Works matching DE "BIOINFORMATICS software"

Results: 783

Exploring Anticancer Potential in Bajakah Tampala by In Silico Virtual Screening.

Published in:

KnE Life Sciences, 2022, p. 111, doi. 10.18502/kls.v7i5.12517

By:

Yuniarti, L.;
Respati, T.;
Tejasari, M.

Publication type:

Article

1株新型耐甲氧西林金黄色葡萄球菌噬菌体的生物学特性及基因组特征.

Published in:

China Tropical Medicine, 2025, v. 25, n. 4, p. 474, doi. 10.13604/j.cnki.46-1064/r.2025.04.15

By:

吕梅萍;
裴华;
王彦双;
林翀;
董金会

Publication type:

Article

ZBTB10 as a potential prognosis biomarker and correlates with the tumor immune microenvironment in stomach adenocarcinoma.

Published in:

BMC Gastroenterology, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12876-025-04047-y

By:

Jiang, Yingdi;
Han, Fuhua;
Dai, Lu;
Qiu, Shali;
Zhou, Yanjie;
Wang, Ke;
Lin, Jiang

Publication type:

Article

A comprehensive investigation of identifying miRNA biomarkers and their potential role in age-related cataract by meta-analysis and bioinformatics analysis.

Published in:

Graefe's Archive of Clinical & Experimental Ophthalmology, 2025, v. 263, n. 5, p. 1307, doi. 10.1007/s00417-024-06723-3

By:

Zhang, Kaiyun;
Chen, Li;
Qu, Laiqiang;
Yan, Hong

Publication type:

Article

Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.94029

By:

Harmalkar, Ameya;
Lyskov, Sergey;
Gray, Jeffrey J.

Publication type:

Article

Contributing to the Functional Classification of Missense Variants in RAG1 Protein from Structural Perspective.

Published in:

Experimed, 2025, v. 15, n. 1, p. 31, doi. 10.26650/experimed.1562959

By:

Kutlu, Asli;
Isikgil, Begum;
Firtina, Sinem

Publication type:

Article

MAPK8 and HDAC6: potential biomarkers related to autophagy in diabetic retinopathy based on bioinformatics analysis.

Published in:

Frontiers in Endocrinology, 2025, p. 1, doi. 10.3389/fendo.2025.1487007

By:

Sun, Ruotong;
Zuo, Ling

Publication type:

Article

Cloning, Expression, and Bioinformatics Analysis of the AvFD1 Gene in Amomum villosum Lour.

Published in:

Biology (2079-7737), 2025, v. 14, n. 5, p. 457, doi. 10.3390/biology14050457

By:

Wang, Duo;
Zhu, Yating;
Li, Shuang;
Zhao, Hongyou;
Wang, Chongnan;
Li, Qianxia;
Wang, Yanfang;
Yang, Chunyong;
Li, Ge;
Wang, Yanqian;
Zhang, Lixia

Publication type:

Article

Disrupted expression of long non-coding RNAs in the human oocyte: the possible epigenetic culprits leading to recurrent oocyte maturation arrest.

Published in:

Journal of Assisted Reproduction & Genetics, 2022, v. 39, n. 10, p. 2215, doi. 10.1007/s10815-022-02596-9

By:

Wei, Lina;
Xia, Huayang;
Liang, Zhongkun;
Yu, Hao;
Liang, Zhenjie;
Yang, Xi;
Li, Yi

Publication type:

Article

Predictive Science Center in Russia.

Published in:

Bio-IT World, 2011, v. 10, n. 5, p. 10

By:

GERDEN, EUGENE

Publication type:

Article

A comprehensive Y-STR portrait of Yousafzai's population.

Published in:

International Journal of Legal Medicine, 2017, v. 131, n. 5, p. 1241, doi. 10.1007/s00414-017-1550-5

By:

Tabassum, Sadia;
Ilyas, Muhammad;
Ullah, Inam;
Israr, Muhammad;
Ahmad, Habib

Publication type:

Article

Irys Extract.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 134, doi. 10.1093/bioinformatics/btx437

By:

Arielly, Rani;
Ebenstein, Yuval

Publication type:

Article

MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3477, doi. 10.1093/bioinformatics/btx449

By:

Jun Ding;
Bar-Joseph, Ziv

Publication type:

Article

DeepLoc: prediction of protein subcellular localization using deep learning.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3387, doi. 10.1093/bioinformatics/btx431

By:

Almagro Armenteros, José Juan;
Sønderby, Casper Kaae;
Sønderby, Søren Kaae;
Nielsen, Henrik;
Winther, Ole

Publication type:

Article

VICTOR: genome-based phylogeny and classification of prokaryotic viruses.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3396, doi. 10.1093/bioinformatics/btx440

By:

Meier-Kolthoff, Jan P.;
Göker, Markus

Publication type:

Article

powsimR: power analysis for bulk and single cell RNA-seq experiments.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3486, doi. 10.1093/bioinformatics/btx435

By:

Vieth, Beate;
Ziegenhain, Christoph;
Parekh, Swati;
Enard, Wolfgang;
Hellmann, Ines

Publication type:

Article

The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3489, doi. 10.1093/bioinformatics/btx415

By:

Wiredja, Danica D.;
Koyutürk, Mehmet;
Chance, Mark R.

