Qi Ma

Post Doctoral

Department of Medicine
University of California, San Diego (UCSD)

Department of Medicine
University of California, San Diego (UCSD)
9500 Gilman Dr. MC0648
La Jolla, CA 92093-0648

Email: q1ma @ ucsd .edu; maqiwinner @ gmail .com

My primary research interests are combination of  Bioinformatics and Epigenetics in study of gene transcriptional regulation mechanism in development, homeostasis and diseases.(e.g. Cancer and Neuron degenerative, cardiovascular disease.) My research focus on understanding functional properties of essential genomics regulatory elements such as enhancers in coding gene transcription regulation by comprehensive analyzing and integrating of multiple diversified functional genomic High-throughput sequencing data (NGS) and develop new computational strategies, including contemporary machine learning and deep learning methods to understand and delineate complicated regulatory network that is responsible for orchestrating transcriptional programs in response to diverse physiological or pathological signals, such as microbiota and cancer progression, and multiple drug resistance influenced by human microbiome.

I led the computational analysis of the biological models for major discoveries as below:

  1. Identification ligand dependent eRNA induction on enhancers is a significant mark of active/functional enhancers, which affects enhancer targeted coding gene transcription activation. Identification of "first tier" Estrogen-regulated active enhancers based on the presence of RNA synthesis and the presence of H3K4me1 and H3K27ac and absence of H3K4me3 histone mark in breast cancer MCF7 cells genome-widely.
  2. Identification of a unique anti-pause enhancer (A-PEs) in genome wide, which regulates target gene transcription by Polymerase II promoter proximal pause release.
  3. Dissecting multiple diverse transcription factors/histone mark/co-activators/mediator co-localization at active enhancers. Identification of Interphased architectural Condensin complexes are most robustly recruited factor involved in active enhancer functions among these multiple factors.
  4. demonstration that nuclear organization and nuclear local environmental play an important role in regulating gene transcriptional activation.
  5. Identification the epigenetic signature of the neuronal enhancers required for transcriptional regulation of synaptic plasticity genes during memory formation, linking this to Reelin signaling. The binding of Reelin to its receptor, LRP8, triggers activation of this cohort of LRP8-Reelin-regulated neuronal (LRN) enhancers that serve as the ultimate convergence point of a novel synapse-to-nucleus pathway.
  6. Deciphering Enhancer Activation Requires trans-Recruitment of a Mega Transcription Factor Complex.
  7. Elucidating the epigenetic program of MEF2A and MEF2C transcription factors in mouse cortical neurons mainly through the binding of enhancer regulatory elements in proximity of target genes involved in neuronal plasticity and calcium signaling.
For more details see my Projects


Postdoctoral Research Associate   02/2015-now
The University of California, San Diego (UCSD), CA, USA.
Supervisor: Prof. Michael G Rosenfeld

Ph.D. in Bioinformatics                                     09/2009-02/2015
The University of California, San Diego (UCSD), CA, USA.
of Bioinformatics and Systems Biology
Supervisor: Prof. Michael G Rosenfeld & Prof. Gene Yeo
Thesis: “Understanding the Functional Properties of Enhancers”

M.S. in Biology                                    09/2005-06/2007
Illinois institute of Technology (IIT), Chicago, IL, USA.
Supervisor: Prof. Wei Wang
Thesis: “Functional genomic analysis of the E.coli O157:H7 stain under industrial sanitizers’ stress by Microarray method.”

B.E. in Biology Engineering                              09/2000-09/2004
Beijing Institute of Technology (BIT), Beijing, China.
Supervisor: Prof. Yulin Deng

  • American Cancer Society Post doctoral Fellowship (2016-2019)


Teaching Assistant
The University of California, San Diego (UCSD), CA, USA. Bioinformatics and Systems Biology Program.
Supervisor: Prof. Trey Ideker
The University of California, San Diego (UCSD), CA, USA. Bioinformatics and Systems Biology Program.
Supervisor: Prof. Glenn Tesler


  • Invited Talk/Presentation:

    The functional role of enhancer network in orchestrating transcriptional programs UCLA Department of Anesthesiology & Perioperative Medicine, UCLA Cardiovascular            Research Theme, Feb, 2017, CA

  • Journal Reviewer / Guest Editor (GE): 
    • Journal of Integrative Bioinformatics (JIB): 2015, 2016
    • Epigenetic Diagnosis & Therapy: 2015, 2016
    • Plos One: 2014, 2015
    • Journal of Molecular Cell Biology: 2014, 2015
    • Mutation Research: 2014, 2015
    • Current Bioinformatics: 2014, 2015
    • Genomics: 2014, 2015
    • Medical & Biological Engineering & Computing: 2014, 2015
    • Computers in Biology and Medicine: 2014, 2015
    • Journal of Bioinformatics and Computational Biology: 2014, 2015
    • Journal of Computational Biology: 2016
    • Journal of Genomes and Exomes: 2016
  • Conference Reviewer / Program Committee (PC)
    • 2015 International Conference on Intelligent Computing (ICIC 2015)

