Conferences & Workshops

Math Modeling Workshop
March 27-31, 2017, from 10:00 am – 12:00 pm
UC San Diego, Bonner Hall room 2130
Organized by Dr. Lev Tsimring
Register for the event here

Spring Systems-To-Synthesis (S2S) Meeting
April 6, 2017, from 1:30 – 6:00 pm
MET rooms 143 & 145 at UC San Diego
Register for the event here

Weekly Events

Genetics, Bioinformatics and Systems Biology Colloquium (2016-17)

qBio Seminar Series (2016-17)

Systems Biology Career Development Seminars (Spring 2017)

Monthly Events

San Diego Bioinformatics Users Series (SDBUS)

Systems Biology Club


Key Publications

  1. Harper, JW, Bennett, EJ. Proteome complexity and the forces that drive proteome imbalance. Nature. 2016;537 (7620):328-38. doi: 10.1038/nature19947. PubMed PMID:27629639 PubMed Central PMC5204264.
  2. Din, MO, Danino, T, Prindle, A, Skalak, M, Selimkhanov, J, Allen, K et al.. Synchronized cycles of bacterial lysis for in vivo delivery. Nature. 2016;536 (7614):81-5. doi: 10.1038/nature18930. PubMed PMID:27437587 PubMed Central PMC5048415.
  3. Prindle, A, Liu, J, Asally, M, Ly, S, Garcia-Ojalvo, J, Süel, GM et al.. Ion channels enable electrical communication in bacterial communities. Nature. 2015;527 (7576):59-63. doi: 10.1038/nature15709. PubMed PMID:26503040 PubMed Central PMC4890463.
  4. Hardy, MD, Yang, J, Selimkhanov, J, Cole, CM, Tsimring, LS, Devaraj, NK et al.. Self-reproducing catalyst drives repeated phospholipid synthesis and membrane growth. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (27):8187-92. doi: 10.1073/pnas.1506704112. PubMed PMID:26100914 PubMed Central PMC4500204.
  5. Yoh, SM, Schneider, M, Seifried, J, Soonthornvacharin, S, Akleh, RE, Olivieri, KC et al.. PQBP1 Is a Proximal Sensor of the cGAS-Dependent Innate Response to HIV-1. Cell. 2015;161 (6):1293-305. doi: 10.1016/j.cell.2015.04.050. PubMed PMID:26046437 PubMed Central PMC4503237.
  6. Bouslimani, A, Porto, C, Rath, CM, Wang, M, Guo, Y, Gonzalez, A et al.. Molecular cartography of the human skin surface in 3D. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (17):E2120-9. doi: 10.1073/pnas.1424409112. PubMed PMID:25825778 PubMed Central PMC4418856.
  7. Selimkhanov, J, Taylor, B, Yao, J, Pilko, A, Albeck, J, Hoffmann, A et al.. Systems biology. Accurate information transmission through dynamic biochemical signaling networks. Science. 2014;346 (6215):1370-3. doi: 10.1126/science.1254933. PubMed PMID:25504722 PubMed Central PMC4813785.
  8. Gosselin, D, Link, VM, Romanoski, CE, Fonseca, GJ, Eichenfield, DZ, Spann, NJ et al.. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell. 2014;159 (6):1327-40. doi: 10.1016/j.cell.2014.11.023. PubMed PMID:25480297 PubMed Central PMC4364385.
