Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 2

Results: 54

DLAB: deep learning methods for structure-based virtual screening of antibodies.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 377, doi. 10.1093/bioinformatics/btab660

By:

Schneider, Constantin;
Buchanan, Andrew;
Taddese, Bruck;
Deane, Charlotte M

Publication type:

Article

Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 513, doi. 10.1093/bioinformatics/btab670

By:

Amgad, Mohamed;
Atteya, Lamees A;
Hussein, Hagar;
Mohammed, Kareem Hosny;
Hafiz, Ehab;
Elsebaie, Maha A T;
Mobadersany, Pooya;
Manthey, David;
Gutman, David A;
Elfandy, Habiba;
Cooper, Lee A D

Publication type:

Article

RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST).

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 397, doi. 10.1093/bioinformatics/btab673

By:

Chen, Yi-Pei;
Ferguson, Laura B;
Salem, Nihal A;
Zheng, George;
Mayfield, R Dayne;
Eslami, Mohammed

Publication type:

Article

XGBLC: an improved survival prediction model based on XGBoost.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 410, doi. 10.1093/bioinformatics/btab675

By:

Ma, Baoshan;
Yan, Ge;
Chai, Bingjie;
Hou, Xiaoyu

Publication type:

Article

SMILE: mutual information learning for integration of single-cell omics data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 476, doi. 10.1093/bioinformatics/btab706

By:

Xu, Yang;
Das, Priyojit;
McCord, Rachel Patton

Publication type:

Article

FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 351, doi. 10.1093/bioinformatics/btab696

By:

Lee, Dohyeon;
Song, Giltae

Publication type:

Article

PaReBrick: PArallel REarrangements and BReaks identification toolkit.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 357, doi. 10.1093/bioinformatics/btab691

By:

Zabelkin, Alexey;
Yakovleva, Yulia;
Bochkareva, Olga;
Alexeev, Nikita

Publication type:

Article

first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz).

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 318, doi. 10.1093/bioinformatics/btab690

By:

Singh, Nisha;
Rawal, Hukam C;
Angadi, Ulavappa B;
Sharma, Tilak Raj;
Singh, Nagendra Kumar;
Mondal, Tapan Kumar

Publication type:

Article

FLINO: a new method for immunofluorescence bioimage normalization.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 520, doi. 10.1093/bioinformatics/btab686

By:

Graf, John;
Cho, Sanghee;
McDonough, Elizabeth;
Corwin, Alex;
Sood, Anup;
Lindner, Andreas;
Salvucci, Manuela;
Stachtea, Xanthi;
Schaeybroeck, Sandra Van;
Dunne, Philip D;
Laurent-Puig, Pierre;
Longley, Daniel;
Prehn, Jochen H M;
Ginty, Fiona

Publication type:

Article

Efficient change-points detection for genomic sequences via cumulative segmented regression.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 311, doi. 10.1093/bioinformatics/btab685

By:

Jia, Shengji;
Shi, Lei

Publication type:

Article

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 325, doi. 10.1093/bioinformatics/btab681

By:

Ren, Yunxiao;
Chakraborty, Trinad;
Doijad, Swapnil;
Falgenhauer, Linda;
Falgenhauer, Jane;
Goesmann, Alexander;
Hauschild, Anne-Christin;
Schwengers, Oliver;
Heider, Dominik

Publication type:

Article

Prediction of whole-cell transcriptional response with machine learning.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 404, doi. 10.1093/bioinformatics/btab676

By:

Eslami, Mohammed;
Borujeni, Amin Espah;
Eramian, Hamed;
Weston, Mark;
Zheng, George;
Urrutia, Joshua;
Corbet, Carolyn;
Becker, Diveena;
Maschhoff, Paul;
Clowers, Katie;
Cristofaro, Alexander;
Hosseini, Hamid Doost;
Gordon, D Benjamin;
Dorfan, Yuval;
Singer, Jedediah;
Vaughn, Matthew;
Gaffney, Niall;
Fonner, John;
Stubbs, Joe;
Voigt, Christopher A

Publication type:

Article

Accelerating Big Data Analysis through LASSO-Random Forest Algorithm in QSAR Studies.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 469, doi. 10.1093/bioinformatics/btab659

By:

Motamedi, Fahimeh;
Pérez-Sánchez, Horacio;
Mehridehnavi, Alireza;
Fassihi, Afshin;
Ghasemi, Fahimeh

Publication type:

Article

echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 536, doi. 10.1093/bioinformatics/btab658

By:

Schilder, Brian M;
Humphrey, Jack;
Raj, Towfique

Publication type:

Article

Continual knowledge infusion into pre-trained biomedical language models.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 494, doi. 10.1093/bioinformatics/btab671

By:

Jha, Kishlay;
Zhang, Aidong

Publication type:

Article

Tiara: deep learning-based classification system for eukaryotic sequences.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 344, doi. 10.1093/bioinformatics/btab672

By:

Karlicki, Michał;
Antonowicz, Stanisław;
Karnkowska, Anna

Publication type:

Article

Testing microbiome association using integrated quantile regression models.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 419, doi. 10.1093/bioinformatics/btab668

By:

Wang, Tianying;
Ling, Wodan;
Plantinga, Anna M;
Wu, Michael C;
Zhan, Xiang

Publication type:

Article

SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 586, doi. 10.1093/bioinformatics/btab657

By:

Paci, Paola;
Fiscon, Giulia

Publication type:

Article

ATPdock: a template-based method for ATP-specific protein–ligand docking.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 556, doi. 10.1093/bioinformatics/btab667

By:

Rao, Liang;
Jia, Ning-Xin;
Hu, Jun;
Yu, Dong-Jun;
Zhang, Gui-Jun

Publication type:

Article

ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 369, doi. 10.1093/bioinformatics/btab666

By:

Kaushik, Rahul;
Zhang, Kam Y J

Publication type:

Article

timeOmics: an R package for longitudinal multi-omics data integration.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 577, doi. 10.1093/bioinformatics/btab664

By:

Bodein, Antoine;
Scott-Boyer, Marie-Pier;
Perin, Olivier;
Cao, Kim-Anh Lê;
Droit, Arnaud

Publication type:

Article

Viola: a structural variant signature extractor with user-defined classifications.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 540, doi. 10.1093/bioinformatics/btab662

By:

Sugita, Itsuki;
Matsuyama, Shohei;
Dobashi, Hiroki;
Komura, Daisuke;
Ishikawa, Shumpei

Publication type:

Article

AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 589, doi. 10.1093/bioinformatics/btab661

By:

Wong, Christina;
Li, Bo

Publication type:

Article

SGI: automatic clinical subgroup identification in omics datasets.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 573, doi. 10.1093/bioinformatics/btab656

By:

Buyukozkan, Mustafa;
Suhre, Karsten;
Krumsiek, Jan

Publication type:

Article

VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 391, doi. 10.1093/bioinformatics/btab653

By:

Atta, Lyla;
Sahoo, Arpan;
Fan, Jean

Publication type:

Article

CIndex: compressed indexes for fast retrieval of FASTQ files.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 335, doi. 10.1093/bioinformatics/btab655

By:

Huo, Hongwei;
Liu, Pengfei;
Wang, Chenhui;
Jiang, Hongbo;
Vitter, Jeffrey Scott

Publication type:

Article

Hypergraph-based logistic matrix factorization for metabolite–disease interaction prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 435, doi. 10.1093/bioinformatics/btab652

By:

Ma, Yingjun;
Ma, Yuanyuan

Publication type:

Article

MR-Corr2: a two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 303, doi. 10.1093/bioinformatics/btab646

By:

Cheng, Qing;
Qiu, Tingting;
Chai, Xiaoran;
Sun, Baoluo;
Xia, Yingcun;
Shi, Xingjie;
Liu, Jin

Publication type:

Article

TGSA: protein–protein association-based twin graph neural networks for drug response prediction with similarity augmentation.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 461, doi. 10.1093/bioinformatics/btab650

By:

Zhu, Yiheng;
Ouyang, Zhenqiu;
Chen, Wenbo;
Feng, Ruiwei;
Chen, Danny Z;
Cao, Ji;
Wu, Jian

Publication type:

Article

BioDynaMo: a modular platform for high-performance agent-based simulation.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 453, doi. 10.1093/bioinformatics/btab649

By:

Breitwieser, Lukas;
Hesam, Ahmad;
Montigny, Jean de;
Vavourakis, Vasileios;
Iosif, Alexandros;
Jennings, Jack;
Kaiser, Marcus;
Manca, Marco;
Meglio, Alberto Di;
Al-Ars, Zaid;
Rademakers, Fons;
Mutlu, Onur;
Bauer, Roman

Publication type:

Article

SplicingFactory—splicing diversity analysis for transcriptome data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 384, doi. 10.1093/bioinformatics/btab648

By:

Dankó, Benedek;
Szikora, Péter;
Pór, Tamás;
Szeifert, Alexa;
Sebestyén, Endre

Publication type:

Article

Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 487, doi. 10.1093/bioinformatics/btab647

By:

Pio, Gianvito;
Mignone, Paolo;
Magazzù, Giuseppe;
Zampieri, Guido;
Ceci, Michelangelo;
Angione, Claudio

Publication type:

Article

MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 426, doi. 10.1093/bioinformatics/btab651

By:

Fu, Haitao;
Huang, Feng;
Liu, Xuan;
Qiu, Yang;
Zhang, Wen

Publication type:

Article

Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 503, doi. 10.1093/bioinformatics/btab638

By:

Guo, Shuxia;
Zhao, Xuan;
Jiang, Shengdian;
Ding, Liya;
Peng, Hanchuan

Publication type:

Article

DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 533, doi. 10.1093/bioinformatics/btab624

By:

Brewer, Kenneth I;
Gaffield, Glenn J;
Puri, Malavika;
Breaker, Ronald R

Publication type:

Article

TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 570, doi. 10.1093/bioinformatics/btab619

By:

Zhang, Peter;
Palmisano, Alida;
Kumar, Ravindra;
Li, Ming-Chung;
Doroshow, James H;
Zhao, Yingdong

Publication type:

Article

FIVEx: an interactive eQTL browser across public datasets.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 559, doi. 10.1093/bioinformatics/btab614

By:

Kwong, Alan;
Boughton, Andrew P;
Wang, Mukai;
VandeHaar, Peter;
Boehnke, Michael;
Abecasis, Gonçalo;
Kang, Hyun Min

Publication type:

Article

GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 546, doi. 10.1093/bioinformatics/btab607

By:

Stanton, Richard A;
Vlachos, Nicholas;
Halpin, Alison Laufer

Publication type:

Article

ksrates: positioning whole-genome duplications relative to speciation events in KS distributions.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 530, doi. 10.1093/bioinformatics/btab602

By:

Sensalari, Cecilia;
Maere, Steven;
Lohaus, Rolf

Publication type:

Article

indelPost: harmonizing ambiguities in simple and complex indel alignments.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 549, doi. 10.1093/bioinformatics/btab601

By:

Hagiwara, Kohei;
Edmonson, Michael N;
Wheeler, David A;
Zhang, Jinghui

Publication type:

Article

purgeR: inbreeding and purging in pedigreed populations.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 564, doi. 10.1093/bioinformatics/btab599

By:

López-Cortegano, Eugenio

Publication type:

Article

INTERCAAT: identifying interface residues between macromolecules.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 554, doi. 10.1093/bioinformatics/btab596

By:

Grudman, Steven;
Fajardo, J Eduardo;
Fiser, Andras

Publication type:

Article

Amanida: an R package for meta-analysis of metabolomics non-integral data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 583, doi. 10.1093/bioinformatics/btab591

By:

Llambrich, Maria;
Correig, Eudald;
Gumà, Josep;
Brezmes, Jesús;
Cumeras, Raquel

Publication type:

Article

Unipept Visualizations: an interactive visualization library for biological data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 562, doi. 10.1093/bioinformatics/btab590

By:

Verschaffelt, Pieter;
Collier, James;
Botzki, Alexander;
Martens, Lennart;
Dawyndt, Peter;
Mesuere, Bart

Publication type:

Article

PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 594, doi. 10.1093/bioinformatics/btab589

By:

Fernandez-Gonzalez, Rodrigo;
Balaghi, Negar;
Wang, Kelly;
Hawkins, Ray;
Rothenberg, Katheryn;
McFaul, Christopher;
Schimmer, Clara;
Ly, Michelle;
Carmo, Ana Maria do;
Scepanovic, Gordana;
Erdemci-Tandogan, Gonca;
Castle, Veronica

Publication type:

Article

HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 543, doi. 10.1093/bioinformatics/btab585

By:

Tan, Jie;
Fang, Zhencheng;
Wu, Shufang;
Guo, Qian;
Jiang, Xiaoqing;
Zhu, Huaiqiu

Publication type:

Article

MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 552, doi. 10.1093/bioinformatics/btab584

By:

Barozet, Amélie;
Molloy, Kevin;
Vaisset, Marc;
Zanon, Christophe;
Fauret, Pierre;
Siméon, Thierry;
Cortés, Juan

Publication type:

Article

metID: an R package for automatable compound annotation for LC−MS-based data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 568, doi. 10.1093/bioinformatics/btab583

By:

Shen, Xiaotao;
Wu, Si;
Liang, Liang;
Chen, Songjie;
Contrepois, Kévin;
Zhu, Zheng-Jiang;
Snyder, Michael

Publication type:

Article

PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 444, doi. 10.1093/bioinformatics/btab566

By:

Nam, Seungyoon;
Lee, Sungyoung;
Park, Sungjin;
Lee, Jinhyuk;
Park, Aron;
Kim, Yon Hui;
Park, Taesung

Publication type:

Article

UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data.

Published in:

Bioinformatics, 2022, v. 38, n. 2, p. 527, doi. 10.1093/bioinformatics/btab561

By:

Wang, Shixiang;
Xiong, Yi;
Zhao, Longfei;
Gu, Kai;
Li, Yin;
Zhao, Fei;
Li, Jianfeng;
Wang, Mingjie;
Wang, Haitao;
Tao, Ziyu;
Wu, Tao;
Zheng, Yichao;
Li, Xuejun;
Liu, Xue-Song

Publication type:

Article