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December 2023

Table of Contents - PeerJ (Biology Articles)

December 8, 2023

Riding the wave of innovation: immunoinformatics in fish disease control

Siti Aisyah Razali, Mohd Shahir Shamsir, Nur Farahin Ishak, Chen-Fei Low, Wan-Atirah Azemin

https://doi.org/10.7717/peerj.16419 PubMed 38089909

December 8, 2023

BERT-5mC: an interpretable model for predicting 5-methylcytosine sites of DNA based on BERT

Shuyu Wang, Yinbo Liu, Yufeng Liu, Yong Zhang, Xiaolei Zhu

https://doi.org/10.7717/peerj.16600 PubMed 38089911

December 5, 2023

pH-sensing G protein-coupled orphan receptor GPR68 is expressed in human cartilage and correlates with degradation of extracellular matrix during OA progression

Nazir M. Khan, Martha E. Diaz-Hernandez, William N. Martin, Bhakti Patel, Samir Chihab, Hicham Drissi

https://doi.org/10.7717/peerj.16553 PubMed 38077417

December 18, 2023

Identification and validation of prognostic and tumor microenvironment characteristics of necroptosis index and BIRC3 in clear cell renal cell carcinoma

Kai Wei, Xi Zhang, Dongrong Yang

https://doi.org/10.7717/peerj.16643 PubMed 38130918

December 1, 2023

Temporal and spatial differences in the vaginal microbiome of Chinese healthy women

Limin Du, Xue Dong, Jiarong Song, Tingting Lei, Xianming Liu, Yue Lan, Xu Liu, Jiao Wang, Bisong Yue, Miao He, Zhenxin Fan, Tao Guo

https://doi.org/10.7717/peerj.16438 PubMed 38054020

December 18, 2023

Benchmarking long-read genome sequence alignment tools for human genomics applications

Jonathan LoTempio, Emmanuele Delot, Eric Vilain

https://doi.org/10.7717/peerj.16515 PubMed 38130927

December 5, 2023

Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology

Saber Soleymani, Nathan Gravel, Liang-Chin Huang, Wayland Yeung, Elika Bozorgi, Nathaniel G. Bendzunas, Krzysztof J. Kochut, Natarajan Kannan

https://doi.org/10.7717/peerj.16087 PubMed 38077442

December 7, 2023

LINC01936 inhibits the proliferation and metastasis of lung squamous cell carcinoma probably by EMT signaling and immune infiltration

Qinqin Tian, Xiyao Liu, Ang Li, Hongjiao Wu, Yuning Xie, Hongmei Zhang, Fengjun Wu, Yating Chen, Congcong Bai, Xuemei Zhang

https://doi.org/10.7717/peerj.16447 PubMed 38084139

December 14, 2023

Genome-wide identification of the OMT gene family in Cucumis melo L. and expression analysis under abiotic and biotic stress

Shuoshuo Wang, Chuang Wang, Futang Lv, Pengfei Chu, Han Jin

https://doi.org/10.7717/peerj.16483 PubMed 38107581

December 5, 2023

Fascin actin-bundling protein 1 regulates non-small cell lung cancer progression by influencing the transcription and splicing of tumorigenesis-related genes

Qingchao Sun, Ruixue Liu, Haiping Zhang, Liang Zong, Xiaoliang Jing, Long Ma, Jie Li, Liwei Zhang

https://doi.org/10.7717/peerj.16526 PubMed 38077434

December 18, 2023

Differentially expressed genes in orbital adipose/connective tissue of thyroid-associated orbitopathy

Yan Wang, Yanqiu Liu, Jiping Cai, Tianyi Zong, Ziyin Zhang, Tianhua Xie, Tong Mu, Meili Wu, Qian Yang, Yangningzhi Wang, Xiaolu Wang, Yong Yao

https://doi.org/10.7717/peerj.16569 PubMed 38130930

December 11, 2023

A deep learning method for drug-target affinity prediction based on sequence interaction information mining

Mingjian Jiang, Yunchang Shao, Yuanyuan Zhang, Wei Zhou, Shunpeng Pang

https://doi.org/10.7717/peerj.16625 PubMed 38099302

December 14, 2023

Chargaff’s second parity rule lies at the origin of additive genetic interactions in quantitative traits to make omnigenic selection possible

