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Kenta Nakai
Bronze Contributor
9,850 Points

Contributions by role

Author 270
Editor 9,580

Contributions by subject area

Bioinformatics
Genomics
Gastroenterology and Hepatology
Oncology
Translational Medicine
Computational Biology
Developmental Biology
Cell Biology
Genetics
Orthopedics
Data Mining and Machine Learning
Molecular Biology
Plant Science
Diabetes and Endocrinology
Cardiology
Pathology
Urology
Medical Genetics
Microbiology
Agricultural Science
Virology
Computational Science
Statistics
Evolutionary Studies
Parasitology
Taxonomy
Zoology
Biodiversity
Biogeography
Biochemistry
Food Science and Technology
Drugs and Devices
Biotechnology
Immunology
Otorhinolaryngology
Entomology
Pharmacology
Neurology
Respiratory Medicine
Surgery and Surgical Specialties
Andrology
Veterinary Medicine
Histology
Soil Science
Forestry
Women's Health
Geriatrics
Infectious Diseases
COVID-19
Nutrition
Dermatology
Hematology
Allergy and Clinical Immunology
Bronze Contributor

Kenta Nakai

PeerJ Editor & Author

Summary

Professor of Human Genome Center, the Institute of Medical Science, the University of Tokyo, Japan. Editor of DNA Research and Mathematical Biosciences. Former president of the Japanese Society of Bioinformatics.

Bioinformatics Computational Biology Genomics

Editorial Board Member

PeerJ - the Journal of Life & Environmental Sciences

Work details

Professor

The University of Tokyo
The Institute of Medical Science

Websites

  • ResearcherID
  • Google Scholar
  • Nakai Lab

PeerJ Contributions

  • Articles 3
  • Edited 62
March 15, 2024
Resting heart rate and risk of dementia: a Mendelian randomization study in the international genomics of Alzheimer’s Project and UK Biobank
Xingxing Chen, Yi Zheng, Jun Wang, Blake Yue, Xian Zhang, Kenta Nakai, Lijing L. Yan
https://doi.org/10.7717/peerj.17073 PubMed 38500529
June 26, 2020
Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma
Munmee Dutta, Hidewaki Nakagawa, Hiroaki Kato, Kazuhiro Maejima, Shota Sasagawa, Kaoru Nakano, Aya Sasaki-Oku, Akihiro Fujimoto, Raúl Nicolás Mateos, Ashwini Patil, Hiroko Tanaka, Satoru Miyano, Takushi Yasuda, Kenta Nakai, Masashi Fujita
https://doi.org/10.7717/peerj.9294 PubMed 32617189
May 30, 2017
Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster
Yosvany López, Alexis Vandenbon, Akinao Nose, Kenta Nakai
https://doi.org/10.7717/peerj.3389 PubMed 28584716

