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


Key Publications

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Recent Publications

  1. Troutman, TD, Bennett, H, Sakai, M, Seidman, JS, Heinz, S, Glass, CK et al.. Purification of mouse hepatic non-parenchymal cells or nuclei for use in ChIP-seq and other next-generation sequencing approaches. STAR Protoc. 2021;2 (1):100363. doi: 10.1016/j.xpro.2021.100363. PubMed PMID:33748781 PubMed Central PMC7960533.
  2. Davis, AG, Einstein, JM, Zheng, D, Jayne, ND, Fu, XD, Tian, B et al.. A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. Blood Adv. 2021;5 (5):1310-1323. doi: 10.1182/bloodadvances.2020002090. PubMed PMID:33656539 PubMed Central PMC7948294.
  3. Wheeler, EC, Vu, AQ, Einstein, JM, DiSalvo, M, Ahmed, N, Van Nostrand, EL et al.. Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors. Nat Methods. 2020;17 (6):636-642. doi: 10.1038/s41592-020-0826-8. PubMed PMID:32393832 PubMed Central PMC7357298.
  4. Seidman, JS, Troutman, TD, Sakai, M, Gola, A, Spann, NJ, Bennett, H et al.. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis. Immunity. 2020;52 (6):1057-1074.e7. doi: 10.1016/j.immuni.2020.04.001. PubMed PMID:32362324 PubMed Central PMC7305990.
  5. Garshott, DM, Sundaramoorthy, E, Leonard, M, Bennett, EJ. Distinct regulatory ribosomal ubiquitylation events are reversible and hierarchically organized. Elife. 2020;9 :. doi: 10.7554/eLife.54023. PubMed PMID:32011234 PubMed Central PMC7064338.
  6. Xiong, L, Cao, Y, Cooper, R, Rappel, WJ, Hasty, J, Tsimring, L et al.. Flower-like patterns in multi-species bacterial colonies. Elife. 2020;9 :. doi: 10.7554/eLife.48885. PubMed PMID:31933477 PubMed Central PMC6959979.
  7. Zhai, X, Larkin, JW, Kikuchi, K, Redford, SE, Roy, U, Süel, GM et al.. Statistics of correlated percolation in a bacterial community. PLoS Comput Biol. 2019;15 (12):e1007508. doi: 10.1371/journal.pcbi.1007508. PubMed PMID:31790383 PubMed Central PMC6907856.
  8. 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.
  9. 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.
  10. 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 PubMed Central PMC6988775.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
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A complete list of all our publications can be found here on PubMed