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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

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

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

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

Li W, Liu J, Li Z, Ye R, Chen W, Huang Y, Yuan Y, Zhang Y, Hu H, Zheng P, Fang Z, Tao Z, Song S, Pan R, Zhang J, Tu J, Sheen J, Du H

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice.
Mol Plant. 2023;17(2):240-257 - PMID: 38053337 - PMCID: PMC11271712 - DOI: 10.1016/j.molp.2023.12.002

Fiskin E, Eraslan G, Alora-Palli MB, Leyva-Castillo JM, Kim S, Choe H, Lareau CA, Lau H, Finan EP, Teixeira-Soldano I, LaBere B, Chu A, Woods B, Chou J, Slyper M, Waldman J, Islam S, Schneider L, Phipatanakul W, Platt C, Rozenblatt-Rosen O, Delorey TM, Deguine J, Smith GP, Geha R, Regev A, Xavier RJ

Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis
bioRxiv. 2023;:ePub - DOI: 10.1101/2023.10.29.563503

Lelyveld VS, Fang Z, Szostak JW

Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity.
Science. 2023;382(6669):423-429 - PMID: 37883544 - PMCID: PMC10886449 - DOI: 10.1126/science.adh5339

Nakata T, Li C, Mayassi T, Lin H, Ghosh K, Segerstolpe Å, Diamond EL, Herbst P, Biancalani T, Gaddam S, Parkar S, Lu Z, Jaiswal A, Li B, Creasey EA, Lefkovith A, Daly MJ, Graham DB, Xavier RJ

Genetic vulnerability to Crohn's disease reveals a spatially resolved epithelial restitution program.
Sci Transl Med. 2023;15(719):eadg5252 - PMID: 37878672 - PMCID: PMC10798370 - DOI: 10.1126/scitranslmed.adg5252

Thurimella K, Mohamed AMT, Graham DB, Owens RM, Leanti La Rosa S, Plichta DR, Bacallado S, Xavier RJ

Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics
bioRxiv. 2023;:ePub - DOI: https://doi.org/10.1101/2023.10.23.563620

Shin YH, Bang S, Park SM, Ma X, Cassilly C, Graham D, Xavier R, Clardy J

Revisiting Coley's Toxins: Immunogenic Cardiolipins from Streptococcus pyogenes.
J Am Chem Soc. 2023;145(39):21183-21188 - PMID: 37738205 - PMCID: PMC10557101 - DOI: 10.1021/jacs.3c07727

Parada-Kusz M, Clatworthy AE, Goering ER, Blackwood SM, Salm EJ, Choi C, Combs S, Lee JSW, Rodriguez-Osorio C, Tomita S, Hung DT

A tryptophan metabolite modulates the host response to bacterial infection via kainate receptors.
bioRxiv. 2023;:ePub - PMID: 37645903 - PMCID: PMC10462041 - DOI: 10.1101/2023.08.16.553532

DasGupta S, Zhang S, Szostak JW

Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly.
ACS Cent Sci. 2023;9(8):1670-1678 - PMID: 37637737 - PMCID: PMC10451029 - DOI: 10.1021/acscentsci.3c00547

Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A

Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.
Biophys J. 2023;122(16):3323-3339 - PMID: 37469144 - PMCID: PMC10465710 - DOI: 10.1016/j.bpj.2023.07.009

Ye R, Lin Z, Liu KH, Sheen J, Chen S

Dynamic Proximity Tagging in Living Plant Cells with Pupylation-Based Interaction Tagging.
Methods Mol Biol. 2023;2690:137-147 - PMID: 37450145 - DOI: 10.1007/978-1-0716-3327-4_14

Aitken HRM, Wright TH, Radakovic A, Szostak JW

Small-Molecule Organocatalysis Facilitates In Situ Nucleotide Activation and RNA Copying.
J Am Chem Soc. 2023;145(29):16142-16149 - PMID: 37431761 - PMCID: PMC10375519 - DOI: 10.1021/jacs.3c04635

