Publications for All Faculty

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Ding J, Garber JJ, Uchida A, Lefkovith A, Carter GT, Vimalathas P, Canha L, Dougan M, Staller K, Yarze J, Delorey TM, Rozenblatt-Rosen O, Ashenberg O, Graham DB, Deguine J, Regev A, Xavier RJ

An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission.
Nat Commun. 2024;15(1):3344 - PMID: 38637492 - PMCID: PMC11026436 - DOI: 10.1038/s41467-024-47647-0

Fang Z, Pazienza LT, Zhang J, Tam CP, Szostak JW

Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.
J Am Chem Soc. 2024;146(15):10632-10639 - PMID: 38579124 - PMCID: PMC11027144 - DOI: 10.1021/jacs.4c00323

Li C, Stražar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.
Cell. 2024;187(8):1834-1852.e19 - PMID: 38569543 - PMCID: PMC11071153 - DOI: 10.1016/j.cell.2024.03.014

Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas A, Fitzgerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT

"Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS".
bioRxiv. 2024;:ePub - PMID: 38559044 - PMCID: PMC10980007 - DOI: 10.1101/2024.03.16.585348

Brandt M, Cao Z, Krishna C, Reedy JL, Gu X, Dutko RA, Oliver BA, Tusi BK, Park J, Richey L, Segerstolpe Å, Litwiler S, Creasey EA, Carey KL, Vyas JM, Graham DB, Xavier RJ

Translational genetics identifies a phosphorylation switch in CARD9 required for innate inflammatory responses.
Cell Rep. 2024;43(3):113944 - PMID: 38489265 - PMCID: PMC11008285 - DOI: 10.1016/j.celrep.2024.113944

Radakovic A, Lewicka A, Todisco M, Aitken HRM, Weiss Z, Kim S, Bannan A, Piccirilli JA, Szostak JW

Structure-guided aminoacylation and assembly of chimeric RNAs.
bioRxiv. 2024;:ePub - PMID: 38464152 - PMCID: PMC10925264 - DOI: 10.1101/2024.03.02.583109

Pust MM, Rocha Castellanos DM, Rzasa K, Dame A, Pishchany G, Assawasirisin C, Liss A, Fernandez-Del Castillo C, Xavier RJ

Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm.
Gut. 2024;73(7):1131-1141 - PMID: 38429112 - PMCID: PMC11187374 - DOI: 10.1136/gutjnl-2023-331012

Warnhoff K, Bhattacharya S, Snoozy J, Breen PC, Ruvkun G

Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans
Elife. 2024;12:ePub - PMID: 38349720 - PMCID: PMC10942545 - DOI: 10.7554/eLife.89173

Todisco M, Ding D, Szostak JW

Transient states during the annealing of mismatched and bulged oligonucleotides.
Nucleic Acids Res. 2024;52(5):2174-2187 - PMID: 38348869 - PMCID: PMC10954449 - DOI: 10.1093/nar/gkae091

Neo DM, Clatworthy AE, Hung DT

A dual-plasmid CRISPR/Cas9-based method for rapid and efficient genetic disruption in Mycobacterium abscessus.
J Bacteriol. 2024;206(3):e0033523 - PMID: 38319218 - PMCID: PMC10955840 - DOI: 10.1128/jb.00335-23

Freeman MW, Halvorsen YD, Bond M, Murphy B, Isaacsohn J

Results from a Phase 1 Study Assessing the Pharmacokinetics of the Aldosterone Synthase Inhibitor Baxdrostat in Participants with Varying Degrees of Renal Function.
Clin Pharmacol Drug Dev. 2024;13(4):410-418 - PMID: 38311833 - DOI: 10.1002/cpdd.1371

Ding D, Fang Z, Kim SC, O'Flaherty DK, Jia X, Stone TB, Zhou L, Szostak JW

Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying.
J Am Chem Soc. 2024;146(6):3861-3871 - PMID: 38293747 - PMCID: PMC10870715 - DOI: 10.1021/jacs.3c11158

Sturm A, Sun P, Avila-Pacheco J, Clatworthy AE, Bloom-Ackermann Z, Wuo MG, Gomez JE, Jin S, Clish CB, Kiessling LL, Hung DT

Genetic factors affecting storage and utilization of lipids during dormancy in Mycobacterium tuberculosis.
MBio. 2024;15(2):e0320823 - PMID: 38236034 - PMCID: PMC10865790 - DOI: 10.1128/mbio.03208-23

Sella Y, Broderick NA, Stouffer KM, McEwan DL, Ausubel FM, Casadevall A, Bergman A

