Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 9

Results: 54

Correction to: GSpace: an exact coalescence simulator of recombining genomes under isolation by distance.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2674, doi. 10.1093/bioinformatics/btac193

By:

Virgoulay, Thimothée;
Rousset, François;
Leblois, Raphaël

Publication type:

Article

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

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2673, doi. 10.1093/bioinformatics/btac162

By:

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

Publication type:

Article

LOCAN: a python library for analyzing single-molecule localization microscopy data.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2670, doi. 10.1093/bioinformatics/btac160

By:

Doose, Sören

Publication type:

Article

PANPROVA: pangenomic prokaryotic evolution of full assemblies.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2631, doi. 10.1093/bioinformatics/btac158

By:

Bonnici, Vincenzo;
Giugno, Rosalba

Publication type:

Article

RevUP: an online scoring system for regulatory variants implicated in rare diseases.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2664, doi. 10.1093/bioinformatics/btac157

By:

Correard, Solenne;
Hewitson, Brittany;
van der Lee, Robin;
Wasserman, Wyeth W

Publication type:

Article

HiCARN: resolution enhancement of Hi-C data using cascading residual networks.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2414, doi. 10.1093/bioinformatics/btac156

By:

Hicks, Parker;
Oluwadare, Oluwatosin

Publication type:

Article

BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2571, doi. 10.1093/bioinformatics/btac155

By:

Wu, Yifan;
Gao, Min;
Zeng, Min;
Zhang, Jie;
Li, Min

Publication type:

Article

DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2561, doi. 10.1093/bioinformatics/btac154

By:

Cai, Tian;
Abbu, Kyra Alyssa;
Liu, Yang;
Xie, Lei

Publication type:

Article

PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2659, doi. 10.1093/bioinformatics/btac153

By:

Ogris, Christoph;
Castresana-Aguirre, Miguel;
Sonnhammer, Erik L L

Publication type:

Article

GenRisk: a tool for comprehensive genetic risk modeling.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2651, doi. 10.1093/bioinformatics/btac152

By:

Aldisi, Rana;
Hassanin, Emadeldin;
Sivalingam, Sugirthan;
Buness, Andreas;
Klinkhammer, Hannah;
Mayr, Andreas;
Fröhlich, Holger;
Krawitz, Peter;
Maj, Carlo

Publication type:

Article

AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2628, doi. 10.1093/bioinformatics/btac151

By:

Młokosiewicz, Jakub;
Deszyński, Piotr;
Wilman, Wiktoria;
Jaszczyszyn, Igor;
Ganesan, Rajkumar;
Kovaltsuk, Aleksandr;
Leem, Jinwoo;
Galson, Jacob D;
Krawczyk, Konrad

Publication type:

Article

CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2621, doi. 10.1093/bioinformatics/btac150

By:

Przytycki, Pawel F;
Pollard, Katherine S

Publication type:

Article

NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2648, doi. 10.1093/bioinformatics/btac149

By:

Agostinis, Federico;
Romualdi, Chiara;
Sales, Gabriele;
Risso, Davide

Publication type:

Article

Heterogeneous graph embedding model for predicting interactions between TF and target gene.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2554, doi. 10.1093/bioinformatics/btac148

By:

Huang, Yu-An;
Pan, Gui-Qing;
Wang, Jia;
Li, Jian-Qiang;
Chen, Jie;
Wu, Yang-Han

Publication type:

Article

GraphGONet: a self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2504, doi. 10.1093/bioinformatics/btac147

By:

Bourgeais, Victoria;
Zehraoui, Farida;
Hanczar, Blaise

Publication type:

Article

Variomes: a high recall search engine to support the curation of genomic variants.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2595, doi. 10.1093/bioinformatics/btac146

By:

Pasche, Emilie;
Mottaz, Anaïs;
Caucheteur, Déborah;
Gobeill, Julien;
Michel, Pierre-André;
Ruch, Patrick

Publication type:

Article

spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2645, doi. 10.1093/bioinformatics/btac145

By:

Ospina, Oscar E;
Wilson, Christopher M;
Soupir, Alex C;
Berglund, Anders;
Smalley, Inna;
Tsai, Kenneth Y;
Fridley, Brooke L

Publication type:

Article

Evitar: designing anti-viral RNA therapies against future RNA viruses.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2437, doi. 10.1093/bioinformatics/btac144

By:

Zhang, Dingyao;
Tian, Jingru;
Wang, Yadong;
Lu, Jun

Publication type:

Article

Bayesian method to cluster single-cell RNA sequencing data using copy number alterations.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2512, doi. 10.1093/bioinformatics/btac143