Academic Editor on

June 26, 2025
The potential mechanism of Huangqin for treatment of systemic lupus erythematosus based on network pharmacology, molecular docking and molecular dynamics simulation
Shuting Zheng, Hui Yang, Jialing Wu, Ou Jin, Xi Zhang
https://doi.org/10.7717/peerj.19536 PubMed 40585331
May 20, 2025
Intrinsic factors behind long COVID: exploring the role of nucleocapsid protein in thrombosis
Ahmed Eltayeb, Muhamed Adilović, Maryam Golzardi, Altijana Hromić-Jahjefendić, Alberto Rubio-Casillas, Vladimir N. Uversky, Elrashdy M. Redwan
https://doi.org/10.7717/peerj.19429 PubMed 40416618
May 14, 2025
Construction and validation of a prognostic model for colorectal cancer based on migrasome-related long non-coding RNAs
Qiang Lv, Qingzhu Yang, Hongsheng Chen, Yang Wang, Yuliuming Wang, Xu Hu, Ming Liu
https://doi.org/10.7717/peerj.19443 PubMed 40386228
May 2, 2025
A comprehensive analysis identified an autophagy-related risk model for predicting recurrence and immunotherapy response in stage I lung adenocarcinoma
Hongmei Zheng, Songqing Fan, Hongjing Zang, Jiadi Luo, Long Shu, Jinwu Peng
https://doi.org/10.7717/peerj.19366 PubMed 40330698
February 21, 2025
Construction and verification of a prognostic model for bladder cancer based on disulfidptosis-related angiogenesis genes
Zhihao Zhou, Yuwei Zhang, Yuhua Zhou, Jiayu Gu, Jufa Li, Jianfeng Shao, Ninghan Feng
https://doi.org/10.7717/peerj.18911 PubMed 39995998
February 13, 2025
Proteomics of stress-induced cardiomyopathy: insights from differential expression, protein interaction networks, and functional pathway enrichment in an isoproterenol-induced TTC mouse model
Liuyang Tian, Botao Liu, Ying Ren, Jian Cui, Zhihua Pang
https://doi.org/10.7717/peerj.18984 PubMed 39959819
January 14, 2025
Identification and mechanistic insights of cell senescence-related genes in psoriasis
Guiyan Deng, Cheng Xu, Dunchang Mo
https://doi.org/10.7717/peerj.18818 PubMed 39830966
December 13, 2024
Pepper power: short-term impact of pepper consumption on the gut bacteriome composition in healthy volunteers
Oluwafayoke Owolo, Haruna J. Audu, Ayorinde O. Afolayan, Funmilola A. Ayeni
https://doi.org/10.7717/peerj.18707 PubMed 39686991
September 19, 2024
Similarity-based metric analysis approach for predicting osteogenic differentiation correlation coefficients and discovering the novel osteogenic-related gene FOXA1 in BMSCs
Lingtong Sun, Juan Chen, Li Jun Li, Lingdi Li
https://doi.org/10.7717/peerj.18068 PubMed 39308804
June 19, 2024
VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19
Danusorn Lee, Unitsa Sangket
https://doi.org/10.7717/peerj.17504 PubMed 38912043
March 6, 2024
Unsupervised AI reveals insect species-specific genome signatures
Yui Sawada, Ryuhei Minei, Hiromasa Tabata, Toshimichi Ikemura, Kennosuke Wada, Yoshiko Wada, Hiroshi Nagata, Yuki Iwasaki
https://doi.org/10.7717/peerj.17025 PubMed 38464746
September 28, 2023
DisVar: an R library for identifying variants associated with diseases using large-scale personal genetic information
Khunanon Chanasongkhram, Kasikrit Damkliang, Unitsa Sangket
https://doi.org/10.7717/peerj.16086 PubMed 37790633
August 24, 2023
Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction
Jia Qu, Zihao Song, Xiaolong Cheng, Zhibin Jiang, Jie Zhou
https://doi.org/10.7717/peerj.15889 PubMed 37641598
January 13, 2023
Systematic identification of smORFs in domestic silkworm (Bombyx mori)
Linrong Wan, Wenfu Xiao, Ziyan Huang, Anlian Zhou, Yaming Jiang, Bangxing Zou, Binbin Liu, Cao Deng, Youhong Zhang
