Millard and Muriel Jacobs Genetics and Genomics Laboratory

Articles from CaltechAUTHORS

• Chakrabarty, Yogaditya; Yang, Zheng; et el. (2024) The HRI branch of the integrated stress response selectively triggers mitophagy; Molecular Cell; 10.1016/j.molcel.2024.01.016
• Jacobs-Li, Jessica; Tang, Weiyi; et el. (2023) Single-cell profiling coupled with lineage analysis reveals vagal and sacral neural crest contributions to the developing enteric nervous system; eLife; Vol. 12; e79156; PMCID PMC10627514; 10.7554/elife.79156
• Stundl, Jan; Martik, Megan L.; et el. (2023) Ancient vertebrate dermal armor evolved from trunk neural crest; Proceedings of the National Academy of Sciences of the United States of America; Vol. 120; No. 30; e2221120120; PMCID PMC10372632; 10.1073/pnas.2221120120
• Chen, Xinhong; Wolfe, Damien A.; et el. (2023) Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates; Nature Communications; Vol. 14; Art. No. 3345; PMCID PMC10250345; 10.1038/s41467-023-38582-7
• Inglis, Alison J.; Guna, Alina; et el. (2023) Coupled protein quality control during nonsense-mediated mRNA decay; Journal of Cell Science; Vol. 136; No. 10; Art. No. jcs261216; PMCID PMC10234110; 10.1242/jcs.261216
• Goronzy, Isabel N.; Quinodoz, Sofia A.; et el. (2022) Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription; Cell Reports; Vol. 41; No. 9; Art. No. 111730; PMCID PMC9793828; 10.1016/j.celrep.2022.111730
• Goertsen, David; Goeden, Nick; et el. (2022) Targeting the lung epithelium after intravenous delivery by directed evolution of underexplored sites on the AAV capsid; Molecular Therapy - Methods & Clinical Development; Vol. 26; 331-342; PMCID PMC9372736; 10.1016/j.omtm.2022.07.010
• Yang, Chien-I; Zhu, Zikun; et el. (2022) System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity; iScience; Vol. 25; No. 8; Art. No. 104756; PMCID PMC9356101; 10.1016/j.isci.2022.104756
• Galton, Riley; Fejes-Tóth, Katalin; et el. (2022) Co-option of the piRNA pathway to regulate neural crest specification; Science Advances; Vol. 8; No. 32; Art. No. abn1441; 10.1126/sciadv.abn1441
• Yu, Hang; Speth, Daan R.; et el. (2022) Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep; Applied and Environmental Microbiology; Vol. 88; No. 11; Art. No. e0210921; PMCID PMC9195934; 10.1128/aem.02109-21
• Zhu, Zikun; Wang, Shuai; et el. (2022) Ribosome profiling reveals multiple roles of SecA in cotranslational protein export; Nature Communications; Vol. 13; Art. No. 3393; PMCID PMC9192764; 10.1038/s41467-022-31061-5
• Zhou, Wen; Gao, Fan; et el. (2022) Single-cell deletion analyses show control of pro–T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b; Science Immunology; Vol. 7; No. 71; eabm1920; PMCID PMC9273332; 10.1126/sciimmunol.abm1920
• Ma, Yitong; Budde, Mark W.; et el. (2022) Synthetic mammalian signaling circuits for robust cell population control; Cell; Vol. 185; No. 6; 967-979; PMCID PMC8995209; 10.1016/j.cell.2022.01.026
• Arrastia, Mary V.; Jachowicz, Joanna W.; et el. (2022) Single-cell measurement of higher-order 3D genome organization with scSPRITE; Nature Biotechnology; Vol. 40; No. 1; 64-73; 10.1038/s41587-021-00998-1
• Chen, Peiwei; Luo, Yicheng; et el. (2021) RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility; PLoS Genetics; Vol. 17; No. 9; Art. No. e1009591; PMCID PMC8412364; 10.1371/journal.pgen.1009591
