Publications

Randles, S., Yeo, G. W. RNA dysregulation as a determinant of aging and neurodegenerative vulnerability. Trends in Cell Biology.

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Schafer, D. M., Blue, S. M., Xu, S., Mizrahi, O., Gosztyla, M. L., Street, L., Rothamel, K. L., Kopalle, H., Landry, S. B., Rosales, E. K. F., Tien, R. H., Elmsaouri, S., Coufal, N. G., Jovanovic, M., Yeo, G. W. ARID5A RNA-binding coordinates microglial defense and ferroptosis in iPSCderived models. Nature Communications.

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Tse, J. E., Brothers, W. R., Hayward, R. E., Barbas, S., Sheng, K., Spencer, K. R., DeMeester, K. E., Njomen, E., Williamson, J. R., Liu, D. R., Melillo, B., Yeo, G. W., Cravatt, B. F., Li, H ESCAPE: assigning site-specific activity to covalent ligands in cells by prime editing. bioRxiv [Preprint].

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Fang, J., Lam, D. C., Mah, C. K., Watanabe, R., Tanner, H. M., Comi, T., Cai, Y., Chen, C-Y., te Velthuis, A. J. W., Brangwynne, C. P., Yeo, G. W., Ollmann Saphire, E. Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response. bioRxiv [Preprint].

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Jagannatha, P., Yoon, Y., Landry, S. B. Naritomi, J. T., Zhan, L., Olson, S., Wei, X., Street, L. A., Liu, L., Jeong, J., Quan, C., Reid, J., Soles, L. V., Segeberg, M., Schmok, J. C., Jain, M., Rosales, E. K. F., Chen, V. W., Gosztyla, M. L., Xu, S., Pong, A., Jovanovic, M., Graveley, B. R., Shi, Y., Yeo, G. W. Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection. Molecular Cell.

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Luo, Z., Corchado-Hernandez, A., Brothers, W. R., Aryanpour, Z., Zhao, Z. Z., Zhao, J., Clarke, L., Campbell-Smith, C., Yeo, G. W., Najafabadi, H. S., Fabian, M. R. High-resolution mapping of CCR4-NOT recruitment elements reveals transcriptome-wide drivers of mRNA decay. Cell Systems.

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Chin, A., Bergeman, J., Communal, L., Barutcu, S., Boulais, J., Yeo, G. W., Mes-Masson, A.-M., Lécuyer, E. Localized regulation of cell junction mRNAs is required for epithelial cell integrity. RNA Journal.

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Her, H.-L., Yee, B. A., Xu, S., Boyle, E. A., Rothamel, K. L., Zhao, Z. Z., Blue, S. M., Mueller, J. R., Park, S. S., Nguyen, G. G., Naritomi, J. T., Klie, A., Wei, X., Olson, S., Zhan, L., Aigner, S., Graveley, B. R., Yeo. G. W. Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces. Cell Systems.

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Flanagan, K., Xu, S., Yeo, G. W. Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data. bioRxiv [Preprint]

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Zavolan, M., Yeo, G. W. System-level measurement, modeling, and manipulation of RNA. RNA.

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Sison, S. L.*, Zampa, F.*, Kofman, E. R.*, Choi, S. Y., Jagannatha, P., Nguyen, G. G., Naritomi JT, Shin A, Khorgade A, Jin W, Chen, C.-Y., Sievert, D. M., Mukhopadhyay, S., Mizrahi, O., Blue, S. M., Marina, R. J., Yang, D., Wang, C. C., Pang, Z., Brannan, K. W., Ye, L., Al’Khafaji, A. M., Yeo, G. W.**, Lippi, G.** (*co-first, **co-corresponding). Single-cell and isoform-specific translational profiling of the mouse brain. Nature.

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Yeo, G.W. Organizing research at scale: Reflections on leading multi-team scientific collaborations. Molecular Cell.

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Serres-Bérard, T., Gosztyla, M. L., Nguyen, G., Yeo, G. W., Puymirat, J., Chahine, M. MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy. Elsevier.

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Lindsey, G. L., Hockley, T. K., Gomez, A. V., Marshall, A. C., Brothers, W. R., Finney, C. T., Gross, J., Fox, A. H., Yeo, G. W., Melillo, B., Bond, C. S., Cravatt, B. F.. Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO. Cell Chemical Biology.

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Tankka, A. T., Einstein, J. M., Zhou, C. J., Pham, V. N., Zhang, Y., Naritomi, J. T., Nguyen, G. G., Mendez-Molina, A. N., Hu, Z., Mizrahi, O., Perelis, M., Sarsam, J., Tan, F. E., Kaufman, D. S., Yang, J., Antal, C. E., Yeo, G. W. Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression. Cancer Research.

