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Lee H, Jun YS, Cha OK, Sheen J

Mitogen-activated protein kinases MPK3 and MPK6 are required for stem cell maintenance in the Arabidopsis shoot apical meristem.
Plant Cell Rep. 2019;38(3):311-319 - PMID: 30552452 - PMCID: PMC6573032 - DOI: 10.1007/s00299-018-2367-5

Haberman Y, Schirmer M, Dexheimer PJ, Karns R, Braun T, Kim MO, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Crandall WV, Mack DR, Griffiths AM, Heyman MB, Baker SS, Kellermayer R, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva-Hemker M, Ziring D, Kirschner BS, Keljo DJ, Guthery SL, Cohen SA, Snapper S, Evans J, Dubinsky M, Aronow B, Hyams JS, Kugathasan S, Huttenhower C, Xavier RJ, Denson LA

Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis.
Mucosal Immunol. 2019;12(2):491-502 - PMID: 30542108 - PMCID: PMC6375755 - DOI: 10.1038/s41385-018-0114-4

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ

Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Nat Microbiol. 2019;4(2):293-305 - PMID: 30531976 - PMCID: PMC6342642 - DOI: 10.1038/s41564-018-0306-4

Kim SC, O'Flaherty DK, Zhou L, Lelyveld VS, Szostak JW

Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA.
Proc Natl Acad Sci U S A. 2018;115(52):13318-13323 - PMID: 30509978 - PMCID: PMC6310819 - DOI: 10.1073/pnas.1814367115

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.
Nat Methods. 2018;15(12):992-993 - PMID: 30504875 - PMCID: PMC6620603 - DOI: 10.1038/s41592-018-0225-6

Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.
Sci Transl Med. 2018;10(472):ePub - PMID: 30567928 - DOI: 10.1126/scitranslmed.aap8914

Chen GH, Liu MJ, Xiong Y, Sheen J, Wu SH

TOR and RPS6 transmit light signals to enhance protein translation in deetiolating Arabidopsis seedlings.
Proc Natl Acad Sci U S A. 2018;115(50):12823-12828 - PMID: 30482859 - PMCID: PMC6294885 - DOI: 10.1073/pnas.1809526115

Tan JMJ, Mellouk N, Osborne SE, Ammendolia DA, Dyer DN, Li R, Brunen D, van Rijn JM, Huang J, Czuczman MA, Cemma MA, Won AM, Yip CM, Xavier RJ, MacDuff DA, Reggiori F, Debnath J, Yoshimori T, Kim PK, Fairn GD, Coyaud E, Raught B, Muise AM, Higgins DE, Brumell JH

An ATG16L1-dependent pathway promotes plasma membrane repair and limits Listeria monocytogenes cell-to-cell spread.
Nat Microbiol. 2018;3(12):1472-1485 - PMID: 30478389 - DOI: 10.1038/s41564-018-0293-5

Uniken Venema WT, Voskuil MD, Vich Vila A, van der Vries G, Jansen BH, Jabri B, Faber KN, Dijkstra G, Xavier RJ, Wijmenga C, Graham DB, Weersma RK, Festen EA

Single-cell RNA Sequencing of Blood and Ileal T cells From Patients With Crohn's Disease Reveals Tissue-specific Characteristics and Drug Targets.
Gastroenterology. 2019;156(3):812-815.e22 - PMID: 30391472 - PMCID: PMC6759855 - DOI: 10.1053/j.gastro.2018.10.046

Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.
Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008

Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.
Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008

Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF

Temporal development of the gut microbiome in early childhood from the TEDDY study.
Nature. 2018;562(7728):583-588 - PMID: 30356187 - PMCID: PMC6415775 - DOI: 10.1038/s41586-018-0617-x

Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.
Nature. 2018;562(7728):589-594 - PMID: 30356183 - PMCID: PMC6296767 - DOI: 10.1038/s41586-018-0620-2

Lin XX, Sen I, Janssens GE, Zhou X, Fonslow BR, Edgar D, Stroustrup N, Swoboda P, Yates JR, Ruvkun G, Riedel CG

DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity.
Nat Commun. 2018;9(1):4400 - PMID: 30353013 - PMCID: PMC6199276 - DOI: 10.1038/s41467-018-06624-0

Graham DB, Luo C, O'Connell DJ, Lefkovith A, Brown EM, Yassour M, Varma M, Abelin JG, Conway KL, Jasso GJ, Matar CG, Carr SA, Xavier RJ

Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes.
Nat Med. 2018;24(11):1762-1772 - PMID: 30349087 - PMCID: PMC6312190 - DOI: 10.1038/s41591-018-0203-7

Wang C, Bauckman KA, Ross ASB, Symington JW, Ligon MM, Scholtes G, Kumar A, Chang HW, Twentyman J, Fashemi BE, Xavier RJ, Mysorekar IU

A non-canonical autophagy-dependent role of the ATG16L1T300A variant in urothelial vesicular trafficking and uropathogenic Escherichia coli persistence.
Autophagy. 2019;15(3):527-542 - PMID: 30335568 - PMCID: PMC6351132 - DOI: 10.1080/15548627.2018.1535290

Jin L, Engelhart AE, Zhang W, Adamala KP, Szostak JW

Catalysis of Template-directed Nonenzymatic RNA Copying by Iron (II).
J Am Chem Soc. 2018;140(44):15016-15021 - PMID: 30335371 - PMCID: PMC7547886 - DOI: 10.1021/jacs.8b09617

Dong D, Zhou H, Na SY, Niedra R, Peng Y, Wang H, Seed B, Zhou GL

GPR108, an NF-κB activator suppressed by TIRAP, negatively regulates TLR-triggered immune responses.
PLoS One. 2018;13(10):e0205303 - PMID: 30332431 - PMCID: PMC6192633 - DOI: 10.1371/journal.pone.0205303

Tillman EJ, Richardson CE, Cattie DJ, Reddy KC, Lehrbach NJ, Droste R, Ruvkun G, Kim DH

Endoplasmic Reticulum Homeostasis Is Modulated by the Forkhead Transcription Factor FKH-9 During Infection of Caenorhabditis elegans.
Genetics. 2018;210(4):1329-1337 - PMID: 30287474 - PMCID: PMC6283152 - DOI: 10.1534/genetics.118.301450

Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.
Cell Host Microbe. 2018;24(4):600-610.e4 - PMID: 30308161 - PMCID: PMC6277984 - DOI: 10.1016/j.chom.2018.09.009

Fang C, Lee KK, Nietupski R, Bates RH, Fernandez-Menendez R, Lopez-Roman EM, Guijarro-Lopez L, Yin Y, Peng Z, Gomez JE, Fisher S, Barros-Aguirre D, Hubbard BK, Serrano-Wu MH, Hung DT

Discovery of heterocyclic replacements for the coumarin core of anti-tubercular FadD32 inhibitors.
Bioorg Med Chem Lett. 2018;28(22):3529-3533 - PMID: 30316633 - PMCID: PMC6233306 - DOI: 10.1016/j.bmcl.2018.09.037

Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK

In vivo CRISPR editing with no detectable genome-wide off-target mutations.
Nature. 2018;561(7723):416-419 - PMID: 30209390 - PMCID: PMC6194229 - DOI: 10.1038/s41586-018-0500-9

Ausubel FM

Tracing My Roots: How I Became a Plant Biologist.
Annu Rev Genet. 2018;52:1-20 - PMID: 30192637 - DOI: 10.1146/annurev-genet-120417-031722

Joyce GF, Szostak JW

Protocells and RNA Self-Replication.
Cold Spring Harb Perspect Biol. 2018;10(9):ePub - PMID: 30181195 - PMCID: PMC6120706 - DOI: 10.1101/cshperspect.a034801

Wein MN, Foretz M, Fisher DE, Xavier RJ, Kronenberg HM

Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential.
Trends Endocrinol Metab. 2018;29(10):723-735 - PMID: 30150136 - PMCID: PMC6151151 - DOI: 10.1016/j.tem.2018.08.004
Total: 2481