Functional Genomics

2023
Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer [Internet]. Cell Rep 2023;42(12):113564. Publisher's Version
Schmaier AA, Anderson PF, Chen SM, El-Darzi E, Aivasovsky I, Kaushik MP, Sack KD, Hartzell HC, Parikh SM, Flaumenhaft R, Schulman S. TMEM16E regulates endothelial cell procoagulant activity and thrombosis [Internet]. J Clin Invest 2023;133(11):e163808. Publisher's Version
Chen D-Y, Chin CV, Kenney D, Tavares AH, Khan N, Conway HL, Liu GQ, Choudhary MC, Gertje HP, O'Connell AK, Adams S, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation [Internet]. Nature 2023;615:143-150. Publisher's Version
Durall RT, Huang J, Wojenski L, Huang Y, Gokhale PC, Leeper BA, Nash JO, Ballester PL, Davidson S, Shlien A, Sotirakis E, Bertaux F, Dubus V, Luo J, Wu CJ, Keskin DB, Eagen KP, Shapiro GI, French CA. The BRD4-NUT fusion alone drives malignant transformation of NUT carcinoma [Internet]. Cancer Res 2023;(Oct 11) Publisher's Version
Park DS, Nguyen SC, Isenhart R, Shah PP, Kim W, Barnett RJ, Chandra A, Luppino JM, Harke J, Wai M, Walsh PJ, Abdill RJ, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki MT, Vahedi G, Phillips-Cremins JE, Jain R, Joyce EF. High-throughput Oligopaint screen identifies druggable 3D genome regulators. Nature 2023;620:209–217.
2022
Boekell KL, Brown BJ, Talbot BE, Schlondorff JS. Trpc6 gain-of-function disease mutation enhances phosphatidylserine exposure in murine platelets [Internet]. PLoS One 2022;17(6):e0270431. Publisher's Version
Vora SM, Fontana P, Mao T, Leger V, Zhang Y, Fu T-M, Lieberman J, Gehrke L, Shi M, Wang L, Iwasaki A, Wu H. Targeting stem-loop 1 of the SARS-CoV-2 5' UTR to suppress viral translation and Nsp1 evasion [Internet]. Proc Natl Acad Sci U S A 2022;119(9):e2117198119. Publisher's Version
Coverdell TC, Abraham-Fan R-J, Wu C, Abbott SBG, Campbell JN. Genetic encoding of an esophageal motor circuit [Internet]. Cell Rep 2022;39(11):110962. Publisher's Version
Jutzi JS, Marneth AE, Ciboddo M, Guerra-Moreno A, Jiménez-Santos MJ, Kosmidou A, Dressman JW, Liang H, Hamel R, Lozano P, Rumi E, Doench JG, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A. Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs [Internet]. Blood 2022;140(11):1291-1304. Publisher's Version
Martínez-Noël G, Szajner P, Kramer RE, Boyland KA, Sheikh A, Smith JA, Howley PM. Identification of MicroRNAs That Stabilize p53 in Human Papillomavirus-Positive Cancer Cells. J Virol 2022;96(4)
2021
Tasdemir-Yilmaz OE, Druckenbrod NR, Olukoya OO, Dong W, Yung AR, Bastille I, Pazyra-Murphy MF, Sitko AA, Hale EB, Vigneau S, Gimelbrant AA, Kharchenko PV, Goodrich LV, Segal RA. Diversity of developing peripheral glia revealed by single-cell RNA sequencing [Internet]. Dev Cell 2021;56(17):2516-2535. Publisher's Version
Chu V, Feng Q, Lim Y, Shao S. Selective destabilization of polypeptides synthesized from NMD-targeted transcripts [Internet]. Mol Biol Cell 2021;32(22):ar38. Publisher's Version
2020
Egusquiaguirre SP, Liu S, Tošić I, Jiang K, Walker SR, Nicolais M, Saw TY, Xiang M, Bartel K, Nelson EA, Frank DA. CDK5RAP3 is a co-factor for the oncogenic transcription factor STAT3 [Internet]. Neoplasia 2020;22(1):47-59. Publisher's Version
Cruz FM, Colbert JD, Rock KL. The GTPase Rab39a promotes phagosome maturation into MHC-I antigen-presenting compartments [Internet]. EMBO J 2020;39:e102020. Publisher's Version
Tattikota SG, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh MJ, Yoon S-H, Comjean A, Li F, Dervis F, Hung R-J, Nam J-W, Sui SH, Shim J, Perrimon N. A single-cell survey of Drosophila blood [Internet]. eLife 2020;9:e54818. Publisher's Version
Todd WD, Venner A, Anaclet C, Broadhurst RY, Luca RD, Bandaru SS, Issokson L, Hablitz LM, Cravetchi O, Arrigoni E, Campbell JN, Allen CN, Olson DP, Fuller PM. Suprachiasmatic VIP neurons are required for normal circadian rhythmicity and comprised of molecularly distinct subpopulations [Internet]. Nat Commun 2020;11:4410. Publisher's Version
Takahashi N, Cho P, Selfors LM, Kuiken HJ, Kaul R, Fujiwara T, Harris IS, Zhang T, Gygi SP, Brugge JS. 3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis [Internet]. Mol Cell 2020;80(5):828-844. Publisher's Version
2018
Bodnar NO, Kim KH, Ji Z, Wales TE, Svetlov V, Nudler E, Engen JR, Walz T, Rapoport TA. Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Nat Struct Mol Biol 2018;25(7):616-622.
Takahashi N, Chen H-Y, Harris IS, Stover DG, Selfors LM, Bronson RT, Deraedt T, Cichowski K, Welm AL, Mori Y, Mills GB, Brugge JS. Cancer Cells Co-opt the Neuronal Redox-Sensing Channel TRPA1 to Promote Oxidative-Stress Tolerance [Internet]. Cancer Cell 2018;33(6):985-1003. Publisher's Version

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