Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 10

Results: 52

findPC: An R package to automatically select the number of principal components in single-cell analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2949, doi. 10.1093/bioinformatics/btac235

By:

Zhuang, Haotian;
Wang, Huimin;
Ji, Zhicheng

Publication type:

Article

Deep learning identifies and quantifies recombination hotspot determinants.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2683, doi. 10.1093/bioinformatics/btac234

By:

Li, Yu;
Chen, Siyuan;
Rapakoulia, Trisevgeni;
Kuwahara, Hiroyuki;
Yip, Kevin Y;
Gao, Xin

Publication type:

Article

MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2967, doi. 10.1093/bioinformatics/btac216

By:

Lake, Nicole J;
Zhou, Lily;
Xu, Jenny;
Lek, Monkol

Publication type:

Article

BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2791, doi. 10.1093/bioinformatics/btac213

By:

Boggy, Gregory J;
McElfresh, G W;
Mahyari, Eisa;
Ventura, Abigail B;
Hansen, Scott G;
Picker, Louis J;
Bimber, Benjamin N

Publication type:

Article

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2773, doi. 10.1093/bioinformatics/btac212

By:

Mu, Wancen;
Sarkar, Hirak;
Srivastava, Avi;
Choi, Kwangbom;
Patro, Rob;
Love, Michael I

Publication type:

Article

Relational graph convolutional networks for predicting blood–brain barrier penetration of drug molecules.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2826, doi. 10.1093/bioinformatics/btac211

By:

Ding, Yan;
Jiang, Xiaoqian;
Kim, Yejin

Publication type:

Article

Driver gene detection through Bayesian network integration of mutation and expression profiles.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2781, doi. 10.1093/bioinformatics/btac203

By:

Chen, Zhong;
Lu, You;
Cao, Bo;
Zhang, Wensheng;
Edwards, Andrea;
Zhang, Kun

Publication type:

Article

TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2839, doi. 10.1093/bioinformatics/btac209

By:

Eguchi, Ryohei;
Hamano, Momoko;
Iwata, Michio;
Nakamura, Toru;
Oki, Shinya;
Yamanishi, Yoshihiro

Publication type:

Article

Overcoming biases in causal inference of molecular interactions.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2818, doi. 10.1093/bioinformatics/btac206

By:

Kumar, Sajal;
Song, Mingzhou

Publication type:

Article

AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2937, doi. 10.1093/bioinformatics/btac207

By:

Shine, Morgan;
Zhang, Chengxin;
Pyle, Anna Marie

Publication type:

Article

Design and application of a knowledge network for automatic prioritization of drug mechanisms.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2880, doi. 10.1093/bioinformatics/btac205

By:

Mayers, Michael;
Tu, Roger;
Steinecke, Dylan;
Li, Tong Shu;
Queralt-Rosinach, Núria;
Su, Andrew I

Publication type:

Article

BIODICA: a computational environment for Independent Component Analysis of omics data.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2963, doi. 10.1093/bioinformatics/btac204

By:

Captier, Nicolas;
Merlevede, Jane;
Molkenov, Askhat;
Seisenova, Ainur;
Zhubanchaliyev, Altynbek;
Nazarov, Petr V;
Barillot, Emmanuel;
Kairov, Ulykbek;
Zinovyev, Andrei

Publication type:

Article

SASpector: analysis of missing genomic regions in draft genomes of prokaryotes.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2920, doi. 10.1093/bioinformatics/btac208

By:

Lood, Cédric;
Rojo, Alejandro Correa;
Sinar, Deniz;
Verkinderen, Emma;
Lavigne, Rob;
Noort, Vera van

Publication type:

Article

Impact of protein conformational diversity on AlphaFold predictions.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2742, doi. 10.1093/bioinformatics/btac202

By:

Saldaño, Tadeo;
Escobedo, Nahuel;
Marchetti, Julia;
Zea, Diego Javier;
Donagh, Juan Mac;
Rueda, Ana Julia Velez;
Gonik, Eduardo;
Melani, Agustina García;
Nechcoff, Julieta Novomisky;
Salas, Martín N;
Peters, Tomás;
Demitroff, Nicolás;
Alberti, Sebastian Fernandez;
Palopoli, Nicolas;
Fornasari, Maria Silvina;
Parisi, Gustavo

Publication type:

Article

Boost-RS: boosted embeddings for recommender systems and its application to enzyme–substrate interaction prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2832, doi. 10.1093/bioinformatics/btac201

By:

Li, Xinmeng;
Liu, Li-Ping;
Hassoun, Soha

Publication type:

Article

TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2712, doi. 10.1093/bioinformatics/btac200

By:

Yan, Ke;
Lv, Hongwu;
Guo, Yichen;
Chen, Yongyong;
Wu, Hao;
Liu, Bin

Publication type:

Article

tRNAstudio: facilitating the study of human mature tRNAs from deep sequencing datasets.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2934, doi. 10.1093/bioinformatics/btac198

By:

Murillo-Recio, Marina;
Samper, Ignacio Miguel Martínez de Lejarza;
Domínguez, Cristina Tuñí i;
Pouplana, Lluís Ribas de;
Torres, Adrian Gabriel

Publication type:

Article

Improving confidence in lipidomic annotations by incorporating empirical ion mobility regression analysis and chemical class prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2872, doi. 10.1093/bioinformatics/btac197

By:

Rose, Bailey S;
May, Jody C;
Picache, Jaqueline A;
Codreanu, Simona G;
Sherrod, Stacy D;
McLean, John A

Publication type:

Article

plotsr: visualizing structural similarities and rearrangements between multiple genomes.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2922, doi. 10.1093/bioinformatics/btac196

By:

Goel, Manish;
Schneeberger, Korbinian

Publication type:

Article

InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2918, doi. 10.1093/bioinformatics/btac194

By:

Persson, Emma;
Sonnhammer, Erik L L

Publication type:

Article

Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2863, doi. 10.1093/bioinformatics/btac192

By:

Wei, Yu;
Li, Shanshan;
Li, Zhonglin;
Wan, Ziwei;
Lin, Jianping

Publication type:

Article

VisuStatR: visualizing motility and morphology statistics on images in R.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2970, doi. 10.1093/bioinformatics/btac191

By:

Harmel, Christoph;
Ahmed, Samy Sid;
Koch, Robin;
Tünnermann, Jana;
Distler, Tania;
Imle, Andrea;
Giorgetti, Luca;
Bahn, Emanuel;
Fackler, Oliver T;
Graw, Frederik

Publication type:

Article

PyLiger: scalable single-cell multi-omic data integration in Python.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2946, doi. 10.1093/bioinformatics/btac190

By:

Lu, Lu;
Welch, Joshua D

Publication type:

Article

kc-hits: a tool to aid in the evaluation and classification of chemical carcinogens.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2961, doi. 10.1093/bioinformatics/btac189

By:

Reisfeld, Brad;
Conti, Aline de;
Ghissassi, Fatiha El;
Benbrahim-Tallaa, Lamia;
Gwinn, William;
Grosse, Yann;
Schubauer-Berigan, Mary

Publication type:

Article

TransPPMP: predicting pathogenicity of frameshift and non-sense mutations by a Transformer based on protein features.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2705, doi. 10.1093/bioinformatics/btac188

By:

Nie, Liangpeng;
Quan, Lijun;
Wu, Tingfang;
He, Ruji;
Lyu, Qiang

Publication type:

Article

RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2932, doi. 10.1093/bioinformatics/btac187

By:

Zhang, Hao;
Chang, Qixin;
Yin, Zekun;
Xu, Xiaoming;
Wei, Yanjie;
Schmidt, Bertil;
Liu, Weiguo

Publication type:

Article

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2719, doi. 10.1093/bioinformatics/btac186

By:

Caraballo-Ortiz, Marcos A;
Miura, Sayaka;
Sanderford, Maxwell;
Dolker, Tenzin;
Tao, Qiqing;
Weaver, Steven;
Pond, Sergei L K;
Kumar, Sudhir

Publication type:

Article

Annotating regulatory elements by heterogeneous network embedding.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2899, doi. 10.1093/bioinformatics/btac185

By:

Lu, Yurun;
Feng, Zhanying;
Zhang, Songmao;
Wang, Yong

Publication type:

Article

MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2930, doi. 10.1093/bioinformatics/btac184

By:

Liao, Chun-Chieh;
Fu, Po-Ying;
Huang, Chih-Wei;
Chuang, Chia-Hsien;
Yen, Yun;
Lin, Chung-Yen;
Chen, Shu-Hwa

Publication type:

Article

Network-based cancer heterogeneity analysis incorporating multi-view of prior information.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2855, doi. 10.1093/bioinformatics/btac183

By:

Li, Yang;
Xu, Shaodong;
Ma, Shuangge;
Wu, Mengyun

Publication type:

Article

VIQoR: a web service for visually supervised protein inference and protein quantification.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2757, doi. 10.1093/bioinformatics/btac182

By:

Tsiamis, Vasileios;
Schwämmle, Veit

Publication type:

Article

Integrative analysis of relative abundance data and presence–absence data of the microbiome using the LDM.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2915, doi. 10.1093/bioinformatics/btac181

By:

Zhu, Zhengyi;
Satten, Glen A;
Hu, Yi-Juan

Publication type:

Article

MOSS: multi-omic integration with sparse value decomposition.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2956, doi. 10.1093/bioinformatics/btac179

By:

Gonzalez-Reymundez, Agustin;
Grueneberg, Alexander;
Lu, Guanqi;
Alves, Filipe Couto;
Rincon, Gonzalo;
Vazquez, Ana I

Publication type:

Article

Fast and accurate inference of gene regulatory networks through robust precision matrix estimation.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2802, doi. 10.1093/bioinformatics/btac178

By:

Passemiers, Antoine;
Moreau, Yves;
Raimondi, Daniele

Publication type:

Article

comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values).