By:

Milite, Salvatore;
Bergamin, Riccardo;
Patruno, Lucrezia;
Calonaci, Nicola;
Caravagna, Giulio

Publication type:

Article

scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2642, doi. 10.1093/bioinformatics/btac141

By:

Andreatta, Massimo;
Berenstein, Ariel J;
Carmona, Santiago J

Publication type:

Article

JIND: joint integration and discrimination for automated single-cell annotation.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2488, doi. 10.1093/bioinformatics/btac140

By:

Goyal, Mohit;
Serrano, Guillermo;
Argemi, Josepmaria;
Shomorony, Ilan;
Hernaez, Mikel;
Ochoa, Idoia

Publication type:

Article

Transgene-design: a web application for the design of mammalian transgenes.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2626, doi. 10.1093/bioinformatics/btac139

By:

Mühlhausen, Stefanie;
Hurst, Laurence D

Publication type:

Article

ensemble approach to predict binding hotspots in protein–RNA interactions based on SMOTE data balancing and Random Grouping feature selection strategies.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2452, doi. 10.1093/bioinformatics/btac138

By:

Zhou, Tong;
Rong, Jie;
Liu, Yang;
Gong, Weikang;
Li, Chunhua

Publication type:

Article

BWA-MEME: BWA-MEM emulated with a machine learning approach.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2404, doi. 10.1093/bioinformatics/btac137

By:

Jung, Youngmok;
Han, Dongsu

Publication type:

Article

HAMdetector: a Bayesian regression model that integrates information to detect HLA-associated mutations.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2428, doi. 10.1093/bioinformatics/btac134

By:

Habermann, Daniel;
Kharimzadeh, Hadi;
Walker, Andreas;
Li, Yang;
Yang, Rongge;
Kaiser, Rolf;
Brumme, Zabrina L;
Timm, Jörg;
Roggendorf, Michael;
Hoffmann, Daniel

Publication type:

Article

fastISM: performant in silico saturation mutagenesis for convolutional neural networks.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2397, doi. 10.1093/bioinformatics/btac135

By:

Nair, Surag;
Shrikumar, Avanti;
Schreiber, Jacob;
Kundaje, Anshul

Publication type:

Article

To rarefy or not to rarefy: robustness and efficiency trade-offs of rarefying microbiome data.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2389, doi. 10.1093/bioinformatics/btac127

By:

Hong, Johnny;
Karaoz, Ulas;
Valpine, Perry de;
Fithian, William

Publication type:

Article

Modeling multi-scale data via a network of networks.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2544, doi. 10.1093/bioinformatics/btac133

By:

Gu, Shawn;
Jiang, Meng;
Guzzi, Pietro Hiram;
Milenković, Tijana

Publication type:

Article

Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2496, doi. 10.1093/bioinformatics/btac131

By:

Zhai, Zhiqian;
Lei, Yu L;
Wang, Rongrong;
Xie, Yuying

Publication type:

Article

Phitest for analyzing the homogeneity of single-cell populations.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2639, doi. 10.1093/bioinformatics/btac130

By:

Li, Wei Vivian

Publication type:

Article

COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2661, doi. 10.1093/bioinformatics/btac129

By:

Shi, Andy;
Gaynor, Sheila M;
Dey, Rounak;
Zhang, Haoyu;
Quick, Corbin;
Lin, Xihong

Publication type:

Article

SomaticSiMu: a mutational signature simulator.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2619, doi. 10.1093/bioinformatics/btac128

By:

Chen, David;
Randhawa, Gurjit S;
Soltysiak, Maximillian P M;
Souza, Camila P E de;
Kari, Lila;
Singh, Shiva M;
Hill, Kathleen A

Publication type:

Article

MultiBaC: an R package to remove batch effects in multi-omic experiments.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2657, doi. 10.1093/bioinformatics/btac132

By:

Ugidos, Manuel;
Nueda, María José;
Prats-Montalbán, José M;
Ferrer, Alberto;
Conesa, Ana;
Tarazona, Sonia

Publication type:

Article

StAmP-DB: a platform for structures of polymorphic amyloid fibril cores.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2636, doi. 10.1093/bioinformatics/btac126

By:

Louros, Nikolaos;
van der Kant, Rob;
Schymkowitz, Joost;
Rousseau, Frederic

Publication type:

Article

BamToCov: an efficient toolkit for sequence coverage calculations.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2617, doi. 10.1093/bioinformatics/btac125

By:

Birolo, Giovanni;
Telatin, Andrea

Publication type:

Article

POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2474, doi. 10.1093/bioinformatics/btac124

By:

Holmström, Susanna;
Hautaniemi, Sampsa;
Häkkinen, Antti

Publication type:

Article

Multi-scale deep learning for the imbalanced multi-label protein subcellular localization prediction based on immunohistochemistry images.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2602, doi. 10.1093/bioinformatics/btac123

By:

Wang, Fengsheng;
Wei, Leyi

Publication type:

Article

SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2536, doi. 10.1093/bioinformatics/btac122

By:

Li, Xingyi;
Li, Min;
Xiang, Ju;
Zhao, Zhelin;
Shang, Xuequn

Publication type:

Article

µProteInS—a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2612, doi. 10.1093/bioinformatics/btac115

By:

Souza, Eduardo Vieira de;
Dalberto, Pedro Ferrari;
Machado, Vinicius Pellisoli;
Canedo, Adriana;
Saghatelian, Alan;
Machado, Pablo;
Basso, Luiz Augusto;
Bizarro, Cristiano Valim

Publication type:

Article

localpdb—a Python package to manage protein structures and their annotations.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2633, doi. 10.1093/bioinformatics/btac121

By:

Ludwiczak, Jan;
Winski, Aleksander;
Dunin-Horkawicz, Stanislaw

Publication type:

Article

CobraMod: a pathway-centric curation tool for constraint-based metabolic models.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2654, doi. 10.1093/bioinformatics/btac119

By:

Camborda, Stefano;
Weder, Jan-Niklas;
Töpfer, Nadine

Publication type:

Article

Topological approximate Bayesian computation for parameter inference of an angiogenesis model.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2529, doi. 10.1093/bioinformatics/btac118

By:

Thorne, Thomas;
Kirk, Paul D W;
Harrington, Heather A

Publication type:

Article

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2519, doi. 10.1093/bioinformatics/btac117

By:

Gibbs, Claudia Skok;
Jackson, Christopher A;
Saldi, Giuseppe-Antonio;
Tjärnberg, Andreas;
Shah, Aashna;
Watters, Aaron;
Veaux, Nicholas De;
Tchourine, Konstantine;
Yi, Ren;
Hamamsy, Tymor;
Castro, Dayanne M;
Carriero, Nicholas;
Gorissen, Bram L;
Gresham, David;
Miraldi, Emily R;
Bonneau, Richard

Publication type:

Article

scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2466, doi. 10.1093/bioinformatics/btac110

By:

Soutschek, Michael;
Gross, Fridolin;
Schratt, Gerhard;
Germain, Pierre-Luc

Publication type:

Article

TRScore: a 3D RepVGG-based scoring method for ranking protein docking models.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2444, doi. 10.1093/bioinformatics/btac120

By:

Guo, Linyuan;
He, Jiahua;
Lin, Peicong;
Huang, Sheng-You;
Wang, Jianxin

Publication type:

Article

Single-cell RNA sequencing data analysis based on non-uniform ε−neighborhood network.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2459, doi. 10.1093/bioinformatics/btac114

By:

Jia, Junbo;
Chen, Luonan

Publication type:

Article

HFBSurv: hierarchical multimodal fusion with factorized bilinear models for cancer survival prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2587, doi. 10.1093/bioinformatics/btac113

By:

Li, Ruiqing;
Wu, Xingqi;
Li, Ao;
Wang, Minghui

Publication type:

Article

Advanced graph and sequence neural networks for molecular property prediction and drug discovery.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2579, doi. 10.1093/bioinformatics/btac112

By:

Wang, Zhengyang;
Liu, Meng;
Luo, Youzhi;
Xu, Zhao;
Xie, Yaochen;
Wang, Limei;
Cai, Lei;
Qi, Qi;
Yuan, Zhuoning;
Yang, Tianbao;
Ji, Shuiwang

Publication type:

Article

TSAFinder: exhaustive tumor-specific antigen detection with RNAseq.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2422, doi. 10.1093/bioinformatics/btac116

By:

Sharpnack, Michael F;
Johnson, Travis S;
Chalkley, Robert;
Han, Zhi;
Carbone, David;
Huang, Kun;
He, Kai

Publication type:

Article

YeastMate: neural network-assisted segmentation of mating and budding events in Saccharomyces cerevisiae.

Published in:

Bioinformatics, 2022, v. 38, n. 9, p. 2667, doi. 10.1093/bioinformatics/btac107

By:

Bunk, David;
Moriasy, Julian;
Thoma, Felix;
Jakubke, Christopher;
Osman, Christof;
Hörl, David

Publication type:

Article