<h1 id="millard-and-muriel-jacobs-genetics-and-genomics-laboratory"><a
href="./">Millard and Muriel Jacobs Genetics and Genomics
Laboratory</a></h1>
<h3 id="articles-from-caltechauthors">Articles from <a
href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h3>
<ul>
<li>Kitchen, Sheila A.; Naragon, Thomas H.; et al. (2024) <a
href="https://authors.library.caltech.edu/records/8n92k-h7b39">The
genomic and cellular basis of biosynthetic innovation in rove
beetles</a>; Cell; Vol. 187; No. 14; 1-22; <a
href="https://doi.org/10.1016/j.cell.2024.05.012">10.1016/j.cell.2024.05.012</a></li>
<li>Duan, Mengtong; Dev, Ishaan; et al. (2024) <a
href="https://authors.library.caltech.edu/records/xsahp-v8976">SEMPER:
Stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes
for compact, ratio-tunable multi-gene expression</a>; Cell Systems; <a
href="https://doi.org/10.1016/j.cels.2024.06.001">10.1016/j.cels.2024.06.001</a></li>
<li>Chakrabarty, Yogaditya; Yang, Zheng; et al. (2024) <a
href="https://authors.library.caltech.edu/records/brxbr-2nk64">The HRI
branch of the integrated stress response selectively triggers
mitophagy</a>; Molecular Cell; Vol. 84; No. 6; 1090-1100.e6; PMCID
PMC11062084; <a
href="https://doi.org/10.1016/j.molcel.2024.01.016">10.1016/j.molcel.2024.01.016</a></li>
<li>Jacobs-Li, Jessica; Tang, Weiyi; et al. (2023) <a
href="https://authors.library.caltech.edu/records/bpha3-br295">Single-cell
profiling coupled with lineage analysis reveals vagal and sacral neural
crest contributions to the developing enteric nervous system</a>; eLife;
Vol. 12; e79156; PMCID PMC10627514; <a
href="https://doi.org/10.7554/elife.79156">10.7554/elife.79156</a></li>
<li>Shin, Boyoung; Zhou, Wen; et al. (2023) <a
href="https://authors.library.caltech.edu/records/7x7jk-49y92">Runx
factors launch T cell and innate lymphoid programs via direct and gene
network-based mechanisms</a>; Nature Immunology; Vol. 24; No. 9;
1458-1472; PMCID PMC10673614; <a
href="https://doi.org/10.1038/s41590-023-01585-z">10.1038/s41590-023-01585-z</a></li>
<li>Stundl, Jan; Martik, Megan L.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230725-49196000.18">Ancient
vertebrate dermal armor evolved from trunk neural crest</a>; Proceedings
of the National Academy of Sciences of the United States of America;
Vol. 120; No. 30; e2221120120; PMCID PMC10372632; <a
href="https://doi.org/10.1073/pnas.2221120120">10.1073/pnas.2221120120</a></li>
<li>Chen, Xinhong; Wolfe, Damien A.; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230615-129198000.12">Functional
gene delivery to and across brain vasculature of systemic AAVs with
endothelial-specific tropism in rodents and broad tropism in
primates</a>; Nature Communications; Vol. 14; Art. No. 3345; PMCID
PMC10250345; <a
href="https://doi.org/10.1038/s41467-023-38582-7">10.1038/s41467-023-38582-7</a></li>
<li>Inglis, Alison J.; Guna, Alina; et al. (2023) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230628-257040000.13">Coupled
protein quality control during nonsense-mediated mRNA decay</a>; Journal
of Cell Science; Vol. 136; No. 10; Art. No. jcs261216; PMCID
PMC10234110; <a
href="https://doi.org/10.1242/jcs.261216">10.1242/jcs.261216</a></li>
<li>Chen, Peiwei and Aravin, Alexei A. (2023) <a
href="https://authors.library.caltech.edu/records/m0g2n-4g932">Genetic
control of a sex-specific piRNA program</a>; Current Biology; Vol. 33;
No. 9; 1825-1835.e3; PMCID PMC10431932; <a
href="https://doi.org/10.1016/j.cub.2023.03.057">10.1016/j.cub.2023.03.057</a></li>
<li>Goronzy, Isabel N.; Quinodoz, Sofia A.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20230123-451320900.9">Simultaneous
mapping of 3D structure and nascent RNAs argues against nuclear
compartments that preclude transcription</a>; Cell Reports; Vol. 41;
No. 9; Art. No. 111730; PMCID PMC9793828; <a
href="https://doi.org/10.1016/j.celrep.2022.111730">10.1016/j.celrep.2022.111730</a></li>
<li>Goertsen, David; Goeden, Nick; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220816-373601000">Targeting
the lung epithelium after intravenous delivery by directed evolution of
underexplored sites on the AAV capsid</a>; Molecular Therapy - Methods
&amp; Clinical Development; Vol. 26; 331-342; PMCID PMC9372736; <a
href="https://doi.org/10.1016/j.omtm.2022.07.010">10.1016/j.omtm.2022.07.010</a></li>
<li>Yang, Chien-I; Zhu, Zikun; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220816-373597000">System-wide
analyses reveal essential roles of N-terminal protein modification in
bacterial membrane integrity</a>; iScience; Vol. 25; No. 8; Art.