Publication type:

Article

pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3373, doi. 10.1093/bioinformatics/btx413

By:

Hon, Jiří;
Martínek, Tomáš;
Zendulka, Jaroslav;
Lexa, Matej

Publication type:

Article

BioMake: a GNU make-compatible utility for declarative workflow management.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3502, doi. 10.1093/bioinformatics/btx306

By:

Holmes, Ian H.;
Mungall, Christopher J.

Publication type:

Article

The neXtProt peptide uniqueness checker: a tool for the proteomics community.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3471, doi. 10.1093/bioinformatics/btx318

By:

Schaeffer, Mathieu;
Gateau, Alain;
Teixeira, Daniel;
Michel, Pierre-André;
Zahn-Zabal, Monique;
Lane, Lydie

Publication type:

Article

BioContainers: an open-source and community-driven framework for software standardization.

Published in:

Bioinformatics, 2017, v. 33, n. 16, p. 2580, doi. 10.1093/bioinformatics/btx192

By:

Leprevost, Felipe da Veiga;
Grüning, Björn A.;
Aflitos, Saulo Alves;
Röst, Hannes L.;
Uszkoreit, Julian;
Barsnes, Harald;
Vaudel, Marc;
Moreno, Pablo;
Gatto, Laurent;
Weber, Jonas;
Mingze Bai;
Jimenez, Rafael C.;
Sachsenberg, Timo;
Pfeuffer, Julianus;
Alvarez, Roberto Vera;
Griss, Johannes;
Nesvizhskii, Alexey I.;
Perez-Riverol, Yasset

Publication type:

Article

MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 1090, doi. 10.1093/bioinformatics/btw750

By:

Wei Zhou;
Ruilin Li;
Shuo Yuan;
Chang Chun Liu;
Shaowen Yao;
Jing Luo;
Beifang Niu

Publication type:

Article

RECKONER: read error corrector based on KMC.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 1086, doi. 10.1093/bioinformatics/btw746

By:

Długosz, Maciej;
Deorowicz, Sebastian

Publication type:

Article

BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 608, doi. 10.1093/bioinformatics/btw684

By:

Oyetunde, Tolutola;
Muhan Zhang;
Yixin Chen;
Yinjie Tang;
Cynthia Lo

Publication type:

Article

Combenefit: an interactive platform for the analysis and visualization of drug combinations.

Published in:

Bioinformatics, 2016, v. 32, n. 18, p. 2866, doi. 10.1093/bioinformatics/btw230

By:

Fornari, Chiara;
Mollard, Séverine;
Bramhall, Jo L.;
Richards, Frances M.;
Jodrell, Duncan I.;
Di Veroli, Giovanni Y.;
Wang, Dennis

Publication type:

Article

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

Published in:

2016

By:

Mazandu, Gaston K.;
Chimusa, Emile R.;
Mbiyavanga, Mamana;
Mulder, Nicola J.

Publication type:

Product Review

BioSynther: a customized biosynthetic potential explorer.

Published in:

2016

By:

Weizhong Tu;
Haoran Zhang;
Juan Liu;
Qian-Nan Hu

Publication type:

Product Review

CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies.

Published in:

2016

By:

Jun Chen;
Just, Allan C.;
Schwartz, Joel;
Hou, Lifang;
Jafari, Nadereh;
Zhifu Sun;
Kocher, Jean-Pierre A.;
Baccarelli, Andrea;
Xihong Lin

Publication type:

Product Review

HapFlow: visualizing haplotypes in sequencing data.

Published in:

2016

By:

Sullivan, Mitchell J.;
Bachmann, Nathan L.;
Timms, Peter;
Polkinghorne, Adam

Publication type:

Product Review

IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data.

Published in:

2016

By:

Mischnik, Marcel;
Sacco, Francesca;
Cox, Jürgen;
Schneider, Hans-Christoph;
Schäfer, Matthias;
Hendlich, Manfred;
Crowther, Daniel;
Mann, Matthias;
Klabunde, Thomas

Publication type:

Product Review

BiTrinA--multiscale binarization and trinarization with quality analysis.

