Yi Liu

Yi.Liu

TITLE: Postdoctoral Research Fellow (2011 –
EMAIL: liuy6@nullucla.edu
OFFICE: Boyer 570
WEBSITE: http://liuyi.co
EDUCATION:
PhD Pathology, Case Western Reserve University, 2011
BS Biological Sciences, Peking University, 2005

Research Interests

I’m interested in the role of NF-kB signaling in hematopoiesis.

Tools

PyHRM: High Resolution Melt Analysis in Python (OpenSource)

NFkB gene: A list of NFkB (NFkappaB, NF-κB) target genes hosted on Github. Curated based on Dr. Thomas Gilmore’s list.

Publications

Koushik Roy, Simon Mitchell, Yi Liu, Sho Ohta, Yu-sheng Lin, Marie Oliver Metzig, Stephen L Nutt and Alexander Hoffmann. 2019. The switch from B-cell proliferation to plasma cell differentiation phases requires dynamic NFκB/cRel downregulation. Immunity. PMID: 30850343

Wen-Hsien Liu, Seung Goo Kang, Zhe Huang, Cheng-Jang Wu, Hyun Yong Jin, Christian J. Maine, Yi Liu, Jovan Shepherd, Mohsen Sabouri-Ghomi, Alicia Gonzalez-Martin, Shunbin Xu, Alexander Hoffmann, Ye Zheng, Li-Fan Lu, Nengming Xiao, Guo Fu and Changchun Xiao. 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 D, Birnbaum H, Davis-Turak J, Asagiri M, David M, Goldrath AW and Hoffmann A. 2016. B cell survival and development controlled by the coordination of NFκB 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

Riku Fagerlund

Postdoctoral Research Fellow
rfagerlund@nullucsd.edu
Office: NSB 3318
Phone: 858-822-4673

 

Ph.D. General Microbiology, University of Helsinki (2008)
M.S. General Microbiology, University of Helsinki (2003)

 

Research Interests

Coming soon.

Zhang(Frank) Cheng

TITLE: Postdoctoral Research Fellow
OFFICE: Boyer 535
PHONE: 858-822-4673
EDUCATION:
Ph.D. Biophysics, Nanjing University (2010)
B.S. Biophysics, Nanjing University (2005)

Research Interests

Biological systems are complex systems that can be understood in terms of design principles. Based on this premise, I have carried out my research in these areas:

  1. Design principles of small biological network motifs, with a special focus on interlinked feedback loops.
  2. Roles of reversible phosphorylation in contributing to the dynamical feature of Neurospora circadian clock.
  3. Dynamics of P53 signaling network in response to DNA damage.

Now I am focusing on an HIV project, aiming to construct a comprehensive mathematical model of host immune response to HIV exposure. I will use the model to study the dynamics and effectiveness of the host response and develop therapeutic strategies for HIV infection

 

Publications

Citation Link
Reversible phosphorylation subserves robust circadian rhythms by creating a switch in inactivating the positive element.
Cheng Z, Liu F, Zhang XP, Wang W. Biophys J. 97(11):2867-75. (2009)		 PubMed
Cell fate decision mediated by p53 pulses.
Zhang XP, Liu F, Cheng Z, Wang W. PNAS. 106:12245-50. (2009)		 PubMed
Robustness analysis of cellular memory in an autoactivating positive feedback system.
Cheng Z, Liu F, Zhang XP, Wang W. FEBS Lett. 582:3776-82. (2008)		 PubMed
Linking fast and slow positive feedback loops creates an optimal bistable switch in cell signaling.
Zhang XP, Cheng Z, Liu F, Wang W. Phys Rev E. 76, 031924. (2007)		 PubMed

 

Marcelo Behar

Marcelo Behar

POSITION : Postdoctoral Research Fellow
EMAIL: mbehar@nullucsd.edu
PHONE: 858-822-4673

Education

Ph.D Physics (Biophysics) (2008)
The University of North Carolina. Chapel Hill, NC
Department of Physics and Astronomy
Program in Cellular and Molecular Biophysics (T. Elston Lab, Dept. of Pharmacology)
Dissertation topic: “Dynamic regulation and information transfer in intracellular-signaling pathways”

M.S. Physics (2005)
The University of North Carolina. Chapel Hill, NC
Department of Physics and Astronomy (Y. Wu Lab)
Masters Topic: “NMR study of Anomalous spin relaxation in carbon nanotubes”

Licentiate Physical Sciences (1999)
University of Buenos Aires. Buenos Aires, Argentina

Check out more about me and my research at CellularCrossroads.org

Research Interests

I am interested in dynamical aspects of intracellular signaling events and the mechanisms that impart signal specificity.

My research goal is to understand the functional principles underlying biological networks. To this end, I use mathematical models, single-cell experiments, and multi-scale computational simulations to gain insight about how cells overcome the operational constraints they face when dealing with changing environmental and internal conditions. Many of the most significant advances in the life sciences arose from collaborations that cut across disciplines. My approach to scientific research is multidisciplinary and collaborative. I expect findings to enable novel therapeutic strategies based on the restoration of malfunctioning information pathways or induction of new patterns of information flow to control cellular functions impacted by disease.

