Graduate Publications

381 Publications

2021

1.
Dai W, Li A, Yu N, Nguyen T, Leach R, Wühr M, Kleiner R. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nat Chem Biol. 2021;17(11):1178–1187. PMCID: PMC8551019
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Maerker M, Getwan M, Dowdle M, McSheene J, Gonzalez V, Pelliccia J, Hamilton D, Yartseva V, Vejnar C, Tingler M, Minegishi K, Vick P, Giraldez A, Hamada H, Burdine R, Sheets M, Blum M, Schweickert A. Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5. Nat Commun. 2021;12(1):5482. PMCID: PMC8446035
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Christopher J, Stadler C, Martin C, Morgenstern M, Pan Y, Betsinger C, Rattray D, Mahdessian D, Gingras A-C, Warscheid B, Lehtiö J, Cristea I, Foster L, Emili A, Lilley K. Subcellular proteomics. Nat Rev Methods Primers. 2021;1. PMCID: PMC8451152
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Sohrabi S, Moore R, Murphy C. CeAid: a smartphone application for logging and plotting Caenorhabditis elegans assays. G3 (Bethesda). 2021;11(10). PMCID: PMC8473968
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Chen P, Hussmann J, Yan J, Knipping F, Ravisankar P, Chen P-F, Chen C, Nelson J, Newby G, Sahin M, Osborn M, Weissman J, Adamson B, Liu D. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184(22):5635–5652.e29. PMCID: PMC8584034
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Miangolarra M, Li S, Joanny J-F, Wingreen N, Castellana M. Steric interactions and out-of-equilibrium processes control the internal organization of bacteria. Proc Natl Acad Sci U S A. 2021;118(43). PMCID: PMC8639350
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Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella A, Shen Y, Cowan A, McReynolds M, Kennedy B, Lato A, Campagna S, Singh M, Rabinowitz J. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods. 2021;18(11):1377–1385. PMCID: PMC8733904
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Chitrakar A, Solorio-Kirpichyan K, Prangley E, Rath S, Du J, Korennykh A. Introns encode dsRNAs undetected by RIG-I/MDA5/interferons and sensed via RNase L. Proc Natl Acad Sci U S A. 2021;118(46). PMCID: PMC8609619
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Balaich J, Estrella M, Wu G, Jeffrey P, Biswas A, Zhao L, Korennykh A, Donia M. The human microbiome encodes resistance to the antidiabetic drug acarbose. Nature. 2021;600(7887):110–115. PMCID: 3552296
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King S, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol. 2021;17(11):e1009560. PMCID: PMC8601562
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Colonnetta M, Abrahante J, Schedl P, Gohl D, Deshpande G. CLAMP regulates zygotic genome activation in Drosophila embryos. Genetics. 2021;219(2). PMCID: PMC8633140
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Fang C, Kang Y. E-Cadherin: Context-Dependent Functions of a Quintessential Epithelial Marker in Metastasis. Cancer Res. 2021;81(23):5800–5802. PMID: 34853039
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Farahani P, Lemke S, Dine E, Uribe G, Toettcher J, Nelson C. Substratum stiffness regulates Erk signaling dynamics through receptor-level control. Cell Rep. 2021;37(13):110181. PMCID: PMC8756379
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Stanton A, Goodwin K, Sundarakrishnan A, Jaslove J, Gleghorn J, Pavlovich A, Nelson C. Negative Transpulmonary Pressure Disrupts Airway Morphogenesis by Suppressing Fgf10. Front Cell Dev Biol. 2021;9:725785. PMCID: PMC8673560
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Setru S, Gouveia B, Alfaro-Aco R, Shaevitz J, Stone H, Petry S. A hydrodynamic instability drives protein droplet formation on microtubules to nucleate branches. Nat Phys. 2021;17(4):493–498. PMCID: PMC8865447

2022

1.
Fang C, Kang Y. Cellular plasticity in bone metastasis. Bone. 2022;158:115693. PMCID: PMC8046848
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Wang R, Gallant Étienne, Wilson M, Wu Y, Li A, Gitai Z, Seyedsayamdost M. Algal p-coumaric acid induces oxidative stress and siderophore biosynthesis in the bacterial symbiont Phaeobacter inhibens. Cell Chem Biol. 2022;29(4):670–679.e5. PMCID: PMC8866538
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López J, Duran L, Avalos J. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol. 2022;20(1):35–48. PMCID: 5812522
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Nofal M, Wang T, Yang L, Jankowski C, Li S, Han S, Parsons L, Frese A, Gitai Z, Anthony T, Wühr M, Sabatini D, Rabinowitz J. GCN2 adapts protein synthesis to scavenging-dependent growth. Cell Syst. 2022;13(2):158–172.e9. PMCID: PMC8961722
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Ravindran P, McFann S, Thornton R, Toettcher J. A synthetic gene circuit for imaging-free detection of signaling pulses. Cell Syst. 2022;13(2):131–142.e13. PMCID: PMC8857027
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Hill K, Lovett B, Schwarzbauer J. Heparan sulfate is necessary for the early formation of nascent fibronectin and collagen I fibrils at matrix assembly sites. J Biol Chem. 2022;298(1):101479. PMCID: PMC8801470
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Doherty C, Amargant F, Shvartsman S, Duncan F, Gavis E. Bidirectional communication in oogenesis: a dynamic conversation in mice and Drosophila. Trends Cell Biol. 2022;32(4):311–323. PMCID: PMC8917990
1.
Tyl M, Betsinger C, Cristea I. Virus-host protein interactions as footprints of human cytomegalovirus replication. Curr Opin Virol. 2022;52:135–147. PMCID: PMC8844139
1.
Tamura T, Zhang J, Madan V, Biswas A, Schwoerer M, Cafiero T, Heller B, Wang W, Ploss A. Generation and characterization of genetically and antigenically diverse infectious clones of dengue virus serotypes 1-4. Emerg Microbes Infect. 2022;11(1):227–239. PMCID: PMC8745371
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Combs A, Silhavy T. The sacrificial adaptor protein Skp functions to remove stalled substrates from the β-barrel assembly machine. Proc Natl Acad Sci U S A. 2022;119(1). PMCID: PMC8740687