https://doi.org/10.7717/peerj.14682 PubMed 36655040
December 13, 2022
Predicting RNA secondary structure by a neural network: what features may be learned?
Elizaveta I. Grigorashvili, Zoe S. Chervontseva, Mikhail S. Gelfand
https://doi.org/10.7717/peerj.14335 PubMed 36530406
November 4, 2022
APPINetwork: an R package for building and computational analysis of protein–protein interaction networks
Simon Gosset, Annie Glatigny, Mélina Gallopin, Zhou Yi, Marion Salé, Marie-Hélène Mucchielli-Giorgi
https://doi.org/10.7717/peerj.14204 PubMed 36353604
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
March 24, 2022
A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma
Weiqing Wang, Ming Xiang, Hui Liu, Xiao Chu, Zhaoyun Sun, Liang Feng
https://doi.org/10.7717/peerj.13057 PubMed 35356464
March 1, 2022
Genome wide expression analysis of circular RNAs in mammary epithelial cells of cattle revealed difference in milk synthesis
Syed Mudasir Ahmad, Basharat Bhat, Zainab Manzoor, Mashooq Ahmad Dar, Qamar Taban, Eveline M. Ibeagha-Awemu, Nadeem Shabir, Mohd Isfaqul Hussain, Riaz A. Shah, Nazir A. Ganai
https://doi.org/10.7717/peerj.13029 PubMed 35251787
December 2, 2021
CNV-P: a machine-learning framework for predicting high confident copy number variations
Taifu Wang, Jinghua Sun, Xiuqing Zhang, Wen-Jing Wang, Qing Zhou
https://doi.org/10.7717/peerj.12564 PubMed 34917425
October 26, 2021
Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma
Bing-Bing Shang, Jun Chen, Zhi-Guo Wang, Hui Liu
https://doi.org/10.7717/peerj.12315 PubMed 34754620
August 27, 2021
SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda
https://doi.org/10.7717/peerj.12087 PubMed 34532161
July 1, 2021
In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds
Consolata Gakii, Billiah Kemunto Bwana, Grace Gathoni Mugambi, Esther Mukoya, Paul O. Mireji, Richard Rimiru
https://doi.org/10.7717/peerj.11691 PubMed 34249514
May 21, 2021
The landscape of tumors-infiltrate immune cells in papillary thyroid carcinoma and its prognostic value
Yanyi Huang, Tao Yi, Yushu Liu, Mengyun Yan, Xinli Peng, Yunxia Lv
https://doi.org/10.7717/peerj.11494 PubMed 34055497
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
https://doi.org/10.7717/peerj.10906 PubMed 33828908
February 22, 2021
Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis
Chenkai Wang, Nenggui Xu, Shuai Cui
https://doi.org/10.7717/peerj.10885 PubMed 33665027
February 3, 2021
Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina
Linrong Wan, Anlian Zhou, Wenfu Xiao, Bangxing Zou, Yaming Jiang, Jinshu Xiao, Cao Deng, Youhong Zhang
https://doi.org/10.7717/peerj.10818 PubMed 33604192
November 24, 2020
DPM1 expression as a potential prognostic tumor marker in hepatocellular carcinoma
Ming Li, Shengli Xia, Ping Shi
https://doi.org/10.7717/peerj.10307 PubMed 33282554
November 20, 2020
Genome-wide identification and analysis of the thiolase family in insects
Shou-Min Fang
https://doi.org/10.7717/peerj.10393 PubMed 33240678
August 17, 2020
CMTM6 significantly relates to PD-L1 and predicts the prognosis of gastric cancer patients
Xin Li, Ling Chen, Chuan Gu, Qiaoli Sun, Jia Li
https://doi.org/10.7717/peerj.9536 PubMed 32874775
July 21, 2020
Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage
Pengyu Chen, Mingrui Song, Yutian Wang, Songyun Deng, Weisheng Hong, Xianrong Zhang, Bin Yu
https://doi.org/10.7717/peerj.9484 PubMed 32742785
June 19, 2020
Alveolar soft-part sarcoma (ASPS) resembles a mesenchymal stromal progenitor: evidence from meta-analysis of transcriptomic data
