Works matching IS 13674803 AND DT 2020 AND VI 36 AND IP 3

Results: 61

DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 942, doi. 10.1093/bioinformatics/btz677

By:

Li, Tingyang;
Tripathi, Ashootosh;
Yu, Fengan;
Sherman, David H;
Rao, Arvind

Publication type:

Article

A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 880, doi. 10.1093/bioinformatics/btz673

By:

Kumar, Ashwani;
Hosseinnia, Ali;
Gagarinova, Alla;
Phanse, Sadhna;
Kim, Sunyoung;
Aly, Khaled A;
Zilles, Sandra;
Babu, Mohan

Publication type:

Article

Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 742, doi. 10.1093/bioinformatics/btz676

By:

Wu, Yufeng

Publication type:

Article

Automatic local resolution-based sharpening of cryo-EM maps.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 765, doi. 10.1093/bioinformatics/btz671

By:

Ramírez-Aportela, Erney;
Vilas, Jose Luis;
Glukhova, Alisa;
Melero, Roberto;
Conesa, Pablo;
Martínez, Marta;
Maluenda, David;
Mota, Javier;
Jiménez, Amaya;
Vargas, Javier;
Marabini, Roberto;
Sexton, Patrick M;
Carazo, Jose Maria;
Sorzano, Carlos Oscar S

Publication type:

Article

Partition: a surjective mapping approach for dimensionality reduction.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 676, doi. 10.1093/bioinformatics/btz661

By:

Millstein, Joshua;
Battaglin, Francesca;
Barrett, Malcolm;
Cao, Shu;
Zhang, Wu;
Stintzing, Sebastian;
Heinemann, Volker;
Lenz, Heinz-Josef

Publication type:

Article

CRDS: Consensus Reverse Docking System for target fishing.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 959, doi. 10.1093/bioinformatics/btz656

By:

Lee, Aeri;
Kim, Dongsup

Publication type:

Article

Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 910, doi. 10.1093/bioinformatics/btz674

By:

Rossetti, Blair J;
Wilbert, Steven A;
Welch, Jessica L Mark;
Borisy, Gary G;
Nagy, James G

Publication type:

Article

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 698, doi. 10.1093/bioinformatics/btz675

By:

Desvignes, Thomas;
Loher, Phillipe;
Eilbeck, Karen;
Ma, Jeffery;
Urgese, Gianvito;
Fromm, Bastian;
Sydes, Jason;
Aparicio-Puerta, Ernesto;
Barrera, Victor;
Espín, Roderic;
Thibord, Florian;
Ros, Xavier Bofill-De;
Londin, Eric;
Telonis, Aristeidis G;
Ficarra, Elisa;
Friedländer, Marc R;
Postlethwait, John H;
Rigoutsos, Isidore;
Hackenberg, Michael;
Vlachos, Ioannis S

Publication type:

Article

Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 819, doi. 10.1093/bioinformatics/btz672

By:

Chen, Ziyi;
Ji, Chengyang;
Shen, Qin;
Liu, Wei;
Qin, F Xiao-Feng;
Wu, Aiping

Publication type:

Article

ChaperISM: improved chaperone binding prediction using position-independent scoring matrices.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 735, doi. 10.1093/bioinformatics/btz670

By:

Gutierres, M B B;
Bonorino, C B C;
Rigo, M M

Publication type:

Article

Regulatory annotation of genomic intervals based on tissue-specific expression QTLs.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 690, doi. 10.1093/bioinformatics/btz669

By:

Xu, Tianlei;
Jin, Peng;
Qin, Zhaohui S

Publication type:

Article

miComplete: weighted quality evaluation of assembled microbial genomes.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 936, doi. 10.1093/bioinformatics/btz664

By:

Hugoson, Eric;
Lam, Wai Tin;
Guy, Lionel

Publication type:

Article

pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 961, doi. 10.1093/bioinformatics/btz657

By:

Lee, Yoonji;
Baumhardt, Jordan M;
Pei, Jimin;
Chook, Yuh Min;
Grishin, Nick V

Publication type:

Article

A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 842, doi. 10.1093/bioinformatics/btz667

By:

Peng, Cheng;
Wang, Jun;
Asante, Isaac;
Louie, Stan;
Jin, Ran;
Chatzi, Lida;
Casey, Graham;
Thomas, Duncan C;
Conti, David V

Publication type:

Article

Accurate estimation of microbial sequence diversity with Distanced.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 728, doi. 10.1093/bioinformatics/btz668

By:

Hackmann, Timothy J

Publication type:

Article

CROSSalive: a web server for predicting the in vivo structure of RNA molecules.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 940, doi. 10.1093/bioinformatics/btz666

By:

Ponti, Riccardo Delli;
Armaos, Alexandros;
Vandelli, Andrea;
Tartaglia, Gian Gaetano

Publication type:

Article

MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 872, doi. 10.1093/bioinformatics/btz655

