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Jun Chen
PeerJ Editor, Author & Reviewer
3,080 Points

Contributions by role

Author 405
Preprint Author 140
Reviewer 30
Editor 2,505

Contributions by subject area

Bioinformatics
Genomics
Statistics
Microbiology
Gynecology and Obstetrics
Gastroenterology and Hepatology
Public Health
Biodiversity
Ecology
Mathematical Biology
Computational Biology
Molecular Biology
Epidemiology
Genetics
Oncology
Nephrology
Pediatrics
Hematology
Medical Genetics
Evolutionary Studies
Taxonomy
Computational Science
Data Science
Biotechnology
Mycology
Cardiology
Metabolic Sciences
Cell Biology
Science Policy
Urology
Biochemistry
Respiratory Medicine

Jun Chen

PeerJ Editor, Author & Reviewer

Summary

Assistant Professor of Biostatistics, Mayo Clinic. Ph.D., University of Pennsylvania. My research concerns the development and application of powerful and robust statistical methods for high-dimensional "omics" data, arising from modern high-throughput technologies such as microarray and next-generation sequencing. I am particularly interested in methods for microbiome sequencing data. Much of this effort is motivated by ongoing collaborations in projects that study the role of the human microbiome in disease pathogenesis using metagenomic sequencing.

Research interests include statistical genetics, genomics and metagenomics; and high-dimensional statistics.

Bioinformatics Computational Biology Genetics Genomics Statistics

Section Editor

Bioinformatics and Genomics

Editorial Board Member

PeerJ - the Journal of Life & Environmental Sciences

Work details

Associate Professor of Biostatistics

Mayo Clinic
Division of Biomedical Statistics and Informatics
Dr. Chen's methodology development focuses on efficiently modeling microbiome sequencing data, taking into account its inherent structure and large variability. The ultimate goal of his research is to provide tools to integrate the microbiome data into practice of individualized medicine.

Websites

  • Google Scholar
  • My Publications

PeerJ Contributions

  • Articles 3
  • Preprints 2
  • Edited 22
April 2, 2018
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
Li Chen, James Reeve, Lujun Zhang, Shengbing Huang, Xuefeng Wang, Jun Chen
https://doi.org/10.7717/peerj.4600 PubMed 29629248
January 7, 2016
Impact of demographics on human gut microbial diversity in a US Midwest population
Jun Chen, Euijung Ryu, Matthew Hathcock, Karla Ballman, Nicholas Chia, Janet E Olson, Heidi Nelson
https://doi.org/10.7717/peerj.1514 PubMed 26839739
November 26, 2015
Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery
Elizabeth A. Baldwin, Marina Walther-Antonio, Allison M. MacLean, Daryl M. Gohl, Kenneth B. Beckman, Jun Chen, Bryan White, Douglas J. Creedon, Nicholas Chia
https://doi.org/10.7717/peerj.1398 PubMed 26644969
March 7, 2018 - Version: 3
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
Li Chen, James Reeve, Lujun Zhang, Shengbing Huang, Xuefeng Wang, Jun Chen
https://doi.org/10.7287/peerj.preprints.3417v3
November 17, 2015 - Version: 1
Impact of demographics on human gut microbial diversity in a US Midwest population
Jun Chen, Euijung Ryu, Matthew Hathcock, Karla Ballman, Nicholas Chia, Janet E Olson, Heidi Nelson
https://doi.org/10.7287/peerj.preprints.1512v1

