Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 19

Results: 53

Corrigendum to: Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3387, doi. 10.1093/bioinformatics/btab610

By:

Nlebedim, Valentine U;
Chaudhuri, Roy R;
Walters, Kevin

Publication type:

Article

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3120, doi. 10.1093/bioinformatics/btab354

By:

Huang, Neng;
Nie, Fan;
Ni, Peng;
Luo, Feng;
Gao, Xin;
Wang, Jianxin

Publication type:

Article

KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3277, doi. 10.1093/bioinformatics/btab351

By:

Ignatieva, Anastasia;
Lyngsø, Rune B;
Jenkins, Paul A;
Hein, Jotun

Publication type:

Article

VIRUSBreakend: Viral Integration Recognition Using Single Breakends.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3115, doi. 10.1093/bioinformatics/btab343

By:

Cameron, Daniel L;
Jacobs, Nina;
Roepman, Paul;
Priestley, Peter;
Cuppen, Edwin;
Papenfuss, Anthony T

Publication type:

Article

High-complexity regions in mammalian genomes are enriched for developmental genes.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3388, doi. 10.1093/bioinformatics/btab639

By:

Pirogov, Anton;
Pfaffelhuber, Peter;
Börsch-Haubold, Angelika;
Haubold, Bernhard

Publication type:

Article

Erratum to: abPOA: an SIMD-based C library for fast partial order alignment using adaptive band.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3384, doi. 10.1093/bioinformatics/btab587

By:

Gao, Yan;
Liu, Yongzhuang;
Ma, Yanmei;
Liu, Bo;
Wang, Yadong;
Xing, Yi

Publication type:

Article

Corrigendum to: Utilizing image and caption information for biomedical document classification.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3389, doi. 10.1093/bioinformatics/btab568

By:

Li, Pengyuan;
Jiang, Xiangying;
Zhang, Gongbo;
Trabucco, Juan Trelles;
Raciti, Daniela;
Smith, Cynthia;
Ringwald, Martin;
Marai, G Elisabeta;
Arighi, Cecilia;
Shatkay, Hagit

Publication type:

Article

Improving deep learning-based protein distance prediction in CASP14.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3190, doi. 10.1093/bioinformatics/btab355

By:

Guo, Zhiye;
Wu, Tianqi;
Liu, Jian;
Hou, Jie;
Cheng, Jianlin

Publication type:

Article

topology of data: opportunities for cancer research.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3091, doi. 10.1093/bioinformatics/btab553

By:

Loughrey, Ciara F;
Fitzpatrick, Padraig;
Orr, Nick;
Jurek-Loughrey, Anna

Publication type:

Article

Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3386, doi. 10.1093/bioinformatics/btab510

By:

Chen, Jia-Bin;
Dong, Shan-Shan;
Yao, Shi;
Duan, Yuan-Yuan;
Hu, Wei-Xin;
Chen, Hao;
Wang, Nai-Ning;
Chen, Xiao-Feng;
Hao, Ruo-Han;
Thynn, Hlaing Nwe;
Guo, Ming-Rui;
Zhang, Yu-Jie;
Rong, Yu;
Chen, Yi-Xiao;
Zhou, Fu-Ling;
Guo, Yan;
Yang, Tie-Lin

Publication type:

Article

CLEP: a hybrid data- and knowledge-driven framework for generating patient representations.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3311, doi. 10.1093/bioinformatics/btab340

By:

Bharadhwaj, Vinay Srinivas;
Ali, Mehdi;
Birkenbihl, Colin;
Mubeen, Sarah;
Lehmann, Jens;
Hofmann-Apitius, Martin;
Hoyt, Charles Tapley;
Domingo-Fernández, Daniel

Publication type:

Article

ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3152, doi. 10.1093/bioinformatics/btab339

By:

Hu, Fengyuan;
Lu, Jia;
Matheson, Louise S;
Díaz-Muñoz, Manuel D;
Saveliev, Alexander;
Xu, Jinbo;
Turner, Martin

Publication type:

Article

Alignment free sequence comparison methods and reservoir host prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3337, doi. 10.1093/bioinformatics/btab338

By:

Lee, Bill;
Smith, David K;
Guan, Yi

Publication type:

Article

Differential gene expression analysis for multi-subject single-cell RNA-sequencing studies with aggregateBioVar.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3243, doi. 10.1093/bioinformatics/btab337

By:

Thurman, Andrew L;
Ratcliff, Jason A;
Chimenti, Michael S;
Pezzulo, Alejandro A

Publication type:

Article

iCircDA-LTR: identification of circRNA–disease associations based on Learning to Rank.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3302, doi. 10.1093/bioinformatics/btab334

By:

Wei, Hang;
Xu, Yong;
Liu, Bin

Publication type:

Article

Study of real-valued distance prediction for protein structure prediction with deep learning.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3197, doi. 10.1093/bioinformatics/btab333