Bakhyt T. Matkarimov, Murat K. Saparbaev

https://doi.org/10.7717/peerj.16671 PubMed 38107580

December 4, 2023

taxalogue: a toolkit to create comprehensive CO1 reference databases

Niklas W. Noll, Christoph Scherber, Livia Schäffler

https://doi.org/10.7717/peerj.16253 PubMed 38077427

December 4, 2023

Identification of novel biomarkers in obstructive sleep apnea via integrated bioinformatics analysis and experimental validation

Kai Zhang, Caizhen Wang, Yunxiao Wu, Zhifei Xu

https://doi.org/10.7717/peerj.16608 PubMed 38077447

December 18, 2023

A machine learning-based model for clinical prediction of distal metastasis in chondrosarcoma: a multicenter, retrospective study

Jihu Wei, Shijin Lu, Wencai Liu, He Liu, Lin Feng, Yizi Tao, Zhanglin Pu, Qiang Liu, Zhaohui Hu, Haosheng Wang, Wenle Li, Wei Kang, Chengliang Yin, Zhe Feng

https://doi.org/10.7717/peerj.16485 PubMed 38130920

December 5, 2023

miR-4270 suppresses hepatocellular carcinoma progression by inhibiting DNMT3A-mediated methylation of HGFAC promoter

Qiang Zou, Shasha Cao

https://doi.org/10.7717/peerj.16566 PubMed 38077422

December 1, 2023

Identification of cytokine-induced cell communications by pan-cancer meta-analysis

Yining Liu, Min Zhao, Hong Qu

https://doi.org/10.7717/peerj.16221 PubMed 38054018

December 6, 2023

Pharmacoscreening, molecular dynamics, and quantum mechanics of inermin from Panax ginseng: a crucial molecule inhibiting exosomal protein target associated with coronary artery disease progression

Janakiraman V, Sudhan M, Abubakar Wani, Sheikh F. Ahmad, Ahmed Nadeem, Ashutosh Sharma, Shiek S. S. J. Ahmed

https://doi.org/10.7717/peerj.16481 PubMed 38077444

December 12, 2023

Involvement of plasminogen activator inhibitor-1 in p300/p53-mediated age-related atrial fibrosis

Yingyu Lai, Jintao He, Xiaoyan Gao, Dewei Peng, Huishan Zhou, Yuwen Xu, Xueshan Luo, Hui Yang, Mengzhen Zhang, Chunyu Deng, Shulin Wu, Yumei Xue, Feng Zhou, Fang Rao

https://doi.org/10.7717/peerj.16545 PubMed 38107584

December 13, 2023

CXCL10-based gene cluster model serves as a potential diagnostic biomarker for premature ovarian failure

Ying Qin, Canliang Wen, Huijiao Wu

https://doi.org/10.7717/peerj.16659 PubMed 38107572

December 11, 2023

The Aurora kinase inhibitor AT9283 inhibits Burkitt lymphoma growth by regulating Warburg effect

Kaiming Jiang, Lihong Bai, Canfei Wang, Xiang Xiao, Zhao Cheng, Hongling Peng, Sufang Liu

https://doi.org/10.7717/peerj.16581 PubMed 38099309

December 19, 2023

A pyroptosis-related signature in colorectal cancer: exploring its prognostic value and immunological characteristics

Peicheng Jiang, Jin Fan, Shenglin Huang, Luying Liu, Minghua Bai, Quanquan Sun, Jinwen Shen, Na Zhang, Dong Liu, Ning Zhou, Yanru Feng, Jin Jiang, Ji Zhu

https://doi.org/10.7717/peerj.16631 PubMed 38144182

December 1, 2023

Identification of potential glioma drug resistance target proteins based on ultra-performance liquid chromatography-mass spectrometry differential proteomics

Da Li, Jun Yan, Kang Li, Qingcheng Yang, Liping Bian, Bencheng Lin, Xiaohua Liu, Zhuge Xi

https://doi.org/10.7717/peerj.16426 PubMed 38054015

December 15, 2023

Genome-wide identification and expression analysis of growth-regulating factors in Dendrobium officinale and Dendrobium chrysotoxum

Shuying Zhu, Hongman Wang, Qiqian Xue, Huasong Zou, Wei Liu, Qingyun Xue, Xiao-Yu Ding

https://doi.org/10.7717/peerj.16644 PubMed 38111654

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