Cytoscape Tutorial for Beginners 2018
Tuesday, June 5, 2018
9:30 am – 12:30 pm
UC San Diego, BRF2 Room 3A04
Register Here

qBIO Seminar Series
Mondays, April 2 – June 4
3:00 pm – 4:00 pm
UC San Diego, NSB 1205
Complete schedule here

Career Development Seminar Series
Tuesdays, April 3 – June 5
4:00 pm – 5:00 pm
UC San Diego, BRF2 Rm 1102
Complete schedule here

Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, April 5 – Jun 7
12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall Auditorium
Complete schedule here

 

Publications

Key Publications

  1. Martinez-Corral, R, Liu, J, Süel, GM, Garcia-Ojalvo, J. Bistable emergence of oscillations in growing Bacillus subtilis biofilms. Proc. Natl. Acad. Sci. U.S.A. 2018;115 (36):E8333-E8340. doi: 10.1073/pnas.1805004115. PubMed PMID:30127028 PubMed Central PMC6130386.
  2. Link, VM, Duttke, SH, Chun, HB, Holtman, IR, Westin, E, Hoeksema, MA et al.. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell. 2018;173 (7):1796-1809.e17. doi: 10.1016/j.cell.2018.04.018. PubMed PMID:29779944 PubMed Central PMC6003872.
  3. Muse, ED, Yu, S, Edillor, CR, Tao, J, Spann, NJ, Troutman, TD et al.. Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP in macrophages. Proc. Natl. Acad. Sci. U.S.A. 2018;115 (20):E4680-E4689. doi: 10.1073/pnas.1714518115. PubMed PMID:29632203 PubMed Central PMC5960280.
  4. Zhang, W, Bojorquez-Gomez, A, Velez, DO, Xu, G, Sanchez, KS, Shen, JP et al.. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat. Genet. 2018;50 (4):613-620. doi: 10.1038/s41588-018-0091-2. PubMed PMID:29610481 PubMed Central PMC5893414.
  5. Cowell, AN, Istvan, ES, Lukens, AK, Gomez-Lorenzo, MG, Vanaerschot, M, Sakata-Kato, T et al.. Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics. Science. 2018;359 (6372):191-199. doi: 10.1126/science.aan4472. PubMed PMID:29326268 PubMed Central PMC5925756.
  6. Li, Y, Jin, M, O'Laughlin, R, Bittihn, P, Tsimring, LS, Pillus, L et al.. Multigenerational silencing dynamics control cell aging. Proc. Natl. Acad. Sci. U.S.A. 2017;114 (42):11253-11258. doi: 10.1073/pnas.1703379114. PubMed PMID:29073021 PubMed Central PMC5651738.
  7. Erickson, DW, Schink, SJ, Patsalo, V, Williamson, JR, Gerland, U, Hwa, T et al.. A global resource allocation strategy governs growth transition kinetics of Escherichia coli. Nature. 2017;551 (7678):119-123. doi: 10.1038/nature24299. PubMed PMID:29072300 PubMed Central PMC5901684.
  8. Dekker, J, Belmont, AS, Guttman, M, Leshyk, VO, Lis, JT, Lomvardas, S et al.. The 4D nucleome project. Nature. 2017;549 (7671):219-226. doi: 10.1038/nature23884. PubMed PMID:28905911 PubMed Central PMC5617335.
  9. Ou, HD, Phan, S, Deerinck, TJ, Thor, A, Ellisman, MH, O'Shea, CC et al.. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science. 2017;357 (6349):. doi: 10.1126/science.aag0025. PubMed PMID:28751582 PubMed Central PMC5646685.
  10. Gosselin, D, Skola, D, Coufal, NG, Holtman, IR, Schlachetzki, JCM, Sajti, E et al.. An environment-dependent transcriptional network specifies human microglia identity. Science. 2017;356 (6344):. doi: 10.1126/science.aal3222. PubMed PMID:28546318 PubMed Central PMC5858585.
  11. Diao, Y, Fang, R, Li, B, Meng, Z, Yu, J, Qiu, Y et al.. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat. Methods. 2017;14 (6):629-635. doi: 10.1038/nmeth.4264. PubMed PMID:28417999 PubMed Central PMC5490986.
  12. Liu, J, Martinez-Corral, R, Prindle, A, Lee, DD, Larkin, J, Gabalda-Sagarra, M et al.. Coupling between distant biofilms and emergence of nutrient time-sharing. Science. 2017;356 (6338):638-642. doi: 10.1126/science.aah4204. PubMed PMID:28386026 PubMed Central PMC5645014.
  13. Shen, JP, Zhao, D, Sasik, R, Luebeck, J, Birmingham, A, Bojorquez-Gomez, A et al.. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat. Methods. 2017;14 (6):573-576. doi: 10.1038/nmeth.4225. PubMed PMID:28319113 PubMed Central PMC5449203.
  14. 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 PubMed Central PMC5497501.
  15. 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.
  16. 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.
  17. 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):81-85. doi: 10.1038/nature18930. PubMed PMID:27437587 PubMed Central PMC5048415.
  18. 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.
  19. 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.
  20. 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.
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Recent Publications