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Cereda, V. A. M. S., Sharma, A., Flanagan, K., Elmsaouri, S., Steiner, S., Benassi, S., Reis-de-Oliveira, G., Whiteley, J. T., Chandrabhatta, A., Diniz Mendes, A. P., Randolph-Moore, L., Xenitopoulos, D., Jetzer, M., Oefner, R., Benner, C., Santos, R., Yeo, G. W., Marchetto, M. C. Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding. bioRxiv [Preprint]

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Dame, H. B., Kopalle, H., Miñana, B., Klaft, Z., Fahey, J. B., McWatters, D. C., Rao, V., Suresh, R., Aigner, S., Hammer, M. F., Yuskaitis, C. J., Wong, M., Teaney, N., Zhang, C., Thompson, M., Lehner, B., Bennett, C. F., Valcárcel, J., Yeo, G. W., Burge, C. B., Dulla, C. G., Oudin, M. J. A splice-switching antisense oligonucleotide approach for pediatric genetic epilepsies. bioRxiv [Preprint]

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Le, P., Lal, N. K., Xu, S., Mumford, S., Huang, M., Yang, D., Mizrahi, O., Hoover, B., Yee, B., Mei, Y., Rothamel, K., Her, H.-L., Blue, S. M., Shneider, N. A., Yeo, G. W. KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS. bioRxiv [Preprint]

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Huang, M., Ladha, F. A., Wang, Y., Trembley, M. A., Yin, H.-M., Zheng, R., Prondzynski, M., Tharani, Y., Akerberg, A. A., Aigner, S., Yee, B. A., Mayourian, J., Morton, S. U., Bezzerides, V. J., Pu, W. T., Yeo, G. W., Chen, K., Burns, C. G., Burns, C. E. Dosage-sensitive RBFOX2 autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome. bioRxiv [Preprint]

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Gomberg, T. A., Elmsaouri, S., Kopalle, H. M., Baughn, M. W., Beccari, M. S., McAlonis-Downes, M., Artates, J. W., Pant, D., Mak, H., Smargon, A. A., Sander, T. C., Garcia, E., Lee, D. P., Cleveland, D. W., Yeo, G. W. Dual-targeting snRNA gene therapy rescues STMN2 and 1 UNC13A splicing in TDP-432 proteinopathies. bioRxiv [Preprint]

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Glasner, D. R., Todd, C., Cook, B., D’Urso, A., Khosla, S., Estrada, E., Wagner, J. D., Bartels, M. D., Hung, C.-T., Ford, P., Prych, J., Hatch, K. S., Yee, B. A., Ego, K. M., Liang, Q., Holland, S. R., Case, J. B., Corbett, K. D., Diamond, M. S., Lee, B., Yeo, G. W., Herzik, M. A. Jr., Van Nostrand, E. L., Daugherty, M. D. The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition. Nature Microbiology.

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Li, Y., Li, Z., Li, Y., Rhine, K., Ranamukhaarachchi, S., Shuo, Q., Jang, H., Villazon, J., Bai, Z., Fraley, S. I., Yeo, G. W., Fan, R., Shi, L. Imaging Cellular Metabolic Rewiring with SuMMIT-SRS. bioRxiv [Preprint]

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Smargon, A. A., Pant, D., Gomberg, T. A., Fagre, C., Glynne, S., Nguyen, J., Naritomi, J. T., Gilbert, W. V., Yeo, G. W. Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs. Nature Chemical Biology.

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Flores, B. N., Yu, S. B., Cohen, I. V., Fanok, M. H., Luan, W., Maciuca, R. D., Sun, L.D., Tsai, R. M., Vissers, M., Smits, L., Bunte, T. M., Bakardjiev, A., Balasundar, S., Calvert, M. E. K., Chin, M. Y., Dobbins, S. K., Dowdle, W. E., Fang, M., Heuberger, J. A. A. C., Ha, C. L., Huang, F., Miyamoto, T., Osipov, M., Madrid San Martin, L., Saund, K., Tatarakis, D., Vu, A. Q., Xiong, C., Yeo, G. W., Groeneveld, G. J., van den Berg, L. H., Dhuria, S., Estrada, A. A., Jennings, D., Sandmann, T., Ho, C., Scearce-Levie, K., Yulyaningsih, E., Walker, A. K., Di Paolo, G., Kane, L. A., Troyer, M. D., Lewcock, J. W. Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in a randomized clinical trial. Nat Commun.

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Wang, J., Cao, W., Wang, K., Wang, X., Dalvi, A., Prasad, G., Liang, Q., Her. H.-L., Wang, M., Yang, Q., Yeo, G. W., Neal, D. E., Khan, M., Rosin, C. D., Paturi, R., Bergen, L. EvidenceBench: A Benchmark for Extracting Evidence from Biomedical Papers. COLM Conference Papers.

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Xiang, J. S.*, Zhao, K. X., Tadri, L., Tamaru, K., Yee, B. A., Rothamel, K., Schmok, J. C., Mueller, J. R., Park, S. S., Madrigal, A. A., McVicar, R. N., Kwong, E. M., Croker, B. A., Clark, A. E., Carlin, A. F., Acevedo, C., McCole, D., O'Leary, S. E., Hai, R., Leibel, S. L., Yeo, G. W.* Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites. bioRxiv [Preprint']. (*co-corresponding)

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Rhine, K., Epstein, E., Carlson, N. M., Ge, X., Mizrahi, O., Kamat, A., Hermann, A., Brothers, W. R., Ravits, J., Bennett, E. J., Pekkurnaz, G., Yeo, G. W. RNA triggers chronic stress during neuronal aging. bioRxiv [Preprint].

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Mizrahi, O.*, Corley. M.*, Feldman, O.*, Fröhlking, T.*, Sun, L.*, Ziesel, A.*, Antczak, M., Bernetti, M., Elhajjajy, S. I., Huang, W., Nguyen, G. G., Park, S. S., Perez Martell, R. I., Trinity, L., Xu, K., Zok, T., Bussi, G., Jabbari, H., Orenstein, Y., Aviran, S.**, Meyer, M. M.**, Yeo, G. W.** Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data (*co-first; **co-corresponding). RNA.

