Works matching IS 13674803 AND DT 2020 AND VI 36 AND IP 4

Results: 61

Thermodynamically consistent estimation of Gibbs free energy from data: data reconciliation approach.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1219, doi. 10.1093/bioinformatics/btz741

By:

Salike, Saman;
Bhatt, Nirav

Publication type:

Article

EvoEF2: accurate and fast energy function for computational protein design.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1135, doi. 10.1093/bioinformatics/btz740

By:

Huang, Xiaoqiang;
Zhang, Yang

Publication type:

Article

SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1074, doi. 10.1093/bioinformatics/btz734

By:

Yu, Bin;
Qiu, Wenying;
Chen, Cheng;
Ma, Anjun;
Jiang, Jing;
Zhou, Hongyan;
Ma, Qin

Publication type:

Article

Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1030, doi. 10.1093/bioinformatics/btz733

By:

Li, Ziwei;
He, Bo;
Feng, Weixing

Publication type:

Article

The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1296, doi. 10.1093/bioinformatics/btz732

By:

Bender, Julian;
Schmidt, Carla

Publication type:

Article

Hexa-Longin domain scaffolds for inter-Rab signalling.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 990, doi. 10.1093/bioinformatics/btz739

By:

Sanchez-Pulido, Luis;
Ponting, Chris P

Publication type:

Article

Topology-based classification of tetrads and quadruplex structures.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1129, doi. 10.1093/bioinformatics/btz738

By:

Popenda, Mariusz;
Miskiewicz, Joanna;
Sarzynska, Joanna;
Zok, Tomasz;
Szachniuk, Marta

Publication type:

Article

Metric learning on expression data for gene function prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1182, doi. 10.1093/bioinformatics/btz731

By:

Makrodimitris, Stavros;
Reinders, Marcel J T;
Ham, Roeland C H J van

Publication type:

Article

Meltos: multi-sample tumor phylogeny reconstruction for structural variants.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1082, doi. 10.1093/bioinformatics/btz737

By:

Ricketts, Camir;
Seidman, Daniel;
Popic, Victoria;
Hormozdiari, Fereydoun;
Batzoglou, Serafim;
Hajirasouliha, Iman

Publication type:

Article

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1213, doi. 10.1093/bioinformatics/btz736

By:

Li, Yuanyue;
Kuhn, Michael;
Gavin, Anne-Claude;
Bork, Peer

Publication type:

Article

simurg: simulate bacterial pangenomes in R.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1273, doi. 10.1093/bioinformatics/btz735

By:

Ferrés, Ignacio;
Fresia, Pablo;
Iraola, Gregorio

Publication type:

Article

A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1066, doi. 10.1093/bioinformatics/btz725

By:

Liu, Sen;
Wang, Yuping;
Tong, Wuning;
Wei, Shiwei

Publication type:

Article

CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1208, doi. 10.1093/bioinformatics/btz730

By:

Parsons, Rex;
Parsons, Richard;
Garner, Nicholas;
Oster, Henrik;
Rawashdeh, Oliver

Publication type:

Article

Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1252, doi. 10.1093/bioinformatics/btz728

By:

Yao, Ruijie;
Qian, Jiaqiang;
Huang, Qiang

Publication type:

Article

T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1191, doi. 10.1093/bioinformatics/btz727

By:

Bogaerts-Márquez, María;
Barrón, Maite G;
Fiston-Lavier, Anna-Sophie;
Vendrell-Mir, Pol;
Castanera, Raúl;
Casacuberta, Josep M;
González, Josefa

Publication type:

Article

bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1174, doi. 10.1093/bioinformatics/btz726

By:

Tang, Wenhao;
Bertaux, François;
Thomas, Philipp;
Stefanelli, Claire;
Saint, Malika;
Marguerat, Samuel;
Shahrezaei, Vahid

Publication type:

Article

L1EM: a tool for accurate locus specific LINE-1 RNA quantification.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1167, doi. 10.1093/bioinformatics/btz724

By:

McKerrow, Wilson;
Fenyö, David

Publication type:

Article

Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 985, doi. 10.1093/bioinformatics/btz729

By:

Goig, Galo A;
Torres-Puente, Manuela;
Mariner-Llicer, Carla;
Villamayor, Luis M;
Chiner-Oms, Álvaro;
Gil-Brusola, Ana;
Borrás, Rafael;
Espadas, Iñaki Comas

