TITLE: Graduate Student (PhD)
PROGRAM: Microbiology, Immunology, and Molecular Genetics (MIMG) (2014 – 2019)
EMAIL: kango@nullucla.edu
OFFICE: Boyer Hall 570
PHONE: 310-794-9970
EDUCATION:
M.S. in Chemistry, UC San Diego – 2013
B.S. in Pharmacological Chemistry, UC San Diego – 2008

Biography

My research is focused on understanding the mechanisms underlying the activation of gene transcription by NFκB RelA subunit. This is done by elucidating specific attributes of RelA that contribute to its ability to activate and regulate inflammatory gene expression programs by employing a panel of RelA mutations and examining their impact on transcription. By using biochemical analysis, mathematical model-aided analysis approach, RNA and ChIP-seq analyses, we find specialized, non-overlapping functions in DNA binding and transcriptional activation in RelA. My hobbies include playing beach volleyball, badminton, baking, and volunteering for Buddhist temple events.

Awards and Fellowships

MIMG Warsaw Fellowship, 2017-2018

Sidney Rittenberg Award, 2015

Publications

Fortmann KT, Lewis RD, Ngo KA, Fagerlund R, Hoffmann A. 2015. “A Regulated, Ubiquitin-Independent Degron in IκBα.” Journal of Molecular Biology. PMID: 26191773

Tsui R, Kearns JD, Lynch C, Vu D, Ngo KA, Basak S, Ghosh G, Hoffmann A. 2015. “IκBβ enhances the generation of the low-affinity NFκB/RelA homodimer.” Nature Communications. PMID: 25946967.

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 Reports. PMID: 25497099

Staff Research Associate  & Director of SDCSB Next Gen Gene Expression Analysis Core

birnbaumharry@nullgmail.com
Office: NSB 3209
Phone: 610-764-6695

B.A. Mathematics, University of Pennsylvania – 2012

More about the Next-Gen Gene Expression Core

Publications:

Mukherjee, S.P., Behar, M., Birnbaum, H.A, Hoffmann, A., Wright, P.E., Ghosh, G.
Analysis of the RelA:CBP/p300 interaction reveals its involvement in NFkB-driven transcription
PLOS Biology, 11:e1001647

TITLE: Asst. Project Scientist & Director of Light Microscopy
EMAIL: jadvargas@nullucla.edu
OFFICE: Boyer 570
EDUCATION:
Ph.D. Biology, The Salk Institute | University of California, San Diego – 2012
M.S. Molecular and Cellular Physiology, Southern Illinois University  – 2007
B.S. Biological Sciences, University of California, Irvine – 2003
B.S. Chemistry, University of California, Irvine – 2003

Research Interests

My current research interests are in developing image based assays for mammalian cell signaling systems that utilized live-cell approaches to view signaling events in real time at a single cell level to reveal events and mechanisms obscured by population averaging biochemical approaches. I am interesting in assays with workflows amenable to automation that can be used to generate functional data for the design and validation of mathematical models of gene regulatory networks.

Publications

Hobbies | Activities

In my spare time I try to stay fit doing judo 柔道 or gymnastics or playing volleyball at the beach. I also am a photography enthusiast and spend a lot of time taking random pictures of buildings or landscapes that catch my eye.  I’m a Mac.

TITLE: Postdoctoral Research Fellow
OFFICE: Boyer 535
PHONE: 858-822-4673
EDUCATION:
PhD- Computational Biology: University of Heidelberg, Heidelberg Germany (2012)
M.Sc- Chemical Engineering: Indian Institute of Science, Bangalore (2008)

TITLE: Postdoctoral scholar
EMAIL: b4taylor@nullucla.edu
OFFICE: Boyer 570
EDUCATION:
B.S. (Biomedical Engineering) University of Virginia (2009)
Ph.D. (Bioengineering) University of California San Diego (2015)

Research Interests

NF-κB controls some of the most potent antiviral and antibacterial machinery that mammalian cells possess. It’s activated by hundreds of different signals, be they exogenous, endogenous, or synthetic. Tens of negative feedback regulators of NF-κB have been identified, which all serve to attenuate its activity. And while proper activation of NF-κB is a hallmark of a functional inflammatory response, improper activation is associated with pathologies in conditions ranging from Alzheimer’s to cancer to atherosclerosis.