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Nicholson-Shaw, T., Dowdle, M. E., Ajaj, Y., Perelis, M., Fulzele, A, Yeo, G. W., Bennett, E. J., Lykke-Andersen, J. Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor. RNA.

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Rhine, K., Li, R., Kopalle, H. M., Rothamel, K., Ge, X., Epstein, E., Mizrahi, O., Madrigal, A. A., Her, H.-L., Gomberg, T. A., Hermann, A., Schwartz, J. L., Daniels, A. J., Manor, U., Ravits, J., Signer, R. A. J., Bennett, E. J., Yeo, G. W. Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. Nature Neuroscience.

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Research Briefing

Yu, T., Liang, Q., Xu, S., Yeo, G. W. Identification of RBP binding sites using RNA deaminases. Methods in Enzymology.

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Hsu P.*, Choi E. J.*, Wong W. H., Lin Y. H., Vandenburgh S. A., Liu Y. C., Yao P., Indralingam C. S., Yeo G. W., Zuniga E. I., Goldrath A. W., Wang W.**, Chang J.T.** Foxo1 regulates intestinal tissue–resident memory CD8 T cell biology in an anatomic compartment– and context-specific manner (*co-first; **co-corresponding). Science Immunology

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Song, Y.*, Fothergill, L. J.*, Lee, K. S., Liu, B. Y., Koo, A., Perelis, M., Diwakarla, S., Callaghan, B., Huang, J., Wykosky, J., Furness, J. B.**, & Yeo, G. W.** Stratification of enterochromaffin cells by single-cell expression analysis. (*co-first; **co-corresponding) eLife.

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Tajik A., Tsao E., Jahangiri S., Seale B., Yee B. A., Naritomi J. T., Balde Z., Cathelin S., Keyvani Chahi A., Li L., Chen H. T., Wong N., Liu L., Joshi P., Moreira S., McCloskey C. W., Khan S., Rothamel K. L., Boutzen H., Bansal S., Zeng A. G. X., Aigner S., Lu Y., Dick J. E., Kislinger T., Khokha R., Minden M. D., Gingras A.-C., Yeo G. W., Hope K. J. Stress Granules Underlie Acute Myeloid Leukemia Stem Cell Survival and Stress Adaptation. bioRxiv [Preprint]

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Mei Y., Gosztyla M. L., Tan X., Dozier L. E., Wilkinson B., McKetney J., Lee J., Chen M., Tsai D., Kopalle H., Gritsenko M. A., Hartel N., Graham N. A., Flores I., Gilmore-Hall S. K., Xu S., Marquez C. A., Liu S. N., Fong D., Chen J., Licon K., Hong D., Wright S. N., Kreisberg J. F., Nott A., Smith R. D., Qian W. J., Swaney D. L., Iakoucheva L. M., Krogan N. J., Patrick G. N., Zhou Y., Feng G., Coba M. P.*, Yeo G. W.*, Ideker T* (*co-corresponding). Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. Cell Systems

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Glasner D. R., Todd C., Cook B., D’Urso A., Khosla S., Estrada E., Wagner J. D., Bartels M. D., Ford P., Prych J., Hatch K., Yee B. A., Ego K. M., Liang Q., Holland S. R., Case J. B., Corbett K .D., Diamond M. S., Yeo G. W., Herzik M. A. Jr, Van Nostrand E. L., Daugherty M. D. Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex. bioRxiv [Preprint]

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Qiu X., Kemker C., Goebel G. L., Lampe P., Wallis N., Schiller D., Bigler K., Jiang M., Sievers S., Yeo G. W., Wu P. Phenylpyrazoles as Inhibitors of the m6A RNA-Binding Protein YTHDF2. JACS Au

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Kim H. Y.*, Mizrahi O.*, Lee W., Rosenthal S. B., Han C., Yee B. A., Blue S. M., Diaz J., Jonnalagadda J., Hokutan K., Jang H., Ma C. T., Bobkov A., Sergienko E., Jackson M. R., Stefanovic B., Kisseleva T., Yeo G. W.**, Brenner D. A.** (*co-first; **co-corresponding). LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis. bioRxiv [Preprint].

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Xiang J. S.*, Schafer D. M.*, Rothamel K. L., Yeo G. W. (*co-first). Decoding protein-RNA interactions using CLIP-based methodologies. Nature Reviews Genetics.

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Reina-Campos M.*, Monell A.*, Ferry A., Luna V., Cheung K. P., Galletti G., Scharping N. E., Takehara K. K., Quon S., Challita P. P., Boland B. Lin Y. H., Wong W. H., Indralingam C. S., Neadeau H., Alarcón S., Yeo G. W., Chang J. T., Heeg M.**, Goldrath A. W.** (* co-first; **co-corresponding). Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. Nature.

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Alecki C., Rizwan J., Le P., Jacob-Tomas S., Comaduran M. F., Verbrugghe M., Xu J. M. S., Minotti S., Lynch J., Biswas J., Wu T., Durham H. D., Yeo G. W., Vera M. Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis. Nature Communications.