REPRESENTATIVE PUBLICATIONS                                        * Indicate co-first author/equal contribution;

  • Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release. Liu Wen*, Qi Ma*, Kaki Wong, Wenbo Li, Kenny Ohgi, Jie Zhang, Aneel K. Aggarwal, and Michael G. Rosenfeld. Cell 155, no. 7 (December 19, 2013): 1581–1595. doi:10.1016/j.cell.2013.10.056. http://www.sciencedirect.com/science/article/pii/S0092867413014748
  • Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ERa-Regulated Transcriptional Program. Feng Yang*, Qi Ma*, Zhijie Liu, Wenbo Li, Yuliang Tan, Chunyu Jin, Wubin Ma, Yiren Hu, Jia Shen, Kenneth A. Ohgi, Francesca Telese, Wen Liu, and Michael G. Rosenfeld, Molecular Cell (May, 2017) Volume 66, Issue 3, p321–331.e6, 4 https://doi.org/10.1016/j.molcel.2017.03.019
  • LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation. Telese Francesca, Qi Ma, Patricia Montilla Perez, Dimple Notani, Soohwan Oh, Wenbo Li, Davide Comoletti, Kenneth A. Ohgi, Havilah Taylor, and Michael G. Rosenfeld. Neuron, p696–710, April 16, 2015. doi:10.1016/j.neuron.2015.03.033. http://www.cell.com/neuron/abstract/S0896-6273(15)00257-3
  • Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation. Wenbo Li*, Yiren Hu*, Soohwan Oh*, Qi Ma*, Xiang Zhou, Daria Merkurjev, Zhijie Liu, Xiaoyuan Song, Aaron Yun Chen, Bogdan Tanasa, Kenny Ohgi, Jie Zhang, Xin He, Wen Liu, and Michael G. Rosenfeld, Molecular Cell, 59, 188-202 (2015) http://www.sciencedirect.com/science/article/pii/S1097276515004414
  • Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex. Liu Zhijie, Daria Merkurjev, Feng Yang, Wenbo Li, Soohwan Oh, Meyer J. Friedman, Xiaoyuan Song, Feng Zhang, Qi Ma, Kenneth A. Ohgi, Anna Kro- nes, Michael G. Rosenfeld,. Cell 159, no. 2 (September 10, 2014): 358–73. doi:10.1016/j.cell.2014.08.027. http://www.cell.com/abstract/S0092-8674(14)01097-6
  • Genome-Wide Epigenetic Analysis of MEF2A and MEF2C Transcription Factors in Mouse Cortical Neurons.
    Qi Ma, and Francesca Telese. Communicative & Integrative Biology, vol. 8, no. 6, pp. e1087624–11, 00. doi:10.1080/19420889.2015.1087624. http://dx.doi.org/10.1080/19420889.2015.1087624
  • The Histone H4 Lysine 16 Acetyltransferase hMOF Regulates the Outcome of Autophagy. Füllgrabe Jens, Melinda A. Lynch-Day, Nina Heldring, Wenbo Li, Robert B. Struijk, Qi Ma, Ola Hermanson, Michael G. Rosenfeld, Daniel J. Klionsky, and Bertrand Joseph. Nature, 500, 468-471 (July 17, 2013). doi:10.1038/nature12313. http://www.nature.com/nature/journal/v500/n7463/abs/nature12313.html
  • A Novel Neuron-specific Histone H4K20 Demethylase LSD1n Promotes Transcriptional Elongation and is Essential for Learning and Memory. Jianxun Wang, Francesca Telese, Yuliang Tan, Wenbo Li, Xin He, Harihar Basnet, Qi Ma, Daria Merkurjev, Xiaoyan Zhu, Zhijie Liu, Jie Zhang, Kenny Ohgi, Havilah Taylor, Todd S. Macfarlan, Samuel L. Pfaff, Michael G. Rosenfeld, Nature Neuroscience 18, 1256–1264 (2015) http://www.nature.com/neuro/journal/v18/n9/abs/nn.4069.html
  • The Protein Architecture of Human Secretory Vesicles Reveals Differential Regulation of Signaling Molecule Secretion by Protein Kinases. Bark Steven J., Jill Wegrzyn, Laurent Taupenot, Michael Ziegler, Daniel T. O’Connor, Qi Ma, Michael Smoot, Trey Ideker, and Vivian Hook. PLoS ONE 7, no. 8 (August 16, 2012): e41134. doi:10.1371/journal.pone.0041134.                                                                                                                                                                         http://dx.doi.org/10.1371/journal.pone.0041134
  • mHMM (Multivariate Hidden Markov Model) Application in Studying BRD4 and JMJD6 Function Cooperatively on Promoter-Proximal Polymerase-II (Pol II) Pausing Release. Qi Ma, Wen Liu, and Michael G. Rosenfeld. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 515–515. BCB ’12. New York, NY, USA: ACM, 2012. doi:10.1145/2382936.2383005. http://dl.acm.org/citation.cfm?id=2383005
  • Bayesian network (BN) structure learning inference application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal Polymerase-II (Pol II) pausing release. Qi Ma, Wen Liu, Michael. G. Rosenfeld. Pacific Symposium on Biocomputing (PSB) 2014. January 03-07, 2014, Big Island of Hawaii. Page 47. ISBN 978-9-8145-9634-3.
  • Thyroid hormone receptor beta and NCOA4 regulate terminal erythrocyte differentiation.
    Gao, X., Lee, H.-Y., Li, W., Platt, R.J., Barrasa, M.I., Ma, Q., Elmes, R.R., Rosenfeld, M.G., and Lodish, H.F. (2017).  PNAS 201711058.


