Publications for All Faculty

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Pawlak M, DeTomaso D, Schnell A, Meyer Zu Horste G, Lee Y, Nyman J, Dionne D, Regan BML, Singh V, Delorey T, Schramm MA, Wang C, Wallrapp A, Burkett PR, Riesenfeld SJ, Anderson AC, Regev A, Xavier RJ, Yosef N, Kuchroo VK

Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling.
Immunity. 2022;55(9):1663-1679.e6 - PMID: 36070768 - PMCID: PMC9808605 - DOI: 10.1016/j.immuni.2022.08.007

Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O'Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J, Belgium IBD Consortium, Cedars-Sinai IBD, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, NIHR IBD BioResource, Regeneron Genetics Center, SHARE Consortium, SPARC IBD Network, UK IBD Genetics Consortium, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility.
Nat Genet. 2022;54(9):1275-1283 - PMID: 36038634 - PMCID: PMC9700438 - DOI: 10.1038/s41588-022-01156-2

Chou CH, Mohanty S, Kang HA, Kong L, Avila-Pacheco J, Joshi SR, Ueda I, Devine L, Raddassi K, Pierce K, Jeanfavre S, Bullock K, Meng H, Clish C, Santori FR, Shaw AC, Xavier RJ

Metabolomic and transcriptomic signatures of influenza vaccine response in healthy young and older adults.
Aging Cell. 2022;21(9):e13682 - PMID: 35996998 - PMCID: PMC9470889 - DOI: 10.1111/acel.13682

Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F

Prokaryotic innate immunity through pattern recognition of conserved viral proteins.
Science. 2022;377(6607):eabm4096 - PMID: 35951700 - PMCID: PMC10028730 - DOI: 10.1126/science.abm4096

Xue H, Meng J, Lei P, Cao Y, An X, Jia M, Li Y, Liu H, Sheen J, Liu X, Yu F

ARF2-PIF5 interaction controls transcriptional reprogramming in the ABS3-mediated plant senescence pathway.
EMBO J. 2022;41(19):e110988 - PMID: 35942625 - PMCID: PMC9531305 - DOI: 10.15252/embj.2022110988

Ruvkun G, Lehrbach N

Regulation and Functions of the ER-Associated Nrf1 Transcription Factor.
Cold Spring Harb Perspect Biol. 2022;15(1):ePub - PMID: 35940907 - PMCID: PMC9808582 - DOI: 10.1101/cshperspect.a041266

Bae M, Cassilly CD, Liu X, Park SM, Tusi BK, Chen X, Kwon J, Filipčík P, Bolze AS, Liu Z, Vlamakis H, Graham DB, Buhrlage SJ, Xavier RJ, Clardy J

Akkermansia muciniphila phospholipid induces homeostatic immune responses.
Nature. 2022;608(7921):168-173 - PMID: 35896748 - PMCID: PMC9328018 - DOI: 10.1038/s41586-022-04985-7

Wu LF, Liu Z, Roberts SJ, Su M, Szostak JW, Sutherland JD

Template-Free Assembly of Functional RNAs by Loop-Closing Ligation.
J Am Chem Soc. 2022;144(30):13920-13927 - PMID: 35880790 - PMCID: PMC9354263 - DOI: 10.1021/jacs.2c05601

Meng Y, Zhang N, Li J, Shen X, Sheen J, Xiong Y

TOR kinase, a GPS in the complex nutrient and hormonal signaling networks to guide plant growth and development.
J Exp Bot. 2022;73(20):7041-7054 - PMID: 35781569 - PMCID: PMC9664236 - DOI: 10.1093/jxb/erac282

Chen X, Jaiswal A, Costliow Z, Herbst P, Creasey EA, Oshiro-Rapley N, Daly MJ, Carey KL, Graham DB, Xavier RJ

pH sensing controls tissue inflammation by modulating cellular metabolism and endo-lysosomal function of immune cells.
Nat Immunol. 2022;23(7):1063-1075 - PMID: 35668320 - PMCID: PMC9720675 - DOI: 10.1038/s41590-022-01231-0

Brunkard JO, Chang C, Mayer BJ, Meyer C, Sheen J

ConducTORs of a Signaling Symphony: Metabolic and Hormone Responses Converge on TOR and EIN2 in plants.
Fac Rev. 2022;11:12 - PMID: 35719129 - PMCID: PMC9190210 - DOI: 10.12703/r-01-000008

Warrier T, Romano KP, Clatworthy AE, Hung DT

Integrated genomics and chemical biology herald an era of sophisticated antibacterial discovery, from defining essential genes to target elucidation.
Cell Chem Biol. 2022;29(5):716-729 - PMID: 35523184 - PMCID: PMC9893512 - DOI: 10.1016/j.chembiol.2022.04.006

