Publications for All Faculty

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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 - 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
Todd ZR, Szabla R, Szostak JW, Sasselov DD

UV photostability of three 2-aminoazoles with key roles in prebiotic chemistry on the early earth.

Chem Commun (Camb). 2019;55(70):10388-10391 - PMID: 31380533 - PMCID: PMC9631353 - DOI: 10.1039/c9cc05265h
Plichta DR, Graham DB, Subramanian S, Xavier RJ

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships.

Cell. 2019;178(5):1041-1056 - PMID: 31442399 - PMCID: PMC6778965 - DOI: 10.1016/j.cell.2019.07.045
Total: 2446