQC: a visual quality control report for variant evaluation.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5370, doi. 10.1093/bioinformatics/btz560

By:

Yan, Melissa Y;
Ferguson, Betsy;
Bimber, Benjamin N

Publication type:

Article

scRNABatchQC: multi-samples quality control for single cell RNA-seq data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5306, doi. 10.1093/bioinformatics/btz601

By:

Liu, Qi;
Sheng, Quanhu;
Ping, Jie;
Ramirez, Marisol Adelina;
Lau, Ken S;
Coffey, Robert J;
Shyr, Yu

Publication type:

Article

Sequence tube maps: making graph genomes intuitive to commuters.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5318, doi. 10.1093/bioinformatics/btz597

By:

Beyer, Wolfgang;
Novak, Adam M;
Hickey, Glenn;
Chan, Jeffrey;
Tan, Vanessa;
Paten, Benedict;
Zerbino, Daniel R

Publication type:

Article

geneCo: a visualized comparative genomic method to analyze multiple genome structures.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5303, doi. 10.1093/bioinformatics/btz596

By:

Jung, Jaehee;
Kim, Jong Im;
Yi, Gangman

Publication type:

Article

PyMethylProcess—convenient high-throughput preprocessing workflow for DNA methylation data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5379, doi. 10.1093/bioinformatics/btz594

By:

Levy, Joshua J;
Titus, Alexander J;
Salas, Lucas A;
Christensen, Brock C

Publication type:

Article

MPRAscore: robust and non-parametric analysis of massively parallel reporter assays.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5351, doi. 10.1093/bioinformatics/btz591

By:

Niroula, Abhishek;
Ajore, Ram;
Nilsson, Björn

Publication type:

Article

CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5361, doi. 10.1093/bioinformatics/btz598

By:

Vieira, Vítor;
Rocha, Miguel

Publication type:

Article

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5396, doi. 10.1093/bioinformatics/btz588

By:

Arnedo-Pac, Claudia;
Mularoni, Loris;
Muiños, Ferran;
Gonzalez-Perez, Abel;
Lopez-Bigas, Nuria

Publication type:

Article

SquiggleKit: a toolkit for manipulating nanopore signal data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5372, doi. 10.1093/bioinformatics/btz586

By:

Ferguson, James M;
Smith, Martin A

Publication type:

Article

amplimap: a versatile tool to process and analyze targeted NGS data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5349, doi. 10.1093/bioinformatics/btz582

By:

Koelling, Nils;
Bernkopf, Marie;
Calpena, Eduardo;
Maher, Geoffrey J;
Miller, Kerry A;
Ralph, Hannah K;
Goriely, Anne;
Wilkie, Andrew O M

Publication type:

Article

Predicting promoters in phage genomes using PhagePromoter.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5301, doi. 10.1093/bioinformatics/btz580

By:

Sampaio, Marta;
Rocha, Miguel;
Oliveira, Hugo;
Dias, Oscar

Publication type:

Article

diSTruct v1.0: generating biomolecular structures from distance constraints.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5337, doi. 10.1093/bioinformatics/btz578

By:

Taubert, Oskar;
Reinartz, Ines;
Meyerhenke, Henning;
Schug, Alexander

Publication type:

Article

DISPOT: a simple knowledge-based protein domain interaction statistical potential.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5374, doi. 10.1093/bioinformatics/btz587

By:

Narykov, Oleksandr;
Bogatov, Dmytro;
Korkin, Dmitry

Publication type:

Article

TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5339, doi. 10.1093/bioinformatics/btz573

By:

Puente-Santamaria, Laura;
Wasserman, Wyeth W;
Peso, Luis del

Publication type:

Article

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5315, doi. 10.1093/bioinformatics/btz572

By:

Dijkstra, Maurits J J;
Ploeg, Atze J van der;
Feenstra, K Anton;
Fokkink, Wan J;
Abeln, Sanne;
Heringa, Jaap

Publication type:

Article

sAOP: linking chemical stressors to adverse outcomes pathway networks.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5391, doi. 10.1093/bioinformatics/btz570

By:

Aguayo-Orozco, Alejandro;
Audouze, Karine;
Siggaard, Troels;
Barouki, Robert;
Brunak, Søren;
Taboureau, Olivier

Publication type:

Article

Genetic association testing using the GENESIS R/Bioconductor package.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5346, doi. 10.1093/bioinformatics/btz567

By:

Gogarten, Stephanie M;
Sofer, Tamar;
Chen, Han;
Yu, Chaoyu;
Brody, Jennifer A;
Thornton, Timothy A;
Rice, Kenneth M;
Conomos, Matthew P

Publication type:

Article

The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5359, doi. 10.1093/bioinformatics/btz566

By:

Sands, Caroline J;
Wolfer, Arnaud M;
Correia, Gonçalo D S;
Sadawi, Noureddin;
Ahmed, Arfan;
Jiménez, Beatriz;
Lewis, Matthew R;
Glen, Robert C;
Nicholson, Jeremy K;
Pearce, Jake T M

Publication type:

Article

MEpurity: estimating tumor purity using DNA methylation data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5298, doi. 10.1093/bioinformatics/btz555

By:

Liu, Bowen;
Yang, Xiaofei;
Wang, Tingjie;
Lin, Jiadong;
Kang, Yongyong;
Jia, Peng;
Ye, Kai

Publication type:

Article

MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5321, doi. 10.1093/bioinformatics/btz554

By:

Puttick, Mark N

Publication type:

Article

PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5313, doi. 10.1093/bioinformatics/btz568

By:

Saethang, Thammakorn;
Hodge, Kenneth;
Yang, Chin-Rang;
Zhao, Yue;
Kimkong, Ingorn;
Knepper, Mark A;
Pisitkun, Trairak

Publication type:

Article

VeriNA3d: an R package for nucleic acids data mining.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5334, doi. 10.1093/bioinformatics/btz553

By:

Gallego, Diego;
Darré, Leonardo;
Dans, Pablo D;
Orozco, Modesto

Publication type:

Article

HDX-Viewer: interactive 3D visualization of hydrogen–deuterium exchange data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5331, doi. 10.1093/bioinformatics/btz550

By:

Bouyssié, David;
Lesne, Jean;
Locard-Paulet, Marie;
Albigot, Renaud;
Burlet-Schiltz, Odile;
Marcoux, Julien

Publication type:

Article

DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5328, doi. 10.1093/bioinformatics/btz543

By:

Aureli, Simone;
Marino, Daniele Di;
Raniolo, Stefano;
Limongelli, Vittorio

Publication type:

Article

Benchmarking fold detection by DaliLite v.5.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5326, doi. 10.1093/bioinformatics/btz536

By:

Holm, Liisa

Publication type:

Article

RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5357, doi. 10.1093/bioinformatics/btz534

By:

Chagas, Vinicius S;
Groeneveld, Clarice S;
Oliveira, Kelin G;
Trefflich, Sheyla;
Almeida, Rodrigo C de;
Ponder, Bruce A J;
Meyer, Kerstin B;
Jones, Steven J M;
Robertson, A Gordon;
Castro, Mauro A A

Publication type:

Article

JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5309, doi. 10.1093/bioinformatics/btz533

By:

Tamposis, Ioannis A;
Tsirigos, Konstantinos D;
Theodoropoulou, Margarita C;
Kontou, Panagiota I;
Tsaousis, Georgios N;
Sarantopoulou, Dimitra;
Litou, Zoi I;
Bagos, Pantelis G

Publication type:

Article

ValTrendsDB: bringing Protein Data Bank validation information closer to the user.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5389, doi. 10.1093/bioinformatics/btz532

By:

Horský, Vladimír;
Bendová, Veronika;
Toušek, Dominik;
Koča, Jaroslav;
Svobodová, Radka

Publication type:

Article

CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5341, doi. 10.1093/bioinformatics/btz516

By:

Jang, Yeongjun;
Seo, Jihae;
Jang, Insu;
Lee, Byungwook;
Kim, Sun;
Lee, Sanghyuk

Publication type:

Article

Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5344, doi. 10.1093/bioinformatics/btz526

By:

Hernandez-Ferrer, Carles;
Wellenius, Gregory A;
Tamayo, Ibon;
Basagaña, Xavier;
Sunyer, Jordi;
Vrijheid, Martine;
Gonzalez, Juan R

Publication type:

Article

Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5393, doi. 10.1093/bioinformatics/btz523

By:

Wait, Eric;
Winter, Mark;
Cohen, Andrew R

Publication type:

Article

CytoGPS: a web-enabled karyotype analysis tool for cytogenetics.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5365, doi. 10.1093/bioinformatics/btz520

By:

Abrams, Zachary B;
Zhang, Lin;
Abruzzo, Lynne V;
Heerema, Nyla A;
Li, Suli;
Dillon, Tom;
Rodriguez, Ricky;
Coombes, Kevin R;
Payne, Philip R O

Publication type:

Article

KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5354, doi. 10.1093/bioinformatics/btz519

By:

Li, Zhaojun;
Li, Xutong;
Liu, Xiaohong;
Fu, Zunyun;
Xiong, Zhaoping;
Wu, Xiaolong;
Tan, Xiaoqin;
Zhao, Jihui;
Zhong, Feisheng;
Wan, Xiaozhe;
Luo, Xiaomin;
Chen, Kaixian;
Jiang, Hualiang;
Zheng, Mingyue

Publication type:

Article

TCR3d: The T cell receptor structural repertoire database.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5323, doi. 10.1093/bioinformatics/btz517

By:

Gowthaman, Ragul;
Pierce, Brian G

Publication type:

Article

The NEW ESID online database network.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5367, doi. 10.1093/bioinformatics/btz525

By:

Scheible, Raphael;
Rusch, Stephan;
Guzman, David;
Mahlaoui, Nizar;
Ehl, Stephan;
Kindle, Gerhard

Publication type:

Article

Interactive exploration of heterogeneous biological networks with Biomine Explorer.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5385, doi. 10.1093/bioinformatics/btz509

By:

Podpečan, Vid;
Ramšak, Živa;
Gruden, Kristina;
Toivonen, Hannu;
Lavrač, Nada

Publication type:

Article

DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5128, doi. 10.1093/bioinformatics/btz464

By:

Shi, Qiang;
Chen, Weiya;
Huang, Siqi;
Jin, Fanglin;
Dong, Yinghao;
Wang, Yan;
Xue, Zhidong

Publication type:

Article

New algorithms for detecting multi-effect and multi-way epistatic interactions.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5078, doi. 10.1093/bioinformatics/btz463

By:

Ansarifar, Javad;
Wang, Lizhi

Publication type:

Article

AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5121, doi. 10.1093/bioinformatics/btz459

By:

Zhang, Yuqi;
Sanner, Michel F

Publication type:

Article

Graphlet Laplacians for topology-function and topology-disease relationships.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5226, doi. 10.1093/bioinformatics/btz455

By:

Windels, Sam F L;
Malod-Dognin, Noël;
Pržulj, Nataša

Publication type:

Article

DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5113, doi. 10.1093/bioinformatics/btz454

By:

Pagès, Guillaume;
Grudinin, Sergei

Publication type:

Article

A scalable method for parameter identification in kinetic models of metabolism using steady-state data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5216, doi. 10.1093/bioinformatics/btz445

By:

Srinivasan, Shyam;
Cluett, William R;
Mahadevan, Radhakrishnan

Publication type:

Article

MTTFsite: cross-cell type TF binding site prediction by using multi-task learning.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5067, doi. 10.1093/bioinformatics/btz451

By:

Zhou, Jiyun;
Lu, Qin;
Gui, Lin;
Xu, Ruifeng;
Long, Yunfei;
Wang, Hongpeng

Publication type:

Article

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5103, doi. 10.1093/bioinformatics/btz449

By:

Xue, Albert Y;
Yu, Angela M;
Lucks, Julius B;
Bagheri, Neda

Publication type:

Article

Improving data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5257, doi. 10.1093/bioinformatics/btz421

By:

Morais, Camilo L M;
Santos, Marfran C D;
Lima, Kássio M G;
Martin, Francis L

Publication type:

Article

Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5146, doi. 10.1093/bioinformatics/btz447

By:

Zyla, Joanna;
Marczyk, Michal;
Domaszewska, Teresa;
Kaufmann, Stefan H E;
Polanska, Joanna;
Weiner, January

Publication type:

Article

DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5155, doi. 10.1093/bioinformatics/btz453

By:

Ye, Chengzhong;
Speed, Terence P;
Salim, Agus

Publication type:

Article