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Shukla S., Schwartz J. L., Walsh C., Wong W. M., Patel V., Hsieh Y. P., Onwuasoanya C., Chen S., Offenhäusser A., Cauwenberghs G., Santoro F., Muotri A. R., Yeo G. W., Chalasani S. H., Jahed Z. Supra- and sub-threshold intracellular-like recording of 2D and 3D neuronal networks using nanopillar electrode arrays. Microsystems & Nanoengineering.

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Liang Q., Xiang J., Yeo G. W,*, Corbett K. D.*. Rational design yields RNA-binding zinc finger domains with altered sequence specificity (*co-corresponding). RNA.

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Al-azzam N., To J. H., Gautam V., Street L. A., Nguyen C. B., Naritomi J. T., Lam D. C., Madrigal A. A., Lee B., Jin W., Avina A., Mizrahi O., Mueller J. R., Ford W., Schiavon C. R., Rebello E., Vu A. Q., Blue S. M., Madakamutil Y. L., Manor U., Rothstein J. D., Coyne A. N., Jovanovic M., Yeo G. W. Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes. Neuron.

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Schmok J. C., Yeo, G.W. Strategies for programmable manipulation of alternative splicing. Current Opinion in Genetics & Development.

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Anczukow, O., Allain, F. H.-T., Angarola, B. L., Black, D. L., Brooks, A. N., Cheng, C., Conesa, A., Crosse, E. I., Eyras, E., Guccione, E., Lu, S. X., Neugebauer, K. M., Sehgal, P., Song, X., Tothova, Z., Valcárcel, J., Weeks, K. M., Yeo, G. W., Thomas-Tikhonenko, A. Steering research on mRNA splicing in cancer towards clinical translation. Nature Reviews Cancer.

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Street L.*, Rothamel K. L.*, Brannan K. W.*, Jin W., Bokor B., Dong K. D., Rhine K., Madrigal A. A., Al-Azzam N., Kim Kim J., Ma Y., Abdou A., Wolin E., Doron-Mandel E., Ahdout J., Mujumdar M., Jovanovic M.**, Yeo G. W.**. Large-scale map of RNA binding protein interactomes across the mRNA life-cycle (*co-first; **co-corresponding). Molecular Cell.

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Gosztyla, M. L., Zhan, L., Olson, S., Wei, X., Naritomi, J., Nguyen, G., Street, L., Goda, G. A., Cavazos, F. F., Schmok, J. C., Jain, M., Syed, E. U., Kwon, E., Jin, W., Kofman, E.,Tankka, A. T., Li, A., Gonzalez, V., Lécuyer, E., Dominguez, D., Jovanovic, M., Graveley, B. R., Yeo, G. W. Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. Molecular Cell.

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Megagiannis P.*, Mei Y.*, Yan R. E., Yuan L., Wilde J. J., Eckersberg H., Suresh R., Tan X., Chen H., Farmer W. T., Cha K., Le P. U., Catoire H., Rochefort D., Kwan T., Yee B. A., Dion P., Krishnaswamy A., Cloutier J. F., Stifani S., Petrecca K., Yeo G. W., Murai K. K., Feng G., Rouleau G. A., Ideker T.**, Sanjana N. E., Zhou Y.** Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes (*co-first, **co-corresponding). Cell Reports.

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Liang Q.*, Yu T.*, Kofman E., Jagannatha P., Rhine K., Yee B. A., Corbett K. D.**, Yeo G. W.** High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues (*co-first, **co-corresponding). Nature Communications.

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Okholm T. L. H., Kamstrup A. B., Nielsen M. M., Hollensen A. K., Graversgaard M. L., Kristensen L. S., Vang S., Park S. S., Yeo G. W., Dyrskjøt L., Kjems J., Pedersen J. S., Damgaard C. K. circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA. eLife.

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Her, H.-L., Rothamel, K. L., Nguyen, G. G., Boyle, E. A., Yeo, G. W. Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data. Cell Genomics.

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Jagannatha, P., Tankka, A. T., Lorenz, D. A., Yu, T., Yee, B. A., Brannan, K. W., Zhou, C. J., Underwood, J. G., Yeo, G.W. Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution. Genome Research.

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Hawkins, S., Mondaini, A., Namboori, S. C., Nguyen, G. G., Yeo, G. W., Javed, A., Bhinge, A. ePRINT: exonuclease assisted mapping of protein-RNA interactions. Genome Biology.

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Lin, L., Zhao, J., Kubota, N., Li, Z., Lam, Y-L., Nguyen, L. P., Yang, L., Pokharel, S. P., Blue, S. M., Yee, B. A., Chen, R., Yeo, G. W., Chen, C-W., Chen, L., Zheng, S. Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. Neuron.

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Xu S., Nguyen G. G., Naritomi J. T., Kopalle H. M., Yee B. A., Rothamel K. L., Boyle E. A., Yeo G. W. Protocol to process crosslinking and immunoprecipitation data into annotated binding sites. STAR Protocols.

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Mah, C. K., Ahmed, N., Lopez, N. A., Lam, D. C., Pong, A., Monell, A., Kern, C., Han, Y., Prasad, G., Cesnik, A. J., Lundberg, E., Zhu, Q., Carter, H., Yeo, G. W. Bento: a toolkit for subcellular analysis of spatial transcriptomics data. Genome Biology.

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Enustun E., Armbruster E. G., Lee J., Zhang S., Yee B. A., Gu Y., Deep A., Naritomi J. T., Liang Q., Aigner S., Adler B. A., Cress B. F., Doudna J. A., Chaikeeratisak V., Cleveland D. W., Ghassemian M., Yeo G. W., Pogliano J., Corbett K. D.. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. Nucleic Acids Research.

