Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 2

Results: 45

DBDIpy: a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad088

By:

Weidner, Leopold;
Hemmler, Daniel;
Rychlik, Michael;
Schmitt-Kopplin, Philippe

Publication type:

Article

Correction to: HOMELETTE: a unified interface to homology modelling software.

Published in:: 2023
Publication type:: Correction Notice

LDmat: efficiently queryable compression of linkage disequilibrium matrices.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad092

By:

Weiner, Rockwell J;
Lakhani, Chirag;
Knowles, David A;
Gürsoy, Gamze

Publication type:

Article

Literature-based discovery: addressing the issue of the subpar evaluation methodology.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad090

By:

Moreau, Erwan

Publication type:

Article

Multimodal representation learning for predicting molecule–disease relations.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad085

By:

Wen, Jun;
Zhang, Xiang;
Rush, Everett;
Panickan, Vidul A;
Li, Xingyu;
Cai, Tianrun;
Zhou, Doudou;
Ho, Yuk-Lam;
Costa, Lauren;
Begoli, Edmon;
Hong, Chuan;
Gaziano, J Michael;
Cho, Kelly;
Lu, Junwei;
Liao, Katherine P;
Zitnik, Marinka;
Cai, Tianxi

Publication type:

Article

DaTeR: error-correcting phylogenetic chronograms using relative time constraints.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad084

By:

Mondal, Abhijit;
Rangel, L Thiberio;
Payette, Jack G;
Fournier, Gregory P;
Bansal, Mukul S

Publication type:

Article

APL@voro—interactive visualization and analysis of cell membrane simulations.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad083

By:

Kern, Martin;
Jaeger-Honz, Sabrina;
Schreiber, Falk;
Sommer, Bjorn

Publication type:

Article

The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad080

By:

Morris, John H;
Soman, Karthik;
Akbas, Rabia E;
Zhou, Xiaoyuan;
Smith, Brett;
Meng, Elaine C;
Huang, Conrad C;
Cerono, Gabriel;
Schenk, Gundolf;
Rizk-Jackson, Angela;
Harroud, Adil;
Sanders, Lauren;
Costes, Sylvain V;
Bharat, Krish;
Chakraborty, Arjun;
Pico, Alexander R;
Mardirossian, Taline;
Keiser, Michael;
Tang, Alice;
Hardi, Josef

Publication type:

Article

GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad081

By:

Dickson, Andrew;
Asgari, Ehsaneddin;
McHardy, Alice C;
Mofrad, Mohammad R K

Publication type:

Article

A novel strategy for dynamic modeling of genome-scale interaction networks.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad079

By:

Borzou, Pooya;
Ghaisari, Jafar;
Izadi, Iman;
Eshraghi, Yasin;
Gheisari, Yousof

Publication type:

Article

wpLogicNet: logic gate and structure inference in gene regulatory networks.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad072

By:

Malekpour, Seyed Amir;
Shahdoust, Maryam;
Aghdam, Rosa;
Sadeghi, Mehdi

Publication type:

Article

Patpat: a public proteomics dataset search framework.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad076

By:

Liao, Weiheng;
Zhang, Xuelian

Publication type:

Article

scBGEDA: deep single-cell clustering analysis via a dual denoising autoencoder with bipartite graph ensemble clustering.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad075

By:

Wang, Yunhe;
Yu, Zhuohan;
Li, Shaochuan;
Bian, Chuang;
Liang, Yanchun;
Wong, Ka-Chun;
Li, Xiangtao

Publication type:

Article

Optimal gap-affine alignment in O(s) space.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad074

By:

Marco-Sola, Santiago;
Eizenga, Jordan M;
Guarracino, Andrea;
Paten, Benedict;
Garrison, Erik;
Moreto, Miquel

Publication type:

Article

WMDS.net: a network control framework for identifying key players in transcriptome programs.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad071

By:

Cheng, Xiang;
Amanullah, Md;
Liu, Weigang;
Liu, Yi;
Pan, Xiaoqing;
Zhang, Honghe;
Xu, Haiming;
Liu, Pengyuan;
Lu, Yan

Publication type:

Article

ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad077

By:

Zhang, Weijie;
Shan, Yichu;
Zhao, Lili;
Liang, Zhen;
Liu, Chao;
Zhang, Lihua;
Zhang, Yukui

Publication type:

Article

A unified approach to protein domain parsing with inter-residue distance matrix.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad070

By:

Zhu, Kun;
Su, Hong;
Peng, Zhenling;
Yang, Jianyi

Publication type:

Article

PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad068

By:

Yu, Xinyi;
Xiao, Jiashun;
Cai, Mingxuan;
Jiao, Yuling;
Wan, Xiang;
Liu, Jin;
Yang, Can

Publication type:

Article

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad067

By:

Guo, Dan;
Föll, Melanie Christine;
Bemis, Kylie Ariel;
Vitek, Olga

Publication type:

Article

NMRtist: an online platform for automated biomolecular NMR spectra analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad066

By:

Klukowski, Piotr;
Riek, Roland;
Güntert, Peter

Publication type:

Article

Benchmarking tools for a priori identifiability analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad065

By:

Barreiro, Xabier Rey;
Villaverde, Alejandro F

Publication type:

Article

PyGenePlexus: a Python package for gene discovery using network-based machine learning.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad064

By:

