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.
2022 – NIH-NIAID K08 career development award
2020 – UCLA CTSI KL2 career development award
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. NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages. Q.J. Cheng, Ohta, S., Sheu, K.M., Spreafico, R., Adelaja, A., Talor, B., Hoffmann, A. Science, 2018 June 18.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
I am interested in studying transcriptional regulation. My current project aims to elucidate a role of GAF as a mediator of gene expression in type I IFN signaling mainly through RNA-seq and ChIP-seq. I aspire to pursue MD/PhD and become a physician-scientist as a next step after graduation. When I am not in lab, I like watching anime and listening to songs nobody has heard of.
Awardee, Bruins-In-Genomics Summer Program Grant (June 2017-2018)
Best Poster Award, Bruins-In-Genomics Summer Grant (August 2017)
Most Dedicated Volunteer Award, BFPC (May 2017)
Dean’s List (Fall 2017 – present)
Honors College Program, UCLA (Fall 2017 – present)
My research investigates the dynamics of the transcription factor ISGF3 under type I and III interferon stimulation by analyzing components of the JAK-STAT pathway, such as STAT1, JAK1, and TYK2. I am an avid music fan, avocado enthusiast, and I enjoy being at the bench conducting experiments.
CARE Scholar (Fall 2018 – Present)
UCLA Regents Scholar (2017)
My work focuses around bioinformatics and data analysis for the lab. I am currently working on analyzing ChIP-seq and RNA-seq data, along with performing DNA motif-oriented analysis to investigate DNA-binding mechanisms of RelA. In my spare time, I enjoy playing and listening to music, playing and watching sports, and experiencing the variety of cuisines that Los Angeles has to offer.
My current research focuses on how inflammation impacts early B lymphopoiesis and upstream hematopoiesis in aging. By using quantitative muti-color flow cytometry analysis, in vivo bone marrow chimera experiments, mathematical modeling, and single-cell transcriptomic profiling, we can pin down the stage that is substantially impacted by the activation of inflammatory signaling and the discrepancy between cell-surface marker and transcriptomic profiles between developmental stages. My hobbies include film/digital photography and cooking.
Warsaw Fellowship, Jul. 2018, University of California, Los Angeles, CA, United States
Top Poster Award, Jun. 2018, Immunology, Inflammation, Infection, and Transplantation research theme retreat, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
Sidney C. Rittenberg Award, Dec. 2015, University of California, Los Angeles, CA, United States
Koushik Roy, Simon Mitchell, Yi Liu, Sho Ohta, Yu-Sheng Lin, Marie Oliver Metzig, Stephen L Nutt and Alexander Hoffmann, A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation, Immunity, Immunity. 2019 Mar 19;50(3):616-628
Riku Fagerlund, Marcelo Behar, Karen T. Fortmann, Y. Eason Lin, Jesse D. Vargas, and Alexander Hoffmann, Anatomy of a negative feedback loop: the case of IκBα, J R Soc Interface. 2015 Sep 6;12(110):0262
Tsung-Feng Wu, Tony Minghung Yen, Yuanyuan Han, Yu-Jui Chiu, Eason Y.-S. Lin and Yu-Hwa Lo, A light-sheet microscope compatible with mobile devices for label-free intracellular imaging and biosensing, Lab Chip. 2014 Sep 7;14(17):3341-8
