Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 6

Results: 66

MRGCN: cancer subtyping with multi-reconstruction graph convolutional network using full and partial multi-omics dataset.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad353

By:

Yang, Bo;
Yang, Yan;
Wang, Meng;
Su, Xueping

Publication type:

Article

ESPERANTO: a GLP-field sEmi-SuPERvised toxicogenomics metadAta curatioN TOol.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad405

By:

Lieto, Emanuele Di;
Serra, Angela;
Inkala, Simo Iisakki;
Saarimäki, Laura Aliisa;
Giudice, Giusy del;
Fratello, Michele;
Hautanen, Veera;
Annala, Maria;
Federico, Antonio;
Greco, Dario

Publication type:

Article

UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad391

By:

Ocetkiewicz, Krzysztof M;
Czaplewski, Cezary;
Krawczyk, Henryk;
Lipska, Agnieszka G;
Liwo, Adam;
Proficz, Jerzy;
Sieradzan, Adam K;
Czarnul, Paweł

Publication type:

Article

Interpretable deep learning architectures for improving drug response prediction performance: myth or reality?

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad390

By:

Li, Yihui;
Hostallero, David Earl;
Emad, Amin

Publication type:

Article

HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad389

By:

Wang, Xiaotao;
Yue, Feng

Publication type:

Article

WarpSTR: determining tandem repeat lengths using raw nanopore signals.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad388

By:

Sitarčík, Jozef;
Vinař, Tomáš;
Brejová, Broňa;
Krampl, Werner;
Budiš, Jaroslav;
Radvánszky, Ján;
Lucká, Mária

Publication type:

Article

Biologically informed variational autoencoders allow predictive modeling of genetic and drug-induced perturbations.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad387

By:

Doncevic, Daria;
Herrmann, Carl

Publication type:

Article

Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad386

By:

Fischer, Jonas;
Schulz, Marcel H

Publication type:

Article

MolClustPy: a Python package to characterize multivalent biomolecular clusters.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad385

By:

Chattaraj, Aniruddha;
Nalagandla, Indivar;
Loew, Leslie M;
Blinov, Michael L

Publication type:

Article

Ensemble deep learning of embeddings for clustering multimodal single-cell omics data.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad382

By:

Yu, Lijia;
Liu, Chunlei;
Yang, Jean Yee Hwa;
Yang, Pengyi

Publication type:

Article

Cell shape characterization, alignment, and comparison using FlowShape.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad383

By:

Bavel, Casper van;
Thiels, Wim;
Jelier, Rob

Publication type:

Article

NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad372

By:

Abrar, Mohammed Abid;
Kaykobad, M;
Rahman, M Saifur;
Samee, Md Abul Hassan

Publication type:

Article

Finding motifs using DNA images derived from sparse representations.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad378

By:

Chu, Shane K;
Stormo, Gary D

Publication type:

Article

Mistle: bringing spectral library predictions to metaproteomics with an efficient search index.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad376

By:

Nowatzky, Yannek;
Benner, Philipp;
Reinert, Knut;
Muth, Thilo

Publication type:

Article

MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad373

By:

Pan, Tony C;
Chockalingam, Sriram P;
Aluru, Maneesha;
Aluru, Srinivas

Publication type:

Article

MASH Native: a unified solution for native top-down proteomics data processing.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad359

By:

Larson, Eli J;
Pergande, Melissa R;
Moss, Michelle E;
Rossler, Kalina J;
Wenger, R Kent;
Krichel, Boris;
Josyer, Harini;
Melby, Jake A;
Roberts, David S;
Pike, Kyndalanne;
Shi, Zhuoxin;
Chan, Hsin-Ju;
Knight, Bridget;
Rogers, Holden T;
Brown, Kyle A;
Ong, Irene M;
Jeong, Kyowon;
Marty, Michael T;
McIlwain, Sean J;
Ge, Ying

Publication type:

Article

GRETTA: an R package for mapping in silico genetic interaction and essentiality networks.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad381

By:

Takemon, Yuka;
Marra, Marco A

Publication type:

Article

Dicodon-based measures for modeling gene expression.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad380

By:

Alonso, Andres M;
Diambra, Luis

Publication type:

Article

Correction to: Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts.

