Jian Ma

About

Jian Ma is the Ray and Stephanie Lane Professor of Computational Biology at the School of Computer Science, Carnegie Mellon University, a position he has held since September 2021. Prior to this, he served as a Full Professor from July to August 2021 and as an Associate Professor from January 2016 to June 2021. He is also affiliated faculty in Machine Learning at Carnegie Mellon. Before joining Carnegie Mellon, Jian Ma was an Associate Professor with tenure and Assistant Professor in the Bioengineering department at the University of Illinois at Urbana-Champaign, where he was also a faculty member of the Carl R. Woese Institute for Genomic Biology, Biophysics and Computational Biology, and an affiliate faculty member in Computer Science. He completed his postdoctoral training at UC Santa Cruz under David Haussler from 2007 to 2009, earned his Ph.D. in Computer Science from Penn State University in 2006 under Webb Miller, and holds M.S. and B.S. degrees in Computer Science from Fudan University in Shanghai, China. Jian Ma's research interests focus on computational biology, with particular emphasis on 3D epigenomics and comparative genomics. His work integrates computational and machine learning approaches to understand the spatial organization of the genome and its regulatory mechanisms. He has been recognized with numerous honors including being named an ACM Fellow, ISCB Fellow, and AAAS Fellow in 2025 and 2022 respectively, receiving the Allen Newell Award for Research…

Research topics

• Biology
• Genetics
• Cell biology
• Computational biology
• Computer Science
• Artificial Intelligence
• Computer vision
• Physics
• Psychology
• Gerontology

Selected publications

• CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity

  Nature Biotechnology · 2020 · 282 citations

  DOI

• Fasting-induced FGF21 signaling activates hepatic autophagy and lipid degradation via JMJD3 histone demethylase

  Nature Communications · 2020 · 210 citations

  Autophagy is essential for cellular survival and energy homeostasis under nutrient deprivation. Despite the emerging importance of nuclear events in autophagy regulation, epigenetic control of autophagy gene transcription remains unclear. Here, we report fasting-induced Fibroblast Growth Factor-21 (FGF21) signaling activates hepatic autophagy and lipid degradation via Jumonji-D3 (JMJD3/KDM6B) histone demethylase. Upon FGF21 signaling, JMJD3 epigenetically upregulates global autophagy-network gen…

  DOI

• Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

  Nature Cell Biology · 2023 · 170 citations

  PublisherOA PDFDOI

• TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

  Genome Research · 2020 · 150 citations

  activation. Our results demonstrate a largely "hardwired" genome organization with specific genes moving small mean distances relative to speckles during cell differentiation or a physiological transition, suggesting an important role of nuclear speckles in gene expression regulation.

  DOI

• SPIN reveals genome-wide landscape of nuclear compartmentalization

  Genome biology · 2021 · 133 citations

  Senior authorCorresponding

  We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for modulating genome function. As a proof-of-principle, we use SPIN to integrate nuclear compartment mapping (TSA-seq and DamID) and chromatin interaction data (Hi-C) from K562 cells to identify 10 spatial compartmentalization states genome-wide relative to nuclear speckles, lamina, and putative…

  DOI

Recent grants

• NIH Grant R21HG006464

  NIH · $383k · 2015

• Multiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data Integration

  NIH · $10.4M · 2020–2026

• Spatial omics technologies to map the senescent cell microenvironment

  NIH · $916k · 2021–2023

Frequent coauthors

• Yang Zhang

  San Diego Biomedical Research Institute

  97 shared

• Yuchuan Wang

  San Diego Biomedical Research Institute

  73 shared

• Omid Gholamalamdari

  University of Illinois Urbana-Champaign

  71 shared

• Bas van Steensel

  The Netherlands Cancer Institute

  69 shared

• Andrew S. Belmont

  University of Illinois Urbana-Champaign

  69 shared

• Liguo Zhang

  University of Illinois Urbana-Champaign

  67 shared

• Tom van Schaik

  Oncode Institute

  64 shared

• David M. Gilbert

  San Diego Biomedical Research Institute

  64 shared

Labs

• Ma LaboratoryPI

  Not provided

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