Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 22

Results: 56

CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4298, doi. 10.1093/bioinformatics/btab654

By:

Rogers, Mark F;
Gaunt, Tom R;
Campbell, Colin

Publication type:

Article

On the stability of log-rank test under labeling errors.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4297, doi. 10.1093/bioinformatics/btab693

By:

Galili, Ben;
Samohi, Anat;
Yakhini, Zohar

Publication type:

Article

Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4296, doi. 10.1093/bioinformatics/btab692

By:

Levy-Jurgenson, Alona;
Tekpli, Xavier;
Yakhini, Zohar

Publication type:

Article

Bayesian modeling of spatial molecular profiling data via Gaussian process.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4129, doi. 10.1093/bioinformatics/btab455

By:

Li, Qiwei;
Zhang, Minzhe;
Xie, Yang;
Xiao, Guanghua

Publication type:

Article

Fast numerical optimization for genome sequencing data in population biobanks.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4148, doi. 10.1093/bioinformatics/btab452

By:

Li, Ruilin;
Chang, Christopher;
Tanigawa, Yosuke;
Narasimhan, Balasubramanian;
Hastie, Trevor;
Tibshirani, Robert;
Rivas, Manuel A

Publication type:

Article

efam: an expanded, metaproteome-supported HMM profile database of viral protein families.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4202, doi. 10.1093/bioinformatics/btab451

By:

Zayed, Ahmed A;
Lücking, Dominik;
Mohssen, Mohamed;
Cronin, Dylan;
Bolduc, Ben;
Gregory, Ann C;
Hargreaves, Katherine R;
Piehowski, Paul D;
III, Richard A White;
Huang, Eric L;
Adkins, Joshua N;
Roux, Simon;
Moraru, Cristina;
Sullivan, Matthew B

Publication type:

Article

Normalization by distributional resampling of high throughput single-cell RNA-sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4123, doi. 10.1093/bioinformatics/btab450

By:

Brown, Jared;
Ni, Zijian;
Mohanty, Chitrasen;
Bacher, Rhonda;
Kendziorski, Christina

Publication type:

Article

convolutional neural network for common coordinate registration of high-resolution histology images.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4216, doi. 10.1093/bioinformatics/btab447

By:

Daly, Aidan C;
Geras, Krzysztof J;
Bonneau, Richard

Publication type:

Article

Methylation-eQTL analysis in cancer research.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4014, doi. 10.1093/bioinformatics/btab443

By:

Liu, Yusha;
Baggerly, Keith A;
Orouji, Elias;
Manyam, Ganiraju;
Chen, Huiqin;
Lam, Michael;
Davis, Jennifer S;
Lee, Michael S;
Broom, Bradley M;
Menter, David G;
Rai, Kunal;
Kopetz, Scott;
Morris, Jeffrey S

Publication type:

Article

Improving sequence-based modeling of protein families using secondary-structure quality assessment.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4083, doi. 10.1093/bioinformatics/btab442

By:

Malbranke, Cyril;
Bikard, David;
Cocco, Simona;
Monasson, Rémi

Publication type:

Article

Detecting copy number alterations in RNA-Seq using SuperFreq.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4023, doi. 10.1093/bioinformatics/btab440

By:

Flensburg, Christoffer;
Oshlack, Alicia;
Majewski, Ian J

Publication type:

Article

Humanization of antibodies using a machine learning approach on large-scale repertoire data.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4041, doi. 10.1093/bioinformatics/btab434

By:

Marks, Claire;
Hummer, Alissa M;
Chin, Mark;
Deane, Charlotte M

Publication type:

Article

MecCog: a knowledge representation framework for genetic disease mechanism.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4180, doi. 10.1093/bioinformatics/btab432

By:

Kundu, Kunal;
Darden, Lindley;
Moult, John

Publication type:

Article

ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4253, doi. 10.1093/bioinformatics/btab431

By:

Tangaro, Marco A;
Defazio, Giuseppe;
Fosso, Bruno;
Licciulli, Vito Flavio;
Grillo, Giorgio;
Donvito, Giacinto;
Lavezzo, Enrico;
Baruzzo, Giacomo;
Pesole, Graziano;
Santamaria, Monica

Publication type:

Article

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4193, doi. 10.1093/bioinformatics/btab429

By:

Lee, Joon-Yong;
Bilbao, Aivett;
Conant, Christopher R;
Bloodsworth, Kent J;
Orton, Daniel J;
Zhou, Mowei;
Wilson, Jesse W;
Zheng, Xueyun;
Webb, Ian K;
Li, Ailin;
Hixson, Kim K;
Fjeldsted, John C;
Ibrahim, Yehia M;
Payne, Samuel H;
Jansson, Christer;
Smith, Richard D;
Metz, Thomas O

Publication type:

Article

BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4172, doi. 10.1093/bioinformatics/btab422

By:

Cheng, Jun;
Bendjama, Kaïdre;
Rittner, Karola;
Malone, Brandon

Publication type:

Article

framework to decipher the genetic architecture of combinations of complex diseases: applications in cardiovascular medicine.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4137, doi. 10.1093/bioinformatics/btab417

By:

Yin, Liangying;
Chau, Carlos Kwan-Long;
Lin, Yu-Ping;
Rao, Shitao;
Xiang, Yong;
Sham, Pak-Chung;
So, Hon-Cheong

Publication type:

Article

EnMCB: an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4282, doi. 10.1093/bioinformatics/btab415

By:

Yu, Xin;
Kong, De-Xin

Publication type:

Article

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4064, doi. 10.1093/bioinformatics/btab414

By:

Markin, Alexey;
Eulenstein, Oliver

Publication type:

Article

cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4251, doi. 10.1093/bioinformatics/btab413

By:

Zhang, Wei;
Wei, Lei;
Huang, Jiaqi;
Zhong, Bixi;
Li, Jiaqi;
Xu, Hanwen;
He, Shuying;
Liu, Yu;
Liu, Juhong;
Lv, Hairong;
Wang, Xiaowo

Publication type:

Article

Oligator: a flexible interface to draw oligosaccharide structures and generate their theoretical tandem mass spectra.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4261, doi. 10.1093/bioinformatics/btab412

By:

Lollier, Virginie;
Fanuel, Mathieu;
Ropartz, David;
Tessier, Dominique;
Rogniaux, Hélène

Publication type:

Article

scDetect: a rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4115, doi. 10.1093/bioinformatics/btab410

By:

Shen, Yifei;
Chu, Qinjie;
Timko, Michael P;
Fan, Longjiang

Publication type:

Article

Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4006, doi. 10.1093/bioinformatics/btab394

By:

Wolff, Joachim;
Backofen, Rolf;
Grüning, Björn

Publication type:

Article

UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4240, doi. 10.1093/bioinformatics/btab392

By:

Ramos-Rodríguez, Mireia;
Subirana-Granés, Marc;
Pasquali, Lorenzo

Publication type:

Article

Interfacing Seurat with the R tidy universe.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4100, doi. 10.1093/bioinformatics/btab404

By:

Mangiola, Stefano;
Doyle, Maria A;
Papenfuss, Anthony T

Publication type:

Article

Bistability in cell signalling and its significance in identifying potential drug-targets.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4156, doi. 10.1093/bioinformatics/btab395

By:

Halder, Suvankar;
Ghosh, Sumana;
Chattopadhyay, Joydev;
Chatterjee, Samrat

Publication type:

Article

SAMF: a self-adaptive protein modeling framework.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4075, doi. 10.1093/bioinformatics/btab411

By:

Ding, Wenze;
Xu, Qijiang;
Liu, Siyuan;
Wang, Tong;
Shao, Bin;
Gong, Haipeng;
Liu, Tie-Yan

Publication type:

Article

LevioSAM: fast lift-over of variant-aware reference alignments.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4243, doi. 10.1093/bioinformatics/btab396

By:

Mun, Taher;
Chen, Nae-Chyun;
Langmead, Ben

Publication type:

Article

CyAnno: a semi-automated approach for cell type annotation of mass cytometry datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4164, doi. 10.1093/bioinformatics/btab409

By:

Kaushik, Abhinav;
Dunham, Diane;
He, Ziyuan;
Manohar, Monali;
Desai, Manisha;
Nadeau, Kari C;
Andorf, Sandra

Publication type:

Article

PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4048, doi. 10.1093/bioinformatics/btab408

By:

Almodaresi, Fatemeh;
Zakeri, Mohsen;
Patro, Rob

Publication type:

Article

Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4033, doi. 10.1093/bioinformatics/btab406

By:

Wang, Chen;
Konecki, Daniel M;
Marciano, David C;
Govindarajan, Harikumar;
Williams, Amanda M;
Wastuwidyaningtyas, Brigitta;
Bourquard, Thomas;
Katsonis, Panagiotis;
Lichtarge, Olivier

Publication type:

Article

Tfcancer: a manually curated database of transcription factors associated with human cancers.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4288, doi. 10.1093/bioinformatics/btab405

By:

Huang, Qingqing;
Tan, Zhengtang;
Li, Yanjing;
Wang, Wenzhu;
Lang, Mei;
Li, Changying;
Guo, Zhiyun

Publication type:

Article

DeepChargePredictor: a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4255, doi. 10.1093/bioinformatics/btab389

By:

Wang, Jike;
Sun, Huiyong;
Chen, Jiawen;
Jiang, Dejun;
Wang, Zhe;
Wu, Zhenxing;
Chen, Xi;
Cao, Dongsheng;
Hou, Tingjun

Publication type:

Article

Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4091, doi. 10.1093/bioinformatics/btab403

By:

Zuo, Chunman;
Dai, Hao;
Chen, Luonan

Publication type:

Article

Peel learning for pathway-related outcome prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4108, doi. 10.1093/bioinformatics/btab402

