Main
Peng Zhou
Investigator at Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS). Using a combination of classical genetics, comparative genomics and multi-omics approaches, I work to understand the regulatory mechanism of gene expression during plant development and under stress conditions, identify key cis-regulatory elements and transcription factors for crop improvement. My research interests also include constructing plant gene regulatory networks, training machine learning models to predict temporal/spatial gene expression patterns, as well as understanding the molecular mechanism of heterosis.
Education
Ph.D. Plant Pathology & Bioinformatics
University of Minnesota, Twin Cities
St. Paul US
2015 - 2009
- Advidor: Nevin D. Young
M.S. Forensic Genetics
Xi’an Jiaotong University
Xi’an CN
2009 - 2007
B.E. Biological Engineering & Computer Science
Xi’an Jiaotong University
Xi’an CN
2007 - 2003
Research Experience
Investigator & Professor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)
Beijing CN
present - 2021
Post Doctoral Associate
University of Minnesota, Twin Cities
St. Paul US
2021 - 2016
- Advisor: Nathan M. Springer
AgroInformatics Analyst
University of Minnesota, Twin Cities
St. Paul US
2016 - 2015
Representative Publications
A complete assembly of the sorghum BTx623 reference genome
Plant Commun. 2024, 5: 100977.
N/A
2024
- Deng Y*, Zhou P*, Li F*, Wang J*, Xie K*, Liang H, Wang C, Liu B, Zhu Z, Zhou W, et al
Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information
Plant Cell. 2022, 34: 514-534.
N/A
2022
- Zhou P, Enders TA, Myers ZA, Magnusson E, Crisp PA, Noshay J, …, Springer NM
- Impact Factor = 11.277
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions
Plant Cell. 2020, 32: 1377-1396.
N/A
2020
- Zhou P, Li Z, Magnusson E, Cano FAG, Crisp PA, Noshay J, Grotewold E, HirschC, Briggs SP, Springer NM
- Impact Factor = 11.277
Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development
Molecular Plant. 2019, 12: 410-425.
N/A
2019
- Zhou P, Hirsch CN, Briggs SP, Springer NM
- Impact Factor = 10.812
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
BMC Genomics. 2017, 18: 261.
N/A
2017
- Zhou P, Silverstein KAT, Ramaraj T, Guhlin J, Denny R, Liu J, …, Young ND
Other Publications
- Citation = 3430
- H-index = 22
- I10-index = 29
Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions
G3. 2024:jkae274.
N/A
2024
- Ellison EL, Zhou P, Chu Y-H, Hermanson P, Gomez-Cano L, Myers ZA, Abnave A, Gray J, Hirsch CN, Grotewold E, Springer NM
Intraspecific diploidization of a halophyte root fungus drives heterosis
Nat Commun. 2024:15(1):5872.
N/A
- Li Z, Zhu Z, Qian K, Tang B, Han B, Zhong Z, Fu T, Zhou P#, Stukenbrock EH, Martin FM#, Yuan Z#
Mutator transposon insertions within maize genes often provide a novel outward reading promoter
Genetics. 2023:225(3):iyad171.
N/A
2023
- Ellison EL, Zhou P, Hermanson P, Chu Y-H, Read A, Hirsch CN, Grotewold E, Springer NM.
Transcriptome Analysis of Developing Wheat Grains at Rapid Expanding Phase Reveals Dynamic Gene Expression Patterns
Biology. 2022, 11: 281.
N/A
2022
- Guan J, Wang Z, Liu S, Kong X, Wang F, Sun G, Geng S, Mao L#, Zhou P#, Li A#
Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins
Proc Natl Acad Sci U S A.. 2021. 118 (47) e2109332118.
N/A
2021
- Birdseye D, de Boer LA, Bai H, Zhou P, Shen Z, Schmelz EA, Springer NM, Briggs SP
Widespread imprinting of transposable elements and young genes in the maize endosperm
PLoS Genetics. 2021;17: e1009491.
N/A
- Anderson SN, Zhou P, Higgins K, Brandvain Y, Springer NM
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons
Genetics. 2021, 217: 1–13.
N/A
- Noshay JM, Marand AP, Anderson SN, Zhou P, Guerra MKM, Lu Z, et al
Single-parent expression drives dynamic gene expression complementation in maize hybrids
Plant Journal. 2021, 105: 93–107.
N/A
- Li Z, Zhou P, Della Coletta R, Zhang T, Brohammer AB, H O’Connor C, et al.
