Publications
All publications can also be found on Dr. Yeo’s ORCiD page and Pubmed
2024
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Bento: a toolkit for subcellular analysis of spatial transcriptomics data
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 Bio.
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Transcriptome regulation by PARP13 in basal and antiviral states in human cells
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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Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies
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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Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting
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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Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion
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.
2023
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LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function
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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Computational cell–cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment
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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Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics
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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Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM
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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Localized synthesis of molecular chaperones sustains neuronal proteostasis
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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A phage nucleus-associated RNA-binding protein is required for jumbo phage infection
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. bioRxiv [Preprint]
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circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA
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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Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery
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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Xiphoid nucleus of the midline thalamus controls cold-induced food seeking
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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RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression
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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A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.
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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HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence
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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FLARE: A fast and flexible workflow for identifying RNA editing foci
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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Stratification of enterochromaffin cells by single-cell expression analysis
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. (2023). Stratification of enterochromaffin cells by single-cell expression analysis. bioRxiv [Preprint].
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Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration
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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Large-scale map of RNA binding protein interactomes across the mRNA life-cycle
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). BioRxiv [Preprint].
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Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders
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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Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling
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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Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites
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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Proteomic discovery of chemical probes that perturb protein complexes in human cells
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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Remodeling oncogenic transcriptomes by small molecules targeting NONO
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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Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death
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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RNA binding protein DDX5 restricts RORγt+ Treg suppressor function to promote intestine inflammation
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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Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection
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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In vivo screening unveils pervasive RNA-binding protein dependencies in leukemic stem cells and identifies ELAVL1 as a therapeutic target. Blood Cancer Discovery
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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RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding protein
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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An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington’s disease models.
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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Small intestine and colon tissue-resident memory CD8+ T cells exhibit molecular heterogeneity and differential dependence on Eomes
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.
2022
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Engineered U1 snRNAs to modulate alternatively spliced exons
Hatch S. T., Smargon A. A., & Yeo G. W. (2022). Engineered U1 snRNAs to modulate alternatively spliced exons. Methods.
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RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine
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The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.
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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VPS13A and VPS13C influence lipid droplet abundance
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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Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP
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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Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma
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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Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites
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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Aging RNA granule dynamics in neurodegeneration.
Rhine K., Al-Azzam N., Yu T., Yeo G. W. Aging RNA granule dynamics in neurodegeneration. Frontiers in Molecular Biosciences.
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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.
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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Prions induce an early Arc response and a subsequent reduction in mGluR5 in the hippocampus.
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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Examination of the Cell Cycle Dependence of Cytosine and Adenine Base Editors.
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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The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors
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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Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis
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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Illuminating RNA biology through imaging
Le P., Ahmed N., & Yeo G. W. Illuminating RNA biology through imaging. Nature Cell Biology.
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Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans
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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AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay.
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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Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms
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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The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction
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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Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq
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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Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML
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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Crosstalk between CRISPR-Cas9 and the human transcriptome
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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APEX Proximity Labeling of Stress Granule Proteins
Elmsaouri S., Markmiller S., Yeo G. W. APEX Proximity Labeling of Stress Granule Proteins. Methods in Molecular Biology.
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MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy
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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We made the cover of Science Translational Medicine! -
The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients
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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SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp
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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Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings
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Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model
Li H., Lovci M. T., Kwon Y.-S., Rosenfeld M. G., Fu X.-D.§, & Yeo G. W.§. (§ co-corresponding) Proceedings of the National Academy of Sciences USA
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Divergent transcription from active promoters
Seila A. C., Calabrese J. M., Levine S. S., Yeo G. W., Rahl P. B., Flynn R. A., Young R. A., & Sharp P. A. Science
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The PIWI proteins SMEDWI2 and SMEDWI3 are required for stem cell function and piRNA expression in planarians
Palakodeti D., Smielewska M., Liu Y., Yeo G. W.§, & Graveley B. R.§ (§ co-corresponding) RNA
2007
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The EJC factor eIFAIII modulates synaptic strength and neuronal protein expression
Giorgi C., Yeo G. W., Stone M. E., Katz D. B., Burge C., Turrigiano C., & Moore M. J. Cell
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Immunoglobulin light chains in zebrafish: genomic configurations and inversional rearrangements between (V(L)-J(L)C(L)) gene clusters
Zimmerman A. M., Yeo G. W., Howe K., Maddox B. J., & Steiner L. A. Developmental and Comparative Immunology
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Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements in mammalian genomes
Yeo G. W.§, Van Nostrand E. L., & Liang Y. T. (§ corresponding) PLoS Genetics
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Alternative events identified in human embryonic stem cells and neural progenitors
Yeo G. W.§ , Xiang-dong X., Liang Y. T., Muotri A. M., Carson C., Coufal N., & Gage F. H.§. (§ co-corresponding) PLoS Computational Biology
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A regulator of dscam mutually exclusive splicing fidelity
Olson S., Blanchette M., Park J., Savva Y., Yeo G. W., Yeakley J., Rio D., & Graveley B. Nature Structural and Molecular Biology
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RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells
Calabrese J. M., Seila A. C., Yeo G. W., & Sharp P. A. Proceedings pf the National Academy of Sciences USA
2006
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Inference of splicing regulatory activities by sequence neighborhood analysis
Stadler M. B., Shomron N., Yeo G. W., Schneider A., Xiao X., & Burge C. B. PLoS Genetics
2005
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A combinatorial code for splicing silencing: UAGG and GGGG motifs
Han K.§, Yeo G. W.§, An P., Burge C. B., & Grabowski P. (§ co-first authors) PLoS Biology
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Identification and analysis of alternative splicing events conserved in human and mouse
Yeo G. W.§, Van Nostrand E. L., Holste E., Poggio D. T., & Burge C. B.§. (§ co-corresponding) Proceedings of the National Academy of Sciences USA
2004
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Variation in alternative splicing across human tissues
Yeo G. W., Holste D., Kreiman G., & Burge C. B. Genome Biology
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Variation in the splicing regulatory elements and their organization in vertebrate genomes
Yeo G. W., Hoon S., Venkatesh B., & Burge C. B. Proceedings of the National Academy of Sciences USA
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RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
Fairbrother W. G., Yeo G. W., Yeh R., Goldstein P., Mawson M., Sharp P. A., & Burge C. B. Nucleic Acids Research
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Maximum entropy modeling of short sequence motifs with applications to RNA splicing signalsSell it.
Yeo G. W., & Burge C. B. Journal of Computational Biology
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Non-classical splicing mutations in the coding and non-coding regions of the ATM gene: a comparison of cDNA with maximum entropy estimates of splice junction strengths
Eng L., Coutinho G., Nahas S., Yeo G. W., Tanouye R., Drk T., Burge C. B., & Gatti R. A. Human Mutation
2003
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Regularized least-squares classification
Rifkin R., Yeo G. W., & Poggio T. Advances in Learning Theory: Methods, Model and Applications, NATO Science Series III: Computer and System Sciences, Vol. 190, ISO Press, Amsterdam