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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. Abe, Y, Kofman, ER, Ouyang, Z, Cruz-Becerra, G, Spann, NJ, Seidman, JS et al.. A TLR4/TRAF6-dependent signaling pathway mediates NCoR coactivator complex formation for inflammatory gene activation. Proc Natl Acad Sci U S A. 2024;121 (2):e2316104121. doi: 10.1073/pnas.2316104121. PubMed PMID:38165941 PubMed Central PMC10786282.
  2. 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.
  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 PubMed Central PMC6988775.
  4. 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.
  5. 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.
  6. 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.
  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. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
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Recent Publications

  1. Jado, JC, Dow, M, Carolino, K, Klie, A, Fonseca, GJ, Ideker, T et al.. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Sci Rep. 2024;14 (1):13989. doi: 10.1038/s41598-024-63943-7. PubMed PMID:38886371 PubMed Central PMC11183241.
  2. Abe, Y, Kofman, ER, Ouyang, Z, Cruz-Becerra, G, Spann, NJ, Seidman, JS et al.. A TLR4/TRAF6-dependent signaling pathway mediates NCoR coactivator complex formation for inflammatory gene activation. Proc Natl Acad Sci U S A. 2024;121 (2):e2316104121. doi: 10.1073/pnas.2316104121. PubMed PMID:38165941 PubMed Central PMC10786282.
  3. Abe, Y, Kofman, ER, Almeida, M, Ouyang, Z, Ponte, F, Mueller, JR et al.. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. Mol Cell. 2023;83 (19):3421-3437.e11. doi: 10.1016/j.molcel.2023.08.029. PubMed PMID:37751740 PubMed Central PMC10591845.
  4. Ottilie, S, Luth, MR, Hellemann, E, Goldgof, GM, Vigil, E, Kumar, P et al.. Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol. 2022;5 (1):128. doi: 10.1038/s42003-022-03076-7. PubMed PMID:35149760 PubMed Central PMC8837787.
  5. Ozturk, K, Carter, H. Predicting functional consequences of mutations using molecular interaction network features. Hum Genet. 2022;141 (6):1195-1210. doi: 10.1007/s00439-021-02329-5. PubMed PMID:34432150 PubMed Central PMC8873243.
  6. Einstein, JM, Perelis, M, Chaim, IA, Meena, JK, Nussbacher, JK, Tankka, AT et al.. Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer. Mol Cell. 2021;81 (15):3048-3064.e9. doi: 10.1016/j.molcel.2021.06.014. PubMed PMID:34216543 PubMed Central PMC8359670.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
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A complete list of all our publications can be found here on PubMed