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

Publications

Key Publications

  1. Liao, MJ, Din, MO, Tsimring, L, Hasty, J. Rock-paper-scissors: Engineered population dynamics increase genetic stability. Science. 2019;365 (6457):1045-1049. doi: 10.1126/science.aaw0542. PubMed PMID:31488693 .
  2. Lee, DD, Galera-Laporta, L, Bialecka-Fornal, M, Moon, EC, Shen, Z, Briggs, SP et al.. Magnesium Flux Modulates Ribosomes to Increase Bacterial Survival. Cell. 2019;177 (2):352-360.e13. doi: 10.1016/j.cell.2019.01.042. PubMed PMID:30853217 PubMed Central PMC6814349.
  3. Antonova-Koch, Y, Meister, S, Abraham, M, Luth, MR, Ottilie, S, Lukens, AK et al.. Open-source discovery of chemical leads for next-generation chemoprotective antimalarials. Science. 2018;362 (6419):. doi: 10.1126/science.aat9446. PubMed PMID:30523084 PubMed Central PMC6516198.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  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. 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.
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Recent Publications

  1. Cowell, AN, Winzeler, EA. Advances in omics-based methods to identify novel targets for malaria and other parasitic protozoan infections. Genome Med. 2019;11 (1):63. doi: 10.1186/s13073-019-0673-3. PubMed PMID:31640748 PubMed Central PMC6805675.
  2. Sakai, M, Troutman, TD, Seidman, JS, Ouyang, Z, Spann, NJ, Abe, Y et al.. Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity. Immunity. 2019;51 (4):655-670.e8. doi: 10.1016/j.immuni.2019.09.002. PubMed PMID:31587991 PubMed Central PMC6800814.
  3. Liao, MJ, Din, MO, Tsimring, L, Hasty, J. Rock-paper-scissors: Engineered population dynamics increase genetic stability. Science. 2019;365 (6457):1045-1049. doi: 10.1126/science.aaw0542. PubMed PMID:31488693 .
  4. Castro, A, Ozturk, K, Pyke, RM, Xian, S, Zanetti, M, Carter, H et al.. Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes. BMC Med Genomics. 2019;12 (Suppl 6):107. doi: 10.1186/s12920-019-0544-1. PubMed PMID:31345234 PubMed Central PMC6657029.
  5. Martinez-Corral, R, Liu, J, Prindle, A, Süel, GM, Garcia-Ojalvo, J. Metabolic basis of brain-like electrical signalling in bacterial communities. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2019;374 (1774):20180382. doi: 10.1098/rstb.2018.0382. PubMed PMID:31006362 PubMed Central PMC6553584.
  6. Lee, DD, Galera-Laporta, L, Bialecka-Fornal, M, Moon, EC, Shen, Z, Briggs, SP et al.. Magnesium Flux Modulates Ribosomes to Increase Bacterial Survival. Cell. 2019;177 (2):352-360.e13. doi: 10.1016/j.cell.2019.01.042. PubMed PMID:30853217 PubMed Central PMC6814349.
  7. Jin, M, Li, Y, O'Laughlin, R, Bittihn, P, Pillus, L, Tsimring, LS et al.. Divergent Aging of Isogenic Yeast Cells Revealed through Single-Cell Phenotypic Dynamics. Cell Syst. 2019;8 (3):242-253.e3. doi: 10.1016/j.cels.2019.02.002. PubMed PMID:30852250 PubMed Central PMC6514117.
  8. Fonseca, GJ, Tao, J, Westin, EM, Duttke, SH, Spann, NJ, Strid, T et al.. Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. Nat Commun. 2019;10 (1):414. doi: 10.1038/s41467-018-08236-0. PubMed PMID:30679424 PubMed Central PMC6345992.
  9. Antonova-Koch, Y, Meister, S, Abraham, M, Luth, MR, Ottilie, S, Lukens, AK et al.. Open-source discovery of chemical leads for next-generation chemoprotective antimalarials. Science. 2018;362 (6419):. doi: 10.1126/science.aat9446. PubMed PMID:30523084 PubMed Central PMC6516198.
  10. Winzeler, EA. An improbable journey: Creativity helped me make the transition from art to curing malaria. J. Biol. Chem. 2019;294 (2):405-409. doi: 10.1074/jbc.AW118.005229. PubMed PMID:30401750 PubMed Central PMC6333892.
  11. Cooper, R, Tsimring, L, Hasty, J. Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions. Bio Protoc. 2018;8 (16):. doi: 10.21769/BioProtoc.2970. PubMed PMID:30370317 PubMed Central PMC6200413.
  12. Hoeksema, MA, Glass, CK. Nature and nurture of tissue-specific macrophage phenotypes. Atherosclerosis. 2019;281 :159-167. doi: 10.1016/j.atherosclerosis.2018.10.005. PubMed PMID:30343819 PubMed Central PMC6399046.
  13. Davis-Turak, J, Johnson, TL, Hoffmann, A. Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. Nucleic Acids Res. 2018;46 (20):10598-10607. doi: 10.1093/nar/gky870. PubMed PMID:30272246 PubMed Central PMC6237756.
  14. Fulzele, A, Bennett, EJ. Ubiquitin diGLY Proteomics as an Approach to Identify and Quantify the Ubiquitin-Modified Proteome. Methods Mol. Biol. 2018;1844 :363-384. doi: 10.1007/978-1-4939-8706-1_23. PubMed PMID:30242721 PubMed Central PMC6791129.
  15. Eckhardt, M, Zhang, W, Gross, AM, Von Dollen, J, Johnson, JR, Franks-Skiba, KE et al.. Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018;8 (11):1474-1489. doi: 10.1158/2159-8290.CD-17-1018. PubMed PMID:30209081 PubMed Central PMC6375299.
  16. Chaix, A, Lin, T, Le, HD, Chang, MW, Panda, S. Time-Restricted Feeding Prevents Obesity and Metabolic Syndrome in Mice Lacking a Circadian Clock. Cell Metab. 2019;29 (2):303-319.e4. doi: 10.1016/j.cmet.2018.08.004. PubMed PMID:30174302 .
  17. 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.
  18. Larkin, JW, Zhai, X, Kikuchi, K, Redford, SE, Prindle, A, Liu, J et al.. Signal Percolation within a Bacterial Community. Cell Syst. 2018;7 (2):137-145.e3. doi: 10.1016/j.cels.2018.06.005. PubMed PMID:30056004 PubMed Central PMC6214369.
  19. 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.
  20. 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;37 (47):6152-6165. doi: 10.1038/s41388-018-0349-2. PubMed PMID:29995872 PubMed Central PMC6329670.
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A complete list of all our publications can be found here on PubMed