My research focuses on bioinformatics and data analysis. My main project involves methylation data from patients infected with cytomegalovirus post kidney transplant. I am also implementing deep learning techniques to study liver pathology images. Outside of the lab, I enjoy hiking and learning about other disciplines such as history, philosophy, and economics.
My work focuses around bioinformatics and data analysis for the lab. My current research develops single cell RNA sequencing methods for reconstructing heterogeneous time course trajectories from snapshot time series data. I have previously worked on analyzing ChIP-seq and RNA-seq data, along with performing DNA motif-oriented analysis to investigate DNA-binding mechanisms of RelA. In the UCLA BIG Summer program, I used genomic landscapes in small cell lung cancer cell lines to predict drug sensitivities. Outside the lab, some of my interests include playing the piano and guitar, engaging in community service projects for science education and mentorship, playing and watching sports, trying new cuisines, and analyzing sports data.
I joined the Hoffmann lab in June 2020. I work primarily with Dr. Quen Cheng. My research focuses on analyzing RNA-seq and ChIP-seq datasets to understand the variable outcomes of immune cells upon infection. Outside of the lab, I enjoy swimming, hiking and playing the piano.”.
As a developing physician scientist and Hematopathologist-in-training, I am interested in understanding how inflammatory signaling in the bone marrow microenvironment may influence hematopoiesis and human bone marrow disorders.
Azar, S., Buen, F., Chia, J.J., Ma, Y., Caron, J. Dry, S. Bhuta, S. Abemayor, E. Spindle cell lipoma arising from the supraglottis: a case report and review of the literature. Head and Neck Pathology. [In press manuscript number HANP-D-20-00412R1; accepted for publication 11/19/2020.]
Chia J.J., Zhu T., Chyou S., Dasoveanu D.C., Carballo C., Tian S., Magro C.M., Rodeo S., Spiera R.F., Ruddle N.H., McGraw T.E., Browning J.L., Lafyatis R., Gordon J.K., Lu T.T. Dendritic cells maintain adipose-derived stromal cells in skin fibrosis. J Clin Invest. 2016 Nov 1;126(11):4331-4345. PMID: 27721238; PMCID: PMC5096920.
Dasoveanu D.C., Shipman W.D., Chia J.J., Chyou S., Lu T.T. Regulation of lymph node vascular-stromal compartment by dendritic cells. Trends in immunology. 2016; 37(11):764-777. PMID: 27638128; PMCID: PMC5492966.
Chia, J.J. & Lu, T.T. Update on macrophages and innate immunity in scleroderma. Curr Opin Rheumatol 27, 530-536 (2015). PMID: 26352734; PMCID: PMC4763869.
Hains, L.E., Loram, L.C., Taylor, F., Strand, K., Wieseler, J.L., Barrientos, R., Young, J.J., Frank, M.G., Sobesky, J., Martin, T.J., Eisenach, J.C., Maier, S.F., Johnson, J.D., Fleshner, M.R., & Watkins, L.R. 2011. Prior laparotomy or corticosterone potentiates lipopolysaccharide-induced fever and sickness behaviors. J Neuroimmunol. 2011 Oct 28;239(1-2):53-60. PMID: 21907418; PMCID: PMC3205218.
Chia, D.J., Young, J.J., Mertens, A.R., Rotwein, P.R. 2010. Distinct alterations in chromatin organization of the two IGF-I promoters precede growth hormone-induced activation of IGF-I gene transcription. Mol Endocrinol. 2010 Apr;24(4):779-89. PMID: 20160126; PMCID: PMC2852351.
Young, J.J., Mehdi, A., Stohl, L., Levin, L.R., Buck, J., Wagner, J.,Stessin, A.M. 2008. ‘Soluble’ adenylyl cyclase-generated cyclic AMP promotes fast migration in PC12 cells. J Neurosci Res. 2008 Jan;86(1):118-24. PMID: 17680672; PMCID: PMC2587045.
2019: Translational Research Fund project support, Department of Pathology, UCLA
2018: Herman L. Jacobius Prize in Pathology, Weill Cornell Medicine of Cornell University
2015: Outstanding Poster Award, Weill Cornell Graduate School of Cornell University
2014-2015: T32 funding award to the Immunology and Microbial Pathogenesis Program of Weill Cornell Graduate School of Cornell University
2009 – 2011: T32 to the Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program
2006 – 2007: Undergraduate Research Assistantship funding award, University of Colorado
2006: Leibowitz Fellowship Undergraduate Prize, Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program
2004 – 2007: Puksta Scholarship, University of Colorado
2004 – 2007: Norlin Scholarship, University of Colorado
UCLA Alumni Scholar (2019-present)
I’m a hybrid between an engineer and a biologist, with research interests centered on infection and immunity across scales. I want to study human immunity from the perspectives of systems biology and robotics. In my current work, by combining experimental tools and techniques with computational modeling, I aim to dissect how the dynamics of B-lymphocytes across scales – gene regulatory networks, cell-cell interactions, and population-level competitive selection – shape the evolution of highly specific, robust, and diverse antibody responses.