No. 104756; PMCID PMC9356101; <a
href="https://doi.org/10.1016/j.isci.2022.104756">10.1016/j.isci.2022.104756</a></li>
<li>Galton, Riley; Fejes-Tóth, Katalin; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220811-456719000">Co-option
of the piRNA pathway to regulate neural crest specification</a>; Science
Advances; Vol. 8; No. 32; Art. No. abn1441; <a
href="https://doi.org/10.1126/sciadv.abn1441">10.1126/sciadv.abn1441</a></li>
<li>Yu, Hang; Speth, Daan R.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220721-8119000">Community
Structure and Microbial Associations in Sediment-Free Methanotrophic
Enrichment Cultures from a Marine Methane Seep</a>; Applied and
Environmental Microbiology; Vol. 88; No. 11; Art. No. e0210921; PMCID
PMC9195934; <a
href="https://doi.org/10.1128/aem.02109-21">10.1128/aem.02109-21</a></li>
<li>Zhu, Zikun; Wang, Shuai; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220614-222089000">Ribosome
profiling reveals multiple roles of SecA in cotranslational protein
export</a>; Nature Communications; Vol. 13; Art. No. 3393; PMCID
PMC9192764; <a
href="https://doi.org/10.1038/s41467-022-31061-5">10.1038/s41467-022-31061-5</a></li>
<li>Zhou, Wen; Gao, Fan; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20220523-164956000">Single-cell
deletion analyses show control of pro–T cell developmental speed and
pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b</a>; Science
Immunology; Vol. 7; No. 71; eabm1920; PMCID PMC9273332; <a
href="https://doi.org/10.1126/sciimmunol.abm1920">10.1126/sciimmunol.abm1920</a></li>
<li>Ma, Yitong; Budde, Mark W.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200909-145940519">Synthetic
mammalian signaling circuits for robust cell population control</a>;
Cell; Vol. 185; No. 6; 967-979; PMCID PMC8995209; <a
href="https://doi.org/10.1016/j.cell.2022.01.026">10.1016/j.cell.2022.01.026</a></li>
<li>Arrastia, Mary V.; Jachowicz, Joanna W.; et al. (2022) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200813-130113364">Single-cell
measurement of higher-order 3D genome organization with scSPRITE</a>;
Nature Biotechnology; Vol. 40; No. 1; 64-73; <a
href="https://doi.org/10.1038/s41587-021-00998-1">10.1038/s41587-021-00998-1</a></li>
<li>Chen, Peiwei; Luo, Yicheng; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200826-094353695">RDC
complex executes a dynamic piRNA program during Drosophila
spermatogenesis to safeguard male fertility</a>; PLoS Genetics; Vol. 17;
No. 9; Art. No. e1009591; PMCID PMC8412364; <a
href="https://doi.org/10.1371/journal.pgen.1009591">10.1371/journal.pgen.1009591</a></li>
<li>Buchman, Anna; Shriner, Isaiah; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200811-125007941">Engineered
reproductively isolated species drive reversible population
replacement</a>; Nature Communications; Vol. 12; Art. No. 3281; <a
href="https://doi.org/10.1038/s41467-021-23531-z">10.1038/s41467-021-23531-z</a></li>
<li>Chen, Peiwei; Kotov, Alexei A.; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200826-100150960">piRNA-mediated
gene regulation and adaptation to sex-specific transposon expression in
D. melanogaster male germline</a>; Genes and Development; Vol. 35;
No. 11-12; 914-935; PMCID PMC8168559; <a
href="https://doi.org/10.1101/gad.345041.120">10.1101/gad.345041.120</a></li>