Preliminary evidence for chaotic signatures in host-microbe interactions.
mSystems. 2024;9(2):e0111023 - PMID: 38197647 - PMCID: PMC10878097 - DOI: 10.1128/msystems.01110-23

Sheen J

The new horizon of plant auxin signaling via cell-surface co-receptors.
Cell Res. 2024;34(5):343-344 - PMID: 38182889 - PMCID: PMC11061107 - DOI: 10.1038/s41422-023-00921-0

Meisel JD, Miranda M, Skinner OS, Wiesenthal PP, Wellner SM, Jourdain AA, Ruvkun G, Mootha VK

Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism.
Cell. 2024;187(3):659-675.e18 - PMID: 38215760 - PMCID: PMC10919891 - DOI: 10.1016/j.cell.2023.12.010

Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ

Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course.
Cell Host Microbe. 2024;32(2):209-226.e7 - PMID: 38215740 - PMCID: PMC10923022 - DOI: 10.1016/j.chom.2023.12.013

Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS, Lifelines Cohort Study, Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J

Host genetic regulation of human gut microbial structural variation.
Nature. 2024;625(7996):813-821 - PMID: 38172637 - PMCID: PMC10808065 - DOI: 10.1038/s41586-023-06893-w

Tellier J, Tarasova I, Nie J, Smillie CS, Fedele PL, Cao WHJ, Groom JR, Belz GT, Bhattacharya D, Smyth GK, Nutt SL

Unraveling the diversity and functions of tissue-resident plasma cells.
Nat Immunol. 2024;25(2):330-342 - PMID: 38172260 - DOI: 10.1038/s41590-023-01712-w

McMurray JJV, Solomon SD, Lock JP, Massaro JM, Zhu F, Zhou W, Skali H, Lewis EF, Freeman MW, Halvorsen YC

Meta-analysis of risk of major adverse cardiovascular events in adults with type 2 diabetes treated with bexagliflozin.
Diabetes Obes Metab. 2023;26(3):971-979 - PMID: 38151752 - DOI: 10.1111/dom.15394

Babbe H, Sundberg TB, Tichenor M, Seierstad M, Bacani G, Berstler J, Chai W, Chang L, Chung M, Coe K, Collins B, Finley M, Guletsky A, Lemke CT, Mak PA, Mathur A, Mercado-Marin EV, Metkar S, Raymond DD, Rives ML, Rizzolio M, Shaffer PL, Smith R, Smith J, Steele R, Steffens H, Suarez J, Tian G, Majewski N, Volak LP, Wei J, Desai PT, Ong LL, Koudriakova T, Goldberg SD, Hirst G, Kaushik VK, Ort T, Seth N, Graham DB, Plevy S, Venable JD, Xavier RJ, Towne JE

Identification of highly selective SIK1/2 inhibitors that modulate innate immune activation and suppress intestinal inflammation.
Proc Natl Acad Sci U S A. 2023;121(1):e2307086120 - PMID: 38147543 - PMCID: PMC10769863 - DOI: 10.1073/pnas.2307086120

Heo HY, Zou G, Baek S, Kim JS, Mylonakis E, Ausubel FM, Gao H, Kim W

A Methylazanediyl Bisacetamide Derivative Sensitizes Staphylococcus aureus Persisters to a Combination of Gentamicin And Daptomycin.
Adv Sci (Weinh). 2023;11(9):e2306112 - PMID: 38126676 - PMCID: PMC10916567 - DOI: 10.1002/advs.202306112

Kong L, Pokatayev V, Lefkovith A, Carter GT, Creasey EA, Krishna C, Subramanian S, Kochar B, Ashenberg O, Lau H, Ananthakrishnan AN, Graham DB, Deguine J, Xavier RJ

The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon.
Immunity. 2023;56(12):2855 - PMID: 38091954 - DOI: 10.1016/j.immuni.2023.10.017

Stražar M, Xavier RJ

Cytotoxic Th1 cells mushroom after fungal exposures in Crohn's disease.
Immunity. 2023;56(12):2679-2681 - PMID: 38091949 - DOI: 10.1016/j.immuni.2023.11.012

Gentry EC, Collins SL, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu HH, Zuffa S, Yan T, Avila-Pacheco J, Plichta DR, Aron AT, Wang M, Jarmusch AK, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland B, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish CB, Xavier RJ, Chu H, Baker ES, Patterson AD, Knight R, Siegel D, Dorrestein PC

Reverse metabolomics for the discovery of chemical structures from humans.
Nature. 2023;626(7998):419-426 - PMID: 38052229 - PMCID: PMC10849969 - DOI: 10.1038/s41586-023-06906-8
Total: 2498