By:

Li, Jin;
Xu, Jinbo

Publication type:

Article

Reactome and the Gene Ontology: digital convergence of data resources.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3343, doi. 10.1093/bioinformatics/btab325

By:

Good, Benjamin M;
Auken, Kimberly Van;
Hill, David P;
Mi, Huaiyu;
Carbon, Seth;
Balhoff, James P;
Albou, Laurent-Philippe;
Thomas, Paul D;
Mungall, Christopher J;
Blake, Judith A;
D'Eustachio, Peter

Publication type:

Article

Feature-weighted ordinal classification for predicting drug response in multiple myeloma.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3270, doi. 10.1093/bioinformatics/btab320

By:

Ma, Ziyang;
Ahn, Jeongyoun

Publication type:

Article

MAT2: manifold alignment of single-cell transcriptomes with cell triplets.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3263, doi. 10.1093/bioinformatics/btab250

By:

Zhang, Jinglong;
Zhang, Xu;
Wang, Ying;
Zeng, Feng;
Zhao, Xing-Ming

Publication type:

Article

Clustering single-cell RNA-seq data by rank constrained similarity learning.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3235, doi. 10.1093/bioinformatics/btab276

By:

Mei, Qinglin;
Li, Guojun;
Su, Zhengchang

Publication type:

Article

MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3144, doi. 10.1093/bioinformatics/btab249

By:

Apostolides, Michael;
Jiang, Yue;
Husić, Mia;
Siddaway, Robert;
Hawkins, Cynthia;
Turinsky, Andrei L;
Brudno, Michael;
Ramani, Arun K

Publication type:

Article

PrecisionProDB: improving the proteomics performance for precision medicine.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3361, doi. 10.1093/bioinformatics/btab218

By:

Cao, Xiaolong;
Xing, Jinchuan

Publication type:

Article

pDriver: a novel method for unravelling personalized coding and miRNA cancer drivers.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3285, doi. 10.1093/bioinformatics/btab262

By:

Pham, Vu V H;
Liu, Lin;
Bracken, Cameron P;
Nguyen, Thin;
Goodall, Gregory J;
Li, Jiuyong;
Le, Thuc D

Publication type:

Article

RVAgene: generative modeling of gene expression time series data.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3252, doi. 10.1093/bioinformatics/btab260

By:

Mitra, Raktim;
MacLean, Adam L

Publication type:

Article

CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3385, doi. 10.1093/bioinformatics/btab258

By:

Ovchinnikov, Alexey;
Verona, Isabel Pérez;
Pogudin, Gleb;
Tribastone, Mirco

Publication type:

Article

Identification of cell-type-specific marker genes from co-expression patterns in tissue samples.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3228, doi. 10.1093/bioinformatics/btab257

By:

Qiu, Yixuan;
Wang, Jiebiao;
Lei, Jing;
Roeder, Kathryn

Publication type:

Article

Cooperative sequence clustering and decoding for DNA storage system with fountain codes.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3136, doi. 10.1093/bioinformatics/btab246

By:

Jeong, Jaeho;
Park, Seong-Joon;
Kim, Jae-Won;
No, Jong-Seon;
Jeon, Ha Hyeon;
Lee, Jeong Wook;
No, Albert;
Kim, Sunghwan;
Park, Hosung

Publication type:

Article

MaveRegistry: a collaboration platform for multiplexed assays of variant effect.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3382, doi. 10.1093/bioinformatics/btab215

By:

Kuang, Da;
Weile, Jochen;
Kishore, Nishka;
Nguyen, Maria;
Rubin, Alan F;
Fields, Stanley;
Fowler, Douglas M;
Roth, Frederick P

Publication type:

Article

Atomic-level evolutionary information improves protein–protein interface scoring.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3175, doi. 10.1093/bioinformatics/btab254

By:

Quignot, Chloé;
Granger, Pierre;
Chacón, Pablo;
Guerois, Raphael;
Andreani, Jessica

Publication type:

Article

Protlego: a Python package for the analysis and design of chimeric proteins.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3182, doi. 10.1093/bioinformatics/btab253

By:

Ferruz, Noelia;
Noske, Jakob;
Höcker, Birte

Publication type:

Article

novel systematic approach for cancer treatment prognosis and its applications in oropharyngeal cancer with microRNA biomarkers.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3106, doi. 10.1093/bioinformatics/btab242

By:

He, Shenghua;
Lian, Chunfeng;
Thorstad, Wade;
Gay, Hiram;
Zhao, Yujie;
Ruan, Su;
Wang, Xiaowei;
Li, Hua

Publication type:

Article

Fundamental gene network rewiring at the second order within and across mammalian systems.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3293, doi. 10.1093/bioinformatics/btab240

By:

Sharma, Ruby;
Kumar, Sajal;
Song, Mingzhou

Publication type:

Article

EPS: automated feature selection in case–control studies using extreme pseudo-sampling.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3372, doi. 10.1093/bioinformatics/btab214

By:

Shemirani, Ruhollah;
Wenric, Stephane;
Kenny, Eimear;
Ambite, José Luis

Publication type:

Article

VCFShark: how to squeeze a VCF file.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3358, doi. 10.1093/bioinformatics/btab211

By:

Deorowicz, Sebastian;
Danek, Agnieszka;
Kokot, Marek

Publication type:

Article

Generalized Read-Across prediction using genra-py.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3380, doi. 10.1093/bioinformatics/btab210

By:

Shah, Imran;
Tate, Tia;
Patlewicz, Grace

Publication type:

Article

MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3220, doi. 10.1093/bioinformatics/btab239

By:

Gerniers, Alexander;
Bricard, Orian;
Dupont, Pierre

Publication type:

Article

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3128, doi. 10.1093/bioinformatics/btab238

By:

Markowski, Julia;
Kempfer, Rieke;
Kukalev, Alexander;
Irastorza-Azcarate, Ibai;
Loof, Gesa;
Kehr, Birte;
Pombo, Ana;
Rahmann, Sven;
Schwarz, Roland F

Publication type:

Article

Early cancer detection from genome-wide cell-free DNA fragmentation via shuffled frog leaping algorithm and support vector machine.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3099, doi. 10.1093/bioinformatics/btab236

By:

Liu, Linjing;
Chen, Xingjian;
Wong, Ka-Chun

Publication type:

Article

Optimal Bayesian supervised domain adaptation for RNA sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3212, doi. 10.1093/bioinformatics/btab228

By:

Boluki, Shahin;
Qian, Xiaoning;
Dougherty, Edward R

Publication type:

Article

Fast identification of differential distributions in single-cell RNA-sequencing data with waddR.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3204, doi. 10.1093/bioinformatics/btab226

By:

Schefzik, Roman;
Flesch, Julian;
Goncalves, Angela

Publication type:

Article

HPOFiller: identifying missing protein–phenotype associations by graph convolutional network.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3328, doi. 10.1093/bioinformatics/btab224

By:

Liu, Lizhi;
Mamitsuka, Hiroshi;
Zhu, Shanfeng

Publication type:

Article

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3364, doi. 10.1093/bioinformatics/btab222

By:

Zhang, Ruoshi;
Mirdita, Milot;
Karin, Eli Levy;
Norroy, Clovis;
Galiez, Clovis;
Söding, Johannes

Publication type:

Article

ASHLEYS: automated quality control for single-cell Strand-seq data.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3356, doi. 10.1093/bioinformatics/btab221

By:

Gros, Christina;
Sanders, Ashley D;
Korbel, Jan O;
Marschall, Tobias;
Ebert, Peter

Publication type:

Article

Protein contact map refinement for improving structure prediction using generative adversarial networks.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3168, doi. 10.1093/bioinformatics/btab220

By:

Subramaniya, Sai Raghavendra Maddhuri Venkata;
Terashi, Genki;
Jain, Aashish;
Kagaya, Yuki;
Kihara, Daisuke

Publication type:

Article

ShinyCell: simple and sharable visualization of single-cell gene expression data.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3374, doi. 10.1093/bioinformatics/btab209

By:

Ouyang, John F;
Kamaraj, Uma S;
Cao, Elaine Y;
Rackham, Owen J L

Publication type:

Article

Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3351, doi. 10.1093/bioinformatics/btab208

By:

Hu, Qiang;
Hutson, Alan;
Liu, Song;
Morgan, Martin;
Liu, Qian

Publication type:

Article

FUNGI: FUsioN Gene Integration toolset.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3353, doi. 10.1093/bioinformatics/btab206

By:

Cervera, Alejandra;
Rausio, Heidi;
Kähkönen, Tiia;
Andersson, Noora;
Partel, Gabriele;
Rantanen, Ville;
Paciello, Giulia;
Ficarra, Elisa;
Hynninen, Johanna;
Hietanen, Sakari;
Carpén, Olli;
Lehtonen, Rainer;
Hautaniemi, Sampsa;
Huhtinen, Kaisa

Publication type:

Article

PecanPy: a fast, efficient and parallelized Python implementation of node2vec.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3377, doi. 10.1093/bioinformatics/btab202

By:

Liu, Renming;
Krishnan, Arjun

Publication type:

Article

KEC: unique sequence search by K-mer exclusion.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3349, doi. 10.1093/bioinformatics/btab196

By:

Beran, Pavel;
Stehlíková, Dagmar;
Cohen, Stephen P;
Čurn, Vladislav

Publication type:

Article

NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes.

Published in:

Bioinformatics, 2021, v. 37, n. 19, p. 3369, doi. 10.1093/bioinformatics/btab189

By:

Mailhot, Olivier;
Najmanovich, Rafael

Publication type:

Article