Publications for All Faculty

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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
Total: 2498