Luke H. Stockwin
https://doi.org/10.7717/peerj.9394 PubMed 32596059
May 26, 2020
The high expression of MTH1 and NUDT5 predict a poor survival and are associated with malignancy of esophageal squamous cell carcinoma
Jing-Jing Wang, Teng-Hui Liu, Jin Li, Dan-Ni Li, Xin-Yuan Tian, Qiu-Geng Ouyang, Jian-Ping Cai
https://doi.org/10.7717/peerj.9195 PubMed 32518727
April 3, 2020
Weighted gene correlation network analysis reveals novel biomarkers associated with mesenchymal stromal cell differentiation in early phase
Bin Xiao, Guozhu Wang, Weiwei Li
https://doi.org/10.7717/peerj.8907 PubMed 32280568
March 18, 2020
Identification of a three-m6A related gene risk score model as a potential prognostic biomarker in clear cell renal cell carcinoma
Yiqiao Zhao, Zijia Tao, Xiaonan Chen
https://doi.org/10.7717/peerj.8827 PubMed 32219036
February 5, 2020
Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.)
Lin Zhang, Wei Chen, Ben Shi
https://doi.org/10.7717/peerj.8467 PubMed 32071809
December 20, 2019
Expression and prognostic analyses of ITGA11, ITGB4 and ITGB8 in human non-small cell lung cancer
Pancheng Wu, Yanyu Wang, Yijun Wu, Ziqi Jia, Yang Song, Naixin Liang
https://doi.org/10.7717/peerj.8299 PubMed 31875161
December 18, 2019
A systematic review of the application of machine learning in the detection and classification of transposable elements
Simon Orozco-Arias, Gustavo Isaza, Romain Guyot, Reinel Tabares-Soto
https://doi.org/10.7717/peerj.8311 PubMed 31976169
December 9, 2019
Pelvic floor pressure distribution profile in urinary incontinence: a classification study with feature selection
Adriano Carafini, Isabel C.N. Sacco, Marcus Fraga Vieira
https://doi.org/10.7717/peerj.8207 PubMed 31844587
November 1, 2019
The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species
Ruchishree Konhar, Manish Debnath, Santosh Vishwakarma, Atanu Bhattacharjee, Durai Sundar, Pramod Tandon, Debasis Dash, Devendra Kumar Biswal
https://doi.org/10.7717/peerj.7756 PubMed 31695964
October 25, 2019
Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis
Zhendong Liu, Ruotian Zhang, Xin Chen, Penglei Yao, Tao Yan, Wenwu Liu, Jiawei Yao, Andrei Sokhatskii, Ilgiz Gareev, Shiguang Zhao
https://doi.org/10.7717/peerj.7782 PubMed 31667013
October 25, 2019
Investigating the significance of tumor-infiltrating immune cells for the prognosis of lung squamous cell carcinoma
Yueyan Zhu, Xiaoqin Zhang
https://doi.org/10.7717/peerj.7918 PubMed 31667016
September 6, 2019
Crucial lncRNAs associated with adipocyte differentiation from human adipose-derived stem cells based on co-expression and ceRNA network analyses
Kana Chen, Shujie Xie, Wujun Jin
https://doi.org/10.7717/peerj.7544 PubMed 31534842
June 7, 2018
Beef tenderness and intramuscular fat proteomic biomarkers: muscle type effect
Brigitte Picard, Mohammed Gagaoua, Marwa Al-Jammas, Leanne De Koning, Albéric Valais, Muriel Bonnet
https://doi.org/10.7717/peerj.4891 PubMed 29892502
September 28, 2017
Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data
Tomasz Dzida, Mudassar Iqbal, Iryna Charapitsa, George Reid, Henk Stunnenberg, Filomena Matarese, Korbinian Grote, Antti Honkela, Magnus Rattray
https://doi.org/10.7717/peerj.3742 PubMed 28970965
September 11, 2017
Genome-wide identification of the MADS-box transcription factor family in pear (Pyrus bretschneideri) reveals evolution and functional divergence
Runze Wang, Meiling Ming, Jiaming Li, Dongqing Shi, Xin Qiao, Leiting Li, Shaoling Zhang, Jun Wu
