Publications for All Faculty

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Ast T, Meisel JD, Patra S, Wang H, Grange RMH, Kim SH, Calvo SE, Orefice LL, Nagashima F, Ichinose F, Zapol WM, Ruvkun G, Barondeau DP, Mootha VK

Hypoxia Rescues Frataxin Loss by Restoring Iron Sulfur Cluster Biogenesis.

Cell. 2019;177(6):1507-1521.e16 - PMID: 31031004 - PMCID: PMC6911770 - DOI: 10.1016/j.cell.2019.03.045
Tam JM, Reedy JL, Lukason DP, Kuna SG, Acharya M, Khan NS, Negoro PE, Xu S, Ward RA, Feldman MB, Dutko RA, Jeffery JB, Sokolovska A, Wivagg CN, Lassen KG, Le Naour F, Matzaraki V, Garner EC, Xavier RJ, Kumar V, van de Veerdonk FL, Netea MG, Miranti CK, Mansour MK, Vyas JM

Tetraspanin CD82 Organizes Dectin-1 into Signaling Domains to Mediate Cellular Responses to Candida albicans.

J Immunol. 2019;202(11):3256-3266 - PMID: 31010852 - PMCID: PMC6529278 - DOI: 10.4049/jimmunol.1801384
Grünewald J, Zhou R, Garcia SP, Iyer S, Lareau CA, Aryee MJ, Joung JK

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors.

Nature. 2019;569(7756):433-437 - PMID: 30995674 - PMCID: PMC6657343 - DOI: 10.1038/s41586-019-1161-z
Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ

Adaptive Evolution within Gut Microbiomes of Healthy People.

Cell Host Microbe. 2019;25(5):656-667.e8 - PMID: 31028005 - PMCID: PMC6749991 - DOI: 10.1016/j.chom.2019.03.007
Lehrbach NJ, Ruvkun G

Endoplasmic reticulum-associated SKN-1A/Nrf1 mediates a cytoplasmic unfolded protein response and promotes longevity.

Elife. 2019;8:ePub - PMID: 30973820 - PMCID: PMC6459674 - DOI: 10.7554/eLife.44425
Kurilshikov A, van den Munckhof IC, Chen L, Bonder MJ, Schraa K, Rutten J, Riksen NP, de Graaf J, Oosting M, Sanna S, Joosten LA, van der Graaf M, Brand T, Koonen DP, van Faassen MJ, Slagboom PE, Xavier RJ, Kuipers F, Hofker M, Wijmenga C, Netea MG, Zhernakova A, Fu J

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study.

Circ Res. 2019;124(12):1808-1820 - PMID: 30971183 - DOI: 10.1161/CIRCRESAHA.118.314642
Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ

Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Nat Microbiol. 2019;4(5):898 - PMID: 30971771 - DOI: 10.1038/s41564-019-0442-5
Lehrbach NJ, Breen PC, Ruvkun G

Protein Sequence Editing of SKN-1A/Nrf1 by Peptide:N-Glycanase Controls Proteasome Gene Expression.

Cell. 2019;177(3):737-750.e15 - PMID: 31002798 - PMCID: PMC6574124 - DOI: 10.1016/j.cell.2019.03.035
Brown EM, Kenny DJ, Xavier RJ

Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity.

Annu Rev Immunol. 2019;37:599-624 - PMID: 31026411 - DOI: 10.1146/annurev-immunol-042718-041841
Hyams JS, Davis Thomas S, Gotman N, Haberman Y, Karns R, Schirmer M, Mo A, Mack DR, Boyle B, Griffiths AM, LeLeiko NS, Sauer CG, Keljo DJ, Markowitz J, Baker SS, Rosh J, Baldassano RN, Patel A, Pfefferkorn M, Otley A, Heyman M, Noe J, Oliva-Hemker M, Rufo PA, Strople J, Ziring D, Guthery SL, Sudel B, Benkov K, Wali P, Moulton D, Evans J, Kappelman MD, Marquis MA, Sylvester FA, Collins MH, Venkateswaran S, Dubinsky M, Tangpricha V, Spada KL, Saul B, Wang J, Serrano J, Hommel K, Marigorta UM, Gibson G, Xavier RJ, Kugathasan S, Walters T, Denson LA

Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study.

Lancet. 2019;393(10182):1708-1720 - PMID: 30935734 - PMCID: PMC6501846 - DOI: 10.1016/S0140-6736(18)32592-3
Walton T, Zhang W, Li L, Tam CP, Szostak JW

The mechanism of nonenzymatic template copying with imidazole-activated nucleotides.

Angew Chem Int Ed Engl. 2019;58(32):10812-10819 - PMID: 30908802 - DOI: 10.1002/anie.201902050
Warnhoff K, Ruvkun G

Molybdenum cofactor transfer from bacteria to nematode mediates sulfite detoxification.

