Silver Contributor

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Silver 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

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

October 9, 2025

DNA-based prediction of external ear morphology in the Chinese population: an exploratory study

Xindi Wang, Zibo Zhao, Jingting Wu, Yuan Li, Yufei Yang, Bo Liu, Chengye Zhou, Chuanxu Wang, Xiaogang Chen, Feng Song

https://doi.org/10.7717/peerj.20169 PubMed 41084627

October 3, 2025

Reconstruction of masked sequences via inverse mapping of incomplete information natural vectors

Patrick Ding, Guoqing Hu, Hongyu Yu, Stephen S.-T. Yau

https://doi.org/10.7717/peerj.20126 PubMed 41059407

September 18, 2025

Fine-tuning protein language models unlocks the potential of underrepresented viral proteomes

Rajan Sawhney, Barbra D. Ferrell, Thibaut Dejean, Zachary Schreiber, William Harrigan, Shawn W. Polson, K. Eric Wommack, Mahdi Belcaid

https://doi.org/10.7717/peerj.19919 PubMed 40985030

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

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