Academic Editor on

November 23, 2023
Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change?
Hee Yeon Kim, Tae Hyun Kim, Jeong Hwan Shin, Kwangrae Cho, Heon-Kyun Ha, Anbok Lee, Young Jin Kim
https://doi.org/10.7717/peerj.16366 PubMed 38025669
October 12, 2023
An application of topological data analysis in predicting sumoylation sites
Xiaoxi Lin, Yaru Gao, Fengchun Lei
https://doi.org/10.7717/peerj.16204 PubMed 37846308
March 21, 2022
An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2
Sk. Sarif Hassan, Vaishnavi Kodakandla, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Tarek Mohamed Abd El-Aziz, Kazuo Takayama, Ramesh Kandimalla, Amos Lal, Ángel Serrano-Aroca, Gajendra Kumar Azad, Alaa A.A. Aljabali, Giorgio Palù, Gaurav Chauhan, Parise Adadi, Murtaza Tambuwala, Adam M. Brufsky, Wagner Baetas-da-Cruz, Debmalya Barh, Vasco Azevedo, Nikolas G. Bazan, Bruno Silva Andrade, Raner José Santana Silva, Vladimir N. Uversky
https://doi.org/10.7717/peerj.13136 PubMed 35341060
February 15, 2022
A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
Gaurav Vaidya, Nico Cellinese, Hilmar Lapp
https://doi.org/10.7717/peerj.12618 PubMed 35186448
November 17, 2020
Analysis of genes and underlying mechanisms involved in foam cells formation and atherosclerosis development
Kai Zhang, Xianyu Qin, Xianwu Zhou, Jianrong Zhou, Pengju Wen, Shaoxian Chen, Min Wu, Yueheng Wu, Jian Zhuang
https://doi.org/10.7717/peerj.10336 PubMed 33240650
October 29, 2020
A 14 immune-related gene signature predicts clinical outcomes of kidney renal clear cell carcinoma
Yong Zou, Chuan Hu
https://doi.org/10.7717/peerj.10183 PubMed 33194402
August 14, 2020
Identifying disease-associated signaling pathways through a novel effector gene analysis
Zhenshen Bao, Bing Zhang, Li Li, Qinyu Ge, Wanjun Gu, Yunfei Bai
https://doi.org/10.7717/peerj.9695 PubMed 32864216
February 19, 2020
The E2F family as potential biomarkers and therapeutic targets in colon cancer
Haibo Yao, Fang Lu, Yanfei Shao
https://doi.org/10.7717/peerj.8562 PubMed 32117628
November 26, 2019
Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
Haiping Zhang, Jian Zou, Ying Yin, Bo Zhang, Yaling Hu, Jingjing Wang, Huijun Mu
https://doi.org/10.7717/peerj.8096 PubMed 31788359
August 28, 2019
HiLDA: a statistical approach to investigate differences in mutational signatures
Zhi Yang, Priyatama Pandey, Darryl Shibata, David V. Conti, Paul Marjoram, Kimberly D. Siegmund
https://doi.org/10.7717/peerj.7557 PubMed 31523512
May 1, 2019
Predicting gene expression using DNA methylation in three human populations
Huan Zhong, Soyeon Kim, Degui Zhi, Xiangqin Cui
https://doi.org/10.7717/peerj.6757 PubMed 31106051
December 10, 2018
A direct approach to estimating false discovery rates conditional on covariates
Simina M. Boca, Jeffrey T. Leek
https://doi.org/10.7717/peerj.6035 PubMed 30581661
August 8, 2018
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
Jacob T. Nearing, Gavin M. Douglas, André M. Comeau, Morgan G.I. Langille
https://doi.org/10.7717/peerj.5364 PubMed 30123705
July 12, 2018
Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome
Jun Miyoshi, Vanessa Leone, Kentaro Nobutani, Mark W. Musch, Kristina Martinez-Guryn, Yunwei Wang, Sawako Miyoshi, Alexandria M. Bobe, A. Murat Eren, Eugene B. Chang
https://doi.org/10.7717/peerj.5166 PubMed 30013837
April 11, 2018
Empirical evaluation of data normalization methods for molecular classification
Huei-Chung Huang, Li-Xuan Qin
https://doi.org/10.7717/peerj.4584 PubMed 29666754
November 30, 2017
BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters
Gong Cheng, Quan Lu, Ling Ma, Guocai Zhang, Liang Xu, Zongshan Zhou
https://doi.org/10.7717/peerj.3948 PubMed 29204317
October 17, 2017
How to normalize metatranscriptomic count data for differential expression analysis
Heiner Klingenberg, Peter Meinicke
https://doi.org/10.7717/peerj.3859 PubMed 29062598
September 8, 2017
Variance component testing for identifying differentially expressed genes in RNA-seq data
Sheng Yang, Fang Shao, Weiwei Duan, Yang Zhao, Feng Chen
https://doi.org/10.7717/peerj.3797 PubMed 28929020
July 7, 2017
The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research
Valentin Amrhein, Fränzi Korner-Nievergelt, Tobias Roth
https://doi.org/10.7717/peerj.3544 PubMed 28698825
January 19, 2017
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Xun Zhu, Travers Ching, Xinghua Pan, Sherman M. Weissman, Lana Garmire
https://doi.org/10.7717/peerj.2888 PubMed 28133571
August 30, 2016
A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units
Matthew A. Jackson, Jordana T. Bell, Tim D. Spector, Claire J. Steves
https://doi.org/10.7717/peerj.2341 PubMed 27635321
February 18, 2016
Problems in using p-curve analysis and text-mining to detect rate of p-hacking and evidential value
Dorothy V.M. Bishop, Paul A. Thompson
https://doi.org/10.7717/peerj.1715 PubMed 26925335