Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 7

Results: 52

Erratum to: A data-adaptive Bayesian regression approach for polygenic risk prediction.

Published in:

2022

By:

Song, Shuang;
Hou, Lin;
Liu, Jun S

Publication type:

Correction Notice

Fast and compact matching statistics analytics.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1838, doi. 10.1093/bioinformatics/btac064

By:

Cunial, Fabio;
Denas, Olgert;
Belazzougui, Djamal

Publication type:

Article

deep dilated convolutional residual network for predicting interchain contacts of protein homodimers.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1904, doi. 10.1093/bioinformatics/btac063

By:

Roy, Raj S;
Quadir, Farhan;
Soltanikazemi, Elham;
Cheng, Jianlin

Publication type:

Article

fastANCOM: a fast method for analysis of compositions of microbiomes.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2039, doi. 10.1093/bioinformatics/btac060

By:

Zhou, Chao;
Wang, Huimin;
Zhao, Hongyu;
Wang, Tao

Publication type:

Article

metaboprep: an R package for preanalysis data description and processing.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1980, doi. 10.1093/bioinformatics/btac059

By:

Hughes, David A;
Taylor, Kurt;
McBride, Nancy;
Lee, Matthew A;
Mason, Dan;
Lawlor, Deborah A;
Timpson, Nicholas J;
Corbin, Laura J

Publication type:

Article

LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1816, doi. 10.1093/bioinformatics/btac058

By:

Lin, Jyun-Hong;
Chen, Liang-Chi;
Yu, Shu-Chi;
Huang, Yao-Ting

Publication type:

Article

Plotgardener: cultivating precise multi-panel figures in R.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2042, doi. 10.1093/bioinformatics/btac057

By:

Kramer, Nicole E;
Davis, Eric S;
Wenger, Craig D;
Deoudes, Erika M;
Parker, Sarah M;
Love, Michael I;
Phanstiel, Douglas H

Publication type:

Article

DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1895, doi. 10.1093/bioinformatics/btac056

By:

Guo, Sai-Sai;
Liu, Jun;
Zhou, Xiao-Gen;
Zhang, Gui-Jun

Publication type:

Article

FUNKI: interactive functional footprint-based analysis of omics data.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2075, doi. 10.1093/bioinformatics/btac055

By:

Hernansaiz-Ballesteros, Rosa;
Holland, Christian H;
Dugourd, Aurelien;
Saez-Rodriguez, Julio

Publication type:

Article

SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1888, doi. 10.1093/bioinformatics/btac053

By:

Singh, Jaspreet;
Litfin, Thomas;
Singh, Jaswinder;
Paliwal, Kuldip;
Zhou, Yaoqi

Publication type:

Article

Noise-Transfer2Clean: denoising cryo-EM images based on noise modeling and transfer.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2022, doi. 10.1093/bioinformatics/btac052

By:

Li, Hongjia;
Zhang, Hui;
Wan, Xiaohua;
Yang, Zhidong;
Li, Chengmin;
Li, Jintao;
Han, Renmin;
Zhu, Ping;
Zhang, Fa

Publication type:

Article

DisEnrich: database of enriched regions in human dark proteome.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1870, doi. 10.1093/bioinformatics/btac051

By:

Medvedev, Kirill E;
Pei, Jimin;
Grishin, Nick V

Publication type:

Article

SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1830, doi. 10.1093/bioinformatics/btac050

By:

Bennett, Christopher;
Thornton, Micah;
Park, Chanhee;
Henry, Gervaise;
Zhang, Yun;
Malladi, Venkat;
Kim, Daehwan

Publication type:

Article

Vivarium: an interface and engine for integrative multiscale modeling in computational biology.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1972, doi. 10.1093/bioinformatics/btac049

By:

Agmon, Eran;
Spangler, Ryan K;
Skalnik, Christopher J;
Poole, William;
Peirce, Shayn M;
Morrison, Jerry H;
Covert, Markus W

Publication type:

Article

NerLTR-DTA: drug–target binding affinity prediction based on neighbor relationship and learning to rank.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1964, doi. 10.1093/bioinformatics/btac048

By:

Ru, Xiaoqing;
Ye, Xiucai;
Sakurai, Tetsuya;
Zou, Quan

Publication type:

Article

mixture model for determining SARS-Cov-2 variant composition in pooled samples.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1809, doi. 10.1093/bioinformatics/btac047

By:

Valieris, Renan;
Drummond, Rodrigo D;
Defelicibus, Alexandre;
Dias-Neto, Emmanuel;
Rosales, Rafael A;
Silva, Israel Tojal da

Publication type:

Article

Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2070, doi. 10.1093/bioinformatics/btac046

By:

Librado, Pablo;
Orlando, Ludovic

Publication type:

Article

EDTox: an R Shiny application to predict the endocrine disruption potential of compounds.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2066, doi. 10.1093/bioinformatics/btac045

By:

Sakhteman, Amirhossein;
Ghosh, Arindam;
Fortino, Vittorio

Publication type:

Article

TMQuery: a database of precomputed template modeling scores for assessment of protein structural similarity.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2062, doi. 10.1093/bioinformatics/btac044

By:

Price, Stephen;
Tombeur, Stéphane;
Hudson, Alexander;
Sathiyamoorthy, Nanda Kumar;
Smyth, Paul;
Singh, Anjana;
Peccianti, Mara;
Baroncelli, Elisa;
Essaghir, Ahmed;
Ferlenghi, Ilaria;
Phogat, Sanjay Kumar;
Singh, Gurpreet

Publication type:

Article

ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2033, doi. 10.1093/bioinformatics/btac043

By:

Cherif, Emira;
Thiam, Fatou Seck;
Salma, Mohammad;
Rivera-Ingraham, Georgina;
Justy, Fabienne;
Deremarque, Theo;
Breugnot, Damien;
Doudou, Jean-Claude;
Gozlan, Rodolphe Elie;
Combe, Marine

Publication type:

Article

StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2046, doi. 10.1093/bioinformatics/btac042

By:

Cameron, Daniel L;
Dong, Ruining;
Papenfuss, Anthony T

Publication type:

Article

RawHummus: an R Shiny app for automated raw data quality control in metabolomics.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2072, doi. 10.1093/bioinformatics/btac040

By:

Dong, Yonghui;
Kazachkova, Yana;
Gou, Meng;
Morgan, Liat;
Wachsman, Tal;
Gazit, Ehud;
Birkler, Rune Isak Dupont

Publication type:

Article

SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1801, doi. 10.1093/bioinformatics/btac041

By:

Hui, Sandra;
Nielsen, Rasmus

Publication type:

Article

Cross-dependent graph neural networks for molecular property prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2003, doi. 10.1093/bioinformatics/btac039

By:

Ma, Hehuan;
Bian, Yatao;
Rong, Yu;
Huang, Wenbing;
Xu, Tingyang;
Xie, Weiyang;
Ye, Geyan;
Huang, Junzhou

Publication type:

Article

GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2036, doi. 10.1093/bioinformatics/btac037

By:

Hong, Chen;
Thiele, Robin;
Feuerbach, Lars

Publication type:

Article

ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1988, doi. 10.1093/bioinformatics/btac030

By:

Cilibrasi, Luca;
Pinoli, Pietro;
Bernasconi, Anna;
Canakoglu, Arif;
Chiara, Matteo;
Ceri, Stefano

Publication type:

Article

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2049, doi. 10.1093/bioinformatics/btac018

By:

Vollger, Mitchell R;
Kerpedjiev, Peter;
Phillippy, Adam M;
Eichler, Evan E

Publication type:

Article

BioThings SDK: a toolkit for building high-performance data APIs in biomedical research.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2077, doi. 10.1093/bioinformatics/btac017

By:

Lelong, Sebastien;
Zhou, Xinghua;
Afrasiabi, Cyrus;
Qian, Zhongchao;
Cano, Marco Alvarado;
Tsueng, Ginger;
Xin, Jiwen;
Mullen, Julia;
Yao, Yao;
Avila, Ricardo;
Taylor, Greg;
Su, Andrew I;
Wu, Chunlei

Publication type:

Article

ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1877, doi. 10.1093/bioinformatics/btac016

By:

Abanades, Brennan;
Georges, Guy;
Bujotzek, Alexander;
Deane, Charlotte M

Publication type:

Article

Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1956, doi. 10.1093/bioinformatics/btac015

By:

Xiao, Di;
Kim, Hani Jieun;
Pang, Ignatius;
Yang, Pengyi

Publication type:

Article

Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1920, doi. 10.1093/bioinformatics/btac036

By:

Baruzzo, Giacomo;
Cesaro, Giulia;
Camillo, Barbara Di

Publication type:

Article

BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1995, doi. 10.1093/bioinformatics/btac035

By:

Li, Min;
Lu, Zhangli;
Wu, Yifan;
Li, YaoHang

Publication type:

Article

Inverse Potts model improves accuracy of phylogenetic profiling.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1794, doi. 10.1093/bioinformatics/btac034

By:

Fukunaga, Tsukasa;
Iwasaki, Wataru

Publication type:

Article

AlzCode: a platform for multiview analysis of genes related to Alzheimer's disease.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2030, doi. 10.1093/bioinformatics/btac033

By:

Lin, Cui-Xiang;
Li, Hong-Dong;
Deng, Chao;
Erhardt, Shannon;
Wang, Jun;
Peng, Xiaoqing;
Wang, Jianxin

Publication type:

Article

massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2015, doi. 10.1093/bioinformatics/btac032