<li>Hutchins, Erica J.; Piacentino, Michael L.; et al. (2021) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20210302-141852646">Transcriptomic
Identification of Draxin-Responsive Targets During Cranial Neural Crest
EMT</a>; Frontiers in Physiology; Vol. 12; Art. No. 624037; PMCID
PMC7886793; <a
href="https://doi.org/10.3389/fphys.2021.624037">10.3389/fphys.2021.624037</a></li>
<li>Finn, Paul B.; Bhimsaria, Devesh; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200818-152604358">Single
position substitution of hairpin pyrrole-imidazole polyamides imparts
distinct DNA-binding profiles across the human genome</a>; PLoS ONE;
Vol. 15; No. 12; Art. No. e0243905; <a
href="https://doi.org/10.1371/journal.pone.0243905">10.1371/journal.pone.0243905</a></li>
<li>Sun, Simo; Shinya, Ryoji; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20201022-112712963">Telomere-to-Telomere
Genome Assembly of Bursaphelenchus okinawaensis Strain SH1</a>;
Microbiology Resource Announcements; Vol. 9; No. 43; Art. No. e01000-20;
PMCID PMC7585841; <a
href="https://doi.org/10.1128/mra.01000-20">10.1128/mra.01000-20</a></li>
<li>Khazaei, Tahmineh; Williams, Rory L.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200813-144241318">Metabolic
multistability and hysteresis in a model aerobe-anaerobe microbiome
community</a>; Science Advances; Vol. 6; No. 33; Art. No. eaba0353;
PMCID PMC7423363; <a
href="https://doi.org/10.1126/sciadv.aba0353">10.1126/sciadv.aba0353</a></li>
<li>Zhang, Yandong; Sohn, Changho; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200803-104852533">Detecting
protein and post-translational modifications in single cells with
iDentification and qUantification sEparaTion (DUET)</a>; Communications
Biology; Vol. 3; Art. No. 420; <a
href="https://doi.org/10.1038/s42003-020-01132-8">10.1038/s42003-020-01132-8</a></li>
<li>Walton, Sophie J.; Wang, Han; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191028-093454817">Caenorhabditis
elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene
Expression</a>; Genetics; Vol. 215; No. 4; 1039-1054; PMCID PMC7404228;
<a
href="https://doi.org/10.1534/genetics.120.302923">10.1534/genetics.120.302923</a></li>
<li>He, Peng; Williams, Brian A.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200618-081148283">The
changing mouse embryo transcriptome at whole tissue and single-cell
resolution</a>; Nature; Vol. 583; No. 7818; 760-767; <a
href="https://doi.org/10.1038/s41586-020-2536-x">10.1038/s41586-020-2536-x</a></li>
<li>Koromila, Theodora; Gao, Fan; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191125-141648000">Odd-paired
is a pioneer-like factor that coordinates with Zelda to control gene
expression in embryos</a>; eLife; Vol. 9; Art. No. e59610; PMCID
PMC7417190; <a
href="https://doi.org/10.7554/eLife.59610">10.7554/eLife.59610</a></li>
<li>Quintero-Cadena, Porfirio; Lenstra, Tineke L.; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191031-131636300">RNA
Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional
Bursting</a>; Molecular Cell; Vol. 79; No. 2; 207-220; <a
href="https://doi.org/10.1016/j.molcel.2020.05.030">10.1016/j.molcel.2020.05.030</a></li>
<li>Yu, Hang and Leadbetter, Jared R. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200408-160710037">Bacterial