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Busa V. F., Ando Y., Aigner S., Yee B. A., Yeo G. W., Leung A. K. L. Transcriptome regulation by PARP13 in basal and antiviral states in human cells. iScience.

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Medina-Munoz H. C., Kofman E., Jagannatha P., Boyle E. A., Yu T., Jones K. L., Mueller J. R., Lykins G. D., Doudna A. T., Park S. S., Blue S. M., Ranzau B. L., Kohli R. M., Komor A. C., Yeo G. W. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. Nature Communications.

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Keehner, J., Abeles, S. R., Longhurst, C. A., Horton, L. E., Myers, F. E., Riggs-Rodriguez, L., Ahmad, M., Baxter, S., Boussina, A., Cantrell, K., Cardenas, P., De Hoff, P., El-Kareh, R., Holland, J., Ikeda, D., Kurashige, K., Laurent, L. C., SEARCH Alliance Lucas, A., Pride, D., Sathe, S., Tran, A. R., Vasylyeva, T. I., Yeo, G. W., Knight, R., Wertheim, J. O., Torriani, F. J. Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting. Clinical Infectious Diseases.

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Schmok J. C., Jain M., Street L. A., Tankka A. T., Schafer D., Her H-L., Elmsaouri S., Gosztyla M. L., Boyle E. A., Jagannatha P., Luo E-C., Kwon E. J., Jovanovic M., Yeo G. W. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nature Biotechnology.

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Research Summary

Lewis B.M., Cho C.Y., Her, H.-L., Mizrahi O., Hunter T.,* Yeo G.W.* LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function (*co-corresponding). RNA.

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Pong A., Mah C. K., Yeo G. W., Lewis N. E. Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment. Current Opinion in Biotechnology.

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Matteson N. L., Hassler G. W., Kurzban E., Schwab M. A., Perkins S. A., Gangavarapu K., Levy J. I., Parker E., Pride D., Hakim A., De Hoff P. D., Cheung W., Castro-Martinez A., Rivera A., Veder A., Rivera A., Wauer C., Holmes J., Wilson J., Ngo S. N., Plascencia A., Lawrence E. S., Smoot E. W., Eisner E. R., Tsai R., Chacón M., Baer N. A., Seaver P., Salido R. A., Aigner S., Ngo T. T., Barber T., Ostrander T., Fielding-Miller R., Simmons E. H., Zazueta O. E., Serafin-Higuera I., Sanchez-Alavez M., Moreno-Camacho J. L., García-Gil A., Murphy Schafer A. R., McDonald E., Corrigan J., Malone J. D., Stous S., Shah S., Moshiri N., Weiss A., Anderson C., Aceves C. M., Spencer E. G., Hufbauer E. C., Lee J. J., King A. J., Ramesh K. S., Nguyen K. N., Saucedo K., Robles-Sikisaka R., Fisch K. M., Gonias S. L., Birmingham A., McDonald D., Karthikeyan S., Martin N. K., Schooley R. T., Negrete A. J., Reyna H. J., Chavez J. R., Garcia M. L., Cornejo-Bravo J. M., Becker D., Isaksson M., Washington N. L., Lee W., Garfein R. S., Luna-Ruiz Esparza M. A., Alcántar-Fernández J., Henson B., Jepsen K., Olivares-Flores B., Barrera-Badillo G., Lopez-Martínez I., Ramirez-Gonzalez J. E., Flores-León R., Kingsmore S. F., Sanders A., Pradenas A., White B., Matthews G., Hale M., McLawhon R. W., Reed S. L., Winbush T., McHardy I. H., Fielding R. A., Nicholson L., Quigley M. M., Harding A., Mendoza A., Bakhtar O., Browne S. H., Olivas Flores J., Rincon Rodrı́guez D. G., Gonzalez Ibarra M., Robles Ibarra L. C., Arellano Vera B. J., Gonzalez Garcia J., Harvey-Vera A., Knight R., Laurent L. C., Yeo G. W., Wertheim J. O., Ji X., Worobey M., Suchard M. A., Andersen K. G., Campos-Romero A., Wohl S., Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell.

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Boyle E.A., Goldberg G., Schmok J.C., Burgado J., Izidro Layng F., Grunwald H.A., Balotin K.M., Cuoco M.S., Chang K.C., Ecklu-Mensah G., Arakaki A.K.S., Ahmed N., Garcia Arceo X., Jagannatha P., Pekar J., Iyer M.; DASL Alliance; Yeo G.W. Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM. PLoS ONE

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Alecki C., Rizwan J., Le P., Jacob-Tomas S., Xu S., Minotti S., Wu T., Durham H., Yeo G. W., Vera M. Localized synthesis of molecular chaperones sustains neuronal proteostasis. bioRxiv [Preprint].

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Okholm T. L. H., Kamstrup A. B., Nielsen M. M., Hollensen A. K., Graversgaard M. L., Kristensen L. S., Vang S., Park S. S., Yeo G. W., Dyrskjøt L., Kjems J., Pedersen J. S., Damgaard C. K. circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA. bioRxiv [Preprint].

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Liu Z., Wang J., Shi Y., Yee B. A., Terrey M., Zhang Q., Lee J. C., Lin K. I., Wang A. H., Ackerman S. L., Yeo G. W., Cui H., Yang X. L. Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery. Nucleic Acids Research.

