Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 8

Results: 71

libSBOLj3: a graph-based library for design and data exchange in synthetic biology.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad525

By:

Mısırlı, Göksel

Publication type:

Article

DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad526

By:

Feng, Zhenhuan;
Fang, Peiyang;
Zheng, Hui;
Zhang, Xiaofei

Publication type:

Article

Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad522

By:

Jablonski, Kim Philipp;
Beerenwinkel, Niko

Publication type:

Article

Pretrained transformer models for predicting the withdrawal of drugs from the market.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad519

By:

Mazuz, Eyal;
Shtar, Guy;
Kutsky, Nir;
Rokach, Lior;
Shapira, Bracha

Publication type:

Article

Gonomics: uniting high performance and readability for genomics with Go.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad516

By:

Au, Eric H;
Fauci, Christiana;
Luo, Yanting;
Mangan, Riley J;
Snellings, Daniel A;
Shoben, Chelsea R;
Weaver, Seth;
Simpson, Shae K;
Lowe, Craig B

Publication type:

Article

VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad528

By:

Hepp, Benjamin;
Lorieux, Florence;
Degaugue, Augustin;
Oberto, Jacques

Publication type:

Article

scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad505

By:

Yan, Xuhua;
Zheng, Ruiqing;
Chen, Jinmiao;
Li, Min

Publication type:

Article

Few-shot biomedical named entity recognition via knowledge-guided instance generation and prompt contrastive learning.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad496

By:

Chen, Peng;
Wang, Jian;
Lin, Hongfei;
Zhao, Di;
Yang, Zhihao

Publication type:

Article

CoCoNat: a novel method based on deep learning for coiled-coil prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad495

By:

Madeo, Giovanni;
Savojardo, Castrense;
Manfredi, Matteo;
Martelli, Pier Luigi;
Casadio, Rita

Publication type:

Article

crosshap: R package for local haplotype visualization for trait association analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad518

By:

Marsh, Jacob I;
Petereit, Jakob;
Johnston, Brady A;
Bayer, Philipp E;
Fernandez, Cassandria G Tay;
Al-Mamun, Hawlader A;
Batley, Jacqueline;
Edwards, David

Publication type:

Article

CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad503

By:

Du, Bing-Xue;
Long, Yahui;
Li, Xiaoli;
Wu, Min;
Shi, Jian-Yu

Publication type:

Article

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad511

By:

Davidson, Russell B;
Coletti, Mark;
Gao, Mu;
Piatkowski, Bryan;
Sreedasyam, Avinash;
Quadir, Farhan;
Weston, David J;
Schmutz, Jeremy;
Cheng, Jianlin;
Skolnick, Jeffrey;
Parks, Jerry M;
Sedova, Ada

Publication type:

Article

dRFEtools: dynamic recursive feature elimination for omics.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad513

By:

Benjamin, Kynon J M;
Katipalli, Tarun;
Paquola, Apuã C M

Publication type:

Article

AARDVARK: an automated reversion detector for variants affecting resistance kinetics.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad509

By:

Moreno, Thaidy;
Magana, Joaquin;
Quigley, David A

Publication type:

Article

StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad506

By:

Aguilera-Mendoza, Longendri;
Ayala-Ruano, Sebastián;
Martinez-Rios, Felix;
Chavez, Edgar;
García-Jacas, César R;
Brizuela, Carlos A;
Marrero-Ponce, Yovani

Publication type:

Article

Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad494

By:

Subramaniya, Sai Raghavendra Maddhuri Venkata;
Terashi, Genki;
Kihara, Daisuke

Publication type:

Article

Bayesian multitask learning for medicine recommendation based on online patient reviews.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad491

By:

Cheng, Yichen;
Xia, Yusen;
Wang, Xinlei

Publication type:

Article

Predicting thermostability difference between cellular protein orthologs.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad504

By:

Fang, Jianwen

Publication type:

Article

FGCNSurv: dually fused graph convolutional network for multi-omics survival prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad472

By:

Wen, Gang;
Li, Limin

Publication type:

Article

Protein–ligand binding affinity prediction exploiting sequence constituent homology.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad502

By:

Abdel-Rehim, Abbi;
Orhobor, Oghenejokpeme;
Hang, Lou;
Ni, Hao;
King, Ross D

Publication type:

Article

Anomaly detection in mixed high-dimensional molecular data.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad501

By:

Buck, Lena;
Schmidt, Tobias;
Feist, Maren;
Schwarzfischer, Philipp;
Kube, Dieter;
Oefner, Peter J;
Zacharias, Helena U;
Altenbuchinger, Michael;
Dettmer, Katja;
Gronwald, Wolfram;
Spang, Rainer

Publication type:

Article

Correction to: Joint registration of multiple point clouds for fast particle fusion in localization microscopy.

