Selected Publications

Kodali S, Proietti L, Valcarcel G, López-Rubio AV, Pessina P, Eder T, Shi J, Jen A, Lupión-Garcia N, Starner AC, Bartels MD, Cui Y, Sands CM, Planas-Riverola A, Martínez A, Velasco-Hernandez T, Tomás-Daza L, Alber B, Manhart G, Mayer IM, Kollmann K, Fatica A, Menendez P, Shishkova E, Rau RE, Javierre BM, Coon J, Chen Q, Van Nostrand EL, Sardina JL, Grebien F, Di Stefano B. (2024 26 Oct). RNA sequestration in P-bodies sustains myeloid leukaemia. Nat Cell Biol. 26(10):1745-1758.

Xu L, Peng F, Luo Q, Ding Y, Yuan F, Zheng L, He W, Zhang SS, Fu X, Liu J, Mutlu AS, Wang S, Nehring RB, Li X, Tang Q, Li C, Lv X, Dobrolecki LE, Zhang W, Han D, Zhao N, Jaehnig E, Wang J, Wu W, Graham DA, Li Y, Chen R, Peng W, Chen Y, Catic A, Zhang Z, Zhang B, Mustoe AM, Koong AC, Miles G, Lewis MT, Wang MC, Rosenberg SM, O'Malley BW, Westbrook TF, Xu H, Zhang XH, Osborne CK, Li JB, Ellis MJ, Rimawi MF, Rosen JM, Chen X. (2024 Oct 14) IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer. Cell. Epub ahead of print.

Scacchetti A, Shields EJ, Trigg NA, Wilusz JE, Conine CC, Bonasio R. (2024 Oct 3) A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3’ termini. Mol Cell. 84(19):3843-3859.

Song Z, Bae B, Schnabl S, Yuan F, De Zoysa T, Akinyi M, Le Roux C, Choquet K, Whipple A, Van Nostrand E. (2024 Sep 21) Mapping snoRNA-target RNA interactions in an RNA binding protein-dependent manner with chimeric eCLIP. bioRxiv. [Preprint]

Bhola M, Abe K, Orozco P, Rahnamoun H, Avila-Lopez P, Taylor E, Muhammad N, Liu B, Patel P, Marko JF, Starner AC, He C, Van Nostrand EL, Mondragón A, Lauberth SM. (2024 Sep 5). RNA interacts with topoisomerase I to adjust DNA topology. Mol Cell. 84(17):3192-3208.

Meena JK, Wang JH, Neill NJ, Keough D, Putluri N, Katsonis P, Koire AM, Lee H, Bowling EA, Tyagi S, Orellana M, Dominguez-Vidaña R, Li H, Eagle K, Danan C, Chung HC, Yang AD, Wu W, Kurley SJ, Ho BM, Zoeller JR, Olson CM, Meerbrey KL, Lichtarge O, Sreekumar A, Dacso CC, Guddat LW, Rejman D, Hocková D, Janeba Z, Simon LM, Lin CY, Pillon MC, Westbrook TF. (2024 Sep 4). MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer. Cancer Discovery 14(9):1699-1716.

Dao K, Jungers CF, Djuranovic S, Mustoe AM. (2024 Aug 5). U-rich elements drive pervasive cryptic splicing in 3' UTR massively parallel reporter assays. bioRxiv [Preprint]

Zhao Z, Liu A, Citu C, Enduru N, Chen X, Manuel A, Sinha T, Gorski D, Fernandes B, Yu M, Schulz P, Simon L, Soto C. (2024 Aug 1). Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease. Res Sq [Preprint]

Chung DC, Deng X, Yalamanchili HK, Revelli JP, Han AL, Tadros B, Richman R, Dias M, Alavi Naini F, Boeynaems S, Hyman BT, Zoghbi HY. (2024 Jul 31). The big tau splice isoform resists Alzheimer's-related pathological changes. BioRxiv. 2024.07.30.605685

Itai T, Yan F, Liu A, Dai Y, Iwaya C, Curtis SW, Leslie EJ, Simon LM, Jia P, Chen X, Iwata J, Zhao Z. (2024 Jul 18). Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts. HGG Adv. 5 (3):100313.

Dai Y, Itai T, Pei G, Yan F, Chu Y, Jiang X, Weinberg S, Mukhopadhyay N, Marazita ML, Simon LM, Jia P and Zhao Z. (2024 Jul 18) DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development. HGG Adv. 5(3):100312

Yan F, Suzuki A, Iwaya C, Pei G, Chen X, Yoshioka H, Yu M, Simon LM, Iwata J and Zhao Z. (2024 Jun 27). Single-cell multiomics decodes regulatory programs for mouse secondary palate development. Nat Communications. 15(1):821.