Mancuso, Christopher A;
Liu, Renming;
Krishnan, Arjun

Publication type:

Article

Efficient penalized generalized linear mixed models for variable selection and genetic risk prediction in high-dimensional data.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad063

By:

St-Pierre, Julien;
Oualkacha, Karim;
Bhatnagar, Sahir Rai

Publication type:

Article

Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad046

By:

Zhou, Zhongliang;
Yeung, Wayland;
Gravel, Nathan;
Salcedo, Mariah;
Soleymani, Saber;
Li, Sheng;
Kannan, Natarajan

Publication type:

Article

CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad053

By:

Oarga, Alexandru;
Bannerman, Bridget P;
Júlvez, Jorge

Publication type:

Article

The adapted Activity-By-Contact model for enhancer–gene assignment and its application to single-cell data.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad062

By:

Hecker, Dennis;
Ardakani, Fatemeh Behjati;
Karollus, Alexander;
Gagneur, Julien;
Schulz, Marcel H

Publication type:

Article

GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad061

By:

Chang, Daniel;
Gupta, Vinod K;
Hur, Benjamin;
Cunningham, Kevin Y;
Sung, Jaeyun

Publication type:

Article

MFR-DTA: a multi-functional and robust model for predicting drug–target binding affinity and region.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad056

By:

Hua, Yang;
Song, Xiaoning;
Feng, Zhenhua;
Wu, Xiaojun

Publication type:

Article

How to optimally sample a sequence for rapid analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad057

By:

Frith, Martin C;
Shaw, Jim;
Spouge, John L

Publication type:

Article

TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad060

By:

Agarwal, Aman;
Zhao, Fengdi;
Jiang, Yuchao;
Chen, Li

Publication type:

Article

Potent antibiotic design via guided search from antibacterial activity evaluations.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad059

By:

Chen, Lu;
Yu, Liang;
Gao, Lin

Publication type:

Article

MS1Connect: a mass spectrometry run similarity measure.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad058

By:

Lin, Andy;
Kaiser, Brooke L Deatherage;
Hutchison, Janine R;
Bilmes, Jeffrey A

Publication type:

Article

Binding peptide generation for MHC Class I proteins with deep reinforcement learning.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad055

By:

Chen, Ziqi;
Zhang, Baoyi;
Guo, Hongyu;
Emani, Prashant;
Clancy, Trevor;
Jiang, Chongming;
Gerstein, Mark;
Ning, Xia;
Cheng, Chao;
Min, Martin Renqiang

Publication type:

Article

AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad052

By:

Kang, Yanlei;
Elofsson, Arne;
Jiang, Yunliang;
Huang, Weihong;
Yu, Minzhe;
Li, Zhong

Publication type:

Article

BLTSA: pseudotime prediction for single cells by branched local tangent space alignment.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad054

By:

Li, Limin;
Zhao, Yameng;
Li, Huiran;
Zhang, Shuqin

Publication type:

Article

CAPLA: improved prediction of protein–ligand binding affinity by a deep learning approach based on a cross-attention mechanism.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad049

By:

Jin, Zhi;
Wu, Tingfang;
Chen, Taoning;
Pan, Deng;
Wang, Xuejiao;
Xie, Jingxin;
Quan, Lijun;
Lyu, Qiang

Publication type:

Article

Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad051

By:

Zhiyanov, Anton;
Engibaryan, Narek;
Nersisyan, Stepan;
Shkurnikov, Maxim;
Tonevitsky, Alexander

Publication type:

Article

Adversarial dense graph convolutional networks for single-cell classification.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad043

By:

Wang, Kangwei;
Li, Zhengwei;
You, Zhu-Hong;
Han, Pengyong;
Nie, Ru

Publication type:

Article

CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells.

Published in:: 2023
Publication type:: Correction Notice

NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad038

By:

Abid, Dhoha;
Brent, Michael R

Publication type:

Article

Mapache: a flexible pipeline to map ancient DNA.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad028

By:

Neuenschwander, Samuel;
Dávalos, Diana I Cruz;
Anchieri, Lucas;
Mota, Bárbara Sousa da;
Bozzi, Davide;
Rubinacci, Simone;
Delaneau, Olivier;
Rasmussen, Simon;
Malaspinas, Anna-Sapfo

Publication type:

Article

Dealing with dimensionality: the application of machine learning to multi-omics data.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad021

By:

Feldner-Busztin, Dylan;
Nisantzis, Panos Firbas;
Edmunds, Shelley Jane;
Boza, Gergely;
Racimo, Fernando;
Gopalakrishnan, Shyam;
Limborg, Morten Tønsberg;
Lahti, Leo;
Polavieja, Gonzalo G de

Publication type:

Article

Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad018

By:

L'Yi, Sehi;
Keller, Mark S;
Dandawate, Ariaki;
Taing, Len;
Chen, Chen-Hao;
Brown, Myles;
Meyer, Clifford A;
Gehlenborg, Nils

Publication type:

Article

SLGNN: synthetic lethality prediction in human cancers based on factor-aware knowledge graph neural network.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad015

By:

Zhu, Yan;
Zhou, Yuhuan;
Liu, Yang;
Wang, Xuan;
Li, Junyi

Publication type:

Article

NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btac848

By:

Stolfi, Paola;
Mastropietro, Andrea;
Pasculli, Giuseppe;
Tieri, Paolo;
Vergni, Davide

Publication type:

Article