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Articles by Thomas PD
Identification and verification of ferroptosis-related core gene in postmenopausal osteoporosis based on bioinformatics analysis
Identification and verification of ferroptosis-related core gene in postmenopausal osteoporosis based on bioinformatics analysis 1Department of Orthopedic, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang, Guizhou Province, China 2Tumor Research Laboratory, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, China 3Emergency Department, The Affiliated Hospital of Guizhou Medical University, Guiyang, China DOI 10.7717/peerj.20666 Academic Editor Vladimir Uversky Subject...
Genome-wide identification of SMALL AUXIN UP RNA (SAUR) gene family and its expression profiles in response to abiotic stress and auxin in tea plants (Camellia sinensis)
Genome-wide identification of SMALL AUXIN UP RNA (SAUR) gene family and its expression profiles in response to abiotic stress and auxin in tea plants (Camellia sinensis) 1College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China 2Dabie Mountain Laboratory, Xinyang, Henan, China 3College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang, China 4College of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China 5Henan Key...
Optimized Gaussian naïve Bayes for prostate cancer detection in White patients using gene expression data
Optimized Gaussian naïve Bayes for prostate cancer detection in White patients using gene expression data 1Faculty of Engineering and Informatics, Universitas Multimedia Nusantara, Tangerang, Banten, Indonesia 2Faculty of Electronic Engineering and Technology, Universiti Malaysia Perlis, Perlis, Malaysia 3Marshfield Clinic Research Institute, Marshfield, United States DOI 10.7717/peerj-cs.3405 Academic Editor Consolato Sergi Subject Areas Bioinformatics, Computational Biology, Algorithms and...
Robust phylogenetic profile clustering for Saccharomyces cerevisiae proteins
Robust phylogenetic profile clustering for Saccharomyces cerevisiae proteins Department of Biology, McGill University, Montreal, Quebec, Canada DOI 10.7717/peerj.19370 Academic Editor Ugo Bastolla Subject Areas Bioinformatics, Computational Biology, Evolutionary Studies Keywords Gene origins, Phylogenetic profiles, Clustering, Intrinsic disorder, Prion-like, Protein function Copyright © Licence This is an open access article distributed under the terms of the Creative Commons Attribution...
The DUF348 domains of resuscitation promoting factor 2 play important roles in the enzymatic and biological activities in Rhodococcus erythropolis KB1
The DUF348 domains of resuscitation promoting factor 2 play important roles in the enzymatic and biological activities in Rhodococcus erythropolis KB1 1School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, Gansu province, China 2School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu province, China DOI 10.7717/peerj.18561 Academic Editor Bernardo Franco Subject Areas Biochemistry, Bioengineering, Bioinformatics, Microbiology Keywords...
An experimental analysis of graph representation learning for Gene Ontology based protein function prediction
An experimental analysis of graph representation learning for Gene Ontology based protein function prediction 1Faculty of Fundamental Sciences, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam 2Department of Information and Communication Engineering, Myongji University, Yongin, Republic of South Korea DOI 10.7717/peerj.18509 Academic Editor Vladimir Uversky Subject Areas Bioinformatics, Computational Biology, Data Mining and Machine Learning Keywords Protein...
Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing
Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing 1Department of Biological Sciences, Auburn University, Auburn, AL, United States of America 2Department of Biological Sciences, University of Alabama - Tuscaloosa, Tuscaloosa, AL, United States of America 3Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America 4Absci, Vancouver, WA, United States of America...
Unraveling genomic features and phylogenomics through the analysis of three Mexican endemic Myotis genomes
Edgar G. Gutiérrez conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft. Jesus E. Maldonado conceived and designed the experiments, performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.
De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing
De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb.
Protein family neighborhood analyzer-ProFaNA
Materials and Methods Availability and code The algorithm, instructions and sample results of the presented tool are available at http://bioinfo.sggw.edu.pl/neighborhood_analysis. Code of ProFaNA algorithm without data is stored at https://www.github.com/steven0seagal/ProFaNA (DOI 10.5281/zenodo.7993764). Source of data All bacterial genome sequences available from IMG/M—Integrated Microbial Genomes and Microbiomes service (https://img.jgi.doe.gov/) were downloaded in December 2020.
Comprehensive analysis of fatty acid metabolism-related gene signatures for predicting prognosis in patients with prostate cancer
Comprehensive analysis of fatty acid metabolism-related gene signatures for predicting prognosis in patients with prostate cancer , , , , , , , , , , , 1Lanzhou University Second Hospital, Lanzhou, Gansu, China 2Department of Urology, Key Laboratory of Urological Diseases in Gansu Province, Lanzhou University Second Hospital, lanzhou, Gansu, China 3Department of Orthopaedic People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, Henan, China 4School of Basic...
The application of multi-omics and systems biology to identify therapeutic targets in chronic kidney disease
Chronic kidney disease (CKD) constitutes a class of renal disorders diagnosed on the basis of progressive renal failure, which leads to characteristic pathological hallmarks of interstitial fibrosis and inflammation [1, 2]. CKD can also be non-progressive; moreover, diabetes, hypertension and ageing contribute as the primary causes, increasing cardiovascular disease risk [3].
Bracken: estimating species abundance in metagenomics data
Metagenomics is a rapidly growing field of study, driven in part by our ability to generate enormous amounts of DNA sequence rapidly and inexpensively. Since the human genome was first published in 2001 (The International Human Genome Sequencing Consortium, 2001; Venter et al., 2001), sequencing technology has become approximately one million times faster and cheaper, making it possible for individual labs to generate as much sequence data as the entire Human Genome Project in just a few days.
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