By:

Ahmed, Rafsan;
Baali, Ilyes;
Erten, Cesim;
Hoxha, Evis;
Kazan, Hilal

Publication type:

Article

Learning from the ligand: using ligand-based features to improve binding affinity prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 758, doi. 10.1093/bioinformatics/btz665

By:

Boyles, Fergus;
Deane, Charlotte M;
Morris, Garrett M

Publication type:

Article

HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 938, doi. 10.1093/bioinformatics/btz654

By:

Whitwell, Harry J;
DiMaggio, Peter

Publication type:

Article

Fast and accurate correction of optical mapping data via spaced seeds.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 682, doi. 10.1093/bioinformatics/btz663

By:

Salmela, Leena;
Mukherjee, Kingshuk;
Puglisi, Simon J;
Muggli, Martin D;
Boucher, Christina

Publication type:

Article

Improved representation of sequence bloom trees.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 721, doi. 10.1093/bioinformatics/btz662

By:

Harris, Robert S;
Medvedev, Paul

Publication type:

Article

A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 828, doi. 10.1093/bioinformatics/btz660

By:

Moreno-Mayar, J Víctor;
Korneliussen, Thorfinn Sand;
Dalal, Jyoti;
Renaud, Gabriel;
Albrechtsen, Anders;
Nielsen, Rasmus;
Malaspinas, Anna-Sapfo

Publication type:

Article

COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 982, doi. 10.1093/bioinformatics/btz658

By:

Lose, Thoba;
Heusden, Peter van;
Christoffels, Alan

Publication type:

Article

EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 976, doi. 10.1093/bioinformatics/btz659

By:

Bartolome, Jordi;
Alves, Rui;
Solsona, Francesc;
Teixido, Ivan

Publication type:

Article

neoepiscope improves neoepitope prediction with multivariant phasing.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 713, doi. 10.1093/bioinformatics/btz653

By:

Wood, Mary A;
Nguyen, Austin;
Struck, Adam J;
Ellrott, Kyle;
Nellore, Abhinav;
Thompson, Reid F

Publication type:

Article

Gene relevance based on multiple evidences in complex networks.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 865, doi. 10.1093/bioinformatics/btz652

By:

Nanni, Noemi Di;
Gnocchi, Matteo;
Moscatelli, Marco;
Milanesi, Luciano;
Mosca, Ettore

Publication type:

Article

Accurate loop calling for 3D genomic data with cLoops.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 666, doi. 10.1093/bioinformatics/btz651

By:

Cao, Yaqiang;
Chen, Zhaoxiong;
Chen, Xingwei;
Ai, Daosheng;
Chen, Guoyu;
McDermott, Joseph;
Huang, Yi;
Guo, Xiaoxiao;
Han, Jing-Dong J

Publication type:

Article

NExUS: Bayesian simultaneous network estimation across unequal sample sizes.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 798, doi. 10.1093/bioinformatics/btz636

By:

Das, Priyam;
Peterson, Christine B;
Do, Kim-Anh;
Akbani, Rehan;
Baladandayuthapani, Veerabhadran

Publication type:

Article

MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 956, doi. 10.1093/bioinformatics/btz649

By:

Marcos-Alcalde, Iñigo;
López-Viñas, Eduardo;
Gómez-Puertas, Paulino

Publication type:

Article

MeLAD: an integrated resource for metalloenzyme-ligand associations.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 904, doi. 10.1093/bioinformatics/btz648

By:

Li, Gen;
Su, Yu;
Yan, Yu-Hang;
Peng, Jia-Yi;
Dai, Qing-Qing;
Ning, Xiang-Li;
Zhu, Cheng-Long;
Fu, Chen;
McDonough, Michael A;
Schofield, Christopher J;
Huang, Cheng;
Li, Guo-Bo

Publication type:

Article

NACHO: an R package for quality control of NanoString nCounter data.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 970, doi. 10.1093/bioinformatics/btz647

By:

Canouil, Mickaël;
Bouland, Gerard A;
Bonnefond, Amélie;
Froguel, Philippe;
Hart, Leen M 't;
Slieker, Roderick C

Publication type:

Article

StrainHub: a phylogenetic tool to construct pathogen transmission networks.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 945, doi. 10.1093/bioinformatics/btz646

By:

Schneider, Adriano de Bernardi;
Ford, Colby T;
Hostager, Reilly;
Williams, John;
Cioce, Michael;
Çatalyürek, Ümit V;
Wertheim, Joel O;
Janies, Daniel

Publication type:

Article

DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 813, doi. 10.1093/bioinformatics/btz645

By:

Woo, Godwin;
Fernandez, Michael;
Hsing, Michael;
Lack, Nathan A;
Cavga, Ayse Derya;
Cherkasov, Artem

Publication type:

