Selected Publications

Bose R, Saleem I, Mustoe AM. Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol. 2024 Jan 3:S2451-9456(23)00440-3.

Qin W, Cheah JS, Xu C, Messing J, Freibaum BD, Boeynaems S, Taylor JP, Udeshi ND, Carr SA, Ting AY. (2023)
Dynamic mapping of proteome trafficking within and between living cells by TransitID. Cell. S0092-8674(23)00596-2.

Boeynaems S, Dorone Y, Zhuang Y, Shabardina V, Huang G, Marian A, Kim G, Sanyal A, Şen NE, Griffith D, Docampo R, Lasker K, Ruiz-Trillo I, Auburger G, Holehouse AS, Kabashi E, Lin Y, Gitler AD. (2023) Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates. Molecular Cell. 83(12):2020-2034.e6.

Bouguenina H, Nicolaou S, Le Bihan YV, Bowling EA, Calderon C, Caldwell JJ, Harrington B, Hayes A, McAndrew PC, Mitsopoulos C, Sialana FJ, Scarpino A, Stubbs M, Thapaliya A, Tyagi S, Wang HZ, Wood F, Burke R, Raynaud F, Choudhary J, van Montfort RLM, Sadok A, Westbrook TF, Collins I, Chopra R. (2023) iTAG an optimized IMiD-induced degron for targeted protein degradation in human and murine cells. iScience. 26(7):107059.

Mitchell D, Cotter J, Saleem I, Mustoe AM. (2023) Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS. NAR. 51(16):8744-8757

LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. (2023) exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. Cell Genom. 3(5):100303.

Ramabadran R, Wang JH, Reyes JM, Guzman AG, Gupta S, Rosas C, Brunetti L, Gundry MC, Tovy A, Long H, Gu T, Cullen SM, Tyagi S, Rux D, Kim JJ, Kornblau SM, Kyba M, Stossi F, Rau RE, Takahashi K, Westbrook TF, Goodell MA. (2023) DNMT3A-coordinated splicing governs the stem state switch towards differentiation in embryonic and haematopoietic stem cells. Nat Cell Biol. 25(4):528-539.

Mustoe AM, Weidmann CA, Weeks KM. (2023) Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis. Acc Chem Res. 56(7):763-775.

Xu A, Liu M, Huang MF, Zhang Y, Hu R, Gingold JA, Liu Y, Zhu D, Chien CS, Wang WC, Liao Z, Yuan F, Hsu CW, Tu J, Yu Y, Rosen T, Xiong F, Jia P, Yang YP, Bazer DA, Chen YW, Li W, Huff CD, Zhu JJ, Aguilo F, Chiou SH, Boles NC, Lai CC, Hung MC, Zhao Z, Van Nostrand EL, Zhao R, Lee DF. (2023) Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation. Nat Commun. 14(1):1694.

Arif W, Mathur B, Saikali MF, Chembazhi UV, Toohill K, Song YJ, Hao Q, Karimi S, Blue SM, Yee BA, Van Nostrand EL, Bangru S, Guzman G, Yeo GW, Prasanth KV, Anakk S, Cummins CL, Kalsotra A. (2023) Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death. Nat Commun. 14(1):551.

Mattick, J.S., Amaral, P.P., Carninci, P., Carpenter, S., Chang, H.Y., Chen, L.L., Chen, R., Dean, C., Dinger, M.E., Fitzgerald, K.A., Gingeras, T.R., Guttman, M., Hirose, T., Huarte, M., Johnson, R., Kanduri, C., Kapranov, P., Lawrence, J.B., Lee, J.T., Mendell, J.T., Mercer, T.R., Moore, K.J., Nakagawa, S., Rinn, J.L., Spector, D.L., Ulitsky, I., Wan, Y., Wilusz, J.E., and Wu, M. (2023) Long non-coding RNAs: Definition, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 

Zhu X, Qi C, Wang R, Lee JH, Shao J, Bei L, Xiong F, Nguyen PT, Li G, Krakowiak J, Koh SP, Simon LM, Han L, Moore TI, Li W. (2022) Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. Cell Reports. 41(5):111576

Benoit Bouvrette LP, Wang X, Boulais J, Kong J, Syed EU, Blue SM, Zhan L, Olson S, Stanton R, Wei X, Yee B, Van Nostrand EL, Fu XD, Burge CB, Graveley BR, Yeo GW, Lécuyer E. (2022) RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins. Nucleic Acids Res.

