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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

Bonfiglio F, Liu X, Smillie C, Pandit A, Kurilshikov A, Bacigalupe R, Zheng T, Nim H, Garcia-Etxebarria K, Bujanda L, Andreasson A, Agreus L, Walter S, Abecasis G, Eijsbouts C, Jostins L, Parkes M, Hughes DA, Timpson N, Raes J, Franke A, Kennedy NA, Regev A, Zhernakova A, Simren M, Camilleri M, D'Amato M

GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome.
Cell Genom. 2021;1(3):None - PMID: 34957435 - PMCID: PMC8654685 - DOI: 10.1016/j.xgen.2021.100069

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

Carey KL, Liu K, Xavier RJ

Innate host defense mechanisms SAC bacteria by regulating phosphoinositide kinases and phosphatases.
Autophagy. 2021;18(2):452-454 - PMID: 34812102 - PMCID: PMC8942526 - DOI: 10.1080/15548627.2021.2002102

Kong L, Moorlag SJCFM, Lefkovith A, Li B, Matzaraki V, van Emst L, Kang HA, Latorre I, Jaeger M, Joosten LAB, Netea MG, Xavier RJ

Single-cell transcriptomic profiles reveal changes associated with BCG-induced trained immunity and protective effects in circulating monocytes.
Cell Rep. 2021;37(7):110028 - PMID: 34788625 - PMCID: PMC8728743 - DOI: 10.1016/j.celrep.2021.110028

Chrissy Bolton ∗
Christopher S. Smillie ∗
Sumeet Pandey ∗
Rasa Elmentaite
Gabrielle Wei
Carmen Argmann
Dominik Aschenbrenner
Kylie R. James
Dermot P.B. McGovern
Marina Macchi
Judy Cho
Dror S. Shouval
Jochen Kammermeier
Sibylle Koletzko
Krithika Bagalopal
Melania Capitani
Athena Cavounidis
Elisabete Pires
Carl Weidinger
James McCullagh
Peter D. Arkwright
Wolfram Haller
Britta Siegmund
Lauren Peters
Luke Jostins
Simon P.L. Travis
Carl A. Anderson
Scott Snapper
Christoph Klein
Eric Schadt
Matthias Zilbauer
Ramnik Xavier
Sarah Teichmann
Aleixo M. Muise
Aviv Regev
Holm H. Uhlig

An integrated taxonomy for monogenic inflammatory bowel disease
Gastroenterology. 2021;:ePub - DOI: https://doi.org/10.1053/j.gastro.2021.11.014

Bolton C, Smillie CS, Pandey S, Elmentaite R, Wei G, Argmann C, Aschenbrenner D, James KR, McGovern DPB, Macchi M, Cho J, Shouval DS, Kammermeier J, Koletzko S, Bagalopal K, Capitani M, Cavounidis A, Pires E, Weidinger C, McCullagh J, Arkwright PD, Haller W, Siegmund B, Peters L, Jostins L, Travis SPL, Anderson CA, Snapper S, Klein C, Schadt E, Zilbauer M, Xavier R, Teichmann S, Muise AM, Regev A, Uhlig HH

An integrated taxonomy for monogenic inflammatory bowel disease.
Gastroenterology. 2021;162(3):859-876 - PMID: 34780721 - PMCID: PMC7616885 - DOI: 10.1053/j.gastro.2021.11.014

Fiskin E, Lareau CA, Ludwig LS, Eraslan G, Liu F, Ring AM, Xavier RJ, Regev A

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
Nat Biotechnol. 2021;40(3):374-381 - PMID: 34675424 - PMCID: PMC10549956 - DOI: 10.1038/s41587-021-01065-5

Fiskin E, Lareau CA, Ludwig LS, Eraslan G, Liu F, Ring AM, Xavier RJ, Regev A

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
Nat Biotechnol. 2021;40(3):374-381 - PMID: 34675424 - PMCID: PMC10549956 - DOI: 10.1038/s41587-021-01065-5

Ke X, You K, Pichaud M, Haiser HJ, Graham DB, Vlamakis H, Porter JA, Xavier RJ

Gut bacterial metabolites modulate endoplasmic reticulum stress.
Genome Biol. 2021;22(1):292 - PMID: 34654459 - PMCID: PMC8518294 - DOI: 10.1186/s13059-021-02496-8
Total: 2489