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Vatanen T, Jabbar KS, Ruohtula T, Honkanen J, Avila-Pacheco J, Siljander H, Stražar M, Oikarinen S, Hyöty H, Ilonen J, Mitchell CM, Yassour M, Virtanen SM, Clish CB, Plichta DR, Vlamakis H, Knip M, Xavier RJ

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.
Cell. 2022;185(26):4921-4936.e15 - PMID: 36563663 - PMCID: PMC9869402 - DOI: 10.1016/j.cell.2022.11.023

Mao K, Breen P, Ruvkun G

The Caenorhabditis elegans ARIP-4 DNA helicase couples mitochondrial surveillance to immune, detoxification, and antiviral pathways.
Proc Natl Acad Sci U S A. 2022;119(49):e2215966119 - PMID: 36445965 - PMCID: PMC9894117 - DOI: 10.1073/pnas.2215966119

Freeman MW, Halvorsen YD, Marshall W, Pater M, Isaacsohn J, Pearce C, Murphy B, Alp N, Srivastava A, Bhatt DL, Brown MJ, BrigHTN Investigators

Phase 2 Trial of Baxdrostat for Treatment-Resistant Hypertension.
N Engl J Med. 2022;388(5):395-405 - PMID: 36342143 - DOI: 10.1056/NEJMoa2213169

Strecker J, Demircioglu FE, Li D, Faure G, Wilkinson ME, Gootenberg JS, Abudayyeh OO, Nishimasu H, Macrae RK, Zhang F

RNA-activated protein cleavage with a CRISPR-associated endopeptidase.
Science. 2022;378(6622):874-881 - PMID: 36423276 - PMCID: PMC10028731 - DOI: 10.1126/science.add7450

Vatanen T, Ang QY, Siegwald L, Sarker SA, Le Roy CI, Duboux S, Delannoy-Bruno O, Ngom-Bru C, Boulangé CL, Stražar M, Avila-Pacheco J, Deik A, Pierce K, Bullock K, Dennis C, Sultana S, Sayed S, Rahman M, Ahmed T, Modesto M, Mattarelli P, Clish CB, Vlamakis H, Plichta DR, Sakwinska O, Xavier RJ

A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning.
Cell. 2022;185(23):4280-4297.e12 - PMID: 36323316 - DOI: 10.1016/j.cell.2022.10.011

Peng V, Cao S, Trsan T, Bando JK, Avila-Pacheco J, Cleveland JL, Clish C, Xavier RJ, Colonna M

Ornithine decarboxylase supports ILC3 responses in infectious and autoimmune colitis through positive regulation of IL-22 transcription.
Proc Natl Acad Sci U S A. 2022;119(45):e2214900119 - PMID: 36279426 - PMCID: PMC9659397 - DOI: 10.1073/pnas.2214900119

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

Results from a phase 1, randomized, double-blind, multiple ascending dose study characterizing the pharmacokinetics and demonstrating the safety and selectivity of the aldosterone synthase inhibitor baxdrostat in healthy volunteers.
Hypertens Res. 2022;46(1):108-118 - PMID: 36266539 - PMCID: PMC9747611 - DOI: 10.1038/s41440-022-01070-4

Halvorsen YD, Lock JP, Frias JP, Tinahones FJ, Dahl D, Conery AL, Freeman MW

A 96-Week, Double-Blind, Randomized, Controlled Trial Comparing Bexagliflozin to Glimepiride as an Adjunct to Metformin for the Treatment of Type 2 Diabetes in Adults.
Diabetes Obes Metab. 2022;25(1):293-301 - PMID: 36178197 - DOI: 10.1111/dom.14875

Strom KR, Szostak JW

Folding and Duplex Formation in Sequence-Defined Aniline Benzaldehyde Oligoarylacetylenes.
J Am Chem Soc. 2022;144(40):18350-18358 - PMID: 36174969 - PMCID: PMC9562438 - DOI: 10.1021/jacs.2c06268

Jagadeesh KA, Dey KK, Montoro DT, Mohan R, Gazal S, Engreitz JM, Xavier RJ, Price AL, Regev A

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics.
Nat Genet. 2022;54(10):1479-1492 - PMID: 36175791 - PMCID: PMC9910198 - DOI: 10.1038/s41588-022-01187-9

Grünewald J, Miller BR, Szalay RN, Cabeceiras PK, Woodilla CJ, Holtz EJB, Petri K, Joung JK

Engineered CRISPR prime editors with compact, untethered reverse transcriptases.
Nat Biotechnol. 2022;41(3):337-343 - PMID: 36163548 - PMCID: PMC10023297 - DOI: 10.1038/s41587-022-01473-1

Rojas-Tapias DF, Brown EM, Temple ER, Onyekaba MA, Mohamed AMT, Duncan K, Schirmer M, Walker RL, Mayassi T, Pierce KA, Ávila-Pacheco J, Clish CB, Vlamakis H, Xavier RJ

Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine.
Nat Microbiol. 2022;7(10):1673-1685 - PMID: 36138166 - PMCID: PMC9728153 - DOI: 10.1038/s41564-022-01224-7

Liu KH, Liu M, Lin Z, Wang ZF, Chen B, Liu C, Guo A, Konishi M, Yanagisawa S, Wagner G, Sheen J

NIN-like protein 7 transcription factor is a plant nitrate sensor.
Science. 2022;377(6613):1419-1425 - PMID: 36137053 - PMCID: PMC9628810 - DOI: 10.1126/science.add1104

Ye R, Wang M, Du H, Chhajed S, Koh J, Liu KH, Shin J, Wu Y, Shi L, Xu L, Chen S, Zhang Y, Sheen J

Glucose-driven TOR-FIE-PRC2 signalling controls plant development.
Nature. 2022;609(7929):986-993 - PMID: 36104568 - PMCID: PMC9530021 - DOI: 10.1038/s41586-022-05171-5

Todisco M, Szostak JW

Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.
Nucleic Acids Res. 2022;50(17):9647-9662 - PMID: 36099434 - PMCID: PMC9508827 - DOI: 10.1093/nar/gkac784

Pedersen TK, Brown EM, Plichta DR, Johansen J, Twardus SW, Delorey TM, Lau H, Vlamakis H, Moon JJ, Xavier RJ, Graham DB

The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease.
Immunity. 2022;55(10):1909-1923.e6 - PMID: 36115338 - PMCID: PMC9890645 - DOI: 10.1016/j.immuni.2022.08.016

Li Y, Watanabe E, Kawashima Y, Plichta DR, Wang Z, Ujike M, Ang QY, Wu R, Furuichi M, Takeshita K, Yoshida K, Nishiyama K, Kearney SM, Suda W, Hattori M, Sasajima S, Matsunaga T, Zhang X, Watanabe K, Fujishiro J, Norman JM, Olle B, Matsuyama S, Namkoong H, Uwamino Y, Ishii M, Fukunaga K, Hasegawa N, Ohara O, Xavier RJ, Atarashi K, Honda K

Identification of trypsin-degrading commensals in the large intestine.
Nature. 2022;609(7927):582-589 - PMID: 36071157 - PMCID: PMC9477747 - DOI: 10.1038/s41586-022-05181-3

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

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

Poulsen BE, Clatworthy AE, Hung DT

The Use of Tn-Seq and the FiTnEss Analysis to Define the Core Essential Genome of Pseudomonas aeruginosa.
Methods Mol Biol. 2022;2377:179-197 - PMID: 34709617 - DOI: 10.1007/978-1-0716-1720-5_10
Total: 41