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Lal N. K., Le P., Aggarwal S., Zhang A., Wang K., Qi T., Pang Z., Yang D., Nudell V., Yeo G. W., Banks A. S., & Ye L. (2023). Xiphoid nucleus of the midline thalamus controls cold-induced food seeking. Nature.

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Abe Y., Kofman E. R., Almeida M., Ouyang Z., Ponte F., Mueller J. R., Cruz-Becerra G., Sakai M., Prohaska T. A., Spann N. J., Resende-Coelho A., Seidman J. S., Stender J. D., Taylor H., Fan W., Link V. M., Cobo I., Schlachetzki J. C. M., Hamakubo T., Jepsen K., Sakai J., Downes M., Evans R. M., Yeo G. W., Kadonaga J. T., Manolagas S. C., Rosenfeld M. G., Glass C. K. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. Molecular Cell.

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Antal C. E., Oh T. G., Aigner S., Luo E.-C.,Yee B. A., Campos T., Tiriac H., Rothamel K. L., Cheng Z., Jiao H., Wang A., Hah N., Lenkiewicz E., Lumibao J. C., Truitt M. L., Estepa G., Banayo E., Bashi S., Esparza E., Munoz R. M., Diedrich J. K., Sodir N. M., Mueller J. R., Fraser C. R., Borazanci E., Propper D., Von Hoff D. D., Liddle C., Yu R. T., Atkins A. R., Han H., Lowy A. M., Barrett M. T., Engle D. D., Evan G. I., Yeo G. W., Downes M., Evans R. M. (2023). A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. Nature Communications.

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Jin W., Brannan K. W., Kapeli K., Park S. S., Tan H. Q., Gosztyla M. L., Mujumdar M., Ahdout J., Henroid B., Rothamel K., Xiang J. S., Wong L., & Yeo G. W. (2023). HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence. Molecular Cell.

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Kofman E., Yee B., Medina-Munoz H. C., Yeo G. W. FLARE: a fast and flexible workflow for identifying RNA editing foci. BMC Bioinformatics.

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Correia J. C., Jannig P. R., Gosztyla M. L., Cervenka I., Ducommun S., Praestholm S. M., Dumont K., Liu Z., Liang Q., Edsgaerd D., Emanuelsson O., Gregorevic P., Westerblad H., Venckunas T., Brazaitis M., Kamandulis S., Lanner J. T., Yeo G. W., Ruas J. L.* Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration. (*corresponding). BioRxiv [Preprint].

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Smargon A. A., Morelli K. M., Yeo G. W. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders. RNA.

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Kejiou N. S., Ilan L., Aigner S.,Luo E., Tonn T., Ozadam H., Lee M., Cole G. B., Rabano I., Rajakulendran N., Yee B. A., Najafabadi H. S., Moraes T. F., Angers S., Yeo G. W., Cenik C., Palazzo A. F.. Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling. Nucleic Acids Research.

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Boyle E. A., Her H-L., Mueller J. R., Naritomi J. T., Nguyen G. G., & Yeo G. W. Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. Cell Genomics.

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Lazear M. R., Remsberg J. R., Jaeger M. G., Rothamel K., Her H-L., DeMeester K. E., Njomen E., Hogg S. J., Rahman J., Whitby L. R., Won S. J., Schafroth M. A., Ogasawara D., Yokoyama M., Lindsey G. L., Li H., Germain J., Barbas S., Vaughan J., Hanigan T. W., Vartabedian V. F., Reinhardt C. J., Dix M. M., Koo S. J., Heo I., Teijaro J. R., Simon G. M., Ghosh B., Abdel-Wahab O., Ahn K., Saghatelian A., Melilo B., Schreiber S. L., Yeo G. W., Cravatt B. F. Molecular Cell.

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Kathman S. G.*†, Koo S. J.†, Lindsey G. L.†, Her H.-L., Blue S. M., Li H., Jaensch S., Remsberg J. R., Ahn K.*, Yeo G. W.*, Ghosh B.*, & Cravatt B. F.* (2023). Remodeling oncogenic transcriptomes by small molecules targeting NONO (*co-corresponding; †co-first). Nature Chemical Biology.

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Arif W., Mathur B., Saikali M. F., Chembazhi U. V., Toohill K., Song Y. J., Hao Q., Karimi S., Blue S. M., Yee B. A., Van Nostrand E. L., Bangru S., Guzman G., Yeo G. W., Prasanth K. V., Anakk S., Cummins C. L., & Kalsotra A. (2023). Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death. Nature Communications.

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Ma S., Yang Q., Chen N., Zheng A., Abbasi N., Wang G., Patel P. R., Cho B. S., Yee B. A., Zhang L., Chu H., Evans S. M., Yeo G. W., Zheng Y., Huang W. J. M.. RNA binding protein DDX5 restricts RORγt+ Treg suppressor function to promote intestine inflammation. Science Advances.

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Quezada L. K., Jin W., Liu Y. C., Kim E. S., He Z., Indralingam C. S., Tysl T., Labarta-Bajo L., Wehrens E. J., Jo Y., Kazane K. R., Hattori C., Zuniga E. I., Yeo G. W., & Chang J. T. (2023). Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. PLoS Biology.