Halvorsen YD, Conery AL, Lock JP, Zhou W, Freeman MW

Bexagliflozin as an adjunct to metformin for the treatment of type 2 diabetes in adults: A 24-week, randomized, double-blind, placebo-controlled trial.
Diabetes Obes Metab. 2023;25(10):2954-2962 - PMID: 37409573 - DOI: 10.1111/dom.15192

Xu J, Kong L, Oliver BA, Li B, Creasey EA, Guzman G, Schenone M, Carey KL, Carr SA, Graham DB, Deguine J, Xavier RJ

Constitutively active autophagy in macrophages dampens inflammation through metabolic and post-transcriptional regulation of cytokine production.
Cell Rep. 2023;42(7):112708 - PMID: 37392388 - PMCID: PMC10503440 - DOI: 10.1016/j.celrep.2023.112708

Strazar M, Park J, Abelin JG, Taylor HB, Pedersen TK, Plichta DR, Brown EM, Eraslan B, Hung YM, Ortiz K, Clauser KR, Carr SA, Xavier RJ, Graham DB

HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.
Immunity. 2023;56(7):1681-1698.e13 - PMID: 37301199 - PMCID: PMC10519123 - DOI: 10.1016/j.immuni.2023.05.009

Zhang SJ, Lowe LA, Anees P, Krishnan Y, Fai TG, Szostak JW, Wang A

Passive endocytosis in model protocells.
Proc Natl Acad Sci U S A. 2023;120(24):e2221064120 - PMID: 37276401 - PMCID: PMC10268330 - DOI: 10.1073/pnas.2221064120

Ding D, Zhang SJ, Szostak JW

Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides.
Nucleic Acids Res. 2023;51(13):6528-6539 - PMID: 37247941 - PMCID: PMC10359593 - DOI: 10.1093/nar/gkad439

Kalam H, Chou CH, Kadoki M, Graham DB, Deguine J, Hung DT, Xavier RJ

Identification of host regulators of Mycobacterium tuberculosis phenotypes uncovers a role for the MMGT1-GPR156 lipid droplet axis in persistence.
Cell Host Microbe. 2023;31(6):978-992.e5 - PMID: 37269834 - PMCID: PMC10373099 - DOI: 10.1016/j.chom.2023.05.009

Fan Z, Deckel Y, Lowe LA, Loo DWK, Yomo T, Szostak JW, Nisler C, Wang A

Lipid Exchange Promotes Fusion of Model Protocells.
Small Methods. 2023;7(12):e2300126 - PMID: 37246261 - DOI: 10.1002/smtd.202300126

Graham DB, Xavier RJ

Conditioning of the immune system by the microbiome.
Trends Immunol. 2023;44(7):499-511 - PMID: 37236891 - DOI: 10.1016/j.it.2023.05.002

DasGupta S, Zhang SJ, Smela MP, Szostak JW

RNA-catalyzed RNA Ligation within Prebiotically Plausible Model Protocells.
Chemistry. 2023;29(43):e202301376 - PMID: 37216492 - DOI: 10.1002/chem.202301376

Johansen J, Atarashi K, Arai Y, Hirose N, Sørensen SJ, Vatanen T, Knip M, Honda K, Xavier RJ, Rasmussen S, Plichta DR

Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan.
Nat Microbiol. 2023;8(6):1064-1078 - PMID: 37188814 - DOI: 10.1038/s41564-023-01370-6

Warnhoff K, Snoozy J, Breen PC, Ruvkun G

Hypoxia-inducible factor promotes cysteine homeostasis in Caenorhabditis elegans.
bioRxiv. 2023;:ePub - PMID: 37205365 - PMCID: PMC10187278 - DOI: 10.1101/2023.05.04.538701

Zhang SJ, Lowe LA, Anees P, Krishnan Y, Fai TG, Szostak JW, Wang A

Passive endocytosis in model protocells.
bioRxiv. 2023;:ePub - PMID: 37205531 - PMCID: PMC10187163 - DOI: 10.1101/2023.01.07.522792

