Bioinformatics Graduate Student (2009-)
Office: NSB 4418
Phone: 858-822-4673
B.A. in Molecular Biology, Princeton University 2004
Fellow, National Science Foundation Graduate Research Program
Research Interests
I am interested in the coupling between transcriptional elongation and splicing. In addition to modeling, I am pursuing a high-throughput assay of splicing events in pathogen response genes.
Publications
| Citation |
Link |
Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways.
Shih VF, Davis-Turak J, Macal M, Huang JQ, Ponomarenko J, Kearns JD, Yu T, Fagerlund R, Asagiri M, Zuniga EI, Hoffmann A.
Nat Immunol. 2012 Dec;13(12):1162-70. |
PubMed |
Human-specific transcriptional networks in the brain.
Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham MC, Gao F, Chen L, Wang GZ, Luo R, Preuss TM, Geschwind DH.
Neuron. 2012 Aug 23;75(4):601-17 |
PubMed |
Transcriptional architecture of the primate neocortex.
Bernard A, Lubbers LS, Tanis KQ, Luo R, Podtelezhnikov AA, Finney EM, McWhorter MM, Serikawa K, Lemon T, Morgan R, Copeland C, Smith K, Cullen V, Davis-Turak J, Lee CK, Sunkin SM, Loboda AP, Levine DM, Stone DJ, Hawrylycz MJ, Roberts CJ, Jones AR, Geschwind DH, Lein ES.
Neuron. 2012 Mar 22;73(6):1083-99 |
PubMed |
A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3′ end formation.
Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu XD.
Genomics. 2011 Oct;98(4):266-71 |
PubMed |
Tauopathy with paired helical filaments in an aged chimpanzee.
Rosen RF, Farberg AS, Gearing M, Dooyema J, Long PM, Anderson DC, Davis-Turak J, Coppola G, Geschwind DH, Par JF, Duong TQ, Hopkins WD, Preuss TM, Walker LC.
J Comp Neurol. 2008 Jul 20;509(3):259-70. |
PubMed |
Chemistry and Biochemistry Graduate Student (2008-)
abcaldwe@nullucsd.edu
Office: 858-822-4673
B.S. Chemistry, Biochemistry,Seattle Pacific University, 2008
Research Interests
I am interested in the mechanisms of IKK activation and regulation in NFκB signaling.
Biology Graduate Student (2007-)
jalmaden@nullucsd.edu
Office: NSB 3320
Phone: 858-822-4673
B.S. Biochemistry and Cell Biology, UCSD
Research Interests
B-cells undergo dramatic expansion during immune response, which involves one of the most rapid proliferation rates known for mammalian cells. B-cell survival and death is highly regulated, and the proliferative program is limited to about 12 divisions.
The NF-kB signaling system plays a critical role in B-cell biology. Two distinct NF-kB activation pathways have been described to induce overlapping sets of NF-kB transcription factors containing the three activation domain containing NF-kB proteins, RelA, RelB, and cRel. My research is focused on understanding which NF-kB dimers control B-cell survival and proliferation. This study is complicated by the overlap of these two B-cell processes, as well as the interdependencies of NF-kB dimers produced by the NF-kB signaling system in response to B-cell activating signals. Using a combination of in depth experimental analysis and mathematical modeling, at both the cellular and molecular levels, I hope to elucidate the homeostatic and dynamic regulation of the NF-kB signaling system in B-cell physiology.
Publications
Sun, S., J. Almaden, et al. (2005). “Assay development and data analysis of receptor-ligand binding based on scintillation proximity assay.” Metab Eng 7(1): 38-44.
Humphries, P. S., J. V. Almaden, et al. (2006). “Pyridine-2-propanoic acids: Discovery of dual PPARalpha/gamma agonists as antidiabetic agents.” Bioorg Med Chem Lett 16(23): 6116-9.
Humphries, P. S., S. Bailey, et al. (2006). “Pyridine-3-propanoic acids: Discovery of dual PPARalpha/gamma agonists as antidiabetic agents.” Bioorg Med Chem Lett 16(23): 6120-3.
Ralph, E. C., J. Almaden, et al. (2008). “Glucose modulation of glucokinase activation by small molecules.” Biochemistry 47(17): 5028-36.
Postdoctoral Research Fellow
bschroefelbauer@nullucsd.edu
Office: NSB 3318
Phone: 858-822-4673
Ph.D. Molecular Biology, Univ of Life Sciences (Austria) 2007
Ph.D. student, Salk Institute 2003-2006
M.S. Biotechnology, Univ of Life Sciences (Austria) 2002
Research Interests
Coming soon.
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
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.
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:
- Design principles of small biological network motifs, with a special focus on interlinked feedback loops.
- Roles of reversible phosphorylation in contributing to the dynamical feature of Neurospora circadian clock.
- 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 |
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:
PMC33436989. 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:
PMC35577938. 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:
PMC33981997.
Behar M., A. Hoffmann. (2010).
Understanding the Temporal Codes of Intra-Cellular Signals. Curr Opin Genet Dev 20(6):684-93. PMCID:
PMC29829316.
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:
PMC25431075. 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:
174969204.
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:
PMC20421763. 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:
PMC25187232. 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:
173632491.
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
j0huang@nullucsd.edu