The antagonistic MYB paralogs RH1 and RH2 govern anthocyanin leaf markings in Medicago truncatula
New Phytologist. 2021, 229: 3330–3344.
N/A
- Wang C, Ji W, Liu Y, Zhou P, Meng Y, Zhang P, et al.
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
Proc Natl Acad Sci U S A.. 2020, 117: 23991–24000.
N/A
2020
- Crisp PA, Marand AP, Noshay JM, Zhou P, Lu Z, Schmitz RJ, et al.
Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids
Plant Physiol. 2020, 182: 318-331.
N/A
- Crisp PA, Hammond R, Zhou P, Vaillancourt B, Lipzen A, Daum C, et al
Monitoring the interplay between transposable element families and DNA methylation in maize
PLoS Genetics. 2019, 15: e1008291.
N/A
2019
- Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, et al
Transposable elements contribute to dynamic genome content in maize
Plant Journal. 2019, 100: 1052-1065.
N/A
- Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O’Connor CH, et al
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model
BMC Genomics. 2017, 18: 578.
N/A
2017
- Moll KM*, Zhou P*, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, et al
Hybrid assembly with long and short reads improves discovery of gene family expansions
BMC Genomics. 2017, 18: 541.
N/A
- Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, et al
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding
BMC Bioinformatics. 2017, 18: 367.
N/A
- Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND
Exploring structural variants in environmentally sensitive gene families
Curr Opin Plant Biol. 2016, 30: 19–24.
N/A
2016
- Young ND, Zhou P, Silverstein KA
Genomic signature of adaptation to climate in Medicago truncatula
Genetics. 2014, 196: 1263–1275.
N/A
2014
- Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND, Tiffin P
Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
Molecular Ecology. 2011, 108: E864-70.
N/A
2013
- Paape T, Bataillon T, Zhou P, J Y Kono T, Briskine R, Young ND, et al
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)
BMC Bioinformatics. 2013, 14: 335.
N/A
- Zhou P, Silverstein KA, Gao L, Walton JD, Nallu S, Guhlin J, et al
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula
Proc Natl Acad Sci U S A. 2013, 22: 3525–3538.
N/A
- Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, et al
Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome)
Genome Biol Evol. 2012, 4: 726–737.
N/A
2012
- Paape T, Zhou P, Branca A, Briskine R, Young N, Tiffin P
The Medicago genome provides insight into the evolution of rhizobial symbioses
Nature. 2011, 480: 520-524.
N/A
2011
- Young ND, Debellé F, Oldroyd GED, …, Zhou P, …, et al
Professional service
Reviewer for journals
N/A
N/A
- Plant Biotechnology Journal
- JIPB
- Plant Physiology
- BMC Biology
- Crop Journal
- The Plant Genome
Conference presentations
Meta gene regulatory networks in maize refine functionally relevant regulatory interactions
Plant and Animal Genome XXVIII Conference
San Diego, CA
2020
Exploring Functional Transcriptomics using Gene Regulatory Networks in Maize.
61st Annual Maize Genetics Conference
St. Louis, MO
2019
Documenting the Manifestations of Heterosis in Co-expression Networks for Maize
Plant and Animal Genome XXVI Conference
San Diego, CA
2018
The Medicago Pan-Genome Reveals Large-scale Variation
Plant and Animal Genome XXII Conference
San Diego, CA
2014
Detecting secreted peptides in plants using SPADA (Secreted Peptide Alignment Discovery Algorithm)
Plant and Animal Genome XXI Conference
San Diego, CA
2013
Population-Scale Deep Sequencing Reveals Extensive Structural Variation in Medicago species
Minnesota Supercomputing Institute Research Exhibition
Minneapolis, MN
2011
Genome Distribution and Population Genetics of Nodule-Specific Cysteine-Rich (NCR) Peptides in Medicago
Plant and Animal Genome XIX Conference
San Diego, CA
A Medicago truncatula Hapmap as a Platform for Exploring the Genetics of Symbiosis
Plant and Animal Genome XVIII Conference
San Diego, CA
2010
Invited Presentations/Seminars
Co-expression based Gene Regulatory Networks Predict Functional Interactions in Maize
N/A
China Agriculture University, Beijing
2019
Transcriptome Dynamics in Maize
N/A
Huazhong Agriculture University, Wuhan
Toward a Medicago Pan-genome: Assembling and Comparing Multiple Genomes
Medicago truncatula Workshop
Noble Research Institute, Ardmore
2016
Assembling and Comparing Multiple High-Quality Medicago Genomes
N/A
Chinese Academy of Agricultural Sciences (CAAS), Beijing