Publications for All Faculty

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Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.
Nat Microbiol. 2020;5(3):486-497 - PMID: 31959971 - PMCID: PMC7047597 - DOI: 10.1038/s41564-019-0655-7

Brady KJS, Ni P, Grant GG, Thorpe CR, Nadler D, Lee A, Shapiro G, Kogosov A, Palmieri TL, Tompkins RG, Schneider JC, Kazis LE, Ryan CM

Translation and Cross-Cultural Validation of the English Young Adult Burn Outcome Questionnaire (YABOQ) in Spanish.
J Burn Care Res. 2020;41(3):640-646 - PMID: 31930334 - PMCID: PMC9834989 - DOI: 10.1093/jbcr/iraa011

Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW

A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2'-deoxynucleotides.
J Am Chem Soc. 2020;142(5):2317-2326 - PMID: 31913615 - PMCID: PMC7577264 - DOI: 10.1021/jacs.9b11239

Chizzolini F, Passalacqua LFM, Oumais M, Dingilian AI, Szostak JW, Lupták A

Large phenotypic enhancement of structured random RNA pools.
J Am Chem Soc. 2020;142(4):1941-1951 - PMID: 31887027 - DOI: 10.1021/jacs.9b11396

Betin V, Penaranda C, Bandyopadhyay N, Yang R, Abitua A, Bhattacharyya RP, Fan A, Avraham R, Livny J, Shoresh N, Hung DT

Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis.
Sci Rep. 2019;9(1):19244 - PMID: 31848386 - PMCID: PMC6917760 - DOI: 10.1038/s41598-019-55633-6

Dreckmann SC, Amini-Nik S, Tompkins RG, Vojvodic M, Jeschke MG

Genome-wide comparisons of gene expression in adult versus elderly burn patients.
PLoS One. 2019;14(12):e0226425 - PMID: 31834907 - PMCID: PMC6910697 - DOI: 10.1371/journal.pone.0226425

Jiang X, Hall AB, Xavier RJ, Alm EJ

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.
PLoS One. 2019;14(12):e0223680 - PMID: 31830054 - PMCID: PMC6907783 - DOI: 10.1371/journal.pone.0223680

Vasquez-Rifo A, Veksler-Lublinsky I, Cheng Z, Ausubel FM, Ambros V

The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans.
Genome Biol. 2019;20(1):270 - PMID: 31823826 - PMCID: PMC6902481 - DOI: 10.1186/s13059-019-1890-1

Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT

Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination.
Nat Med. 2019;25(12):1858-1864 - PMID: 31768064 - PMCID: PMC6930013 - DOI: 10.1038/s41591-019-0650-9

Halvorsen YD, Walford G, Thurber T, Russell H, Massaro M, Freeman MW

A Twelve-Week, Randomized, Double-Blind, Placebo-Controlled, Four-Arm Dose-Finding Phase 2 Study Evaluating Bexagliflozin as a Monotherapy for Adults with Type 2 Diabetes.
Diabetes Obes Metab. 2020;22(4):566-573 - PMID: 31749238 - DOI: 10.1111/dom.13928

Johnson EO, Office E, Kawate T, Orzechowski M, Hung DT

A large-scale chemical-genetic strategy enables design of antimicrobial combination chemotherapy in Mycobacteria.
ACS Infect Dis. 2020;6(1):56-63 - PMID: 31721551 - PMCID: PMC6958538 - DOI: 10.1021/acsinfecdis.9b00373

Zhou L, Kim S, Ho KH, O'Flaherty DK, Giurgiu C, Wright TH, Szostak JW

Non-enzymatic primer extension with strand displacement.
Elife. 2019;8:ePub - PMID: 31702557 - PMCID: PMC6872209 - DOI: 10.7554/eLife.51888

Ogura A, Tsurumi A, Que YA, Almpani M, Zheng H, Tompkins RG, Ryan CM, Rahme LG

Associations between clinical characteristics and the development of multiple organ failure after severe burns in adult patients.
Burns. 2019;45(8):1775-1782 - PMID: 31690472 - DOI: 10.1016/j.burns.2019.02.014

