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October 2022

Table of Contents - PeerJ (Biology Articles)

October 24, 2022

Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress

Wencai Yu, Guanghong Kong, Jinquan Chao, Tuo Yin, Hai Tian, Huajin Ya, Ligang He, Hanyao Zhang

https://doi.org/10.7717/peerj.14251 PubMed 36312747

October 25, 2022

2FAST2Q: a general-purpose sequence search and counting program for FASTQ files

Afonso M. Bravo, Athanasios Typas, Jan-Willem Veening

https://doi.org/10.7717/peerj.14041 PubMed 36312750

October 7, 2022

Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench)

Aixia Zhang, Jingjing Xu, Xin Xu, Junping Wu, Ping Li, Baohua Wang, Hui Fang

https://doi.org/10.7717/peerj.14156 PubMed 36225907

October 10, 2022

Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups

Carla Stout, Susana Schonhuth, Richard Mayden, Nicole L. Garrison, Jonathan W. Armbruster

https://doi.org/10.7717/peerj.14072 PubMed 36248715

October 27, 2022

DHU-Pred: accurate prediction of dihydrouridine sites using position and composition variant features on diverse classifiers

Muhammad Taseer Suleman, Tamim Alkhalifah, Fahad Alturise, Yaser Daanial Khan

https://doi.org/10.7717/peerj.14104 PubMed 36320563

October 17, 2022

Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms

Jianfeng Ma, Jingyun Chen, Mailin Gan, Lei Chen, Ye Zhao, Lili Niu, Yan Zhu, Shunhua Zhang, Xuewei Li, Zongyi Guo, Jinyong Wang, Li Zhu, Linyuan Shen

https://doi.org/10.7717/peerj.14221 PubMed 36275473

October 3, 2022

Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands

Shaojun Tang, Tingting Fan, Lei Jin, Pin Lei, Chenxia Shao, Shenlian Wu, Yi Yang, Yuelin He, Rui Ren, Jun Xu

https://doi.org/10.7717/peerj.14130 PubMed 36213510

October 17, 2022

isomiRTar: a comprehensive portal of pan-cancer 5′-isomiR targeting

Stepan Nersisyan, Aleksandra Gorbonos, Alexey Makhonin, Anton Zhiyanov, Maxim Shkurnikov, Alexander Tonevitsky

https://doi.org/10.7717/peerj.14205 PubMed 36275459

October 3, 2022

SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells

Junjie Zhou, Wenhao Chen, Qianwen He, Dong Chen, Chunguang Li, Congqing Jiang, Zhao Ding, Qun Qian

https://doi.org/10.7717/peerj.14084 PubMed 36213507

October 31, 2022

The complete chloroplast genome sequences of three Broussonetia species and comparative analysis within the Moraceae

Jinhong Yang, Qu Chu, Gang Meng, Weiqing Kong

https://doi.org/10.7717/peerj.14293 PubMed 36340196

October 3, 2022

Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis

Yaofei Zhao, Yaqiong Li, Xiaoxi Zhen, Jinli Zhang, Qianxiang Zhang, Zhaowen Liu, Shupei Hou, Yuanhuai Han, Bin Zhang

https://doi.org/10.7717/peerj.14099 PubMed 36213506

October 18, 2022

The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew

Alessandro M. Varani, Saura R. Silva, Simone Lopes, Jose Beethoven Figueiredo Barbosa, Danilo Oliveira, Maria Alice Corrêa, Ana Paula Moraes, Vitor F.O. Miranda, Francisco Prosdocimi

https://doi.org/10.7717/peerj.14114 PubMed 36275467

October 10, 2022

Differentially expressed genes related to plant height and yield in two alfalfa cultivars based on RNA-seq

Jiangjiao Qi, Xue Yu, Xuzhe Wang, Fanfan Zhang, Chunhui Ma

https://doi.org/10.7717/peerj.14096 PubMed 36248707

October 18, 2022

Clinical associations and genetic interactions of oncogenic BRAF alleles

Sebastian A. Wagner

https://doi.org/10.7717/peerj.14126 PubMed 36275468

October 14, 2022

RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes

Firaol Dida Midekso, Gangman Yi

https://doi.org/10.7717/peerj.14186 PubMed 36262414

October 27, 2022

Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense

Ziwei Li, Yujia Yang, Bin Chen, Bin Xia, Hongyao Li, Yunwei Zhou, Miao He

https://doi.org/10.7717/peerj.14241 PubMed 36320567

October 3, 2022

Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach

Reza Arshinchi Bonab, Seyedehsadaf Asfa, Panagiota Kontou, Gökhan Karakülah, Athanasia Pavlopoulou

https://doi.org/10.7717/peerj.14149 PubMed 36213495

October 6, 2022

Genomic differences between sequence types 1 and 104 of Streptococcus suis Serotype 2

Anusak Kerdsin, Dan Takeuchi, Yukihiro Akeda, Shota Nakamura, Marcelo Gottschalk, Kazunori Oishi

https://doi.org/10.7717/peerj.14144 PubMed 36221266

October 5, 2022

miR2Trait: an integrated resource for investigating miRNA-disease associations

Poornima Babu, Ashok Palaniappan

https://doi.org/10.7717/peerj.14146 PubMed 36217386

October 10, 2022

A conserved role of bam in maintaining metabolic homeostasis via regulating intestinal microbiota in Drosophila

Jiale Wang, Yangyang Zhu, Chao Zhang, Renjie Duan, Fanrui Kong, Xianrui Zheng, Yongzhi Hua

https://doi.org/10.7717/peerj.14145 PubMed 36248714

October 26, 2022

De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn

Hanqing Tang, Josphat K. Saina, Zhi-Cheng Long, Jinming Chen, Can Dai

https://doi.org/10.7717/peerj.14268 PubMed 36317118

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