  1. Martinez-Corral, R, Liu, J, Süel, GM, Garcia-Ojalvo, J. Bistable emergence of oscillations in growing Bacillus subtilis biofilms. Proc. Natl. Acad. Sci. U.S.A. 2018;115 (36):E8333-E8340. doi: 10.1073/pnas.1805004115. PubMed PMID:30127028 PubMed Central PMC6130386.
  2. Zarrinpar, A, Chaix, A, Xu, ZZ, Chang, MW, Marotz, CA, Saghatelian, A et al.. Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun. 2018;9 (1):2872. doi: 10.1038/s41467-018-05336-9. PubMed PMID:30030441 PubMed Central PMC6054678.
  3. Zhou, Y, Xu, Z, Quan, D, Zhang, F, Zhang, H, Xiao, T et al.. Nuclear respiratory factor 1 promotes spheroid survival and mesenchymal transition in mammary epithelial cells. Oncogene. 2018; :. doi: 10.1038/s41388-018-0349-2. PubMed PMID:29995872 .
  4. Cowell, AN, Valdivia, HO, Bishop, DK, Winzeler, EA. Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing. Genome Med. 2018;10 (1):52. doi: 10.1186/s13073-018-0563-0. PubMed PMID:29973248 PubMed Central PMC6032790.
  5. Zhang, W, Ma, J, Ideker, T. Classifying tumors by supervised network propagation. Bioinformatics. 2018;34 (13):i484-i493. doi: 10.1093/bioinformatics/bty247. PubMed PMID:29949979 PubMed Central PMC6022559.
  6. Ozturk, K, Dow, M, Carlin, DE, Bejar, R, Carter, H. The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. J. Mol. Biol. 2018;430 (18 Pt A):2875-2899. doi: 10.1016/j.jmb.2018.06.016. PubMed PMID:29908887 PubMed Central PMC6097914.
  7. Link, VM, Duttke, SH, Chun, HB, Holtman, IR, Westin, E, Hoeksema, MA et al.. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell. 2018;173 (7):1796-1809.e17. doi: 10.1016/j.cell.2018.04.018. PubMed PMID:29779944 PubMed Central PMC6003872.
  8. Xiong, L, Cooper, R, Tsimring, LS. Coexistence and Pattern Formation in Bacterial Mixtures with Contact-Dependent Killing. Biophys. J. 2018;114 (7):1741-1750. doi: 10.1016/j.bpj.2018.02.012. PubMed PMID:29642042 PubMed Central PMC5954290.
  9. Bui, N, Huang, JK, Bojorquez-Gomez, A, Licon, K, Sanchez, KS, Tang, SN et al.. Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Mol. Cancer Ther. 2018;17 (7):1585-1594. doi: 10.1158/1535-7163.MCT-17-0937. PubMed PMID:29636367 PubMed Central PMC6030464.
  10. Muse, ED, Yu, S, Edillor, CR, Tao, J, Spann, NJ, Troutman, TD et al.. Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP in macrophages. Proc. Natl. Acad. Sci. U.S.A. 2018;115 (20):E4680-E4689. doi: 10.1073/pnas.1714518115. PubMed PMID:29632203 PubMed Central PMC5960280.
  11. Zhang, W, Bojorquez-Gomez, A, Velez, DO, Xu, G, Sanchez, KS, Shen, JP et al.. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat. Genet. 2018;50 (4):613-620. doi: 10.1038/s41588-018-0091-2. PubMed PMID:29610481 PubMed Central PMC5893414.
  12. Huang, JK, Carlin, DE, Yu, MK, Zhang, W, Kreisberg, JF, Tamayo, P et al.. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst. 2018;6 (4):484-495.e5. doi: 10.1016/j.cels.2018.03.001. PubMed PMID:29605183 PubMed Central PMC5920724.
  13. Dai, X, Zhu, M, Warren, M, Balakrishnan, R, Okano, H, Williamson, JR et al.. Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress. MBio. 2018;9 (1):. doi: 10.1128/mBio.02375-17. PubMed PMID:29440576 PubMed Central PMC5821080.
  14. Preissl, S, Fang, R, Huang, H, Zhao, Y, Raviram, R, Gorkin, DU et al.. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat. Neurosci. 2018;21 (3):432-439. doi: 10.1038/s41593-018-0079-3. PubMed PMID:29434377 PubMed Central PMC5862073.
  15. Cowell, AN, Istvan, ES, Lukens, AK, Gomez-Lorenzo, MG, Vanaerschot, M, Sakata-Kato, T et al.. Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics. Science. 2018;359 (6372):191-199. doi: 10.1126/science.aan4472. PubMed PMID:29326268 PubMed Central PMC5925756.
  16. Nene, RV, Putnam, CD, Li, BZ, Nguyen, KG, Srivatsan, A, Campbell, CS et al.. Cdc73 suppresses genome instability by mediating telomere homeostasis. PLoS Genet. 2018;14 (1):e1007170. doi: 10.1371/journal.pgen.1007170. PubMed PMID:29320491 PubMed Central PMC5779705.
  17. Yan, J, Chen, SA, Local, A, Liu, T, Qiu, Y, Dorighi, KM et al.. Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Res. 2018;28 (2):204-220. doi: 10.1038/cr.2018.1. PubMed PMID:29313530 PubMed Central PMC5799818.
  18. Spahn, PN, Bath, T, Weiss, RJ, Kim, J, Esko, JD, Lewis, NE et al.. PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep. 2017;7 (1):15854. doi: 10.1038/s41598-017-16193-9. PubMed PMID:29158538 PubMed Central PMC5696473.
  19. Cooper, RM, Tsimring, L, Hasty, J. Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance. Elife. 2017;6 :. doi: 10.7554/eLife.25950. PubMed PMID:29091031 PubMed Central PMC5701796.
  20. Li, Y, Jin, M, O'Laughlin, R, Bittihn, P, Tsimring, LS, Pillus, L et al.. Multigenerational silencing dynamics control cell aging. Proc. Natl. Acad. Sci. U.S.A. 2017;114 (42):11253-11258. doi: 10.1073/pnas.1703379114. PubMed PMID:29073021 PubMed Central PMC5651738.
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A complete list of all our publications can be found here on PubMed