chemolithoautotrophy via manganese oxidation</a>; Nature; Vol. 583;
No. 7816; 453-458; PMCID PMC7802741; <a
href="https://doi.org/10.1038/s41586-020-2468-5">10.1038/s41586-020-2468-5</a></li>
<li>Dalla Benetta, Elena; Antoshechkin, Igor; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20191007-133644493">Genome
Elimination Mediated by Gene Expression from a Selfish Chromosome</a>;
Science Advances; Vol. 6; No. 14; Art. No. eaaz9808; PMCID PMC7124933;
<a
href="https://doi.org/10.1126/sciadv.aaz9808">10.1126/sciadv.aaz9808</a></li>
<li>Gamez, Stephanie; Antoshechkin, Igor; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190904-144412708">The
Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human
Disease Vector</a>; G3; Vol. 10; No. 3; 1051-1062; PMCID PMC7056973; <a
href="https://doi.org/10.1534/g3.119.401006">10.1534/g3.119.401006</a></li>
<li>Basta, David W.; Angeles-Albores, David; et al. (2020) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20200206-163326208">Heat-shock
proteases promote survival of Pseudomonas aeruginosa during growth
arrest</a>; Proceedings of the National Academy of Sciences of the
United States of America; Vol. 117; No. 8; 4358-4367; PMCID PMC7049150;
<a
href="https://doi.org/10.1073/pnas.1912082117">10.1073/pnas.1912082117</a></li>
<li>Tang, Weiyi; Martik, Megan L.; et al. (2019) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190812-093416740">Cardiac
neural crest contributes to cardiomyocytes in amniotes and heart
regeneration in zebrafish</a>; eLife; Vol. 8; Art. No. e47929; PMCID
PMC6721792; <a
href="https://doi.org/10.7554/elife.47929">10.7554/elife.47929</a></li>
<li>Perry, Elena K. and Newman, Dianne K. (2019) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20190419-100142089">The
transcription factors ActR and SoxR differentially affect the phenazine
tolerance of Agrobacterium tumefaciens</a>; Molecular Microbiology; Vol.
112; No. 1; 199-218; PMCID PMC6615960; <a
href="https://doi.org/10.1111/mmi.14263">10.1111/mmi.14263</a></li>
<li>Khazaei, Tahmineh; Barlow, Jacob T.; et al. (2018) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20180802-093834589">RNA
markers enable phenotypic test of antibiotic susceptibility in Neisseria
gonorrhoeae after 10 minutes of ciprofloxacin exposure</a>; Scientific
Reports; Vol. 8; Art. No. 11606; PMCID PMC6072703; <a
href="https://doi.org/10.1038/s41598-018-29707-w">10.1038/s41598-018-29707-w</a></li>
<li>Kim, Jocelyn T.; Liu, Yarong; et al. (2017) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20170718-091900989">Dendritic
cell–targeted lentiviral vector immunization uses pseudotransduction and
DNA-mediated STING and cGAS activation</a>; Science Immunology; Vol. 2;
No. 13; Art. No. eaal1329; PMCID PMC5845465; <a
href="https://doi.org/10.1126/sciimmunol.aal1329">10.1126/sciimmunol.aal1329</a></li>
<li>Seet, Christopher S.; He, Chongbin; et al. (2017) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20170124-111140333">Generation
of mature T cells from human hematopoietic stem and progenitor cells in
artificial thymic organoids</a>; Nature Methods; Vol. 14; No. 5;
521-530; PMCID PMC5426913; <a
href="https://doi.org/10.1038/nmeth.4237">10.1038/nmeth.4237</a></li>
<li>Nath, Ravi D.; Chow, Elly S.; et al. (2016) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20160818-085530875">C.