By:

Abdelmoula, Walid M;
Stopka, Sylwia A;
Randall, Elizabeth C;
Regan, Michael;
Agar, Jeffrey N;
Sarkaria, Jann N;
Wells, William M;
Kapur, Tina;
Agar, Nathalie Y R

Publication type:

Article

ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1930, doi. 10.1093/bioinformatics/btac031

By:

Roquencourt, Camille;
Grassin-Delyle, Stanislas;
Thévenot, Etienne A

Publication type:

Article

MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1911, doi. 10.1093/bioinformatics/btac014

By:

Mao, Jiawei;
Zhu, He;
Liu, Luyao;
Fang, Zheng;
Dong, Mingming;
Qin, Hongqiang;
Ye, Mingliang

Publication type:

Article

XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1947, doi. 10.1093/bioinformatics/btac029

By:

Xiao, Jiashun;
Cai, Mingxuan;
Hu, Xianghong;
Wan, Xiang;
Chen, Gang;
Yang, Can

Publication type:

Article

End-to-end learning of evolutionary models to find coding regions in genome alignments.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1857, doi. 10.1093/bioinformatics/btac028

By:

Mertsch, Darvin;
Stanke, Mario

Publication type:

Article

From viral evolution to spatial contagion: a biologically modulated Hawkes model.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1846, doi. 10.1093/bioinformatics/btac027

By:

Holbrook, Andrew J;
Ji, Xiang;
Suchard, Marc A

Publication type:

Article

LLPSDB v2.0: an updated database of proteins undergoing liquid–liquid phase separation in vitro.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2010, doi. 10.1093/bioinformatics/btac026

By:

Wang, Xi;
Zhou, Xiang;
Yan, Qinglin;
Liao, Shaofeng;
Tang, Wenqin;
Xu, Peiyu;
Gao, Yangzhenyu;
Li, Qian;
Dou, Zhihui;
Yang, Weishan;
Huang, Beifang;
Li, Jinhong;
Zhang, Zhuqing

Publication type:

Article

MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2054, doi. 10.1093/bioinformatics/btac025

By:

Bao, Xiaoqiong;
Zhu, Kaiyu;
Liu, Xuefei;
Chen, Zhihang;
Luo, Ziwei;
Zhao, Qi;
Ren, Jian;
Zuo, Zhixiang

Publication type:

Article

data-adaptive Bayesian regression approach for polygenic risk prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1938, doi. 10.1093/bioinformatics/btac024

By:

Song, Shuang;
Hou, Lin;
Liu, Jun S

Publication type:

Article

Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1781, doi. 10.1093/bioinformatics/btac023

By:

Marin, Maximillian;
Vargas, Roger;
Harris, Michael;
Jeffrey, Brendan;
Epperson, L Elaine;
Durbin, David;
Strong, Michael;
Salfinger, Max;
Iqbal, Zamin;
Akhundova, Irada;
Vashakidze, Sergo;
Crudu, Valeriu;
Rosenthal, Alex;
Farhat, Maha Reda

Publication type:

Article

ProSynAR: a reference aware read merger.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2052, doi. 10.1093/bioinformatics/btac022

By:

Crysup, Benjamin;
Budowle, Bruce;
Woerner, August E

Publication type:

Article

RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1863, doi. 10.1093/bioinformatics/btac021

By:

Platero-Rochart, Daniel;
González-Alemán, Roy;
Hernández-Rodríguez, Erix W;
Leclerc, Fabrice;
Caballero, Julio;
Montero-Cabrera, Luis

Publication type:

Article

SSpro/ACCpro 6: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, deep learning and structural similarity.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2064, doi. 10.1093/bioinformatics/btac019

By:

Urban, Gregor;
Magnan, Christophe N;
Baldi, Pierre

Publication type:

Article

accurate method for identifying recent recombinants from unaligned sequences.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1823, doi. 10.1093/bioinformatics/btac012

By:

Feng, Qian;
Tiedje, Kathryn E;
Ruybal-Pesántez, Shazia;
Tonkin-Hill, Gerry;
Duffy, Michael F;
Day, Karen P;
Shim, Heejung;
Chan, Yao-Ban

Publication type:

Article

Telogator: a method for reporting chromosome-specific telomere lengths from long reads.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 1788, doi. 10.1093/bioinformatics/btac005

By:

Stephens, Zachary;
Ferrer, Alejandro;
Boardman, Lisa;
Iyer, Ravishankar K;
Kocher, Jean-Pierre A

Publication type:

Article

M&Ms: a versatile software for building microbial mock communities.

Published in:

Bioinformatics, 2022, v. 38, n. 7, p. 2057, doi. 10.1093/bioinformatics/btab882

By:

García-García, Natalia;
Tamames, Javier;
Puente-Sánchez, Fernando

Publication type:

Article