http://mmjggl.caltech.edu/
- 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
- Chen, Peiwei and Aravin, Alexei A. (2023) Genetic
control of a sex-specific piRNA program; 10.1101/2022.10.25.513766
- Guna, Alina; Page, Katharine R.; et el. (2023) A
dual sgRNA library design to probe genetic modifiers using genome-wide
CRISPRi screens; PMCID PMC9882262; 10.1101/2023.01.22.525086
- 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; 10.1101/2023.01.12.523844
- 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
- Shin, Boyoung; Zhou, Wen; et el. (2022) Runx
factors launch T cell and innate lymphoid programs via direct and gene
network-based mechanisms; 10.1101/2022.11.18.517146
- 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
- Wang, Megan; Sanfiorenzo, Charles; et el. (2022) A
universal system for streamlined genome integrations with
CRISPR-associated transposases; 10.1101/2022.05.30.494051
- 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
- Tang, Weiyi; Jacobs-Li, Jessica; et el. (2022) Single-cell
profiling coupled with lineage analysis reveals distinct sacral neural
crest contributions to the developing enteric nervous system; 10.1101/2022.05.09.491197
- 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
- Inglis, Alison J.; Guna, Alina; et el. (2022) Coupled
protein quality control during nonsense mediated mRNA decay; 10.1101/2021.12.22.473893
- 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
- Dahlstrom, Kurt M. and Newman, Dianne K. (2021) Paraburkholderia
edwinii protects Aspergillus sp. from phenazines by acting as a toxin
sponge; 10.1101/2021.03.28.437412
- 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
- Khazaei, Tahmineh; Williams, Rory L.; et el. (2020) Metabolic
multi-stability and hysteresis in a model aerobe-anaerobe microbiome
community; 10.1101/2020.02.28.968941
- 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