Published in:: 2023
Publication type:: Correction Notice

networkGWAS: a network-based approach to discover genetic associations.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad370

By:

Muzio, Giulia;
O'Bray, Leslie;
Meng-Papaxanthos, Laetitia;
Klatt, Juliane;
Fischer, Krista;
Borgwardt, Karsten

Publication type:

Article

SEMtree: tree-based structure learning methods with structural equation models.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad377

By:

Grassi, Mario;
Tarantino, Barbara

Publication type:

Article

3D graph contrastive learning for molecular property prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad371

By:

Moon, Kisung;
Im, Hyeon-Jin;
Kwon, Sunyoung

Publication type:

Article

DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad375

By:

Zhang, Tianjiao;
Li, Liangyu;
Sun, Hailong;
Wang, Guohua

Publication type:

Article

Multiscale model of the different modes of cancer cell invasion.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad374

By:

Ruscone, Marco;
Montagud, Arnau;
Chavrier, Philippe;
Destaing, Olivier;
Bonnet, Isabelle;
Zinovyev, Andrei;
Barillot, Emmanuel;
Noël, Vincent;
Calzone, Laurence

Publication type:

Article

Consensus label propagation with graph convolutional networks for single-cell RNA sequencing cell type annotation.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad360

By:

Lewinsohn, Daniel P;
Vigh-Conrad, Katinka A;
Conrad, Donald F;
Scott, Cory B

Publication type:

Article

S1000: a better taxonomic name corpus for biomedical information extraction.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad369

By:

Luoma, Jouni;
Nastou, Katerina;
Ohta, Tomoko;
Toivonen, Harttu;
Pafilis, Evangelos;
Jensen, Lars Juhl;
Pyysalo, Sampo

Publication type:

Article

The NanoFlow Repository.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad368

By:

Arce, Jessie E;
Welsh, Joshua A;
Cook, Sean;
Tigges, John;
Ghiran, Ionita;
Jones, Jennifer C;
Jackson, Andrew;
Roth, Matthew;
Milosavljevic, Aleksandar

Publication type:

Article

Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad367

By:

Jenior, Matthew L;
Glass, Emma M;
Papin, Jason A

Publication type:

Article

mpwR: an R package for comparing performance of mass spectrometry-based proteomic workflows.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad358

By:

Kardell, Oliver;
Breimann, Stephan;
Hauck, Stefanie M

Publication type:

Article

3DMolMS: prediction of tandem mass spectra from 3D molecular conformations.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad354

By:

Hong, Yuhui;
Li, Sujun;
Welch, Christopher J;
Tichy, Shane;
Ye, Yuzhen;
Tang, Haixu

Publication type:

Article

JUMP: replicability analysis of high-throughput experiments with applications to spatial transcriptomic studies.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad366

By:

Lyu, Pengfei;
Li, Yan;
Wen, Xiaoquan;
Cao, Hongyuan

Publication type:

Article

AIRRSHIP: simulating human B cell receptor repertoire sequences.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad365

By:

Sutherland, Catherine;
Cowan, Graeme J M

Publication type:

Article

IsoTools: a flexible workflow for long-read transcriptome sequencing analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad364

By:

Lienhard, Matthias;
van den Beucken, Twan;
Timmermann, Bernd;
Hochradel, Myriam;
Börno, Stefan;
Caiment, Florian;
Vingron, Martin;
Herwig, Ralf

Publication type:

Article

MTM: a multi-task learning framework to predict individualized tissue gene expression profiles.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad363

By:

He, Guangyi;
Chen, Maiyue;
Bian, Yingnan;
Yang, Ence

Publication type:

Article

Optimization-based decoding of Imaging Spatial Transcriptomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad362

By:

Bryan, John P;
Binan, Loïc;
McCann, Cai;
Eldar, Yonina C;
Farhi, Samouil L;
Cleary, Brian

Publication type:

Article

Consistency enhancement of model prediction on document-level named entity recognition.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad361

By:

Jeong, Minbyul;
Kang, Jaewoo

Publication type:

Article

On the representativeness and stability of a set of EFMs.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad356

By:

Guil, Francisco;
Hidalgo, José F;
García, José M

Publication type:

Article

NHGNN-DTA: a node-adaptive hybrid graph neural network for interpretable drug–target binding affinity prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad355

By:

He, Haohuai;
Chen, Guanxing;
Chen, Calvin Yu-Chian

Publication type:

Article

Similarity measures-based graph co-contrastive learning for drug–disease association prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad357

By:

Gao, Zihao;
Ma, Huifang;
Zhang, Xiaohui;
Wang, Yike;
Wu, Zheyu

Publication type:

Article

Accelerated nanopore basecalling with SLOW5 data format.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad352

By:

Samarakoon, Hiruna;
Ferguson, James M;
Gamaarachchi, Hasindu;
Deveson, Ira W

Publication type:

Article

A complete graph-based approach with multi-task learning for predicting synergistic drug combinations.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad351

By:

Wang, Xiaowen;
Zhu, Hongming;
Chen, Danyi;
Yu, Yongsheng;
Liu, Qi;
Liu, Qin

Publication type:

Article

BRGenomics for analyzing high-resolution genomics data in R.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad331

By:

DeBerardine, Michael

Publication type:

Article

Cellenium—a scalable and interactive visual analytics app for exploring multimodal single-cell data.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad349

By:

Jahn, Carsten;
Ibrahim, Mahmoud;
Busch, Jannis;
Lin, Qiong;
Manchanda, Himanshu;
Mohr, Hagen;
Plischke, Dan;
Roider, Helge G;
Steffen, Andreas

Publication type:

Article

The ACPYPE web server for small-molecule MD topology generation.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad350

By:

Kagami, Luciano;
Wilter, Alan;
Diaz, Adrian;
Vranken, Wim

Publication type:

Article

Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad342

By:

Lee, Junseok;
Kim, Sungwon;
Hyun, Dongmin;
Lee, Namkyeong;
Kim, Yejin;
Park, Chanyoung

Publication type:

Article

Nonlinear data fusion over Entity–Relation graphs for Drug–Target Interaction prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad348

By:

Mazzone, Eugenio;
Moreau, Yves;
Fariselli, Piero;
Raimondi, Daniele

Publication type:

Article

KNeMAP: a network mapping approach for knowledge-driven comparison of transcriptomic profiles.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad341

By:

Pavel, Alisa;
Giudice, Giusy del;
Fratello, Michele;
Ghemtio, Leo;
Lieto, Antonio Di;
Yli-Kauhaluoma, Jari;
Xhaard, Henri;
Federico, Antonio;
Serra, Angela;
Greco, Dario

Publication type:

Article

CW-NET for multitype cell detection and classification in bone marrow examination and mitotic figure examination.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad344

By:

Wang, Ching-Wei;
Huang, Sheng-Chuan;
Khalil, Muhammad-Adil;
Hong, Ding-Zhi;
Meng, Shwu-Ing;
Lee, Yu-Ching

Publication type:

Article

Pygenomics: manipulating genomic intervals and data files in Python.

Published in:

Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad346

By:

Tamazian, Gaik;
Cherkasov, Nikolay;
Kanapin, Alexander;
Samsonova, Anastasia

Publication type:

Article

Correction: Surface ID: a geometry-aware system for protein molecular surface comparison.

Published in:: 2023
Publication type:: Correction Notice