Published in:: 2023
Publication type:: Correction Notice

MLNGCF: circRNA–disease associations prediction with multilayer attention neural graph-based collaborative filtering.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad499

By:

Wu, Qunzhuo;
Deng, Zhaohong;
Zhang, Wei;
Pan, Xiaoyong;
Choi, Kup-Sze;
Zuo, Yun;
Shen, Hong-Bin;
Yu, Dong-Jun

Publication type:

Article

Adjusting for gene-specific covariates to improve RNA-seq analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad498

By:

Jeon, Hyeongseon;
Lim, Kyu-Sang;
Nguyen, Yet;
Nettleton, Dan

Publication type:

Article

ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad493

By:

Xiong, Guangzhi;
Bekiranov, Stefan;
Zhang, Aidong

Publication type:

Article

ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad470

By:

Yang, Chen;
Mai, Jiahao;
Cao, Xuan;
Burberry, Aaron;
Cominelli, Fabio;
Zhang, Liangliang

Publication type:

Article

Exploitation of surrogate variables in random forests for unbiased analysis of mutual impact and importance of features.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad471

By:

Voges, Lucas F;
Jarren, Lukas C;
Seifert, Stephan

Publication type:

Article

Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad469

By:

Hartout, Philip;
Počuča, Bojana;
Méndez-García, Celia;
Schleberger, Christian

Publication type:

Article

NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad492

By:

Wierczeiko, Anna;
Pastore, Stefan;
Mündnich, Stefan;
Busch, Anne M;
Dietrich, Vincent;
Helm, Mark;
Butto, Tamer;
Gerber, Susanne

Publication type:

Article

Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad490

By:

Karatzas, Evangelos;
Baltoumas, Fotis A;
Aplakidou, Eleni;
Kontou, Panagiota I;
Stathopoulos, Panos;
Stefanis, Leonidas;
Bagos, Pantelis G;
Pavlopoulos, Georgios A

Publication type:

Article

PACT: a pipeline for analysis of circulating tumor DNA.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad489

By:

Webster, Jace;
Dang, Ha X;
Chauhan, Pradeep S;
Feng, Wenjia;
Shiang, Alex;
Harris, Peter K;
Pachynski, Russell K;
Chaudhuri, Aadel A;
Maher, Christopher A

Publication type:

Article

SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad488

By:

Ginell, Garrett M;
Flynn, Aidan J;
Holehouse, Alex S

Publication type:

Article

Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad487

By:

Liu, Daniel;
Steinegger, Martin

Publication type:

Article

NCOurd: modelling length distributions of NCO events and gene conversion tracts.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad485

By:

Hardarson, Marteinn T;
Palsson, Gunnar;
Halldorsson, Bjarni V

Publication type:

Article

Prediction of pathogenic single amino acid substitutions using molecular fragment descriptors.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad484

By:

Zadorozhny, Anton;
Smirnov, Anton;
Filimonov, Dmitry;
Lagunin, Alexey

Publication type:

Article

KOunt: a reproducible KEGG orthologue abundance workflow.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad483

By:

Mattock, Jennifer;
Martínez-Álvaro, Marina;
Cleveland, Matthew A;
Roehe, Rainer;
Watson, Mick

Publication type:

Article

XGDAG: explainable gene–disease associations via graph neural networks.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad482

By:

Mastropietro, Andrea;
Carlo, Gianluca De;
Anagnostopoulos, Aris

Publication type:

Article

demuxmix: demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad481

By:

Klein, Hans-Ulrich

Publication type:

Article

BEENE: deep learning-based nonlinear embedding improves batch effect estimation.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad479

By:

Rahman, Md Ashiqur;
Tutul, Abdullah Aman;
Sharmin, Mahfuza;
Bayzid, Md Shamsuzzoha

Publication type:

Article

Short-read aligner performance in germline variant identification.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad480

By:

Wilton, Richard;
Szalay, Alexander S

Publication type:

Article

Cancer drug response prediction with surrogate modeling-based graph neural architecture search.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad478

By:

Oloulade, Babatounde Moctard;
Gao, Jianliang;
Chen, Jiamin;
Al-Sabri, Raeed;
Wu, Zhenpeng

Publication type:

Article

USNAP: fast unique dense region detection and its application to lung cancer.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad477

By:

Wong, Serene W H;
Pastrello, Chiara;
Kotlyar, Max;
Faloutsos, Christos;
Jurisica, Igor

Publication type:

Article

MIX-TPI: a flexible prediction framework for TCR–pMHC interactions based on multimodal representations.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad475

By:

Yang, Minghao;
Huang, Zhi-An;
Zhou, Wei;
Ji, Junkai;
Zhang, Jun;
He, Shan;
Zhu, Zexuan

Publication type:

Article

TALAIA: a 3D visual dictionary for protein structures.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad476

By:

Alemany-Chavarria, Mercè;
Rodríguez-Guerra, Jaime;
Maréchal, Jean-Didier

Publication type:

Article

iCpG-Pos: an accurate computational approach for identification of CpG sites using positional features on single-cell whole genome sequence data.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad474

By:

Park, Sehi;
Rehman, Mobeen Ur;
Ullah, Farman;
Tayara, Hilal;
Chong, Kil To

Publication type:

Article

PCGAN: a generative approach for protein complex identification from protein interaction networks.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad473

By:

Pan, Yuliang;
Wang, Yang;
Guan, Jihong;
Zhou, Shuigeng

Publication type:

Article

BERTrand—peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad468

By:

Myronov, Alexander;
Mazzocco, Giovanni;
Król, Paulina;
Plewczynski, Dariusz

Publication type:

Article

ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad467

By:

Wang, Chen;
Govindarajan, Harikumar;
Katsonis, Panagiotis;
Lichtarge, Olivier

Publication type:

Article

TranSyT, an innovative framework for identifying transport systems.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad466

By:

Cunha, Emanuel;
Lagoa, Davide;
Faria, José P;
Liu, Filipe;
Henry, Christopher S;
Dias, Oscar

Publication type:

Article

Dynamic applicability domain (dAD): compound–target binding affinity estimates with local conformal prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad465

By:

Oršolić, Davor;
Šmuc, Tomislav

Publication type:

Article