https://doi.org/10.7717/peerj.3776 PubMed 28924499
April 27, 2017
Prediction of post-translational modification sites using multiple kernel support vector machine
BingHua Wang, Minghui Wang, Ao Li
https://doi.org/10.7717/peerj.3261 PubMed 28462053
April 18, 2017
The evolution of logic circuits for the purpose of protein contact map prediction
Samuel D. Chapman, Christoph Adami, Claus O. Wilke, Dukka B KC
https://doi.org/10.7717/peerj.3139 PubMed 28439455
September 21, 2016
A genetic programming approach to oral cancer prognosis
Mei Sze Tan, Jing Wei Tan, Siow-Wee Chang, Hwa Jen Yap, Sameem Abdul Kareem, Rosnah Binti Zain
https://doi.org/10.7717/peerj.2482 PubMed 27688975
August 24, 2016
Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes
Vaishali P. Waman, Pandurang Kolekar, Mukund R. Ramtirthkar, Mohan M. Kale, Urmila Kulkarni-Kale
https://doi.org/10.7717/peerj.2326 PubMed 27635316
July 7, 2016
Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing
Ramesh Menon, Anand B. Patel, Chaitanya Joshi
https://doi.org/10.7717/peerj.2147 PubMed 27441113
April 19, 2016
BMP2/BMPR1A is linked to tumour progression in dedifferentiated liposarcomas
Hannah L. O’Neill, Amy P. Cassidy, Olivia B. Harris, John W. Cassidy
https://doi.org/10.7717/peerj.1957 PubMed 27114889
November 18, 2014
Bioinformatic analysis of cis-regulatory interactions between progesterone and estrogen receptors in breast cancer
Matloob Khushi, Christine L. Clarke, J. Dinny Graham
https://doi.org/10.7717/peerj.654 PubMed 25426335
October 23, 2014
Associating disease-related genetic variants in intergenic regions to the genes they impact
Geoff Macintyre, Antonio Jimeno Yepes, Cheng Soon Ong, Karin Verspoor
https://doi.org/10.7717/peerj.639 PubMed 25374782
September 23, 2014
Error estimates for the analysis of differential expression from RNA-seq count data
Conrad J. Burden, Sumaira E. Qureshi, Susan R. Wilson
https://doi.org/10.7717/peerj.576 PubMed 25337456
September 4, 2014
Metagenome fragment classification based on multiple motif-occurrence profiles
Naoki Matsushita, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
https://doi.org/10.7717/peerj.559 PubMed 25210663
August 12, 2014
The mitochondrial genome of Paragonimus westermani (Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)
Devendra K. Biswal, Anupam Chatterjee, Alok Bhattacharya, Veena Tandon
https://doi.org/10.7717/peerj.484 PubMed 25165620
November 12, 2013
An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899
Devendra Kumar Biswal, Sudeep Ghatani, Jollin A. Shylla, Ranjana Sahu, Nandita Mullapudi, Alok Bhattacharya, Veena Tandon
https://doi.org/10.7717/peerj.207 PubMed 24255820
November 5, 2013
Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes
Liang Jiang, Hua-Zhang Zhu, Yin-Zhen Xu, Jia-Zuan Ni, Yan Zhang, Qiong Liu
https://doi.org/10.7717/peerj.202 PubMed 24255816
November 5, 2013
Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing
Piroon Jenjaroenpun, Yuliya Kremenska, Vrundha M. Nair, Maksym Kremenskoy, Baby Joseph, Igor V. Kurochkin
https://doi.org/10.7717/peerj.201 PubMed 24255815
October 31, 2013
Construction of microRNA functional families by a mixture model of position weight matrices
Je-Keun Rhee, Soo-Yong Shin, Byoung-Tak Zhang
https://doi.org/10.7717/peerj.199 PubMed 24255813
October 31, 2013
An extended genovo metagenomic assembler by incorporating paired-end information
Afiahayati , Kengo Sato, Yasubumi Sakakibara
https://doi.org/10.7717/peerj.196 PubMed 24281688