Nat Chem Biol. 2019;15(5):480-488 - PMID: 30911177 - PMCID: PMC6470025 - DOI: 10.1038/s41589-019-0249-y
Bhattacharyya RP, Walker M, Boykin R, Son SS, Liu J, Hachey AC, Ma P, Wu L, Choi K, Cummins KC, Benson M, Skerry J, Ryu H, Wong SY, Goldberg MB, Han J, Pierce VM, Cosimi LA, Shoresh N, Livny J, Beechem J, Hung DT

Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA.

Sci Rep. 2019;9(1):4516 - PMID: 30872641 - PMCID: PMC6418090 - DOI: 10.1038/s41598-019-40792-3
Strom KR, Szostak JW, Prywes N

Transfer of Sequence Information and Replication of Diimine Duplexes.

J Org Chem. 2019;84(7):3754-3761 - PMID: 30855962 - PMCID: PMC7547894 - DOI: 10.1021/acs.joc.9b00095
Wein MN, Foretz M, Fisher DE, Xavier RJ, Kronenberg HM

Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential: (Trends Endocrinol. Metab. 29, 723-735, 2018).

Trends Endocrinol Metab. 2019;30(6):407 - PMID: 30837108 - DOI: 10.1016/j.tem.2019.01.009
Lander ES, Baylis F, Zhang F, Charpentier E, Berg P, Bourgain C, Friedrich B, Joung JK, Li J, Liu D, Naldini L, Nie JB, Qiu R, Schoene-Seifert B, Shao F, Terry S, Wei W, Winnacker EL

Adopt a moratorium on heritable genome editing.

Nature. 2019;567(7747):165-168 - PMID: 30867611 - DOI: 10.1038/d41586-019-00726-5
Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L

CRISPResso2 provides accurate and rapid genome editing sequence analysis.

Nat Biotechnol. 2019;37(3):224-226 - PMID: 30809026 - PMCID: PMC6533916 - DOI: 10.1038/s41587-019-0032-3
Mao K, Ji F, Breen P, Sewell A, Han M, Sadreyev R, Ruvkun G

Mitochondrial Dysfunction in C. elegans Activates Mitochondrial Relocalization and Nuclear Hormone Receptor-Dependent Detoxification Genes.

Cell Metab. 2019;29(5):1182-1191.e4 - PMID: 30799287 - PMCID: PMC6506380 - DOI: 10.1016/j.cmet.2019.01.022
Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK

Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.

Nat Biotechnol. 2019;37(3):276-282 - PMID: 30742127 - PMCID: PMC6401248 - DOI: 10.1038/s41587-018-0011-0
Yudanin NA, Schmitz F, Flamar AL, Thome JJC, Tait Wojno E, Moeller JB, Schirmer M, Latorre IJ, Xavier RJ, Farber DL, Monticelli LA, Artis D

Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity.

Immunity. 2019;50(2):505-519.e4 - PMID: 30770247 - PMCID: PMC6594374 - DOI: 10.1016/j.immuni.2019.01.012
Kniazeva M, Ruvkun G

Rhizobium induces DNA damage in Caenorhabditis elegans intestinal cells.

Proc Natl Acad Sci U S A. 2019;116(9):3784-3792 - PMID: 30808764 - PMCID: PMC6397575 - DOI: 10.1073/pnas.1815656116
Wu Y, Shi L, Li L, Fu L, Liu Y, Xiong Y, Sheen J

Integration of nutrient, energy, light and hormone signalling via TOR in plants.

J Exp Bot. 2019;70(8):2227-2238 - PMID: 30715492 - PMCID: PMC6463029 - DOI: 10.1093/jxb/erz028
Collij V, Imhann F, Vich Vila A, Fu J, Dijkstra G, Festen EAM, Voskuil MD, Daly MJ, Xavier RJ, Wijmenga C, Zhernakova A, Weersma RK

SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects.

PLoS One. 2019;14(1):e0211328 - PMID: 30703110 - PMCID: PMC6354981 - DOI: 10.1371/journal.pone.0211328
Penaranda C, Hung DT

Single-Cell RNA Sequencing to Understand Host-Pathogen Interactions.

ACS Infect Dis. 2019;5(3):336-344 - PMID: 30702856 - DOI: 10.1021/acsinfecdis.8b00369
Matsushita-Ishiodori Y, Hanczyc MM, Wang A, Szostak JW, Yomo T

Using Imaging Flow Cytometry to Quantify and Optimize Giant Vesicle Production by Water-in-oil Emulsion Transfer Methods.

Langmuir. 2019;35(6):2375-2382 - PMID: 30645943 - DOI: 10.1021/acs.langmuir.8b03635
Total: 2467