elegans Stress-Induced Sleep Emerges from the Collective Action of
Multiple Neuropeptides</a>; Current Biology; Vol. 26; No. 18; 2446-2455;
PMCID PMC5694219; <a
href="https://doi.org/10.1016/j.cub.2016.07.048">10.1016/j.cub.2016.07.048</a></li>
<li>Babin, Brett M.; Bergkessel, Megan; et al. (2016) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20160120-081453238">SutA
is a bacterial transcription factor expressed during slow growth in
Pseudomonas aeruginosa</a>; Proceedings of the National Academy of
Sciences of the United States of America; Vol. 113; No. 5; E597-E605;
PMCID PMC4747698; <a
href="https://doi.org/10.1073/pnas.1514412113">10.1073/pnas.1514412113</a></li>
<li>Henley, Beverley M.; Williams, Brian A.; et al. (2013) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20130815-073947290">Transcriptional
regulation by nicotine in dopaminergic neurons</a>; Biochemical
Pharmacology; Vol. 86; No. 8; 1074-1083; PMCID PMC3969234; <a
href="https://doi.org/10.1016/j.bcp.2013.07.031">10.1016/j.bcp.2013.07.031</a></li>
<li>Akbari, Omar S.; Amrhein, Henry; et al. (2013) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20131003-143259486">The
Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive
Species and Major Arbovirus Vector</a>; G3; Vol. 3; No. 9; 1493-1509;
PMCID PMC3755910; <a
href="https://doi.org/10.1534/g3.113.006742">10.1534/g3.113.006742</a></li>
<li>Zhang, Jingli A.; Mortazavi, Ali; et al. (2012) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20120511-113721604">Dynamic
Transformations of Genome-wide Epigenetic Marking and Transcriptional
Control Establish T Cell Identity</a>; Cell; Vol. 149; No. 2; 467-482;
PMCID PMC3336965; <a
href="https://doi.org/10.1016/j.cell.2012.01.056">10.1016/j.cell.2012.01.056</a></li>
<li>Imoukhuede, P. I.; Moss, Fraser J.; et al. (2009) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20090903-090332845">Ezrin
Mediates Tethering of the γ-Aminobutyric Acid Transporter GAT1 to Actin
Filaments Via a C-Terminal PDZ-Interacting Domain</a>; Biophysical
Journal; Vol. 96; No. 7; 2949-2960; PMCID PMC2711277; <a
href="https://doi.org/10.1016/j.bpj.2008.11.070">10.1016/j.bpj.2008.11.070</a></li>
<li>Hao, Shengli and Baltimore, David (2009) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20090413-083201541">The
stability of mRNA influences the temporal order of the induction of
genes encoding inflammatory molecules</a>; Nature Immunology; Vol. 10;
No. 3; 281-288; PMCID PMC2775040; <a
href="https://doi.org/10.1038/ni.1699">10.1038/ni.1699</a></li>
<li>Vikalo, Haris; Hassibi, Babak; et al. (2008) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20090916-153943053">Modeling
and Estimation for Real-Time Microarrays</a>; IEEE Journal of Selected
Topics in Signal Processing; Vol. 2; No. 3; 286-296; <a
href="https://doi.org/10.1109/JSTSP.2008.924383">10.1109/JSTSP.2008.924383</a></li>
<li>O’Connell, Ryan M.; Rao, Dinesh S.; et al. (2008) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:OCOjem08">Sustained
expression of microRNA-155 in hematopoietic stem cells causes a
myeloproliferative disorder</a>; Journal of Experimental Medicine; Vol.
205; No. 3; 585-594; PMCID PMC2275382; <a
href="https://doi.org/10.1084/jem.20072108">10.1084/jem.20072108</a></li>
<li>Kannangara, Rubini; Branigan, Caroline; et al. (2007) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:20170408-172815604">The
Transcription Factor WIN1/SHN1 Regulates Cutin Biosynthesis in
Arabidopsis thaliana</a>; Plant Cell; Vol. 19; No. 4; 1278-1294; PMCID
PMC1913754; <a
href="https://doi.org/10.1105/tpc.106.047076">10.1105/tpc.106.047076</a></li>
<li>O’Connell, Ryan M.; Taganov, Konstantin D.; et al. (2007) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:OCOpnas07">MicroRNA-155
is induced during the macrophage inflammatory response</a>; Proceedings
of the National Academy of Sciences of the United States of America;
Vol. 105; No. 5; 1604-1609; PMCID PMC1780072; <a
href="https://doi.org/10.1073/pnas.0610731104">10.1073/pnas.0610731104</a></li>
<li>Taganov, Konstantin D.; Boldin, Mark P.; et al. (2006) <a
href="https://resolver.caltech.edu/CaltechAUTHORS:TAGpnas06">NF-{kappa}B-dependent
induction of microRNA miR-146, an inhibitor targeted to signaling
proteins of innate immune responses</a>; Proceedings of the National
Academy of Sciences of the United States of America; Vol. 103; No. 33;
12481-12486; PMCID PMC1567904; <a
href="https://doi.org/10.1073/pnas.0605298103">10.1073/pnas.0605298103</a></li>
</ul>