Grayeski PJ, Weidmann CA, Kumar J, Lackey L, Mustoe AM, Busan S, Laederach A, Weeks KM. Global 5'-UTR RNA structure regulates translation of a SERPINA1 mRNA. (2022) Nucleic Acids Res. 50(17):9689-9704

Cai WL, Chen JF, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. (2022) Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. eLife 11:e78163

Antony, C., George, S.S., Blum, J., Somers, P., Thorsheim, C.L., Wu-Corts, D.J., Ai, Y., Gao, L., Lv, K., Tremblay, M.G., Moss, T., Tan, K., Wilusz, J.E., Ganley, A.R.D., Pimkin, M., and Paralkar, V.R. (2022) Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell.

Yan F, Simon LM, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z (2022) Spatiotemporal microRNA-gene expression network related to orofacial clefts. J Dent Res.

Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A (2022) Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. Elife 11: e73888.

Yang L, Wilusz JE, Chen LL (2022) Biogenesis and regulatory roles of circular RNAs. Annu Rev Cell Dev Biol.

Pei G, Yan F, Simon LM, Dai Y, Jia P, Zhao Z (2022) deCS: A tool for systematic cell type annotations of single-cell RNA sequencing data among human tissues. Genomics Proteomics Bioinformatics.

Blue SM, Yee BA, Pratt GA, Mueller JR, Park SS, Shishkin AA, Starner AC, Van Nostrand EL, Yeo GW (2022) Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. Nat Protoc 17: 1223-1265.

Olson SW, Turner AW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM (2022) Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 82: 1708-1723.

Ai Y, Liang D, Wilusz JE (2022) CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells. Nucleic Acids Res 50: e65. '

Alexander RP, Kitchen RR, Tosar JP, Roth M, Mestdagh P, Max KEA, Rozowsky J, Kaczor-Urbanowicz KE, Chang J, Balaj L, Losic B, Van Nostrand EL, LaPlante E, Mateescu B, White BS, Yu R, Milosavljevic A, Stolovitzky G, Spengler RM (2022) Open problems in extracellular RNA data analysis: insights from an ERCC online workshop. Front Genet 12: 778416.

Einstein JM, Perelis M, Chaim IA, Meena JK, Nussbacher JK, Tankka AT, Yee BA, Li H, Madrigal AA, Neill NJ, Shankar A, Tyagi S, Westbrook TF, Yeo GW (2021) Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer. Mol Cell 81: 3048-3064.

Jeong HH, Jia J, Dai Y, Simon LM, Zhao Z (2021) Investigating cellular trajectories in the severity of COVID-19 and their transcriptional programs using machine learning approaches. Genes (Basel) 12: 635.

Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart ZD, Pillon MC, Deterding LJ, Borgnia MJ, Stanley RE (2021) Characterization of SARS2 Nsp15 nuclease activity reveals it’s mad about U. Nucleic Acids Res 49: 10136-10149.

Arabzade A, Zhao Y, Varadharajan S, Chen HC, Jessa S, Rivas B, Stuckert AJ, Solis M, Kardian A, Tlais D, Golbourn BJ, Stanton AJ, Chan YS, Olson C, Karlin KL, Kong K, Kupp R, Hu B, Injac SG, Ngo M, Wang PR, De León LA, Sahm F, Kawauchi D, Pfister SM, Lin CY, Hodges HC, Singh I, Westbrook TF, Chintagumpala MM, Blaney SM, Parsons DW, Pajtler KW, Agnihotri S, Gilbertson RJ, Yi J, Jabado N, Kleinman CL, Bertrand KC, Deneen B, Mack SC (2021) ZFTA-RELA dictates oncogenic transcriptional programs to drive aggressive supratentorial ependymoma. Cancer Discov 11: 2200-2215.

