Publications

Key Publications

  1. Humphries, J, Xiong, L, Liu, J, Prindle, A, Yuan, F, Arjes, HA et al.. Species-Independent Attraction to Biofilms through Electrical Signaling. Cell. 2017;168 (1-2):200-209.e12. doi: 10.1016/j.cell.2016.12.014. PubMed PMID:28086091 .
  2. Cremer, J, Segota, I, Yang, CY, Arnoldini, M, Sauls, JT, Zhang, Z et al.. Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel. Proc. Natl. Acad. Sci. U.S.A. 2016;113 (41):11414-11419. doi: 10.1073/pnas.1601306113. PubMed PMID:27681630 PubMed Central PMC5068270.
  3. 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.
  4. 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.
  5. Glass, CK, Natoli, G. Molecular control of activation and priming in macrophages. Nat. Immunol. 2016;17 (1):26-33. doi: 10.1038/ni.3306. PubMed PMID:26681459 PubMed Central PMC4795476.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
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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. Didovyk, A, Tsimring, LS. Synthetic Gene Circuits Learn to Classify. Cell Syst. 2017;4 (2):151-153. doi: 10.1016/j.cels.2017.02.001. PubMed PMID:28231449 .
  5. Carter, H, Marty, R, Hofree, M, Gross, AM, Jensen, J, Fisch, KM et al.. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. 2017;7 (4):410-423. doi: 10.1158/2159-8290.CD-16-1045. PubMed PMID:28188128 .
  6. 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.
  7. 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.
  8. Kramer, MH, Farré, JC, Mitra, K, Yu, MK, Ono, K, Demchak, B et al.. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol. Cell. 2017;65 (4):761-774.e5. doi: 10.1016/j.molcel.2016.12.024. PubMed PMID:28132844 PubMed Central PMC5439305.
  9. 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.
  10. Humphries, J, Xiong, L, Liu, J, Prindle, A, Yuan, F, Arjes, HA et al.. Species-Independent Attraction to Biofilms through Electrical Signaling. Cell. 2017;168 (1-2):200-209.e12. doi: 10.1016/j.cell.2016.12.014. PubMed PMID:28086091 .
  11. 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 .
  12. Yao, J, Pilko, A, Wollman, R. Distinct cellular states determine calcium signaling response. Mol. Syst. Biol. 2016;12 (12):894. . PubMed PMID:27979909 PubMed Central PMC5199124.
  13. Dai, X, Zhu, M, Warren, M, Balakrishnan, R, Patsalo, V, Okano, H et al.. Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth. Nat Microbiol. 2016;2 :16231. doi: 10.1038/nmicrobiol.2016.231. PubMed PMID:27941827 PubMed Central PMC5346290.
  14. Fang, R, Yu, M, Li, G, Chee, S, Liu, T, Schmitt, AD et al.. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 2016;26 (12):1345-1348. doi: 10.1038/cr.2016.137. PubMed PMID:27886167 PubMed Central PMC5143423.
  15. Schmitt, AD, Hu, M, Jung, I, Xu, Z, Qiu, Y, Tan, CL et al.. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Rep. 2016;17 (8):2042-2059. doi: 10.1016/j.celrep.2016.10.061. PubMed PMID:27851967 .
  16. 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.
  17. AkhavanAghdam, Z, Sinha, J, Tabbaa, OP, Hao, N. Dynamic control of gene regulatory logic by seemingly redundant transcription factors. Elife. 2016;5 :. doi: 10.7554/eLife.18458. PubMed PMID:27690227 PubMed Central PMC5047750.
  18. Cremer, J, Segota, I, Yang, CY, Arnoldini, M, Sauls, JT, Zhang, Z et al.. Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel. Proc. Natl. Acad. Sci. U.S.A. 2016;113 (41):11414-11419. doi: 10.1073/pnas.1601306113. PubMed PMID:27681630 PubMed Central PMC5068270.
  19. 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.
  20. 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.
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A complete list of all our publications can be found here on PubMed