• Buchman, Anna; Shriner, Isaiah; et el. (2021) Engineered reproductively isolated species drive reversible population replacement; Nature Communications; Vol. 12; Art. No. 3281; 10.1038/s41467-021-23531-z
• Chen, Peiwei; Kotov, Alexei A.; et el. (2021) piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline; Genes and Development; Vol. 35; No. 11-12; 914-935; PMCID PMC8168559; 10.1101/gad.345041.120
• Hutchins, Erica J.; Piacentino, Michael L.; et el. (2021) Transcriptomic Identification of Draxin-Responsive Targets During Cranial Neural Crest EMT; Frontiers in Physiology; Vol. 12; Art. No. 624037; PMCID PMC7886793; 10.3389/fphys.2021.624037
• Finn, Paul B.; Bhimsaria, Devesh; et el. (2020) Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome; PLoS ONE; Vol. 15; No. 12; Art. No. e0243905; 10.1371/journal.pone.0243905
• Sun, Simo; Shinya, Ryoji; et el. (2020) Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis Strain SH1; Microbiology Resource Announcements; Vol. 9; No. 43; Art. No. e01000-20; PMCID PMC7585841; 10.1128/mra.01000-20
• Khazaei, Tahmineh; Williams, Rory L.; et el. (2020) Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community; Science Advances; Vol. 6; No. 33; Art. No. eaba0353; PMCID PMC7423363; 10.1126/sciadv.aba0353
• Zhang, Yandong; Sohn, Changho; et el. (2020) Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET); Communications Biology; Vol. 3; Art. No. 420; 10.1038/s42003-020-01132-8
• Walton, Sophie J.; Wang, Han; et el. (2020) Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression; Genetics; Vol. 215; No. 4; 1039-1054; PMCID PMC7404228; 10.1534/genetics.120.302923
• He, Peng; Williams, Brian A.; et el. (2020) The changing mouse embryo transcriptome at whole tissue and single-cell resolution; Nature; Vol. 583; No. 7818; 760-767; 10.1038/s41586-020-2536-x
• Koromila, Theodora; Gao, Fan; et el. (2020) Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos; eLife; Vol. 9; Art. No. e59610; PMCID PMC7417190; 10.7554/eLife.59610
• Yu, Hang and Leadbetter, Jared R. (2020) Bacterial chemolithoautotrophy via manganese oxidation; Nature; Vol. 583; No. 7816; 453-458; PMCID PMC7802741; 10.1038/s41586-020-2468-5
• Quintero-Cadena, Porfirio; Lenstra, Tineke L.; et el. (2020) RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting; Molecular Cell; Vol. 79; No. 2; 207-220; 10.1016/j.molcel.2020.05.030
• Dalla Benetta, Elena; Antoshechkin, Igor; et el. (2020) Genome Elimination Mediated by Gene Expression from a Selfish Chromosome; Science Advances; Vol. 6; No. 14; Art. No. eaaz9808; PMCID PMC7124933; 10.1126/sciadv.aaz9808
• Gamez, Stephanie; Antoshechkin, Igor; et el. (2020) The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector; G3; Vol. 10; No. 3; 1051-1062; PMCID PMC7056973; 10.1534/g3.119.401006
• Basta, David W.; Angeles-Albores, David; et el. (2020) Heat-shock proteases promote survival of Pseudomonas aeruginosa during growth arrest; Proceedings of the National Academy of Sciences of the United States of America; Vol. 117; No. 8; 4358-4367; PMCID PMC7049150; 10.1073/pnas.1912082117
• Tang, Weiyi; Martik, Megan L.; et el. (2019) Cardiac neural crest contributes to cardiomyocytes in amniotes and heart regeneration in zebrafish; eLife; Vol. 8; Art. No. e47929; PMCID PMC6721792; 10.7554/elife.47929
• Perry, Elena K. and Newman, Dianne K. (2019) The transcription factors ActR and SoxR differentially affect the phenazine tolerance of Agrobacterium tumefaciens; Molecular Microbiology; Vol. 112; No. 1; 199-218; PMCID PMC6615960; 10.1111/mmi.14263