By:

Li, Yuantong;
Wang, Fei;
Yan, Mengying;
III, Edward Cantu;
Yang, Fan Nils;
Rao, Hengyi;
Feng, Rui

Publication type:

Article

Jutils: a visualization toolkit for differential alternative splicing events.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4272, doi. 10.1093/bioinformatics/btab401

By:

Yang, Guangyu;
Cope, Leslie;
He, Zitong;
Florea, Liliana

Publication type:

Article

MorphoScript: a dedicated analysis to assess the morphology and contractile structures of cardiomyocytes derived from stem cells.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4209, doi. 10.1093/bioinformatics/btab400

By:

Homan, Tess;
Delanoë-Ayari, Hélène;
Meli, Albano C;
Cazorla, Olivier;
Gergely, Csilla;
Mejat, Alexandre;
Chevalier, Philippe;
Moreau, Adrien

Publication type:

Article

Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4056, doi. 10.1093/bioinformatics/btab399

By:

Hübner, Lukas;
Kozlov, Alexey M;
Hespe, Demian;
Sanders, Peter;
Stamatakis, Alexandros

Publication type:

Article

Super LeArner Prediction of NAb Panels (SLAPNAP): a containerized tool for predicting combination monoclonal broadly neutralizing antibody sensitivity.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4187, doi. 10.1093/bioinformatics/btab398

By:

Williamson, Brian D;
Magaret, Craig A;
Gilbert, Peter B;
Nizam, Sohail;
Simmons, Courtney;
Benkeser, David

Publication type:

Article

3DBionotes COVID-19 edition.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4258, doi. 10.1093/bioinformatics/btab397

By:

Macias, Jose Ramon;
Sanchez-Garcia, Ruben;
Conesa, Pablo;
Ramirez-Aportela, Erney;
Gonzalez, Marta Martinez;
Wert-Carvajal, Carlos;
Parra-Perez, Alberto M;
Mora, Joan Segura;
Horrell, Sam;
Thorn, Andrea;
Sorzano, Carlos O S;
Carazo, Jose Maria

Publication type:

Article

powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4269, doi. 10.1093/bioinformatics/btab385

By:

Dong, Xianjun;
Li, Xiaoqi;
Chang, Tzuu-Wang;
Scherzer, Clemens R;
Weiss, Scott T;
Qiu, Weiliang

Publication type:

Article

HEAL: an automated deep learning framework for cancer histopathology image analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4291, doi. 10.1093/bioinformatics/btab380

By:

Wang, Yanan;
Coudray, Nicolas;
Zhao, Yun;
Li, Fuyi;
Hu, Changyuan;
Zhang, Yao-Zhong;
Imoto, Seiya;
Tsirigos, Aristotelis;
Webb, Geoffrey I;
Daly, Roger J;
Song, Jiangning

Publication type:

Article

MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4238, doi. 10.1093/bioinformatics/btab379

By:

Oguztuzun, Cerag;
Yasar, Pelin;
Yavuz, Kerim;
Muyan, Mesut;
Can, Tolga

Publication type:

Article

Sparse allele vectors and the savvy software suite.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4248, doi. 10.1093/bioinformatics/btab378

By:

LeFaive, Jonathon;
Smith, Albert V;
Kang, Hyun Min;
Abecasis, Gonçalo

Publication type:

Article

Semi-supervised peak calling with SPAN and JBR genome browser.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4235, doi. 10.1093/bioinformatics/btab376

By:

Shpynov, Oleg;
Dievskii, Aleksei;
Chernyatchik, Roman;
Tsurinov, Petr;
Artyomov, Maxim N

Publication type:

Article

FBA: feature barcoding analysis for single cell RNA-Seq.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4266, doi. 10.1093/bioinformatics/btab375

By:

Duan, Jialei;
Hon, Gary C

Publication type:

Article

Bathometer: lightning fast depth-of-reads query.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4233, doi. 10.1093/bioinformatics/btab372

By:

Stenzel, U;
Horn, S

Publication type:

Article

CrossTalkeR: analysis and visualization of ligand–receptorne tworks.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4263, doi. 10.1093/bioinformatics/btab370

By:

Nagai, James S;
Leimkühler, Nils B;
Schaub, Michael T;
Schneider, Rebekka K;
Costa, Ivan G

Publication type:

Article

DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4230, doi. 10.1093/bioinformatics/btab366

By:

Grassi, Luigi;
Harris, Claire;
Zhu, Jie;
Hardman, Colin;
Hatton, Diane

Publication type:

Article

SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities.

Published in:

Bioinformatics, 2021, v. 37, n. 22, p. 4285, doi. 10.1093/bioinformatics/btab365

By:

Macnee, Marie;
Pérez-Palma, Eduardo;
Schumacher-Bass, Sarah;
Dalton, Jarrod;
Leu, Costin;
Blankenberg, Daniel;
Lal, Dennis

Publication type:

Article