Publications for All Faculty

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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
Hsu CT, Yuan YH, Lin YC, Lin S, Cheng QW, Wu FH, Sheen J, Shih MC, Lin CS

Efficient and Economical Targeted Insertion in Plant Genomes via Protoplast Regeneration.

CRISPR J. 2021;4(5):752-760 - PMID: 34569819 - PMCID: PMC9639242 - DOI: 10.1089/crispr.2021.0045
Charlesworth AG, Seroussi U, Lehrbach NJ, Renaud MS, Sundby AE, Molnar RI, Lao RX, Willis AR, Woock JR, Aber MJ, Diao AJ, Reinke AW, Ruvkun G, Claycomb JM

Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility.

Nucleic Acids Res. 2021;49(15):8836-8865 - PMID: 34329465 - PMCID: PMC8421154 - DOI: 10.1093/nar/gkab619
Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N

Spatially organized multicellular immune hubs in human colorectal cancer.

Cell. 2021;184(18):4734-4752.e20 - PMID: 34450029 - PMCID: PMC8772395 - DOI: 10.1016/j.cell.2021.08.003
Subramanian S, Xavier RJ

Tuning in to inflammation: A path forward for precise and efficacious microbiome medicines?

Med (N Y). 2021;2(8):892-894 - PMID: 35590164 - DOI: 10.1016/j.medj.2021.07.006
Stražar M, Temba GS, Vlamakis H, Kullaya VI, Lyamuya F, Mmbaga BT, Joosten LAB, van der Ven AJAM, Netea MG, de Mast Q, Xavier RJ

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations.

Nat Commun. 2021;12(1):4845 - PMID: 34381036 - PMCID: PMC8357928 - DOI: 10.1038/s41467-021-25213-2
Brown EM, Arellano-Santoyo H, Temple ER, Costliow ZA, Pichaud M, Hall AB, Liu K, Durney MA, Gu X, Plichta DR, Clish CA, Porter JA, Vlamakis H, Xavier RJ

Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.

Cell Host Microbe. 2021;29(9):1351-1365.e11 - PMID: 34403684 - PMCID: PMC8429246 - DOI: 10.1016/j.chom.2021.07.011
Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK

Augmenting and directing long-range CRISPR-mediated activation in human cells.

Nat Methods. 2021;18(9):1075-1081 - PMID: 34354266 - PMCID: PMC8446310 - DOI: 10.1038/s41592-021-01224-1
Li L, Liu KH, Sheen J

Dynamic Nutrient Signaling Networks in Plants.

Annu Rev Cell Dev Biol. 2021;37:341-367 - PMID: 34351784 - PMCID: PMC8497281 - DOI: 10.1146/annurev-cellbio-010521-015047
Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S, Skelly AN, Okamura Y, Vlamakis H, Li Y, Tanoue T, Takei H, Nittono H, Narushima S, Irie J, Itoh H, Moriya K, Sugiura Y, Suematsu M, Moritoki N, Shibata S, Littman DR, Fischbach MA, Uwamino Y, Inoue T, Honda A, Hattori M, Murai T, Xavier RJ, Hirose N, Honda K

Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians.

Nature. 2021;599(7885):458-464 - PMID: 34325466 - DOI: 10.1038/s41586-021-03832-5
Liu K, Kong L, Graham DB, Carey KL, Xavier RJ

SAC1 regulates autophagosomal phosphatidylinositol-4-phosphate for xenophagy-directed bacterial clearance

Cell Reports. 2021;36(4):109434 - PMID: 34320354 - PMCID: PMC8327279 - DOI: https://doi.org/10.1016/j.celrep.2021.109434
Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease.

Cell Host Microbe. 2021;29(8):1294-1304.e4 - PMID: 34297922 - PMCID: PMC8366279 - DOI: 10.1016/j.chom.2021.06.019
Vadaq N, Schirmer M, Tunjungputri RN, Vlamakis H, Chiriac C, Ardiansyah E, Gasem MH, Joosten L, de Groot PG, Xavier RJ, Netea MG, van der Ven AJAM, de Mast Q

Untargeted plasma metabolome and gut microbiome profiling provide novel insights in the regulation of platelet reactivity in healthy individuals.

Thromb Haemost. 2021;122(4):529-539 - PMID: 34192775 - DOI: 10.1055/a-1541-3706
Xie L, McKenzie CI, Qu X, Mu Y, Wang Q, Bing N, Naidoo K, Alam MJ, Yu D, Gong F, Ang C, Robert R, Marques FZ, Furlotte N, Hinds D, Gasser O, 23andMe Research Team, Xavier RJ, Mackay CR

pH and Proton Sensor GPR65 Determine Susceptibility to Atopic Dermatitis.

J Immunol. 2021;207(1):101-109 - PMID: 34135065 - PMCID: PMC8674371 - DOI: 10.4049/jimmunol.2001363
Arnett A, Moo KG, Flynn KJ, Sundberg TB, Johannessen L, Shamji AF, Gray NS, Decker T, Zheng Y, Gersuk VH, Rahman ZS, Levy DE, Marié IJ, Linsley PS, Xavier RJ, Khor B

The CDK8 inhibitor DCA promotes a tolerogenic chemical immunophenotype in CD4+ T cells via a novel CDK8-GATA3-FOXP3 pathway.

Mol Cell Biol. 2021;41(9):e0008521 - PMID: 34124936 - PMCID: PMC8384069 - DOI: 10.1128/MCB.00085-21
Gligorijević V, Renfrew PD, Kosciolek T, Leman JK, Berenberg D, Vatanen T, Chandler C, Taylor BC, Fisk IM, Vlamakis H, Xavier RJ, Knight R, Cho K, Bonneau R

Structure-based protein function prediction using graph convolutional networks.

Nat Commun. 2021;12(1):3168 - PMID: 34039967 - PMCID: PMC8155034 - DOI: 10.1038/s41467-021-23303-9
Xavier RJ

Translating the human microbiome: a path to improving health.

Genome Med. 2021;13(1):78 - PMID: 33952319 - PMCID: PMC8097784 - DOI: 10.1186/s13073-021-00896-w
Total: 2473