Palit S, Shrestha AK, Thapa S, L Grimm S, Coarfa C, Theis F, Simon LM, Shivanna B. (2024 Jun 19). Leveraging Integrated RNA Sequencing to Decipher Adrenomedullin's Protective Mechanisms in Experimental Bronchopulmonary Dysplasia. Genes (Basel). 15(6):806.

Yan F, Jiang V, Jordan A, Che Y, Liu Y, Cai Q, Xue Y, Li Y, McIntosh J, Chen Z, Vargas J, Nie L, Yao Y, Lee H-H, Wang W, Bigcal J, Badillo M, Meena J, Flowers C, Zhou J, Zhao Z, Simon LM and Wang M. (2024 Jun 9). The HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma. Exp Hematol Oncol. 13(1):14.

Zheng R, Dunlap M, Bobkov GOM, Gonzalez-Figueroa C, Patel KJ, Lyu J, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Le Roux CA, Bartels MD, Vuong A, Flynn RA, Chang HY, Van Nostrand EL, Xiao X, Cheng C. (2024 Jun 6) hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing. Mol Cell. 84 (11):2087-2103.

Morandell J, Monziani A, Lazioli M, Donzel D, Döring J, Pegorar CO, D’Anzi A, Pellegrini M, Mattiello A, Bortolotti D, Bergonzoni G, Tripathi T, Mattis VB, Kovalenko M, Rosati J, Dieterich C, Dassi E, Wheeler VC, Ellederová Z, Wilusz JE, Viero G, Biagioli M. (2024 Jun 3) CircHTT(2,3,4,5,6) – co-evolving with the HTT CAG-repeat tract – modulates Huntington’s disease phenotypes. Mol Ther Nucleic Acids 35: 102234.

Seasock MJ, Shafiquzzaman M, Ruiz-Echartea ME, Kanchi RS, Tran BT, Simon LM, Meyer MD, Erice PA, Lotlikar SL, Wenlock SC, Ochsner SA, Enright A, Carisey AF, Romero F, Rosas IO, King KY, McKenna NJ, Coarfa C, Rodriguez A. (2024 May 27). Let-7 restrains an oncogenic epigenetic circuit in AT2 cells to prevent ectopic formation of fibrogenic transitional cell intermediates and pulmonary fibrosis. bioRxiv [Preprint].

Wright BW and Wilusz JE (2024 May 21) An unexpected path for Malat1 in neurons: Trafficking out of the nucleus for translation. Genes Dev 38: 291-293.

Sharma S, Fazal FM. (2024 May 16) Localization of RNAs to the mitochondria-mechanisms and functions. RNA. 30(6):597-608.

Fuchs Wightman F, Lukin J, Giusti S, Soutschek M, Bragado L, Pozzi B, Gonzalez P, Fededa JP, Schratt G, Fujiwara R, Wilusz JE, Refojo D, de la Mata M. (2024 Apr 12). Influence of RNA circularity on target RNA-directed microRNA degradation. Nucleic Acids Res 52: 3358-3374.

Du C, Waltzer WC, Wilusz JE, Spaliviero M, Darras F, Romanov V. (2024 Feb 28) Circular STAG2 RNA modulates bladder cancer progression via miR-145-5p/TAGLN2 and is considered as biomarker for recurrence. Cancers (Basel) 16: 978

Field S, Dorone Y, Dwyer WP, Cox JA, Raba D, Froehlich J, Blea M, Carmo OMS, Wallace IS, Hastings R, Boeynaems S, Rhee SY. (2024 Feb 19) Arabidopsis thaliana RHAMNOSE 1 condensate formation drives UDP-rhamnose synthesis. bioRxiv. 2024.02.15.580454

Bose R, Saleem I, Mustoe AM. (2024 Jan 18). Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol. 31(1):17-35.

Xiao MS, Wilusz JE. (2024) Purification of circular RNAs using poly(A) tailing followed by RNase R digestion. Methods Mol Biol 2765: 3-19.

Fujiwara R, Zhai SN, Liang D, Shah AP, Tracey M, Ma XK, Fields CJ, Mendoza-Figueroa MS, Meline MC, Tatomer DC, Yang L, Wilusz JE. (2023 Dec 21) IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol Cell. 83(24):4445-4460.

Stringer BW, Gabryelska M, Marri S, Clark L, Lin H, Gantley L, Liu R, Wilusz JE, Conn VM, Conn SJ. (2023 Nov 22) Versatile toolkit for highly-efficient and scarless overexpression of circular RNAs. bioRxiv. 2023.11.21.568171.

Mitchell D, Cotter J, Saleem I, Mustoe AM (2023 Sep 8). Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS. Nucleic Acids Res.;51(16):8744-8757.