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Vujovic A., de Rooij L., Keyvani Chahi A., Chen H.T., Yee B. A., Loganathan S. K., Liu L., Chan D. C. H., Tajik A., Tsao E., Moreira S., Joshi P., Xu J., Wong N., Balde Z., Jahangiri S., Zandi S., Aigner S., Dick J. E., Minden M.D., Schramek D., Yeo G.W., Hope K. J. (2023). In vivo screening unveils pervasive RNA-binding protein dependencies in leukemic stem cells and identifies ELAVL1 as a therapeutic target. Blood Cancer Discovery.

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Benoit Bouvrette L. P., Wang X., Boulais J., Kong, J., Syed E. U., Blue S. M., Zhan L., Olson S., Stanton R., Wei X., Yee B., Van Nostrand E. L., Fu X. -D., Burge C. B., Graveley B. R., Yeo G. W., & Lécuyer E. (2023). RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins. Nucleic Acids Research.

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Morelli K. H., Wu Q., Gosztyla M. L., Liu H., Yao M., Zhang C., Chen J., Marina R. J., Lee K., Jones K. L., Huang M. Y., Li A., Smith-Geater C., Thompson L. M., Duan W., & Yeo G. W. An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington’s disease models. Nature Neuroscience.

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Lin Y. H., Duong H. G., Limary A. E., Kim E. S., Hsu P., Patel S. A., Wong W. H., Indralingam C. S., Liu Y. C., Yao P., Chiang N. R., Vandenburgh S. A., Anderson T. R., Olvera J. G., Ferry A., Takehara K. K., Jin W., Tsai M. S., Yeo G. W., Goldrath A. W., Chang J. T. Small intestine and colon tissue-resident memory CD8+ T cells exhibit molecular heterogeneity and differential dependence on Eomes. Immunity.

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Hatch S. T., Smargon A. A., & Yeo G. W. (2022). Engineered U1 snRNAs to modulate alternatively spliced exons. Methods.

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Long T., Abbasi N., Hernandez J. E., Li Y., Sayed I. M., Ma S., Iemolo A.,Yee B. A., Yeo G. W., Telese F., Ghosh P., Das S., & Huang W. J. M. RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. Gut.

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Kanbar J. N., Ma S., Kim E. S., Kurd N. S., Tsai M. S., Tysl T., Widjaja C. E., Limary A. E., Yee B. A., He Z., Hao Y., Fu X. -D., Yeo G. W., Huang W. J., & Chang J. T. (2022). The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. Journal of Experimental Medicine.

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Chen S., Roberts M. A., Chen C. -Y., Markmiller S., Wei H. -G., Yeo G. W., Granneman J. G., Olzmann J. A., & Ferro-Novick S. VPS13A and VPS13C influence lipid droplet abundance. Contact.

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Lorenz D. A., Her H. -L., Shen K. A., Rothamel K., Hutt K. R., Nojadera A. C., Bruns S. C., Manakov S. A., Yee B. A., Chapman K. B.*, Yeo G. W.* Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP (*co-corresponding). Nature Methods.

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Kameda-Smith M. M., Zhu H., Luo E. -C., Suk Y., Xella A., Yee B. A., Chokshi C., Xing S., Tan F., Fox R. G., Adile A. A., Bakhshihyan D., Brown K., Gwynne W. D., Subapanditha M., Miletic P., Picard D., Burns I., Moffat J., Paruch K., Fleming A., Hope K., Provias J. P., Remke M., Lu Y., Reya T., Venugopal C., Reimand J., Wechsler-Reya R. J.*, Yeo G. W.*, Singh S. K.* Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma (*co-corresponding). Nature Communications.

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Her H.-L., Boyle E. A., Yeo G. W. Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites. Bioinformatics Advances.

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Rhine K., Al-Azzam N., Yu T., Yeo G. W. Aging RNA granule dynamics in neurodegeneration. Frontiers in Molecular Biosciences.

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Karthikeyan S., Levy J. I., De Hoff P., Humphrey G., Birmingham A., Jepsen K., Farmer S., Tubb H. M., Valles T., Tribelhorn C. E., Tsai R., Aigner S., Sathe S., Moshiri N., Henson B., Mark A. M., Hakim A., Baer N. A., Barber T., … Laurent L. C., Yeo G. W., Andersen K. G., Knight R. (2022). Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature.

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Ojeda-Juárez D., Lawrence J. A., Soldau K., Pizzo D. P., Wheeler E., Aguilar-Calvo P., Khuu H., Chen J., Malik A., Funk G., Nam P., Sanchez H., Geschwind M. D., Wu C., Yeo G. W., Chen X., Patrick G. N., & Sigurdson C. J. Prions induce an early Arc response and a subsequent reduction in mGluR5 in the hippocampus. Neurobiology of Disease.

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Burnett C. A., Wong A. T., Vasquez C. A., McHugh C. A., Yeo G. W., Komor A. C. Examination of the Cell Cycle Dependence of Cytosine and Adenine Base Editors. Frontiers in Genome Editing.

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Liu L., Vujovic A., Deshpande N. P., Sathe S., Anande G., Chen H. T. T., Xu J., Minden M. D., Yeo G. W., Unnikrishnan A., Hope K. J., Lu Y. The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors. Nature Communications.

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Krach F., Wheeler E. C., Regensburger M., Boerstler T., Wend H., Vu A. Q., Wang R., Reischl S., Boldt K., Batra R., Aigner S., Ravits J., Winkler J., Yeo G. W., Winner B. Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. Acta Neuropathologica.