Article

Knot_pull—python package for biopolymer smoothing and knot detection.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 953, doi. 10.1093/bioinformatics/btz644

By:

Jarmolinska, Aleksandra I;
Gambin, Anna;
Sulkowska, Joanna I

Publication type:

Article

baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 966, doi. 10.1093/bioinformatics/btz643

By:

Ozuna, A;
Liberto, D;
Joyce, R M;
Arnvig, K B;
Nobeli, I

Publication type:

Article

Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 805, doi. 10.1093/bioinformatics/btz640

By:

Deng, Wenjiang;
Mou, Tian;
Kalari, Krishna R;
Niu, Nifang;
Wang, Liewei;
Pawitan, Yudi;
Vu, Trung Nghia

Publication type:

Article

LightDock goes information-driven.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 950, doi. 10.1093/bioinformatics/btz642

By:

Roel-Touris, Jorge;
Bonvin, Alexandre M J J;
Jiménez-García, Brian

Publication type:

Article

Machine learning empowers phosphoproteome prediction in cancers.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 859, doi. 10.1093/bioinformatics/btz639

By:

Li, Hongyang;
Guan, Yuanfang

Publication type:

Article

AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 978, doi. 10.1093/bioinformatics/btz638

By:

Stolbov, Leonid;
Druzhilovskiy, Dmitry;
Rudik, Anastasia;
Filimonov, Dmitry;
Poroikov, Vladimir;
Nicklaus, Marc

Publication type:

Article

U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 974, doi. 10.1093/bioinformatics/btz637

By:

Gao, Zheng;
Terhorst, Jonathan;
Hout, Cristopher V Van;
Stoev, Stilian

Publication type:

Article

Tersect: a set theoretical utility for exploring sequence variant data.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 934, doi. 10.1093/bioinformatics/btz634

By:

Kurowski, Tomasz J;
Mohareb, Fady

Publication type:

Article

RICOPILI: Rapid Imputation for COnsortias PIpeLIne.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 930, doi. 10.1093/bioinformatics/btz633

By:

Lam, Max;
Awasthi, Swapnil;
Watson, Hunna J;
Goldstein, Jackie;
Panagiotaropoulou, Georgia;
Trubetskoy, Vassily;
Karlsson, Robert;
Frei, Oleksander;
Fan, Chun-Chieh;
Witte, Ward De;
Mota, Nina R;
Mullins, Niamh;
Brügger, Kim;
Lee, S Hong;
Wray, Naomi R;
Skarabis, Nora;
Huang, Hailiang;
Neale, Benjamin;
Daly, Mark J;
Mattheisen, Manuel

Publication type:

Article

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 972, doi. 10.1093/bioinformatics/btz632

By:

Silva, Vinicius da;
Ramos, Marcel;
Groenen, Martien;
Crooijmans, Richard;
Johansson, Anna;
Regitano, Luciana;
Coutinho, Luiz;
Zimmer, Ralf;
Waldron, Levi;
Geistlinger, Ludwig

Publication type:

Article

G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 928, doi. 10.1093/bioinformatics/btz631

By:

Guo, Xin;
Zhang, Bo;
Zeng, Wenqi;
Zhao, Shuting;
Ge, Dongliang

Publication type:

Article

A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 653, doi. 10.1093/bioinformatics/btz630

By:

Wang, Ya;
Qian, Min;
Tang, Deliang;
Herbstman, Julie;
Perera, Frederica;
Wang, Shuang

Publication type:

Article

pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 660, doi. 10.1093/bioinformatics/btz635

By:

Chung, Ren-Hua;
Kang, Chen-Yu

Publication type:

Article

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 704, doi. 10.1093/bioinformatics/btz629

By:

Zhang, Yanju;
Yu, Sha;
Xie, Ruopeng;
Li, Jiahui;
Leier, André;
Marquez-Lago, Tatiana T;
Akutsu, Tatsuya;
Smith, A Ian;
Ge, Zongyuan;
Wang, Jiawei;
Lithgow, Trevor;
Song, Jiangning

Publication type:

Article

KRAB ZNF explorer—the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 980, doi. 10.1093/bioinformatics/btz624

By:

Cylwa, Rafał;
Kiełczewski, Kornel;
Machnik, Marta;
Oleksiewicz, Urszula;
Biecek, Przemysław

Publication type:

Article

Integrating ab initio and template-based algorithms for protein–protein complex structure prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 751, doi. 10.1093/bioinformatics/btz623

By:

Vangaveti, Sweta;
Vreven, Thom;
Zhang, Yang;
Weng, Zhiping

Publication type:

Article

Protein Homeostasis Database: protein quality control in E.coli.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 948, doi. 10.1093/bioinformatics/btz628

By:

Ramakrishnan, Reshmi;
Houben, Bert;
Kreft, Łukasz;
Botzki, Alexander;
Schymkowitz, Joost;
Rousseau, Frederic

Publication type:

Article