  9. Gross, AM, Orosco, RK, Shen, JP, Egloff, AM, Carter, H, Hofree, M et al.. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat. Genet. 2014;46 (9):939-43. doi: 10.1038/ng.3051. PubMed PMID:25086664 PubMed Central PMC4146706.
  10. Engineer, CB, Ghassemian, M, Anderson, JC, Peck, SC, Hu, H, Schroeder, JI et al.. Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development. Nature. 2014;513 (7517):246-50. doi: 10.1038/nature13452. PubMed PMID:25043023 PubMed Central PMC4274335.
  11. Lee, K, Sung, MK, Kim, J, Kim, K, Byun, J, Paik, H et al.. Proteome-wide remodeling of protein location and function by stress. Proc. Natl. Acad. Sci. U.S.A. 2014;111 (30):E3157-66. doi: 10.1073/pnas.1318881111. PubMed PMID:25028499 PubMed Central PMC4121818.
  12. Gorkin, DU, Leung, D, Ren, B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell. 2014;14 (6):762-75. doi: 10.1016/j.stem.2014.05.017. PubMed PMID:24905166 PubMed Central PMC4107214.
  13. Carvunis, AR, Ideker, T. Siri of the cell: what biology could learn from the iPhone. Cell. 2014;157 (3):534-8. doi: 10.1016/j.cell.2014.03.009. PubMed PMID:24766803 PubMed Central PMC4154484.
  14. Prindle, A, Selimkhanov, J, Li, H, Razinkov, I, Tsimring, LS, Hasty, J et al.. Rapid and tunable post-translational coupling of genetic circuits. Nature. 2014;508 (7496):387-91. doi: 10.1038/nature13238. PubMed PMID:24717442 PubMed Central PMC4142690.
  15. St John, PC, Hirota, T, Kay, SA, Doyle, FJ 3rd. Spatiotemporal separation of PER and CRY posttranslational regulation in the mammalian circadian clock. Proc. Natl. Acad. Sci. U.S.A. 2014;111 (5):2040-5. doi: 10.1073/pnas.1323618111. PubMed PMID:24449901 PubMed Central PMC3918757.
  16. Jin, F, Li, Y, Dixon, JR, Selvaraj, S, Ye, Z, Lee, AY et al.. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013;503 (7475):290-4. doi: 10.1038/nature12644. PubMed PMID:24141950 PubMed Central PMC3838900.
  17. Behar, M, Barken, D, Werner, SL, Hoffmann, A. The dynamics of signaling as a pharmacological target. Cell. 2013;155 (2):448-61. doi: 10.1016/j.cell.2013.09.018. PubMed PMID:24120141 PubMed Central PMC3856316.
  18. Hofree, M, Shen, JP, Carter, H, Gross, A, Ideker, T. Network-based stratification of tumor mutations. Nat. Methods. 2013;10 (11):1108-15. doi: 10.1038/nmeth.2651. PubMed PMID:24037242 PubMed Central PMC3866081.
  19. Dutkowski, J, Kramer, M, Surma, MA, Balakrishnan, R, Cherry, JM, Krogan, NJ et al.. A gene ontology inferred from molecular networks. Nat. Biotechnol. 2013;31 (1):38-45. doi: 10.1038/nbt.2463. PubMed PMID:23242164 PubMed Central PMC3654867.
  20. Saito, R, Smoot, ME, Ono, K, Ruscheinski, J, Wang, PL, Lotia, S et al.. A travel guide to Cytoscape plugins. Nat. Methods. 2012;9 (11):1069-76. doi: 10.1038/nmeth.2212. PubMed PMID:23132118 PubMed Central PMC3649846.
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Recent Publications

