Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 4

Results: 46

Identification of protein–protein interaction bridges for multiple sclerosis.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad175

By:

Yazıcı, Gözde;
Kurt Vatandaslar, Burcu;
Aydin Canturk, Ilknur;
Aydinli, Fatmagul I;
Arici Duz, Ozge;
Karakoc, Emre;
Kerman, Bilal E;
Alkan, Can

Publication type:

Article

K-RET: knowledgeable biomedical relation extraction system.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad174

By:

Sousa, Diana F;
Couto, Francisco M

Publication type:

Article

eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad173

By:

Yang, Min;
Qiu, Bo;
He, Guo-You;
Zhou, Jian-Yuan;
Yu, Hao-Jie;
Zhang, Yu-Ying;
Li, Yan-Shang;
Li, Tai-Song;
Guo, Jin-Cheng;
Li, Xue-Cang;
Xie, Jian-Jun

Publication type:

Article

Discriminative pattern discovery for the characterization of different network populations.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad168

By:

Fassetti, Fabio;
Rombo, Simona E;
Serrao, Cristina

Publication type:

Article

Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad188

By:

Ren, Xiaoliang;
Shao, Yanwen;
Zhang, Yiwen;
Ni, Ying;
Bi, Yu;
Li, Runsheng

Publication type:

Article

Decomposing mosaic tandem repeats accurately from long reads.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad185

By:

Masutani, Bansho;
Kawahara, Riki;
Morishita, Shinichi

Publication type:

Article

Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad182

By:

Bu, Deliang;
Wang, Xiao;
Li, Qizhai

Publication type:

Article

streammd: fast low-memory duplicate marking using a Bloom filter.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad181

By:

Leonard, Conrad

Publication type:

Article

Multiscale adaptive differential abundance analysis in microbial compositional data.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad178

By:

Wang, Shulei

Publication type:

Article

SmoothT—a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad176

By:

Staritzbichler, René;
Ristic, Nikola;
Stapke, Tülin;
Hildebrand, Peter W

Publication type:

Article

MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad177

By:

El Khili, Mohamed Reda;
Memon, Safyan Aman;
Emad, Amin

Publication type:

Article

ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad171

By:

Doherty, Hannah M;
Kritikos, George;
Galardini, Marco;
Banzhaf, Manuel;
Moradigaravand, Danesh

Publication type:

Article

Population-based change-point detection for the identification of homozygosity islands.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad170

By:

Prates, Lucas;
Lemes, Renan B;
Hünemeier, Tábita;
Leonardi, Florencia

Publication type:

Article

Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad169

By:

Liu, Yi;
Elsworth, Benjamin L;
Gaunt, Tom R

Publication type:

Article

sInterBase: a comprehensive database of Escherichia coli sRNA–mRNA interactions.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad172

By:

Cohen, Shani;
Maximof, Eden;
Rokach, Shay;
Tadeski, Mor;
Veksler-Lublinsky, Isana

Publication type:

Article

Modular response analysis reformulated as a multilinear regression problem.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad166

By:

Borg, Jean-Pierre;
Colinge, Jacques;
Ravel, Patrice

Publication type:

Article

STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad165

By:

Xu, Jing;
Zhang, Aidi;
Liu, Fang;
Zhang, Xiujun

Publication type:

Article

mlf-core: a framework for deterministic machine learning.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad164

By:

Heumos, Lukas;
Ehmele, Philipp;
Kuhn Cuellar, Luis;
Menden, Kevin;
Miller, Edmund;
Lemke, Steffen;
Gabernet, Gisela;
Nahnsen, Sven

Publication type:

Article

Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad162

By:

Wang, Xuesong;
Hu, Zhihang;
Yu, Tingyang;
Wang, Yixuan;
Wang, Ruijie;
Wei, Yumeng;
Shu, Juan;
Ma, Jianzhu;
Li, Yu

Publication type:

Article

WAVES (Web-based tool for Analysis and Visualization of Environmental Samples)—a web application for visualization of wastewater pathogen sequencing results.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad160

By:

Triska, Petr;
Amman, Fabian;
Endler, Lukas;
Bergthaler, Andreas

Publication type:

Article

Unmixing biological fluorescence image data with sparse and low-rank Poisson regression.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad159

By:

Wang, Ruogu;
Lemus, Alex A;
Henneberry, Colin M;
Ying, Yiming;
Feng, Yunlong;
Valm, Alex M

Publication type:

Article

Boolean network sketches: a unifying framework for logical model inference.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad158

By:

Beneš, Nikola;
Brim, Luboš;
Huvar, Ondřej;
Pastva, Samuel;
Šafránek, David

Publication type:

Article

De novo drug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad157

By:

Fang, Yi;
Pan, Xiaoyong;
Shen, Hong-Bin

Publication type:

Article

Integrative analysis of individual-level data and high-dimensional summary statistics.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad156

By:

Fu, Sheng;
Deng, Lu;
Zhang, Han;
Qin, Jing;
Yu, Kai

Publication type:

Article

HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad154

By:

Ye, Tiantian;
Hu, Yangyang;
Pun, Sydney;
Ma, Wenxiu

Publication type:

Article

Foldcomp: a library and format for compressing and indexing large protein structure sets.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad153

By:

Kim, Hyunbin;
Mirdita, Milot;
Steinegger, Martin

Publication type:

Article

DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad152

By:

Marriott, Heather;
Kabiljo, Renata;
Al Khleifat, Ahmad;
Dobson, Richard J;
Al-Chalabi, Ammar;
Iacoangeli, Alfredo

Publication type:

Article

AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad149

By:

Dong, Chenyang;
Shen, Siqi;
Keleş, Sündüz

Publication type:

Article

Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad148

By:

Zhang, Mingqian;
Zhang, Wenke;
Chen, Yuzhu;
Zhao, Jin;
Wu, Shunyao;
Su, Xiaoquan

Publication type:

Article

Correction to: Multi-omic integration by machine learning (MIMaL).