Simon LM, Flocco C, Burkart F, Methner A, Henke D, Rauer L, Müller CL, Vogel J, Quaisser C, Overmann J, Simon S. (2023 Aug 9). Microbial fingerprints reveal interaction between museum objects, curators, and visitors. iScience.;26(9):107578.

Romero-Perez PS, Dorone Y, Flores E, Sukenik S, Boeynaems S. (2023 Jul 26) When Phased without Water: Biophysics of Cellular Desiccation, from Biomolecules to Condensates. Chem Rev. 123(14):9010-9035.

Qin W, Cheah JS, Xu C, Messing J, Freibaum BD, Boeynaems S, Taylor JP, Udeshi ND, Carr SA, Ting AY. (2023 Jul 20)
Dynamic mapping of proteome trafficking within and between living cells by TransitID. Cell. 186(15):3307-3324.

Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. (2023 Jun 24) Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 24(6):430-447.

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 Jun 15) Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates. Molecular Cell. 83(12):2020-2034.

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 Jun 7) iTAG an optimized IMiD-induced degron for targeted protein degradation in human and murine cells. iScience. 26(7):107059.

Wang M, Deng W, Samuels DC, Zhao Z, Simon LM.(2023 Jun 4). MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data. Genes (Basel).;14(6):1222.

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 Apr 20) 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.

Onuchic P, Boeynaems S. (2023 Apr 19) You're in then you're out. Nat Chem Biol. 19(4):399-400.

Mitchell D, Cotter J, Saleem I, Mustoe AM. (2023 Apr 11) Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS. Nucleic Acids Res. [Preprint]

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 Apr 6) 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 Apr 4) 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 Mar 27) Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation. Nat Commun. 14(1):1694.

Boeynaems S, Ma XR, Yeong V, Ginell GM, Chen JH, Blum JA, Nakayama L, Sanyal A, Briner A, Haver DV, Pauwels J, Ekman A, Schmidt HB, Sundararajan K, Porta L, Lasker K, Larabell C, Hayashi MAF, Kundaje A, Impens F, Obermeyer A, Holehouse AS, Gitler AD. (2023 Mar 9) Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease. bioRxiv. [Preprint]

Boeynaems S, Chong S, Gsponer J, Holt L, Milovanovic D, Mitrea DM, Mueller-Cajar O, Portz B, Reilly JF, Reinkemeier CD, Sabari BR, Sanulli S, Shorter J, Sontag E, Strader L, Stachowiak J, Weber SC, White M, Zhang H, Zweckstetter M, Elbaum-Garfinkle S, Kriwacki R. (2023 Mar 1) Phase Separation in Biology and Disease; Current Perspectives and Open Questions. J Mol Biol. 435(5):167971.

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 Feb 9) Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death. Nat Commun. 14(1):551.

Chen LL, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma XK, Pek JW, Rajewsky N, Salzman J, Wilusz JE, Yang L, Zhao F. (2023 Jan 25). A guide to naming eukaryotic circular RNAs. Nat Cell Biol 25: 1-5.

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. (2023 Jan 6) RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins. Nucleic Acids Res. 51(D1):D1549-D1557.

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 Jan 3) 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 Nov 1) Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. Cell Reports. 41(5):111576

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 Oct 20) Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell. 82(20):3826-3839.

Yang L, Wilusz JE, Chen LL (2022 Oct 6) Biogenesis and regulatory roles of circular RNAs. Annu Rev Cell Dev Biol. 38:263-289.

Grayeski PJ, Weidmann CA, Kumar J, Lackey L, Mustoe AM, Busan S, Laederach A, Weeks KM. (2022 Sep 23) Global 5'-UTR RNA structure regulates translation of a SERPINA1 mRNA. 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 Aug 31) Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. eLife 11:e78163

Yan F, Simon LM, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z (2022 Jun 30) Spatiotemporal microRNA-gene expression network related to orofacial clefts. J Dent Res.

Ai Y, Liang D, Wilusz JE (2022 Jun 24) CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells. Nucleic Acids Res 50: e65.

Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A (2022 Jun 13) Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. Elife 11: e73888.

Olson SW, Turner AW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM (2022 May 5) Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 82: 1708-1723.

Pei G, Yan F, Simon LM, Dai Y, Jia P, Zhao Z (2022 Apr 22) 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 Mar 23) Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. Nat Protoc 17: 1223-1265.

Xiang JS, Mueller JR, Luo EC, Yee BA, Schafer D, Schmok JC, Tan FE, Rothamel K, McVicar RN, Kwong EM, Croker BA, Jones KL, Her HL, Chen CY, Vu AQ, Jin W, Park SS, Le P, Brannan KW, Kofman ER, Li Y, Tankka AT, Dong KD, Song Y, Clark AE, Carlin AF, Van Nostrand EL, Leibel SL, Yeo GW. (2022 Mar 17) Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. Res Sq :rs.3.rs-1394331.