  1. Jean, S, Kiger, AA. RAB21 Activity Assay Using GST-fused APPL1. Bio Protoc. 2016;6 (4):. doi: 10.21769/BioProtoc.1738. PubMed PMID:28251173 PubMed Central PMC5328668.
  2. Jean, S, Kiger, AA. VAMP8-3xHA Uptake Assay in HeLa Cells. Bio Protoc. 2016;6 (4):. . PubMed PMID:28251172 PubMed Central PMC5328665.
  3. Soonthornvacharin, S, Rodriguez-Frandsen, A, Zhou, Y, Galvez, F, Huffmaster, NJ, Tripathi, S et al.. Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation. Nat Microbiol. 2017;2 :17022. doi: 10.1038/nmicrobiol.2017.22. PubMed PMID:28248290 PubMed Central PMC5338947.
  4. Cowell, AN, Loy, DE, Sundararaman, SA, Valdivia, H, Fisch, K, Lescano, AG et al.. Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples. MBio. 2017;8 (1):. doi: 10.1128/mBio.02257-16. PubMed PMID:28174312 PubMed Central PMC5296604.
  5. Stockwell, SR, Rifkin, SA. A living vector field reveals constraints on galactose network induction in yeast. Mol. Syst. Biol. 2017;13 (1):908. . PubMed PMID:28137775 PubMed Central PMC5293160.
  6. Sundaramoorthy, E, Leonard, M, Mak, R, Liao, J, Fulzele, A, Bennett, EJ et al.. ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation. Mol. Cell. 2017;65 (4):751-760.e4. doi: 10.1016/j.molcel.2016.12.026. PubMed PMID:28132843 PubMed Central PMC5321136.
  7. Attali, I, Tobelaim, WS, Persaud, A, Motamedchaboki, K, Simpson-Lavy, KJ, Mashahreh, B et al.. Ubiquitylation-dependent oligomerization regulates activity of Nedd4 ligases. EMBO J. 2017;36 (4):425-440. doi: 10.15252/embj.201694314. PubMed PMID:28069708 .
  8. Saito, R, Rocanin-Arjo, A, You, YH, Darshi, M, Van Espen, B, Miyamoto, S et al.. Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight. 2016;1 (17):e87877. doi: 10.1172/jci.insight.87877. PubMed PMID:27777973 PubMed Central PMC5070958.
  9. Harper, JW, Bennett, EJ. Proteome complexity and the forces that drive proteome imbalance. Nature. 2016;537 (7620):328-38. doi: 10.1038/nature19947. PubMed PMID:27629639 PubMed Central PMC5204264.
  10. Steiner, PJ, Williams, RJ, Hasty, J, Tsimring, LS. Criticality and Adaptivity in Enzymatic Networks. Biophys. J. 2016;111 (5):1078-87. doi: 10.1016/j.bpj.2016.07.036. PubMed PMID:27602735 PubMed Central PMC5018143.
  11. Singec, I, Crain, AM, Hou, J, Tobe, BT, Talantova, M, Winquist, AA et al.. Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling. Stem Cell Reports. 2016;7 (3):527-42. doi: 10.1016/j.stemcr.2016.07.019. PubMed PMID:27569059 PubMed Central PMC5032292.
  12. Shah, M, Su, D, Scheliga, JS, Pluskal, T, Boronat, S, Motamedchaboki, K et al.. A Transcript-Specific eIF3 Complex Mediates Global Translational Control of Energy Metabolism. Cell Rep. 2016;16 (7):1891-902. doi: 10.1016/j.celrep.2016.07.006. PubMed PMID:27477275 PubMed Central PMC4988921.
  13. Eichenfield, DZ, Troutman, TD, Link, VM, Lam, MT, Cho, H, Gosselin, D et al.. Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. Elife. 2016;5 :. doi: 10.7554/eLife.13024. PubMed PMID:27462873 PubMed Central PMC4963201.
  14. Srivas, R, Shen, JP, Yang, CC, Sun, SM, Li, J, Gross, AM et al.. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Mol. Cell. 2016;63 (3):514-25. doi: 10.1016/j.molcel.2016.06.022. PubMed PMID:27453043 PubMed Central PMC5209245.
  15. Din, MO, Danino, T, Prindle, A, Skalak, M, Selimkhanov, J, Allen, K et al.. Synchronized cycles of bacterial lysis for in vivo delivery. Nature. 2016;536 (7614):81-5. doi: 10.1038/nature18930. PubMed PMID:27437587 PubMed Central PMC5048415.
  16. Allison, KA, Sajti, E, Collier, JG, Gosselin, D, Troutman, TD, Stone, EL et al.. Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells. Elife. 2016;5 :. doi: 10.7554/eLife.10134. PubMed PMID:27376549 PubMed Central PMC4931909.
  17. Didovyk, A, Borek, B, Tsimring, L, Hasty, J. Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications. Curr. Opin. Biotechnol. 2016;40 :177-84. doi: 10.1016/j.copbio.2016.06.003. PubMed PMID:27344519 PubMed Central PMC4975649.
  18. Gendron, JM, Webb, K, Yang, B, Rising, L, Zuzow, N, Bennett, EJ et al.. Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction. Mol. Cell Proteomics. 2016;15 (8):2576-93. doi: 10.1074/mcp.M116.058420. PubMed PMID:27185884 PubMed Central PMC4974337.
  19. Borek, B, Hasty, J, Tsimring, L. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules. PLoS ONE. 2016;11 (5):e0153679. doi: 10.1371/journal.pone.0153679. PubMed PMID:27148743 PubMed Central PMC4858293.
  20. Engin, HB, Kreisberg, JF, Carter, H. Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces. PLoS ONE. 2016;11 (4):e0152929. doi: 10.1371/journal.pone.0152929. PubMed PMID:27043210 PubMed Central PMC4820104.
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A complete list of all our publications can be found here on PubMed