Gao Y, Kabotyanski EB, Shepherd JH, Villegas E, Acosta D, Hamor C, Sun T, Montmeyor-Garcia C, He X, Dobrolecki LE, Westbrook TF, Lewis MT, Hilsenbeck SG, Zhang XH, Perou CM, Rosen JM (2021) Tumor suppressor PLK2 may serve as a biomarker in triple-negative breast cancer for improved response to PLK1 therapeutics. Cancer Res Commun 1: 178-193.

Bowling EA, Wang JH, Gong F, Wu W, Neill NJ, Kim IS, Tyagi S, Orellana M, Kurley SJ, Dominguez-Vidaña R, Chung HC, Hsu TY, Dubrulle J, Saltzman AB, Li H, Meena JK, Canlas GM, Chamakuri S, Singh S, Simon LM, Olson CM, Dobrolecki LE, Lewis MT, Zhang B, Golding I, Rosen JM, Young DW, Malovannaya A, Stossi F, Miles G, Ellis MJ, Yu L, Buonamici S, Lin CY, Karlin KL, Zhang XH, Westbrook TF (2021) Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer. Cell 184: 384-403.

Richters A, Doyle SK, Freeman DB, Lee C, Leifer BS, Jagannathan S, Kabinger F, Koren JV, Struntz NB, Urgiles J, Stagg RA, Curtin BH, Chatterjee D, Mathea S, Mikochik PJ, Hopkins TD, Gao H, Branch JR, Xin H, Westover L, Bignan GC, Rupnow BA, Karlin KL, Olson CM, Westbrook TF, Vacca J, Wilfong CM, Trotter BW, Saffran DC, Bischofberger N, Knapp S, Russo JW, Hickson I, Bischoff JR, Gottardis MM, Balk SP, Lin CY, Pop MS, Koehler AN (2021) Modulating androgen receptor-driven transcription in prostate cancer with selective CDK9 inhibitors. Cell Chem Biol 28: 134-147.

Pillon MC, Frazier MN, Dillard LB, Williams JG, Kocaman S, Krahn JM, Perera L, Hayne CK, Gordon J, Stewart ZD, Sobhany M, Deterding LJ, Hsu AL, Dandey VP, Borgnia MJ, Stanley RE (2021) Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics. Nat Commun 12: 636.

Krug K, Jaehnig EJ, Satpathy S, Blumenberg L, Karpova A, Anurag M, Miles G, Mertins P, Geffen Y, Tang LC, Heiman DI, Cao S, Maruvka YE, Lei JT, Huang C, Kothadia RB, Colaprico A, Birger C, Wang J, Dou Y, Wen B, Shi Z, Liao Y, Wiznerowicz M, Wyczalkowski MA, Chen XS, Kennedy JJ, Paulovich AG, Thiagarajan M, Kinsinger CR, Hiltke T, Boja ES, Mesri M, Robles AI, Rodriguez H, Westbrook TF, Ding L, Getz G, Clauser KR, Fenyö D, Ruggles KV, Zhang B, Mani DR, Carr SA, Ellis MJ, Gillette MA, Clinical Proteomic Tumor Analysis Consortium (2020) Proteogenomic landscape of breast cancer tumorigenesis and targeted therapy. Cell 183: 1436-1456.

Dhindsa RS, Copeland BR, Mustoe AM, Goldstein DB (2020) Natural selection shapes codon usage in the human genome. Am J Hum Genet 107: 83-95.

Arnal-Estapé A, Cai WL, Albert AE, Zhao M, Stevens LE, López-Giráldez F, Patel KD, Tyagi S, Schmitt EM, Westbrook TF, Nguyen DX (2020) Tumor progression and chromatin landscape of lung cancer are regulated by the lineage factor GATA6. Oncogene 39: 3726-3737.

Lee H, Zandkarimi F, Zhang Y, Meena JK, Kim J, Zhuang L, Tyagi S, Ma L, Westbrook TF, Steinberg GR, Nakada D, Stockwell BR, Gan B (2020) Energy-stress-mediated AMPK activation inhibits ferroptosis. Nat Cell Biol 22: 225-234.

