I am Yi Liu, a postdoctoral researcher at University of California, Los Angeles (UCLA). I work in Alexander Hoffmann’s Lab in the new Institute of Quantitative and Computational Biology (iQCB) and Dep. of MIMG. My research focuses on how NFkB signaling system regulates the blood regeneration process in our body, either in physiological or pathological conditions. In my spare time, I lead a healthcare-sector-focused investment club. I like creative activities. I share my writings and small software tools on my portfolio of websites.
Blood is one of the most regenerative tissue in our body. In any healthy individual, new blood cells are made to replace old cells in a constant basis. During infection or blood loss, this regenerative capacity is key to survival. All blood cell types came from one cell type – hematopoietic stems cells (HSCs). This process is tightly regulated and precisely balanced to maintain an ideal composition of blood.
However, while much more is understood about functions and regulations of mature blood cells (such as T, B, Dendritic cells), less is known about the regulation of hematopoiesis process: the long development big bang from HSCs to mature blood cells.
My research tackles this question from a specific angle: how a network of NFkB transcription factors dynamicly regulate this process. I utilize the unique spectrum of expertise in Alexander Hoffmann’s lab, including biochemistry, mice models, and computational modeling.
I believe we will be able to understand the big bang of blood. This will help cure diseases of the blood system, including but not limited to leukemia, anemia, lymphoma, bone marrow transplantation, survival to radiation.
Case Western Reserve University (CWRU), Cleveland, OH
Ph.D., Pathology, Immunology Track August 2011
Mentors: Clifford V. Harding, M.D., Ph.D. & W. Henry Boom, M.D.
Dissertation: Negative regulation of type I interferon (IFN-I) in dendritic cells (DCs).
Peking University, Beijing, China
B.S., Biological Sciences July 2005
Passed Level II
Introduction to Mathematical Thinking
Systems Biology, a 5-course specialization by Icahn School of Medicine at Mount Sinai on Coursera. Specialization Certificate earned on September 1, 2015
Li L, Xu X, Lv K, Zheng G, Wang H, Chen S, Huang L, Liu Y, Zhang Y, Tang Z, Zhang L, Wang J, Qiao J, Li H, Wang X, Yao G, Fang C. 2023 Asebogenin suppresses thrombus formation via inhibition of Syk phosphorylation. British Journal of Pharmacology PMID: 36166754
Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. 2021 Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses.
Immunity. PMID: 33979588
Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A. 2019 A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation. Immunity. PMID: 30850343
Liu WH, Kang SG, Huang Z, Wu CJ, Jin HY, Maine CJ, Liu Y, Shepherd J, Sabouri-Ghomi M, Gonzalez-Martin A, Xu S, Hoffmann A, Zheng Y, Lu LF, Xiao N, Fu G and Xiao C. 2016. A miR-155–Peli1–c-Rel pathway controls the generation and function of T follicular helper cells. J. Ex. Med. PMID: 27481129
Almaden JV*, Liu YC*, Yang E, Otero DC, Birnbaum H, Davis-Turak J, Asagiri M, David M, Goldrath AW, Hoffmann A. 2016. B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRel. Blood. PMID: 26773039
Almaden JV, Tsui R, Liu YC, Birnbaum H, Shokhirev MN, Ngo KA, Davis-Turak JC, Otero D, Basak S, Rickert RC, Hoffmann A. 2014. A Pathway Switch Directs BAFF Signaling to Distinct NFκB Transcription Factors in Maturing and Proliferating B Cells. Cell Rep. PMID: 25497099
Liu YC, Simmons DP, Li X, Abbott DW, Boom WH, Harding CV. 2012. TLR2 Signaling Depletes IRAK1 and Inhibits Induction of Type I IFN by TLR7/9. J. Immunology. PMID: 22227568
Simmons DP, Wearsch PA, Canaday DH, Meyerson HJ, Liu YC, Wang Y, Boom WH, Harding CV. 2012. Type I interferon drives a distinctive dendritic cell maturation phenotype that allows continued class II MHC synthesis and antigen processing. J. Immunology. PMID: 22371391
Liu YC, Gray RC, Hardy GA, Kuchtey J, Abbott DW, Emancipator SN, Harding CV. 2010. CpG-B oligodeoxynucleotides inhibit TLR-dependent and -independent induction of type I IFN in dendritic cells. J. Immunology. PMID: 20181884
Simmons DP, Canaday DH, Liu Y, Li Q, Huang A, Boom WH, Harding CV. 2010. Mycobacterium tuberculosis and TLR2 agonists inhibit induction of type I IFN and class I MHC antigen cross processing by TLR9. J. Immunology. PMID: 20660347
Anis MM, Fulton SA, Reba SM, Liu Y, Harding CV, Boom WH. 2008. Modulation of pulmonary dendritic cell function during mycobacterial infection. Infect. Immun. PMID: 18039834
Pennini ME, Liu Y, Yang J, Croniger CM, Boom WH, Harding CV. 2007. CCAAT/enhancer-binding protein beta and delta binding to CIITA promoters is associated with the inhibition of CIITA expression in response to Mtb 19-kDa lipoprotein. J. Immunology PMID: 17982082
Li L, Bin LH, Li F, Liu Y, Chen D, Zhai Z, Shu HB. 2005. TRIP6 is a RIP2-associated common signaling component of multiple NF-kappaB activation pathways. J. Cell Sciences PMID: 15657077
I joined DeepKinase in August 2021 and serves as its Chief Research Officer.
I founded and currently lead Positive Strand Investment Club (PSIC). At PSIC, we apply our diverse talents to studying biotech and pharmaceutical industry. We thrive to identify industry trends, innovative drugs, and potential investment opportunities. Learn more >>.
- DeepKinase: official website for a tyrosine phosphoproteomics company
- GapDB: check stock price gaps
- PyHRM: Free Opensource High Resolution Melt Analysis in Python
- iPyNbViewer: Standalone App for IPython Notebook
- BioLog: A online log system with search filter (List.js)
- TRIALERT: discontinued. automated clinical trial tracking
- LoveLoveBean App: discontinued. automatically fetch, match and notify you L.L.Bean Daily Sales
I learned Chinese Seal Carving from Master Li Shengshi (李盛世). I also help promote his artwork in the United States. Learn more at his website.
During 2009-2010, I spent two years of spare time, wrote/edited about 200 articles about China at ChinaBlog.cc. The articles are in English, aiming to introduce China to the English speaking world. I covered a variety of topics, including Chinese Art, Music, Literature, Travel, Food, and History etc.
PKUBIO.org: Peking University BIO-Net Symposium: A network of Peking University alumni and friends in the field of life sciences.