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Le P., Ahmed N., & Yeo G. W. Illuminating RNA biology through imaging. Nature Cell Biology.

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Tang X. -Z. E., Tan S. X., Hoon S., & Yeo G. W. (2022). Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans. Nature Medicine.

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Cho H., Abshire E. T., Popp M. W., Pröschel C., Schwartz J. L., Yeo G. W., Maquat L. E. AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay. Molecular Cell.

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Nicholson-Shaw A. L., Kofman E. R., Yeo G. W., Pasquinelli A. E.. Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. Nucleic Acids Research.

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Moshiri N., Fisch K. M., Birmingham A., DeHoff P., Yeo G. W., Jepsen K., Laurent L. C., Knight R. The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction. Scientific Reports.

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Blue S. M., Yee B. A., Pratt G. A., Mueller J. R., Park S. S., Shishkin A. A., Starner A. C., Van Nostrand E. L., & Yeo G. W. Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. Nature Protocols.

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Krivdova G., Voisin V., Schoof E. M., Marhon S. A., Murison A., McLeod J. L., Gabra M. M., Zeng A. G. X., Aigner S., Yee B. A., Shishkin A. A., Van Nostrand E. L., Hermans K. G., Trotman-Grant A. C., Mbong N., Kennedy J. A., Gan O. I., Wagenblast E., De Carvalho D. D., Salmena L., Minden M. D., Bader G. D., Yeo G. W, Dick J. E., Lechman E. R. Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML. Cell Reports.

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Smargon A. A., Madrigal A. A., Yee B. A., Dong K. D., Mueller J. R., Yeo G. W.. Crosstalk between CRISPR-Cas9 and the human transcriptome. Nature Communications.

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Elmsaouri S., Markmiller S., Yeo G. W. APEX Proximity Labeling of Stress Granule Proteins. Methods in Molecular Biology.

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Morelli K. H., Jin W., Shathe S., Madrigal A. A., Jones K. L., Schwartz J. L., Bridges T., Mueller J. R., Shankar A., Chaim I. A., Day J. W., Yeo G. W. MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy. Science Translational Medicine.

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Gonzalez C. G., Mills R. H., Kordahi M. C., Carrillo-Terrazas M., Secaira-Morocho H., Widjaja C. E., Tsai M. S., Mittal Y., Yee B. A., Vargas F., Weldon K., Gauglitz J. M., Delaroque C., Sauceda C., Rossitto L. A., Ackermann G., Humphrey G., Swafford A. D., Siegel C. A., Buckey J. C. Jr, Raffals L. E., Sadler C., Lindholm P., Fisch K. M., Valaseck M., Suriawinata A., Yeo G. W., Ghosh P., Chang J. T., Chu H., Dorrestein P., Zhu Q., Chassaing B., Knight R., Gonzalez D. J., Dulai P. S. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients. Cellular and Molecular Gastroenterology and Hepatology.

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Cantú V. J., Salido R. A., Huang S., Rahman G., Tsai R., Valentine H., Magallanes C. G., Aigner S., Baer N. A., Barber T., Belda-Ferre P., Betty M., Bryant M., Casas Maya M., Castro-Martínez A., Chacón M., Cheung W., Crescini E. S., De Hoff P., Eisner E., Farmer S., Hakim A., Kohn L., Lastrella A. L., Lawrence E. S., Morgan S. C., Ngo T. T., Nouri A., Plascencia A., Ruiz C. A., Sathe S., Seaver P., Shwartz T., Smoot E. W., Ostrander R. T., Valles T., Yeo G. W., Laurent L. C., Fielding-Miller R., Knight R.. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. mSystems.

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Cantú V. J., Sanders K., Belda-Ferre P., Salido R. A., Tsai R., Austin B., Jordan W., Asudani M., Walster A., Magallanes C. G., Valentine H., Manjoonian A., Wijaya C., Omaleki V., Aigner S., Baer N. A., Betty M., Castro-Martínez A., Cheung W., De Hoff P., Eisner E., Hakim A., Lastrella A. L., Lawrence E. S., Ngo T. T., Ostrander T., Plascencia A., Sathe S., Smoot E. W., Carlin A. F., Yeo G. W., Laurent L. C., Manlutac A. L., Fielding-Miller R., Knight R. Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings. mSystems. 2022 Aug 30;7(4):e0010922. doi: 10.1128/msystems.00109-22. Epub 2022 Jun 15. PMID: 35703436; PMCID: PMC9426498

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Cantú V. J., Belda-Ferre P., Salido R. A., Tsai R., Austin B., Jordan W., Asudani M., Walster A., Magallanes C. G., Valentine H., Manjoonian A., Wijaya C., Omaleki V., Sanders K., Aigner S., Baer N. A., Betty M., Castro-Martínez A., Cheung W., Crescini E. S., De Hoff P., Eisner E., Hakim A., Kapadia B., Lastrella A. L., Lawrence E. S., Ngo T. T., Ostrander T., Sathe S., Seaver P., Smoot E. W., Carlin A. F., Yeo G. W., Laurent L. C., Manlutac A. L., Fielding-Miller R., Knight R. Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings. mSystems.

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Martinez N. M., Su A., Burns M. C., Nussbacher J. K., Schaening C., Sathe S., Yeo G. W., Gilbert W. V. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. Molecular Cell.

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