We’ve seen tantalizing glimpses that NF-κB activates via intricately-controlled dynamics of translocation to and from the nucleus, and it’s been hypothesized that these patterns might convey information, allowing a cell to discriminate between different inputs using this single transcription factor. However, we’re still unclear on what these specific dynamic codes are, and how the information they convey might be decoded by the cell.

Using single-cell microscopy and automated tracking and measurement, I’m hoping to help crack the NF-κB dynamical code. I think it’s likely that NF-κB dynamics can convey information, not just about the nature of a particular stimulus, but about the disease state of a cell. Knowing what healthy and aberrant NF-κB dynamics look like (and even how to modulate one into the other) could afford new windows into both diagnosis and treatment.

Publications

Selimkhanov J*, Taylor B*, Yao J, et al. Accurate information transmission through dynamic biochemical signaling networks. Science. 2014; 346(6215):1370-1373.

Cheng Z*, Taylor B*, Ourthiague DR, Hoffmann A. Distinct single-cell signaling characteristics are conferred by the MyD88 and TRIF pathways during TLR4 activation. Sci Signal. 2015; 8(385):1-13.

(* denotes equal contribution)

Chemistry & Biochemistry Graduate Student (2009-)

Office: NSB 3318
Phone: 858-822-4673

B.S. Cellular & Molecular Biology, San Diego State University 2009

Research Interests

Coming soon.

Chemistry and Biochemistry Graduate Student (2009-)

Office: NSB 4318
Phone: 858-822-4673

B.S. Chemistry, Boston University 2009

Research Interests

I am interested in the dynamic encoding of stimulus specificity in the canonical NFκB pathway.

TITLE: Bioinformatics and Systems Biology Graduate Student (2008-June 2014)
OFFICE: NSB 3209
PHONE: 520-4717076
EMAIL: mshokhir at ucsd.edu
EDUCATION:
B.S. Computer Science, Biochemistry and Molecular Biophysics, University of Arizona – 2008
LINKEDIN: http://www.linkedin.com/pub/maxim-shokhirev/19/948/62

Research Interests

I am interested in understanding how cell population dynamics are coordinated on the cellular and biochemical levels. A prime example, the mammalian immune response involves seemingly stochastic cellular decisions to respond, divide, and undergo programmed cell death. Understand how immune cells make decisions that result in an effective population response sheds light on the nature of multi-cellular biology and may provide insights into treating immune disorders and cancers. To this end, I have developed computational tools for describing cell population dynamics in terms of stochastic cellular processes, cell tracking software for quantifying time-lapse microscopy movies, performed single-cell RNAseq experiments, ran immunfluorescence studies, and constructed kinetic ODE models which incorporate the cell-cycle, apoptosis, and NFkB signaling. This has allowed me to characterize the responses of primary mouse B cells under diverse conditions in a multi-scale manner.

Publications

1. Shokhirev MN and Alexander Hoffmann (2013) FlowMax: a computational tool for maximum likelihood deconvolution of CFSE time courses. PLoS One.
2. Jiao B, Ma H, Shokhirev MN, Drung A, Yang Q, et al. (2012) Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Cell 149: 630-641.
3. Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F (2010) Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps. J Struct Biol 169: 95-105.
4. Berry RE, Shokhirev MN, Ho AY, Yang F, Shokhireva TK, et al. (2009) Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes. J Am Chem Soc 131: 2313-2327.
5. Knipp M, Yang F, Berry RE, Zhang H, Shokhirev MN, et al. (2007) Spectroscopic and functional characterization of nitrophorin 7 from the blood-feeding insect Rhodnius prolixus reveals an important role of its isoform-specific N-terminus for proper protein function. Biochemistry 46: 13254-13268.
6. Berry RE, Shokhireva T, Filippov I, Shokhirev MN, Zhang H, et al. (2007) Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus. Biochemistry 46: 6830-6843.
7. Borunda, P.; Brewer, C.; Erten, C.; King, N.; Nation Z.; Shokhirev, M. (2005) GSPIM: Graphical Visualization Tool for MIPS Assembly Programming and Simulation. SIGCSE 2005.