• Khazaei, Tahmineh; Barlow, Jacob T.; et el. (2018) RNA markers enable phenotypic test of antibiotic susceptibility in Neisseria gonorrhoeae after 10 minutes of ciprofloxacin exposure; Scientific Reports; Vol. 8; Art. No. 11606; PMCID PMC6072703; 10.1038/s41598-018-29707-w
• Kim, Jocelyn T.; Liu, Yarong; et el. (2017) Dendritic cell–targeted lentiviral vector immunization uses pseudotransduction and DNA-mediated STING and cGAS activation; Science Immunology; Vol. 2; No. 13; Art. No. eaal1329; PMCID PMC5845465; 10.1126/sciimmunol.aal1329
• Seet, Christopher S.; He, Chongbin; et el. (2017) Generation of mature T cells from human hematopoietic stem and progenitor cells in artificial thymic organoids; Nature Methods; Vol. 14; No. 5; 521-530; PMCID PMC5426913; 10.1038/nmeth.4237
• Nath, Ravi D.; Chow, Elly S.; et el. (2016) C. elegans Stress-Induced Sleep Emerges from the Collective Action of Multiple Neuropeptides; Current Biology; Vol. 26; No. 18; 2446-2455; PMCID PMC5694219; 10.1016/j.cub.2016.07.048
• Babin, Brett M.; Bergkessel, Megan; et el. (2016) SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa; Proceedings of the National Academy of Sciences of the United States of America; Vol. 113; No. 5; E597-E605; PMCID PMC4747698; 10.1073/pnas.1514412113
• Henley, Beverley M.; Williams, Brian A.; et el. (2013) Transcriptional regulation by nicotine in dopaminergic neurons; Biochemical Pharmacology; Vol. 86; No. 8; 1074-1083; PMCID PMC3969234; 10.1016/j.bcp.2013.07.031
• Akbari, Omar S.; Amrhein, Henry; et el. (2013) The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector; G3; Vol. 3; No. 9; 1493-1509; PMCID PMC3755910; 10.1534/g3.113.006742
• Zhang, Jingli A.; Mortazavi, Ali; et el. (2012) Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity; Cell; Vol. 149; No. 2; 467-482; PMCID PMC3336965; 10.1016/j.cell.2012.01.056
• Imoukhuede, P. I.; Moss, Fraser J.; et el. (2009) Ezrin Mediates Tethering of the γ-Aminobutyric Acid Transporter GAT1 to Actin Filaments Via a C-Terminal PDZ-Interacting Domain; Biophysical Journal; Vol. 96; No. 7; 2949-2960; PMCID PMC2711277; 10.1016/j.bpj.2008.11.070
• Hao, Shengli and Baltimore, David (2009) The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules; Nature Immunology; Vol. 10; No. 3; 281-288; PMCID PMC2775040; 10.1038/ni.1699
• Vikalo, Haris; Hassibi, Babak; et el. (2008) Modeling and Estimation for Real-Time Microarrays; IEEE Journal of Selected Topics in Signal Processing; Vol. 2; No. 3; 286-296; 10.1109/JSTSP.2008.924383
• O’Connell, Ryan M.; Rao, Dinesh S.; et el. (2008) Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder; Journal of Experimental Medicine; Vol. 205; No. 3; 585-594; PMCID PMC2275382; 10.1084/jem.20072108
• Kannangara, Rubini; Branigan, Caroline; et el. (2007) The Transcription Factor WIN1/SHN1 Regulates Cutin Biosynthesis in Arabidopsis thaliana; Plant Cell; Vol. 19; No. 4; 1278-1294; PMCID PMC1913754; 10.1105/tpc.106.047076
• O’Connell, Ryan M.; Taganov, Konstantin D.; et el. (2007) MicroRNA-155 is induced during the macrophage inflammatory response; Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 5; 1604-1609; PMCID PMC1780072; 10.1073/pnas.0610731104
• Taganov, Konstantin D.; Boldin, Mark P.; et el. (2006) NF-{kappa}B-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses; Proceedings of the National Academy of Sciences of the United States of America; Vol. 103; No. 33; 12481-12486; PMCID PMC1567904; 10.1073/pnas.0605298103