  1. Francesca Telese, Qi Ma, Patricia Montilla Perez, Soohwan Oh, Davide Comoletti, Dimple Norari, Wenbo Li, Michael G. Rosenfeld. “Reelin-LRP8 pathway activates an enhancer code for learning and memory” Neuroepigenetics, Keytone Symposia 2015 on Molecular and Cellular Biology. Feburary 22-26, 2015, Santa Fe, New Mexico, USA.
  2. Dorota Skowronska-Krawczyk, Qi Ma, Michal Schwartz, Kathleen Scully, Michael G. Rosenfeld. “Role of subnuclear structures in transcriptional activation - lesson from human disease” Nature Biotechnology Conference “Genomic Technologies and Biomaterials for Understanding Disease” San Diego, June 23-24, 2014.
  3. Dorota Skowronska-Krawczyk, Qi Ma, Michal Schwartz, Kathleen Scully, Michael G. Rosenfeld. “Required Enhancer: Matrin-3 Structural Interactions for Homeodomain Transcription Programs” 11th EMBL Conference Transcription and Chromatin, Heidelberg, (Germany) August 23-26, 2014.
  4. S. J. Bark; J. L. Wegrzyn; Q. MA; J. Snedecor; L. Taupenot; D. T. O’Connor; V. Hook. UCSD. “Molecular architecture and protein interaction networks of dense-core secretory vesicles from a human adrenal pheochromocytoma: implications in stress and neuropeptide secretion.” Neuroscience 2010 conference, San Diego, Neuronal genomics session (D2 639.18). Nov. 13-17, 2010.
  5. Dorota Skowronska-Krawczyk, Michal Schwartz, Xiaoyuan Song, Qi Ma, Wenbo Li, Dimple Notani, Bogdan Tanasa, Michael G Rosenfeld. “Role of Chromatin in Organogenesis” 2013 LS2 USGEB, Life science Switzerland, Revolution in Biology January 31th, 2013.
  6. Dimple Notani, Wenbo Li, Qi Ma, Bogdan Tanasa, Esperanza Nunez, Daria Merkurjev, Christopher K Glass, Michael G Rosenfeld. “Functional roles of enhancer rnas for oestrogen- dependent transcriptional activation”, Nuclear Receptors: Biological Networks, Genome Dynamics and Disease, Keystone Symposia On Molecular And Cellular Biology, Taos, New Mexico USA, January, 2014.
  7. Qi Ma, Li Tang, Wei Yang, Yulin Deng.“The Formation and Metabolism of Endogenous Catechol Isoquinolines’ Neurotoxins Formed in Parkinson’s Disease by using the HPLC-MS methods”, The 15th Chinese National Chromatography Symposium 2005, Zhouzheng, China, April 2005.
  8. Qi Ma, Li Tang, Wei Yang, Yulin Deng. “The method research of the quantitive measurement of the damage degree on the SH-SY5Y neurons by the free radicals using the HPLC-DAD”, The 15th Chinese National Chromatography Symposium 2005, Zhouzheng, China, April 2005.
  9. Mackintosh, C., Ma, Qi., and Garcia-Bassets, I. NANOG-mediated chromatin alterations in ovarian cancer cells treated with cisplatin. American Society for Cell Biology (ASCB): Annual Meeting. San Diego, CA (2015).
  10. Ranveer S. Jayani, Qi Ma, Dimple Notani, Michael G. Rosenfeld, "Understanding Role of 9p21 Gene Desert SNPs in Cancer, Aging, Diabetes and Cardio-Vascular Diseases". The 21th International Association of Gerontology and Geriatrics (IAGG), 2017 July 23-27 in San Francisco.