Alongside this primary research interest, I love learning about the wonderfully weird biology of exotic “non-model” organisms. I’m also passionate about global development and improving health outcomes among vulnerable populations through my work. I initiated and still contribute towards a web/mobile-based citizen science effort to crowdsource mosquito ecological data for monitoring and predicting mosquito-borne disease outbreaks [Abuzz].
As hobbies, I love hiking, cooking, playing racquet sports, Indian classical and epic music, reading comics from various countries and drawing my own, and reading sci-fi, fantasy, and non-fiction books
1. Using mobile phones as acoustic sensors for high-throughput mosquito surveillance. (2017) eLife 2017;6:e27854
2. Surface tension dominates the biomechanics of insect flight on fluid interfaces. (2016) Journal of Experimental Biology 219, 752-766
2021-2024: Damon Runyon Quantitative Biology Postdoctoral Fellowship
2019-2021: James S McDonnell Foundation (JSMF) 21st Century Postdoctoral Fellowship Award in Understanding Dynamic and Multi-scale Systems
2013-2016 : Howard Hughes Medical Institute (HHMI) Graduate Student Research Fellowship
2015 : DARPA Rising Stars Award
2011 : IIT Bombay Technical Activities Citation
2008 & 2009 : IIT Bombay Institute Academic Prize
2008 : IIT Bombay Heritage Fund Shantilal H Goradia Memorial Scholarship
2003 : Kishore Vaigyanik Protsahan Yojana (KVPY) Fellowship (Government of India & Indian Institute of Science)
2003 : National Talent Search Scholarship (Government of India)
My research focuses on primarily on data analysis and bioinformatics in the lab. My current work deals with RNA-seq and methylation data, more specifically in differential gene expression and differential methylation analysis. I am also investigating the prediction of psoriatic arthritis using genotypic data and machine learning/deep learning techniques. Outside of the lab, I enjoy playing and watching ice hockey and basketball, hiking, and reading up on startup culture and venture capital.
As an infectious diseases physician-scientist, my research is motivated by the mysteries I encounter in my medical practice. One such conundrum is how the same infection can cause highly variable outcomes in different patients. One of the factors that determines infection severity is the “context” in which the immune system is operating. This context can include age, sex, chronic diseases, and importantly, also the recent exposure history of an immune cell. When innate immune cells such as macrophages are exposed to cytokines and pathogen-associated molecules their signaling networks and epigenetic states get re-wired. This reprogramming affects their response to a subsequent infection and may also lead to post-infectious immune dysfunction. My research examines the molecular mechanisms of macrophage reprogramming and how this relates to the variable outcomes of human infections.
Nov 2019 Invited speaker, NIH/NIAID Symposium on Innate Immune Memory
Oct 2018 UCLA Department of Medicine Research Symposium Poster Competition, 3rd place
Sep 2018 Research Innovator Award, Department of Medicine, UCLA
2015-current Fellowship for Specialized Training in Advanced Research (STAR), UCLA
May 2015 Outstanding Fellow Teaching Award, UCLA
July 2013 Commendation of Excellence in Medical Student Teaching, UCLA
Dec 2012 Commendation of Excellence in Medical Student Teaching, UCLA
Dec 2012 Commendation of Excellence in Patient Communication, UCLA
June 2012 Thomas E. Carew Prize for Cardiovascular Research
June 2012 Samuel B. Hamburger Memorial Thesis Award for Outstanding Research Project
Jan 2010 Award for Best Use of Literature, NIH Trainees’ Poster Session
April 2009 Awardee, NIH Short-Term Research Training Grant
1. Type I and type II interferon modulate NFκB signaling via distinct mechanisms. EL Mercado, S Mitchell, J Ho, K Fortmann, A Adelaja, QJ Cheng, G Ghosh, A Hoffmann. Frontiers in Immunology, 2019 June 25.
2. Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions. Q Cheng, F Behzadi, S Sen, S Ohta, R Spreafico, R Teles, R Modlin, A Hoffmann. Scientific Reports, 2019 Mar 27.
3. Duodenoscope-related outbreak of a carbapenem-resistant Klebsiella pneumoniae identified using advanced molecular diagnostics. RM Humphries, S Yang, S Kim, VR Muthusamy, D Russell, A Trout, T Zaroda, QJ Cheng, G Aldrovandi, DZ Uslan, P Hemarajata, Z Rubin. Clin Infect Dis. 2017 Aug 8.
4. Probing chromatin landscape reveals roles of endocardial TBX20 in septation. CJ Boogerd, I Aneas, N Sakabe, RJ Dirschinger, QJ Cheng, B Zhou, J Chen, MA Nobrega, SM Evans. J Clin Invest. 2016 Jun 27.
5. Who provides primary care? An assessment of HIV patient and provider practices and preferences. QJ Cheng, EM Engelage, TR Grogan, JS Currier, RM Hoffman. J AIDS Clin Res. 2014 Nov; 5(11).
7. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana. S Kashiwagi, I Kuraoka, Y Fujiwara, K Hitomi, QJ Cheng, JO Fuss, DS Shin, C Masutani, JA Tainer, F Hanaoka, S Iwai. J. Nucleic Acids 2010, 701472.
8. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. L Fan, JO Fuss, QJ Cheng, AS Arvai, M Hammel, VA Roberts, PK Cooper, JA Tainer. Cell 2008, 133:789.