Lee JWJ, Plichta DR, Asher S, Delsignore M, Jeong T, McGoldrick J, Staller K, Khalili H, Xavier RJ, Chung DC

Association of distinct microbial signatures with premalignant colorectal adenomas.
Cell Host Microbe. 2023;31(5):827-838.e3 - PMID: 37130517 - PMCID: PMC10477964 - DOI: 10.1016/j.chom.2023.04.007

Thakku SG, Lirette J, Murugesan K, Chen J, Theron G, Banaei N, Blainey PC, Gomez J, Wong SY, Hung DT

Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13.
Nat Commun. 2023;14(1):1803 - PMID: 37002219 - PMCID: PMC10064635 - DOI: 10.1038/s41467-023-37183-8

Ding D, Zhou L, Mittal S, Szostak JW

Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication.
J Am Chem Soc. 2023;145(13):7504-7515 - PMID: 36963403 - PMCID: PMC10080680 - DOI: 10.1021/jacs.3c00612

Huang XW, Pan W, Zhong MZ, Chhonker YS, Steele AD, Keohane CE, Mishra B, Felix Raj Lucas LO, Murry DJ, Ausubel FM, Wuest WM, Li CX, Mylonakis E

Biological Evaluation of the Antibacterial Retinoid CD437 in Cutibacterium acnes Infection.
Antimicrob Agents Chemother. 2023;67(4):e0167922 - PMID: 36943064 - PMCID: PMC10112217 - DOI: 10.1128/aac.01679-22

Halvorsen SC, Benita Y, Hopton M, Hoppe B, Gunnlaugsson HO, Korgaonkar P, Vanderburg CR, Nielsen GP, Trepanowski N, Cheah JH, Frosch MP, Schwab JH, Rosenberg AE, Hornicek FJ, Sassi S

Transcriptional Profiling Supports the Notochordal Origin of Chordoma and Its Dependence on a TGFΒ1-TBXT Network.
Am J Pathol. 2023;193(5):532-547 - PMID: 36804377 - DOI: 10.1016/j.ajpath.2023.01.014

Freeman MW, Bond M, Murphy B, Hui J, Isaacsohn J

Results From a Randomized, Open-Label, Crossover Study Evaluating the Effect of the Aldosterone Synthase Inhibitor Baxdrostat on the Pharmacokinetics of Metformin in Healthy Human Subjects.
Am J Cardiovasc Drugs. 2023;23(3):277-286 - PMID: 36790596 - PMCID: PMC9930700 - DOI: 10.1007/s40256-023-00572-x

Brown EM, Clardy J, Xavier RJ

Gut microbiome lipid metabolism and its impact on host physiology.
Cell Host Microbe. 2023;31(2):173-186 - PMID: 36758518 - PMCID: PMC10124142 - DOI: 10.1016/j.chom.2023.01.009

Scheid JF, Eraslan B, Hudak A, Brown EM, Sergio D, Delorey TM, Phillips D, Lefkovith A, Jess AT, Duck LW, Elson CO, Vlamakis H, Plichta DR, Deguine J, Ananthakrishnan AN, Graham DB, Regev A, Xavier RJ

Remodeling of colon plasma cell repertoire within ulcerative colitis patients.
J Exp Med. 2023;220(4):ePub - PMID: 36752797 - PMCID: PMC9949229 - DOI: 10.1084/jem.20220538

Ma P, Amemiya HM, He LL, Gandhi SJ, Nicol R, Bhattacharyya RP, Smillie CS, Hung DT

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states.
Cell. 2023;186(4):877-891.e14 - PMID: 36708705 - PMCID: PMC10014032 - DOI: 10.1016/j.cell.2023.01.002

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(2):444-458.e5 - PMID: 36720220 - PMCID: PMC9957882 - DOI: 10.1016/j.immuni.2023.01.002
Total: 39