Publications for All Faculty

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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
Total: 2446