Mercado N, Schutzius G, Kolter C, Estoppey D, Bergling S, Roma G, Gubser Keller C, Nigsch F, Salathe A, Terranova R, Reece-Hoyes J, Alford J, Russ C, Knehr J, Hoepfner D, Aebi A, Ruffner H, Beck TC, Jagannathan S, Olson CM, Sheppard HE, Elsarrag SZ, Bouwmeester T, Frederiksen M, Lohmann F, Lin CY, Kirkland S (2019) IRF2 is a master regulator of human keratinocyte stem cell fate. Nat Commun 10: 4676.

Hirukawa A, Singh S, Wang J, Rennhack JP, Swiatnicki M, Sanguin-Gendreau V, Zuo D, Daldoul K, Lavoie C, Park M, Andrechek ER, Westbrook TF, Harris LN, Varadan V, Smith HW, Muller WJ (2019) Reduction of Global H3K27me3 enhances HER2/ErbB2 targeted therapy. Cell Rep 29: 249-257.

Kim IS, Gao Y, Welte T, Wang H, Liu J, Janghorban M, Sheng K, Niu Y, Goldstein A, Zhao N, Bado I, Lo HC, Toneff MJ, Nguyen T, Bu W, Jiang W, Arnold J, Gu F, He J, Jebakumar D, Walker K, Li Y, Mo Q, Westbrook TF, Zong C, Rao A, Sreekumar A, Rosen JM, Zhang XH (2019) Immuno-subtyping of breast cancer reveals distinct myeloid cell profiles and immunotherapy resistance mechanisms. Nat Cell Bio 21: 1113-1126.

Olson CM, Liang Y, Leggett A, Park WD, Li L, Mills CE, Elsarrag SZ, Ficarro SB, Zhang T, Düster R, Geyer M, Sim T, Marto JA, Sorger PK, Westover KD, Lin CY, Kwiatkowski N, Gray NS (2019) Development of a selective CDK7 covalent inhibitor reveals predominant cell-cycle phenotype. Cell Chem Biol 26: 792-803.

Mowery CT, Reyes JM, Cabal-Hierro L, Higby KJ, Karlin KL, Wang JH, Kimmerling RJ, Cejas P, Lim K, Li H, Furusawa T, Long HW, Pellman D, Chapuy B, Bustin M, Manalis SR, Westbrook TF, Lin CY, Lane AA (2019) Trisomy of a Down Syndrome critical region globally amplifies transcription via HMGN1 overexpression. Cell Rep 25: 1898-1911.

Rousseaux MWC, Vázquez-Vélez GE, Al-Ramahi I, Jeong HH, Bajić A, Revelli JP, Ye H, Phan ET, Deger JM, Perez AM, Kim JY, Lavery LA, Xu Q, Li MZ, Kang H, Kim JJ, Shulman JM, Westbrook TF, Elledge SJ, Liu Z, Botas J, Zoghbi HY (2018) A druggable genome screen identifies modifiers of a-synuclein levels via a tiered cross-species validation approach. J Neurosci 38: 9286-9301.

Nair A, Chung HC, Sun T, Tyagi S, Dobrolecki LE, Dominguez-Vidana R, Kurley SJ, Orellana M, Renwick A, Henke DM, Katsonis P, Schmitt E, Chan DW, Li H, Mao S, Petrovic I, Creighton CJ, Gutierrez C, Dubrulle J, Stossi F, Tyner JW, Lichtarge O, Lin CY, Zhang B, Scott KL, Hilsenbeck SG, Sun J, Yu X, Osborne CK, Schiff R, Christensen JG, Shields DJ, Rimawi MF, Ellis MJ, Shaw CA, Lewis MT, Westbrook TF (2018) Combinatorial inhibition of PTPN12-regulated receptors leads to a broadly effective therapeutic strategy in triple-negative breast cancer. Nat Med 24: 505-511.

Sack LM, Davoli T, Li MZ, Li Y, Xu Q, Naxerova K, Wooten EC, Bernardi RJ, Martin TD, Chen T, Leng Y, Liang AC, Scorsone KA, Westbrook TF, Wong KK, Elledge SJ (2018) Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns. Cell 173: 499-514.