Publication type:

Article

phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1289, doi. 10.1093/bioinformatics/btz722

By:

Bradley, Patrick H;
Pollard, Katherine S

Publication type:

Article

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1057, doi. 10.1093/bioinformatics/btz721

By:

Li, Fuyi;
Chen, Jinxiang;
Leier, André;
Marquez-Lago, Tatiana;
Liu, Quanzhong;
Wang, Yanze;
Revote, Jerico;
Smith, A Ian;
Akutsu, Tatsuya;
Webb, Geoffrey I;
Kurgan, Lukasz;
Song, Jiangning

Publication type:

Article

ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1270, doi. 10.1093/bioinformatics/btz720

By:

Jin, Hongjian;
Kasper, Lawryn H;
Larson, Jon D;
Wu, Gang;
Baker, Suzanne J;
Zhang, Jinghui;
Fan, Yiping

Publication type:

Article

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1267, doi. 10.1093/bioinformatics/btz719

By:

Bolognini, Davide;
Sanders, Ashley;
Korbel, Jan O;
Magi, Alberto;
Benes, Vladimir;
Rausch, Tobias

Publication type:

Article

Graph embedding on biomedical networks: methods, applications and evaluations.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1241, doi. 10.1093/bioinformatics/btz718

By:

Yue, Xiang;
Wang, Zhen;
Huang, Jingong;
Parthasarathy, Srinivasan;
Moosavinasab, Soheil;
Huang, Yungui;
Lin, Simon M;
Zhang, Wen;
Zhang, Ping;
Sun, Huan

Publication type:

Article

MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1300, doi. 10.1093/bioinformatics/btz717

By:

Trullo, A;
Dufourt, J;
Lagha, M

Publication type:

Article

VikNGS: a C++ variant integration kit for next generation sequencing association analysis.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1283, doi. 10.1093/bioinformatics/btz716

By:

Baskurt, Zeynep;
Mastromatteo, Scott;
Gong, Jiafen;
Wintle, Richard F;
Scherer, Stephen W;
Strug, Lisa J

Publication type:

Article

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1303, doi. 10.1093/bioinformatics/btz715

By:

Breitwieser, Florian P;
Salzberg, Steven L

Publication type:

Article

AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1022, doi. 10.1093/bioinformatics/btz714

By:

Korandla, Deepank R;
Wozniak, Jacob M;
Campeau, Anaamika;
Gonzalez, David J;
Wright, Erik S

Publication type:

Article

SCSsim: an integrated tool for simulating single-cell genome sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1281, doi. 10.1093/bioinformatics/btz713

By:

Yu, Zhenhua;
Du, Fang;
Sun, Xuehong;
Li, Ao

Publication type:

Article

MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1293, doi. 10.1093/bioinformatics/btz712

By:

Fang, Chao;
Li, Zhaoyu;
Xu, Dong;
Shang, Yi

Publication type:

Article

Chordomics: a visualization tool for linking function to phylogeny in microbiomes.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1309, doi. 10.1093/bioinformatics/btz711

By:

McDonnell, Kevin;
Waters, Nicholas;
Howley, Enda;
Abram, Florence

Publication type:

Article

Set cover-based methods for motif selection.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1044, doi. 10.1093/bioinformatics/btz697

By:

Li, Yichao;
Liu, Yating;
Juedes, David;
Drews, Frank;
Bunescu, Razvan;
Welch, Lonnie

Publication type:

Article

DeepMSPeptide: peptide detectability prediction using deep learning.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1279, doi. 10.1093/bioinformatics/btz708

By:

Serrano, Guillermo;
Guruceaga, Elizabeth;
Segura, Victor

Publication type:

Article

scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1262, doi. 10.1093/bioinformatics/btz701

By:

Ye, Congting;
Zhou, Qian;
Wu, Xiaohui;
Yu, Chen;
Ji, Guoli;
Saban, Daniel R;
Li, Qingshun Q

Publication type:

Article

hypeR: an R package for geneset enrichment workflows.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1307, doi. 10.1093/bioinformatics/btz700

By:

Federico, Anthony;
Monti, Stefano

Publication type:

Article

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1286, doi. 10.1093/bioinformatics/btz710

By:

Davín, Adrián A;
Tricou, Théo;
Tannier, Eric;
Vienne, Damien M de;
Szöllősi, Gergely J

Publication type:

Article

Protein–protein interaction site prediction through combining local and global features with deep neural networks.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1114, doi. 10.1093/bioinformatics/btz699

By:

Zeng, Min;
Zhang, Fuhao;
Wu, Fang-Xiang;
Li, Yaohang;
Wang, Jianxin;
Li, Min

Publication type:

Article

Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 994, doi. 10.1093/bioinformatics/btz709

By:

Zhu, Qian;
Tekpli, Xavier;
Troyanskaya, Olga G;
Kristensen, Vessela N

Publication type:

Article

scds: computational annotation of doublets in single-cell RNA sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1150, doi. 10.1093/bioinformatics/btz698

By:

Bais, Abha S;
Kostka, Dennis

Publication type:

Article

PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1052, doi. 10.1093/bioinformatics/btz707

By:

Qing, Xue;
Wang, Meng;
Karssen, Gerrit;
Bucki, Patricia;
Bert, Wim;
Braun-Miyara, Sigal

Publication type:

Article

EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1265, doi. 10.1093/bioinformatics/btz706

By:

Marcet-Houben, Marina;
Gabaldón, Toni

Publication type:

Article

Spectrum: fast density-aware spectral clustering for single and multi-omic data.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1159, doi. 10.1093/bioinformatics/btz704

By:

John, Christopher R;
Watson, David;
Barnes, Michael R;
Pitzalis, Costantino;
Lewis, Myles J

Publication type:

Article

Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1121, doi. 10.1093/bioinformatics/btz703

By:

Alam, Tanvir;
Alazmi, Meshari;
Naser, Rayan;
Huser, Franceline;
Momin, Afaque A;
Astro, Veronica;
Hong, SeungBeom;
Walkiewicz, Katarzyna W;
Canlas, Christian G;
Huser, Raphaël;
Ali, Amal J;
Merzaban, Jasmeen;
Adamo, Antonio;
Jaremko, Mariusz;
Jaremko, Łukasz;
Bajic, Vladimir B;
Gao, Xin;
Arold, Stefan T

Publication type:

Article

EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1014, doi. 10.1093/bioinformatics/btz702

By:

Harmanci, Arif;
Harmanci, Akdes Serin;
Swaminathan, Jyothishmathi;
Gopalakrishnan, Vidya

Publication type:

Article

NERDD: a web portal providing access to in silico tools for drug discovery.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1291, doi. 10.1093/bioinformatics/btz695

By:

Stork, Conrad;
Embruch, Gerd;
Šícho, Martin;
Kops, Christina de Bruyn;
Chen, Ya;
Svozil, Daniel;
Kirchmair, Johannes

Publication type:

Article

Identifying enhancer–promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1037, doi. 10.1093/bioinformatics/btz694

By:

Hong, Zengyan;
Zeng, Xiangxiang;
Wei, Leyi;
Liu, Xiangrong

Publication type:

Article

XMAn v2—a database of Homo sapiens mutated peptides.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1311, doi. 10.1093/bioinformatics/btz693

By:

Flores, Marcela Aguilera;
Lazar, Iulia M

Publication type:

Article

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1260, doi. 10.1093/bioinformatics/btz681

By:

Porubsky, David;
Sanders, Ashley D;
Taudt, Aaron;
Colomé-Tatché, Maria;
Lansdorp, Peter M;
Guryev, Victor

Publication type:

Article

Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1107, doi. 10.1093/bioinformatics/btz691

By:

Hanson, Jack;
Litfin, Thomas;
Paliwal, Kuldip;
Zhou, Yaoqi

Publication type:

Article

VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1277, doi. 10.1093/bioinformatics/btz689

By:

Wang, Jun;
Du, Pu-Feng;
Xue, Xin-Yu;
Li, Guang-Ping;
Zhou, Yuan-Ke;
Zhao, Wei;
Lin, Hao;
Chen, Wei

Publication type:

Article

Non-homogeneous dynamic Bayesian networks with edge-wise sequentially coupled parameters.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1198, doi. 10.1093/bioinformatics/btz690

By:

Kamalabad, Mahdi Shafiee;
Grzegorczyk, Marco

Publication type:

Article