Publications

14. Shinohara H*, Behar M*, Inoue K, Hiroshima M, Yasuda T, Nagashima T, Kimura S, Sanjo H, Maeda S, Yumoto N, Ki S, Akira S, Sako Y, Hoffmann A, Kurosaki T, Okada-Hatakeyama M (2014). Positive Feedback Within a Kinase Signaling Complex Functions as a Switch Mechanism for NF-κB Activation, Science, 344, pp.760-764. PMID: 24833394. (* equal contribution)

13. Behar, M., B.arken, D., Werner, S.L., Hoffmann, A (2013). The Dynamics of Signaling as a Pharmacological Target. Cell, 155, pp.448-461. PMID: 24120141.

The equilibrium, quasi-equilibrium, and out-of equilibrium parts of a signal can be manipulated through different perturbation strategies and, under some conditions, selectively suppressed (or enhanced)

12. Mukherjee SP, Behar M, Birnbaum HA, Hoffmann A, Wright PE, et al. (2013). Analysis of the RelA:CBP/p300 Interaction Reveals NF-κB-Driven Transcription. PLoS Biol 11(9): e1001647. doi:10.1371/journal.pbio.1001647. PMID: 24019758.

11. Behar M, A. Hoffmann. (2103) Tunable Signal Processing through a kinase control cycle: the IKK signaling node. Biophys. J. 105(1):231-41. PMID: 23823243.
10. Basak S., M. Behar, A. Hoffmann. (2012). Lessons from modeling the NFkB pathway. Immunol Rev. 246(1):221-38. PMCID: PMC3343698
9. Jin M., B. Errede, M. Behar, W. Mather, S. Nayak, J. Hasty, H.G.  Dohlman, T. Elston. (2011). Saccharomyces cerevisiae dynamically modifies pheromone gradients to achieve better mating efficiency, Sci Signal 4(186): ra54. PMCID: PMC3557793
8. Schröfelbauer B., S.Polley, M.Behar, G.Ghosh, A. Hoffmann. (2011). NEMO ensures signaling specificity of the pleiotropic IKKb by directing its kinase activity towards IkBa. Mol Cell 13;47(1):111-21. PMCID: PMC3398199
7. Behar M., A. Hoffmann. (2010). Understanding the Temporal Codes of Intra-Cellular Signals. Curr Opin Genet Dev 20(6):684-93. PMCID: PMC2982931
6. Behar, M., N. Hao, R. Shanks, H. G. Dohlman, T. C. Elston. (2008). Dose-to-duration encoding and signaling beyond saturation in intracellular signaling networks. PLoS Comput. Biol. 4:e1000197. PMCID: PMC2543107
5. Hao, N., M. Behar, T. C. Elston, and H. G. Dohlman. (2007). Systems biology analysis of G protein and MAP kinase signaling in yeast. Oncogene 26:3254-3266. PMID: 17496920
4. Behar, M., H. G. Dohlman, T. C. Elston. (2007). Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks. PNAS 104:16146-16151. PMCID: PMC2042176
3. Hao, N, S. Nayak, M. Behar, R. Shanks, M. Nagiec, B. Errede, J. Hasty, T. C. Elston, H. G. Dohlman. (2007). Regulation of cell signaling dynamics by the protein kinase-scaffold Ste5. Mol Cell. 30:649-56. PMCID: PMC2518723
2. Hao, N., M. Behar, S. C. Parnell, M. P. Torres, C. H. Borchers, T. C. Elston, and H. G. Dohlman. (2007). A Systems-Biology Analysis of Feedback Inhibition in the Sho1 Osmotic-Stress-Response Pathway. Curr Biol 17:659-667. PMID: 17363249
1. Behar, M., N. Hao, H. G. Dohlman, and T. C. Elston. (2007). Mathematical and Computational Analysis of Adaptation via Feedback Inhibition in Signal Transduction Pathways. Biophys J 93:806-821. PMCID: PMC1913166
Bryce Alves

POSITION: Postdoctoral Research Fellow
OFFICE: NSB 3318
PHONE : 858-822-4673
EDUCATION:
Ph.D. Cell and Molecular Biology, Univ of Reno, Nevada (2009)
B.S. Microbiology, Boise State Univ (2003)

Research Interests

I’m interested in all things concerning T cells. I received my Ph.D. with studies of T cell cytotoxicity and activation. Currently I’m working on how different IkBs influence T cell proliferation and survival.

Publications

Citation Link
Hydrolysis of tumor cell lipids after cytotoxic T lymphocyte (CTL)-mediated death.
Bryce N. Alves, Jeff Leong, David Tamang, Viki Elliott, Mark Lowe, and Dorothy Hudig.
Int Immunol. 2009 May;21(5):543-53.		 PubMed
Pancreatic lipase-related protein 2 (PLRP2) induction by IL-4 in CTLs and reevaluation of the negative effects of its gene ablation on cytotoxicity.
Bryce N. Alves, Jeff Leong, David Tamang, Viki Elliott, Jillian Edelnant, Doug Redelman, Cherrie A. Singer, Andy R Kuhn, Rita Miller, Mark E Lowe, and Dorothy Hudig.
J Leukoc Biol. 2009 Sep;86(3):701-12.		 PubMed
Lipid-dependent cytotoxicity by the lipase PLRP2 and by PLRP2-positive cytotoxic T lymphocytes (CTLs).
Bryce N. Alves, Kristen Marshall, David L.Tamang, Jeff Leong, Doug Redelman, Viki Elliott, Mark E. Lowe, and Dorothy Hudig.
Cell Biochem Funct. 2009 Jul;27(5):296-308		 PubMed

 

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