Published in:: 2023
Publication type:: Correction Notice

A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad145

By:

Li, Yuxin;
Liu, Xuhua;
Jia, Xueyan;
Jiang, Tao;
Wu, Jianghao;
Zhang, Qianlong;
Li, Junhuai;
Li, Xiangning;
Li, Anan

Publication type:

Article

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

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad144

By:

Skog, Signe;
Örkenby, Lovisa;
Kugelberg, Unn;
Öst, Anita;
Nätt, Daniel

Publication type:

Article

Phenonaut: multiomics data integration for phenotypic space exploration.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad143

By:

Shave, Steven;
Dawson, John C;
Athar, Abdullah M;
Nguyen, Cuong Q;
Kasprowicz, Richard;
Carragher, Neil O

Publication type:

Article

OutSingle: a novel method of detecting and injecting outliers in RNA-Seq count data using the optimal hard threshold for singular values.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad142

By:

Salkovic, Edin;
Sadeghi, Mohammad Amin;
Baggag, Abdelkader;
Salem, Ahmed Gamal Rashed;
Bensmail, Halima

Publication type:

Article

The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad139

By:

Zhang, Ziang;
Sun, Lei

Publication type:

Article

RNAget: an API to securely retrieve RNA quantifications.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad126

By:

Upchurch, Sean;
Palumbo, Emilio;
Adams, Jeremy;
Bujold, David;
Bourque, Guillaume;
Nedzel, Jared;
Graham, Keenan;
Kagda, Meenakshi S;
Assis, Pedro;
Hitz, Benjamin;
Righi, Emilio;
Guigó, Roderic;
Wold, Barbara J;
GA4GH RNA-Seq Task Team;
Brazma, Alvis;
Burchard, Julia;
Capka, Joe;
Cherry, Michael;
Clarke, Laura;
Craft, Brian

Publication type:

Article

dipwmsearch: a Python package for searching di-PWM motifs.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad141

By:

Mille, Marie;
Ripoll, Julie;
Cazaux, Bastien;
Rivals, Eric

Publication type:

Article

IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad140

By:

Yuzeir, Altay;
Bejarano, David Alejandro;
Grein, Stephan;
Hasenauer, Jan;
Schlitzer, Andreas;
Yu, Jiangyan

Publication type:

Article

PreTP-2L: identification of therapeutic peptides and their types using two-layer ensemble learning framework.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad125

By:

Yan, Ke;
Guo, Yichen;
Liu, Bin

Publication type:

Article

Effective and efficient active learning for deep learning-based tissue image analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad138

By:

Meirelles, André L S;
Kurc, Tahsin;
Kong, Jun;
Ferreira, Renato;
Saltz, Joel;
Teodoro, George

Publication type:

Article

An expectation–maximization framework for comprehensive prediction of isoform-specific functions.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad132

By:

Karlebach, Guy;
Carmody, Leigh;
Sundaramurthi, Jagadish Chandrabose;
Casiraghi, Elena;
Hansen, Peter;
Reese, Justin;
Mungall, Christopher J;
Valentini, Giorgio;
Robinson, Peter N

Publication type:

Article

scMCs: a framework for single-cell multi-omics data integration and multiple clusterings.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad133

By:

Ren, Liangrui;
Wang, Jun;
Li, Zhao;
Li, Qingzhong;
Yu, Guoxian

Publication type:

Article

Prediction and curation of missing biomedical identifier mappings with Biomappings.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad130

By:

Hoyt, Charles Tapley;
Hoyt, Amelia L;
Gyori, Benjamin M

Publication type:

Article

DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad073

By:

Packer, Richard J;
Williams, Alex T;
Hennah, William;
Eisenberg, Micaela T;
Shrine, Nick;
Fawcett, Katherine A;
Pearson, Willow;
Guyatt, Anna L;
Edris, Ahmed;
Hollox, Edward J;
Marttila, Mikko;
Rao, Balasubramanya S;
Bratty, John Raymond;
Wain, Louise V;
Dudbridge, Frank;
Tobin, Martin D

Publication type:

Article

Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad113

By:

Cho, Hyun Jae;
Shu, Mia;
Bekiranov, Stefan;
Zang, Chongzhi;
Zhang, Aidong

Publication type:

Article

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.

Published in:

Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad110

By:

Shaffer, Michael;
Borton, Mikayla A;
Bolduc, Ben;
Faria, José P;
Flynn, Rory M;
Ghadermazi, Parsa;
Edirisinghe, Janaka N;
Wood-Charlson, Elisha M;
Miller, Christopher S;
Chan, Siu Hung Joshua;
Sullivan, Matthew B;
Henry, Christopher S;
Wrighton, Kelly C

Publication type:

Article