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2810, doi. 10.1093/bioinformatics/btac177

By:

Park, Aron;
Joo, Minjae;
Kim, Kyungdoc;
Son, Won-Joon;
Lim, GyuTae;
Lee, Jinhyuk;
Kim, Jung Ho;
Lee, Dae Ho;
Nam, Seungyoon

Publication type:

Article

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2700, doi. 10.1093/bioinformatics/btac176

By:

Lo, Chien-Chi;
Shakya, Migun;
Connor, Ryan;
Davenport, Karen;
Flynn, Mark;
Gutiérrez, Adán Myers y;
Hu, Bin;
Li, Po-E;
Jackson, Elais Player;
Xu, Yan;
Chain, Patrick S G

Publication type:

Article

CBNplot: Bayesian network plots for enrichment analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2959, doi. 10.1093/bioinformatics/btac175

By:

Sato, Noriaki;
Tamada, Yoshinori;
Yu, Guangchuang;
Okuno, Yasushi

Publication type:

Article

RegScaf: a regression approach to scaffolding.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2675, doi. 10.1093/bioinformatics/btac174

By:

Li, Mengtian;
Li, Lei M

Publication type:

Article

MorphoTools2: an R package for multivariate morphometric analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2954, doi. 10.1093/bioinformatics/btac173

By:

Šlenker, Marek;
Koutecký, Petr;
Marhold, Karol

Publication type:

Article

BSDE: barycenter single-cell differential expression for case–control studies.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2765, doi. 10.1093/bioinformatics/btac171

By:

Zhang, Mengqi;
Guo, F Richard

Publication type:

Article

rbioapi: user-friendly R interface to biologic web services' API.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2952, doi. 10.1093/bioinformatics/btac172

By:

Rezwani, Moosa;
Pourfathollah, Ali Akbar;
Noorbakhsh, Farshid

Publication type:

Article

LPTD: a novel linear programming-based topology determination method for cryo-EM maps.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2734, doi. 10.1093/bioinformatics/btac170

By:

Behkamal, Bahareh;
Naghibzadeh, Mahmoud;
Pagnani, Andrea;
Saberi, Mohammad Reza;
Nasr, Kamal Al

Publication type:

Article

SimSCSnTree: a simulator of single-cell DNA sequencing data.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2912, doi. 10.1093/bioinformatics/btac169

By:

Mallory, Xian Fan;
Nakhleh, Luay

Publication type:

Article

EDClust: an EM–MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2692, doi. 10.1093/bioinformatics/btac168

By:

Wei, Xin;
Li, Ziyi;
Ji, Hongkai;
Wu, Hao

Publication type:

Article

Context-aware learning for cancer cell nucleus recognition in pathology images.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2892, doi. 10.1093/bioinformatics/btac167

By:

Bai, Tian;
Xu, Jiayu;
Zhang, Zhenting;
Guo, Shuyu;
Luo, Xiao

Publication type:

Article

Analysing high-throughput sequencing data in Python with HTSeq 2.0.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2943, doi. 10.1093/bioinformatics/btac166

By:

Putri, Givanna H;
Anders, Simon;
Pyl, Paul Theodor;
Pimanda, John E;
Zanini, Fabio

Publication type:

Article

PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2927, doi. 10.1093/bioinformatics/btac165

By:

Yeh, Chiann-Ling C;
Amorosi, Clara J;
Showman, Soyeon;
Dunham, Maitreya J

Publication type:

Article

Supervised graph co-contrastive learning for drug–target interaction prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2847, doi. 10.1093/bioinformatics/btac164

By:

Li, Yang;
Qiao, Guanyu;
Gao, Xin;
Wang, Guohua

Publication type:

Article

OMAMO: orthology-based alternative model organism selection.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2965, doi. 10.1093/bioinformatics/btac163

By:

Nicheperovich, Alina;
Altenhoff, Adrian M;
Dessimoz, Christophe;
Majidian, Sina

Publication type:

Article

hacksig: a unified and tidy R framework to easily compute gene expression signature scores.

Published in:

Bioinformatics, 2022, v. 38, n. 10, p. 2940, doi. 10.1093/bioinformatics/btac161

By:

Carenzo, Andrea;
Pistore, Federico;
Serafini, Mara S;
Lenoci, Deborah;
Licata, Armando G;
Cecco, Loris De

Publication type:

Article