Wang A, Szostak JW

Lipid constituents of model protocell membranes.
Emerg Top Life Sci. 2019;3(5):537-542 - PMID: 33523161 - DOI: 10.1042/ETLS20190021

Maheshwari P, Du H, Sheen J, Assmann SM, Albert R

Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling.
PLoS Comput Biol. 2019;15(10):e1007429 - PMID: 31658257 - PMCID: PMC6837631 - DOI: 10.1371/journal.pcbi.1007429

Wright TH, Giurgiu C, Zhang W, Radakovic A, O'Flaherty DK, Zhou L, Szostak JW

Prebiotically Plausible 'Patching' of RNA Backbone Cleavage Through a 3'-5' Pyrophosphate Linkage.
J Am Chem Soc. 2019;141(45):18104-18112 - PMID: 31651170 - PMCID: PMC7577263 - DOI: 10.1021/jacs.9b08237

Johnson EO, Hung DT

A point of inflection and reflection on systems chemical biology.
ACS Chem Biol. 2019;14(12):2497-2511 - PMID: 31613592 - DOI: 10.1021/acschembio.9b00714

Govindan JA, Jayamani E, Ruvkun G

ROS-based lethality of Caenorhabditis elegans mitochondrial electron transport mutants grown on Escherichia coli siderophore iron release mutants.
Proc Natl Acad Sci U S A. 2019;116(43):21651-21658 - PMID: 31591219 - PMCID: PMC6815122 - DOI: 10.1073/pnas.1912628116

Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses.
Immunity. 2019;51(4):696-708.e9 - PMID: 31618654 - PMCID: PMC6991097 - DOI: 10.1016/j.immuni.2019.09.004

Grünewald J, Zhou R, Iyer S, Lareau CA, Garcia SP, Aryee MJ, Joung JK

CRISPR DNA base editors with reduced RNA off-target and self-editing activities.
Nat Biotechnol. 2019;37(9):1041-1048 - PMID: 31477922 - PMCID: PMC6730565 - DOI: 10.1038/s41587-019-0236-6

Elmaleh DR, Farlow MR, Conti PS, Tompkins RG, Kundakovic L, Tanzi RE

Developing Effective Alzheimer's Disease Therapies: Clinical Experience and Future Directions.
J Alzheimers Dis. 2019;71(3):715-732 - PMID: 31476157 - PMCID: PMC6839593 - DOI: 10.3233/JAD-190507

Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, Baxt LA, Begun J, Kuballa P, Gagnon JD, Lassen KG, Regev A, Xavier RJ

Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1.
J Immunol. 2019;203(7):1820-1829 - PMID: 31451676 - PMCID: PMC6761021 - DOI: 10.4049/jimmunol.1800419

Lelyveld VS, O'Flaherty DK, Zhou L, Izgu EC, Szostak JW

DNA polymerase activity on synthetic N3'→P5' phosphoramidate DNA templates.
Nucleic Acids Res. 2019;47(17):8941-8949 - PMID: 31428779 - PMCID: PMC6755091 - DOI: 10.1093/nar/gkz707

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Savova G, Shaw SY, Churchill S, Burke KE, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ

Use of narrative concepts in the EHR to validate genetic determinants of treatment response in a virtual inflammatory bowel disease cohort.
Clin Gastroenterol Hepatol. 2020;18(8):1890-1892 - PMID: 31404664 - PMCID: PMC12476026 - DOI: 10.1016/j.cgh.2019.08.005

Goel G, Tye-Din JA, Qiao SW, Russell AK, Mayassi T, Ciszewski C, Sarna VK, Wang S, Goldstein KE, Dzuris JL, Williams LJ, Xavier RJ, Lundin KEA, Jabri B, Sollid LM, Anderson RP

Cytokine release and gastrointestinal symptoms after gluten challenge in celiac disease.
Sci Adv. 2019;5(8):eaaw7756 - PMID: 31457091 - PMCID: PMC6685723 - DOI: 10.1126/sciadv.aaw7756
Total: 2498