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 Jan 3) Open problems in extracellular RNA data analysis: insights from an ERCC online workshop. Front Genet 12: 778416.

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 Dec 27) 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.

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 Sept 27) ZFTA-RELA dictates oncogenic transcriptional programs to drive aggressive supratentorial ependymoma. Cancer Discov 11: 2200-2215.

Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart ZD, Pillon MC, Deterding LJ, Borgnia MJ, Stanley RE (2021 Sept 27) Characterization of SARS2 Nsp15 nuclease activity reveals it’s mad about U. Nucleic Acids Res 49: 10136-10149.

Maas-Bauer K, Lohmeyer JK, Hirai T, Ramos TL, Fazal FM, Litzenburger UM, Yost KE, Ribado JV, Kambham N, Wenokur AS, Lin PY, Alvarez M, Mavers M, Baker J, Bhatt AS, Chang HY, Simonetta F, Negrin RS. (2021 Sept 9) Invariant natural killer T-cell subsets have diverse graft-versus-host-disease-preventing and antitumor effects. Blood. 138(10):858-870.

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 Aug 5) Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer. Mol Cell 81: 3048-3064.

Yan F, Zhao Z, Simon LM. (2021 Jul 20). EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data. Patterns (N Y).;2(8):100311.

Jeong HH, Jia J, Dai Y, Simon LM, Zhao Z. (2021 Apr 24). Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches. Genes (Basel).;12(5):635.

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 Feb 18) 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 Jan 27) Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics. Nat Commun 12: 636.

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 Jan 21). Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer. Cell. 184 (2):384-403.e21.

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 Nov 25) Proteogenomic landscape of breast cancer tumorigenesis and targeted therapy. Cell 183: 1436-1456.

Dhindsa RS, Copeland BR, Mustoe AM, Goldstein DB (2020 Jul 2) 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 Mar 10) 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 Feb 6) 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 Oct 14) 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 Oct 8) 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 Sept) Immuno-subtyping of breast cancer reveals distinct myeloid cell profiles and immunotherapy resistance mechanisms. Nat Cell Bio 21: 1113-1126.

Stylianou N, Lehman ML, Wang C, Fard AT, Rockstroh A, Fazli L, Jovanovic L, Ward M, Sadowski MC, Kashyap AS, Buttyan R, Gleave ME, Westbrook TF, Williams ED, Gunter JH, Nelson CC, Hollier BG. (2019 Aug 26) Correction: A molecular portrait of epithelial-mesenchymal plasticity in prostate cancer associated with clinical outcome. Oncogene. 38(13):2436.

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 Jun 20) Development of a selective CDK7 covalent inhibitor reveals predominant cell-cycle phenotype. Cell Chem Biol 26: 792-803.

Stylianou N, Lehman ML, Wang C, Fard AT, Rockstroh A, Fazli L, Jovanovic L, Ward M, Sadowski MC, Kashyap AS, Buttyan R, Gleave ME, Westbrook TF, Williams ED, Gunter JH, Nelson CC, Hollier BG. (2019 Feb) A molecular portrait of epithelial-mesenchymal plasticity in prostate cancer associated with clinical outcome. Oncogene. 38(7):913-934.

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 (2018 Nov 13) 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 Oct 24) A Druggable Genome Screen Identifies Modifiers of α-Synuclein Levels via a Tiered Cross-Species Validation Approach. J Neurosci. 38(43):9286-9301.

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 Apr 5) Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns. Cell 173: 499-514.

Dasgupta S, Rajapakshe K, Zhu B, Nikolai BC, Yi P, Putluri N, Choi JM, Jung SY, Coarfa C, Westbrook TF, Zhang XH, Foulds CE, Tsai SY, Tsai MJ, O'Malley BW. (2018 Apr) Metabolic enzyme PFKFB4 activates transcriptional coactivator SRC-3 to drive breast cancer. Nature 556(7700):249-254.

Zeid R, Lawlor MA, Poon E, Reyes JM, Fulciniti M, Lopez MA, Scott TG, Nabet B, Erb MA, Winter GE, Jacobson Z, Polaski DR, Karlin KL, Hirsch RA, Munshi NP, Westbrook TF, Chesler L, Lin CY, Bradner JE. (2018 Apr) Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma. Nat Genet. 50(4):515-523.

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 Mar 26) Combinatorial inhibition of PTPN12-regulated receptors leads to a broadly effective therapeutic strategy in triple-negative breast cancer. Nat Med 24: 505-511.