Zhang SJ, Duzdevich D, Ding D, Szostak JW

Freeze-thaw cycles enable a prebiotically plausible and continuous pathway from nucleotide activation to nonenzymatic RNA copying.
Proc Natl Acad Sci U S A. 2022;119(17):e2116429119 - PMID: 35446612 - PMCID: PMC9169909 - DOI: 10.1073/pnas.2116429119

Thakku SG, Ackerman CM, Myhrvold C, Bhattacharyya RP, Livny J, Ma P, Gomez GI, Sabeti PC, Blainey PC, Hung DT

Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays.
PNAS Nexus. 2022;1(1):pgac021 - PMID: 35450424 - PMCID: PMC9013781 - DOI: 10.1093/pnasnexus/pgac021

Snoozy J, Breen PC, Ruvkun G, Warnhoff K

moc-6/MOCS2A is necessary for molybdenum cofactor synthesis in C. elegans.
MicroPubl Biol. 2022;2022:ePub - PMID: 35224462 - PMCID: PMC8864482 - DOI: 10.17912/micropub.biology.000531

Radakovic A, DasGupta S, Wright TH, Aitken HRM, Szostak JW

Nonenzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides.
Proc Natl Acad Sci U S A. 2022;119(7):ePub - PMID: 35140183 - PMCID: PMC8851484 - DOI: 10.1073/pnas.2116840119

Johannes F. Scheid, Basak Eraslan, Andrew Hudak, Eric Brown, Dallis Sergio, Toni Delorey, Devan Phillips, Ariel Lefkovith, Alison T. Jess, Lennard W. Duck, Charles O. Elson, Hera Vlamakis, Jacques Deguine, Ashwin Ananthakrishnan, Daniel B. Graham, Aviv Regev, Ramnik J. Xavier

Remodeling of human colon plasma cell repertoire in ulcerative colitis
bioRxiv. 2022;:ePub - DOI: https://doi.org/10.1101/2022.02.14.480403

Szamosvári D, Bae M, Bang S, Tusi BK, Cassilly CD, Park SM, Graham DB, Xavier RJ, Clardy J

Lyme Disease, Borrelia burgdorferi, and Lipid Immunogens.
J Am Chem Soc. 2022;144(6):2474-2478 - PMID: 35129341 - DOI: 10.1021/jacs.1c12202

Szamosvári D, Bae M, Bang S, Tusi BK, Cassilly CD, Park SM, Graham DB, Xavier RJ, Clardy J

Lyme Disease, Borrelia burgdorferi, and Lipid Immunogens.
J Am Chem Soc. 2022;144(6):2474-2478 - PMID: 35129341 - DOI: 10.1021/jacs.1c12202

Lin CS, Hsu CT, Yuan YH, Zheng PX, Wu FH, Cheng QW, Wu YL, Wu TL, Lin S, Yue JJ, Cheng YH, Lin SI, Shih MC, Sheen J, Lin YC

DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration.
Plant Physiol. 2022;188(4):1917-1930 - PMID: 35088855 - PMCID: PMC8968427 - DOI: 10.1093/plphys/kiac022

Jasso GJ, Jaiswal A, Varma M, Laszewski T, Grauel A, Omar A, Silva N, Dranoff G, Porter JA, Mansfield K, Cremasco V, Regev A, Xavier RJ, Graham DB

Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing.
PLoS Biol. 2022;20(1):e3001532 - PMID: 35085231 - PMCID: PMC8824371 - DOI: 10.1371/journal.pbio.3001532

Jasso GJ, Jaiswal A, Varma M, Laszewski T, Grauel A, Omar A, Silva N, Dranoff G, Porter JA, Mansfield K, Cremasco V, Regev A, Xavier RJ, Graham DB

Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing.
PLoS Biol. 2022;20(1):e3001532 - PMID: 35085231 - PMCID: PMC8824371 - DOI: 10.1371/journal.pbio.3001532

Jiang W, Bush J, Sheen J

A Versatile and Efficient Plant Protoplast Platform for Genome Editing by Cas9 RNPs.
Front Genome Ed. 2021;3:719190 - PMID: 35005700 - PMCID: PMC8729822 - DOI: 10.3389/fgeed.2021.719190

Walker RL, Vlamakis H, Lee JWJ, Besse LA, Xanthakis V, Vasan RS, Shaw SY, Xavier RJ

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease.
Genome Med. 2021;13(1):188 - PMID: 34915914 - PMCID: PMC8680346 - DOI: 10.1186/s13073-021-01007-5

Ding D, Zhou L, Giurgiu C, Szostak JW

Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates.
Nucleic Acids Res. 2022;50(1):35-45 - PMID: 34893864 - PMCID: PMC8754633 - DOI: 10.1093/nar/gkab1202
Total: 2498