Biology & Life sciences - Table of Contents

March 16, 2021

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer

https://doi.org/10.7717/peerj.10947 PubMed 33777521

March 30, 2021

COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer

Qishun Geng, Zhibo Shen, Lifeng Li, Jie Zhao

https://doi.org/10.7717/peerj.11145 PubMed 33850663

March 2, 2021

Comparative transcriptome analyses of maize seedling root responses to salt stress

Xiaoxiang Zhang, Peng Liu, Chunyan Qing, Cong Yang, Yaou Shen, Langlang Ma

https://doi.org/10.7717/peerj.10765 PubMed 33717668

March 30, 2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Olivier Zablocki, Michelle Michelsen, Marie Burris, Natalie Solonenko, Joanna Warwick-Dugdale, Romik Ghosh, Jennifer Pett-Ridge, Matthew B. Sullivan, Ben Temperton

https://doi.org/10.7717/peerj.11088 PubMed 33850654

March 31, 2021

The classification of EEG-based winking signals: a transfer learning and random forest pipeline

Jothi Letchumy Mahendra Kumar, Mamunur Rashid, Rabiu Muazu Musa, Mohd Azraai Mohd Razman, Norizam Sulaiman, Rozita Jailani, Anwar P.P. Abdul Majeed

https://doi.org/10.7717/peerj.11182 PubMed 33850667

March 15, 2021

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

Sushma Naithani, Daemon Dikeman, Priyanka Garg, Noor Al-Bader, Pankaj Jaiswal

https://doi.org/10.7717/peerj.11052 PubMed 33777532

March 31, 2021

New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics

Alexander Knyshov, Eric R.L. Gordon, Christiane Weirauch

https://doi.org/10.7717/peerj.11019 PubMed 33850647

March 8, 2021

Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis

Feixiang Fan, Zhen Huang, Yongfeng Chen

https://doi.org/10.7717/peerj.11018 PubMed 33732554

March 9, 2021

Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome

Stefan Gavriliuc, Mason R. Stothart, Astrid Henry, Jocelyn Poissant

https://doi.org/10.7717/peerj.10837 PubMed 33854827

March 10, 2021

A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution

Zbigniew Wyżewski, Marcin Gradowski, Marianna Krysińska, Małgorzata Dudkiewicz, Krzysztof Pawłowski

https://doi.org/10.7717/peerj.11051 PubMed 33854844

March 2, 2021

Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat (Triticum aestivum L.)

Yaqian Li, Jinghan Song, Guang Zhu, Zehao Hou, Lin Wang, Xiaoxue Wu, Zhengwu Fang, Yike Liu, Chunbao Gao

https://doi.org/10.7717/peerj.10963 PubMed 33717696

March 10, 2021

Genome-wide identification and expression pattern of SnRK gene family under several hormone treatments and its role in floral scent emission in Hedychium coronarium

Chutian Wang, Farhat Abbas, Yiwei Zhou, Yanguo Ke, Xinyue Li, Yuechong Yue, Yunyi Yu, Rangcai Yu, Yanping Fan

https://doi.org/10.7717/peerj.10883 PubMed 33854831

March 5, 2021

Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis

Chunyang Li, Haopeng Yu, Yajing Sun, Xiaoxi Zeng, Wei Zhang

https://doi.org/10.7717/peerj.10682 PubMed 33717664

March 4, 2021

Differential gene expression in a tripartite interaction: Drosophila, Spiroplasma and parasitic wasps

Victor Manuel Higareda Alvear, Mariana Mateos, Diego Cortez, Cecilia Tamborindeguy, Esperanza Martinez-Romero

https://doi.org/10.7717/peerj.11020 PubMed 33717711

March 2, 2021

The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study

Qi Zeng, Sha Wang, Jia Tan, Lu Chen, Jinwei Wang

https://doi.org/10.7717/peerj.10830 PubMed 33717678

March 23, 2021

Immunoinformatic approach to design a multiepitope vaccine targeting non-mutational hotspot regions of structural and non-structural proteins of the SARS CoV2

Vandana Solanki, Monalisa Tiwari, Vishvanath Tiwari

https://doi.org/10.7717/peerj.11126 PubMed 33828922

March 17, 2021

Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma

Prin Sungwan, Worachart Lert-itthiporn, Atit Silsirivanit, Nathakan Klinhom-on, Seiji Okada, Sopit Wongkham, Wunchana Seubwai

https://doi.org/10.7717/peerj.11067 PubMed 33777535

March 3, 2021

iTRAQ-based comparative proteome analyses of different growth stages revealing the regulatory role of reactive oxygen species in the fruiting body development of Ophiocordyceps sinensis

Xinxin Tong, Fang Wang, Han Zhang, Jing Bai, Qiang Dong, Pan Yue, Xinyi Jiang, Xinrui Li, Li Wang, Jinlin Guo

https://doi.org/10.7717/peerj.10940 PubMed 33717691

March 10, 2021

Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil

Marcelle Oliveira de Almeida, Rodrigo Carvalho, Flavia Figueira Aburjaile, Fabio Malcher Miranda, Janaína Canário Cerqueira, Bertram Brenig, Preetam Ghosh, Rommel Ramos, Rodrigo Bentes Kato, Siomar de Castro Soares, Artur Silva, Vasco Azevedo, Marcus Vinicius Canário Viana

https://doi.org/10.7717/peerj.11079 PubMed 33854845

March 16, 2021

Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots

Liangchen Su, Shuai Liu, Xing Liu, Baihong Zhang, Meijuan Li, Lidan Zeng, Ling Li

https://doi.org/10.7717/peerj.10976 PubMed 33777524

March 31, 2021

Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application

Jakub Hynst, Veronika Navrkalova, Karol Pal, Sarka Pospisilova

https://doi.org/10.7717/peerj.10897 PubMed 33850640

March 24, 2021

LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes

Long Tian, Reza Mazloom, Lenwood S. Heath, Boris A. Vinatzer