Published in:

2016

By:

Müssel, Christoph;
Schmid, Florian;
Blätte, Tamara J.;
Hopfensitz, Martin;
Lausser, Ludwig;
Kestler, Hans A.

Publication type:

Product Review

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.

Published in:

2016

By:

Chao Wang;
Haicang Zhang;
Wei-Mou Zheng;
Dong Xu;
Jianwei Zhu;
Bing Wang;
Kang Ning;
Shiwei Sun;
Shuai Cheng Li;
Dongbo Bu

Publication type:

Product Review

CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads.

Published in:

2016

By:

Borozan, Ivan;
Ferretti, Vincent

Publication type:

Product Review

miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis.

Published in:

2016

By:

Patel, Parth;
Ramachandruni, S. Deepthi;
Kakrana, Atul;
Nakano, Mayumi;
Meyers, Blake C.

Publication type:

Product Review

I-PV: a CIRCOS module for interactive protein sequence visualization.

Published in:

2016

By:

Tanyalcin, Ibrahim;
Al Assaf, Carla;
Gheldof, Alexander;
Stouffs, Katrien;
Lissens, Willy;
Jansen, Anna C.

Publication type:

Product Review

Rust-Bio: a fast and safe bioinformatics library.

Published in:

2016

By:

Köster, Johannes

Publication type:

Product Review

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 292, doi. 10.1093/bioinformatics/btv566

By:

Okonechnikov, Konstantin;
Conesa, Ana;
García-Alcalde, Fernando

Publication type:

Article

FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads.

Published in:

Bioinformatics, 2015, v. 31, n. 19, p. 3207, doi. 10.1093/bioinformatics/btv280

By:

Lam, Ka-Kit;
LaButti, Kurt;
Khalak, Asif;
Tse, David

Publication type:

Article

MetaMapR: pathway independent metabolomic network analysis incorporating unknowns.

Published in:

2015

By:

Grapov, Dmitry;
Wanichthanarak, Kwanjeera;
Fiehn, Oliver

Publication type:

Product Review

PDIviz: analysis and visualization of protein-DNA binding interfaces.

Published in:

2015

By:

Ribeiro, Judemir;
Melo, Francisco;
Schüller, Andreas

Publication type:

Product Review

AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes.

Published in:

2015

By:

Hue Vuong;
Anney Che;
Ravichandran, Sarangan;
Luke, Brian T.;
Collins, Jack R.;
Mudunuri, Uma S.

Publication type:

Product Review

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.

Published in:

2015

By:

Mohiyuddin, Marghoob;
Mu, John C.;
Jian Li;
Asadi, Narges Bani;
Gerstein, Mark B.;
Abyzov, Alexej;
Wong, Wing H.;
Lam, Hugo Y. K.

Publication type:

Product Review

ESPRESSO: taking into account assessment errors on outcome and exposures in power analysis for association studies.

Published in:

2015

By:

Gaye, Amadou;
Burton, Thomas W. Y.;
Burton, Paul R.

Publication type:

Product Review

GS-align for glycan structure alignment and similarity measurement.

Published in:

2015

By:

Hui Sun Lee;
Sunhwan Jo;
Mukherjee, Srayanta;
Sang-Jun Park;
Skolnick, Jeffrey;
Jooyoung Lee;
Wonpil Im

Publication type:

Product Review

ScaffMatch: scaffolding algorithm based on maximum weight matching.

Published in:

2015

By:

Mandric, Igor;
Zelikovsky, Alex

Publication type:

Product Review

FastMotif: spectral sequence motif discovery.

Published in:

2015

By:

Colombo, Nicoló;
Vlassis, Nikos

Publication type:

Product Review

iTagPlot: an accurate computation and interactive drawing tool for tag density plot.

Published in:

2015

By:

Sung-Hwan Kim;
Onyeka Ezenwoye;
Hwan-Gue Cho;
Robertson, Keith D.;
Jeong-Hyeon Choi

Publication type:

Product Review

EpIC: a rational pipeline for epitope immunogenicity characterization.

Published in:

2015

By:

Marciniuk, Kristen;
Trost, Brett;
Napper, Scott

Publication type:

Product Review

Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces.

Published in:

2015

By:

Vázquez, Miguel;
Valencia, Alfonso;
Pons, Tirso

Publication type:

Product Review

miR2GO: comparative functional analysis for microRNAs.

Published in:

2015

By:

Bhattacharya, Anindya;
Yan Cui

Publication type:

Product Review