Scientific content

Doctoral Research

I completed my PhD training (2016) in the department of Developmental and Cell Biology and the Center for Complex Biological Systems at the University of California Irvine with Dr. Ali Mortazavi. My thesis was focused on mapping the dynamic gene regulatory networks during human myeloid differentiation using ATAC-seq and RNA-seq data (Ramirez et al, 2017 Cell Systems). My training included the integration of molecular biology, biochemistry, next-generation sequencing (genomic technologies) and computational approaches.

Macrophage/Monocyte dynamic gene regulatory networks

I participated actively in the STATegra consortium, which mapped molecular dynamics during pre-B cell differentiation using multi-omic data integration (STATegra et al, Scientific Data 2019). My role in STATegra was primarily geared towards data generation and analysis of bulk DNase/ATAC-seq, single-cell RNA-seq, and single-cell ATAC-seq across the pre-B model system. Along with my colleague Camden Jansen, we developed a novel approach using self-organizing maps (SOM) to link scATAC-seq and scRNA-seq data that overcomes these challenges and can generate draft regulatory networks (Jansen, Ramirez et al 2019).

Building GRNs using Self-Organizing Maps (SOM)

Screen Shot 2018-10-19 at 10.42.54 AM
Screen Shot 2018-10-19 at 10.46.30 AM

I was also an active member of the ENCODE consortium during my PhD. Aside from my own thesis work, I was fortunate enough to participate in several research collaborations during my PhD. This included studies on myofibroblast regeneration (Plikus et al 2017 Science. Maksim Plikus lab, UCI), derivation of microglia from human iPSC (Abud et al, Neuron 2017), and transcriptional regulation across several cellular systems (Peter Donovan lab, UCI; Esteban Ballestar lab (Rodriguez-Ubreva et al 2017 Cell Reports).

Current Science (Post doctoral ; 2017-ongoing)

I am currently an NIH funded postdoctoral fellow in the laboratory of Dr. Christophe Benoist and Dr. Diane Mathis at Harvard Medical School. Here, I am working on mapping the FoxP3 genome architecture in regulatory T cells, enhancer interactome, developing technologies for interrogating transcription factor regulation and working as an active member of the ImmGen consortium mapping chromatin dynamics and regulatory logic across the mouse immune system.

Computational software and applications

An R based visualizer and network analysis of chromatin conformation data
Online web app:
RNR and AD conceived the idea for DNA Rchitect.
DNA Rchitect was built and developed with Alos Diallo, Karni Bedirian and Simon Gray

Additional Scientific interests

Apart from work in the innate and adaptive immune systems, I am also interested in studying various disease pathologies in the brain. This extends to understanding how different gene regulatory programs of the same cell type become active in different disease contexts. Moreover development of genomic/imaging technologies and computational software for interrogating gene regulation and various chromatin features are areas of keen interest.

If you would like to contact me, please email me at

Non-science related interests

I play electric/acoustic guitar and listen to music ranging from french house, jazz to electronic. I practice Yoga and enjoy boxing, both as a form of exercise and entertainment. I relish in exploring and spending quality time with loved ones and close friends.



* Denotes equal contributions

14) Deep learning of immune cell differentiation. Alexandra Maslova*, Ricardo N. Ramirez*, Ke Ma, Hugo Schmutz, Chendi Wang, Curtis Fox, Bernard Ng, Christophe Benoist#, Sara Mostafavi#, and the Immunological Genome Project Consortium. #Joint supervision. (PNAS 2020).

13) Perspectives on ENCODE. The ENCODE Project Consortium (Nature 2020).

12) Expanded encyclopaedias of DNA elements in the human and mouse genomes. The ENCODE Project Consortium (Nature 2020).

11) Slug regulates the Dll4-Notch,VEGFR2 axis to control endothelial cell activation and angiogenesis. Nan Hultgren, Jennifer Fang, Mary Ziegler, Ricardo N. Ramirez, Duc Phan, Michaela Hatch, Katrina Welch-Reardon, Antonio Paniagua, Lin Kim, Nathan Shon, Ali Mortazavi, David Williams, Christopher Hughes. (in press 2020).


10) DNA Rchitect: An R based visualizer for network analysis of chromatin interaction data. Ricardo N. Ramirez*, Karni Bedirian*, Simon Gray, Alos Diallo. (Bioinformatics 2019).

9) The cis-regulatory atlas of the mouse immune system. Hideyuki Yoshida, Caleb A. Lareau, Ricardo N. Ramirez, Samuel A. Rose, Barbara Maier, Aleksandra Wroblewska. Fiona Desland, Aleksey Chudnovskiy, Arthur Mortha, Claudia Dominguez, Julie Tellier, Edy Kim, Dan Dwyer, Susan Shinton, Tsukasa Nabekura, YiLin Qi, Bingfei Yu, Michelle Robinette, Kiwook Kim, Amy Wagers, Andrew Rhoads, Stephen Nutt, Brian Brown, Sara Mostafavi, Jason Buenrostro, Christophe Benoist, and the Immunological Genome Project Consortium. (Cell 2019).

8) Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using Linked Self-Organizing Maps. Camden Jansen*, Ricardo N. Ramirez*, Nicole El-AliDavid Gomez-CabreroJesper TegnerMatthias MerkenschlagerAna ConesaAli Mortazavi. (Plos Computational Biology 2019).

7) Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation. Isabel Ferreirós Vidal, Thomas Carroll, Tianyi Zhang, Vincenzo Lagani, Ricardo N. Ramirez, Elizabeth Ing-Simmons, Alicia Garcia, Lee Cooper, Ziwei Liang, Georgios Papoutsoglou, Gopuraja Dharmalingam, Ya Guo, Sonia Tarazona, Sunjay J. Fernandes, Peri Noori, Gilad Silberberg, Amanda G. Fisher, Ioannis Tsamardinos, Ali Mortazavi, Boris Lenhard, Ana Conesa , Jesper Tegner, Matthias Merkenschlager, David Gomez-Cabrero (PLOS Biology 2019).

6) STATegra: a comprehensive multi-omics dataset of B-cell differentiation in mouse.
David Gomez-Cabrero*, Sonia Tarazona*, Isabel Ferreirós-Vidal*, Ricardo N. Ramirez*, Carlos Company*, Andreas Schmidt*, Theo Reijmers*, Veronica von Saint Paul*, Franscesco Marabita, Javier Rodríguez-Ubreva,  Antonio Garcia-Gomez, Thomas Carroll, Lee Cooper, Ziwei Liang, Gopuraja Dharmalingam, Leandro Balzano, Vicenzo Lagani, Ioannis Tsamardinos, Michael Lappe, Dieter Maier, Johan A. Westerhuis, Thomas Hankemeier, Axel Imhof, Esteban Ballestar, Ali Mortazavi, Matthias Merkenschlager, Jesper Tènger, Ana Conesa. (Scientific Data 2019).


5) TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency. Robert A. Sierra, Nathan P. Hoverter, Ricardo N. Ramirez, Linh M. Vuong, Ali Mortazavi, Bradley J. Merrill, Marian L. Waterman, Peter J. Donovan (Development 2018).


4) Dynamic gene regulatory networks of human myeloid differentiation. Ricardo N. Ramirez, Nicole C. El-Ali, Dana Wyman, Ana Conesa, Ali Mortazavi (Cell Systems 2017).

3) iPSC-derived human microglia-like cells to study neurological disease. E.M. Abud1,2,3, R.N. Ramirez4,5, E.S. Martinez1,2,3, L.M. Healy7, C.H.H. Nguyen1,2,3, V.M. Scarfone2, S.E. Marsh1,2,3, A. Madany8, C. Fimbres2,3, C. Caraway2,3, M.D. Torres1,2,3, A. Park2,3, K. Rakez6, A., K.H. Gylys7, A. Mortazavi4,5, J.P. Antel7, M.J. Carson2, W.W. Poon2,3, M. Blurton-Jones. (Neuron 2017). 

2) Regeneration of fat cells from myofibroblasts during wound healing. Maksim V. Plikus1,2, Christian Fernando Guerrero-Juarez2, Mayumi Ito3, Yun Rose Li4, Priya H. Dedhia5, Olga Shestova5, Denise L. Gay1,6, Raul Ramos2, Tsai-Ching Hsi2, Ji Won Oh2, Xiaojie Wang2, Ricardo N. Ramirez, Rabi Murad, Amanda Ramirez2, Sara E. Konopelski2, Arijh Elzein2, Anne Wang1, Rarinthip June Supapannachart1, Zaixin Yang1, Ying Zheng1, Arben Nace1, Amy Guo1, Elsa Treffeisen1, Thomas Andl7, Stefan Offermanns8, Daniel Metzger9, Pierre Chambon9, Ali Mortazavi, Rana K. Gupta10, Bruce A. Hamilton11, Sarah E. Millar1, Patrick Seale5, 12, Warren S. Pear5, Mitchell A. Lazar4, 13, George Cotsarelis (Science, 2017). 

1) Prostaglandin E2 Leads to the Acquisition of DNTM3A-Dependent Tolerogenic Functions in Human Myeloid-Derived Suppressor Cells. Javier Rodríguez-Ubreva,Francesc Català-Moll, Nataša Obermajer, Damiana Álvarez-Errico, Ricardo N. Ramirez, Carlos Company, Roser Vento-Tormo, Gema Moreno-Bueno, Robert P. Edwards, Ali Mortazavi, Pawel Kalinski, Esteban Ballestar. (Cell Reports, 2017).