Publications
All publications can also be found on Dr. Yeo’s ORCiD page and Pubmed
2024
-
Identification of RBP binding sites using RNA deaminases
Yu, T., Liang, Q., Xu, S., Yeo, G. W. Identification of RBP binding sites using RNA deaminases. Methods of Enzymology.
-
Supra- and sub-threshold intracellular-like recording of 2D and 3D neuronal networks using nanopillar electrode arrays
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.
-
Rational design yields RNA-binding zinc finger domains with altered sequence specificity
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.
-
Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes
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.
-
Strategies for programmable manipulation of alternative splicing
Schmok J. C., Yeo, G.W. Strategies for programmable manipulation of alternative splicing. Current Opinion in Genetics & Development.
-
Steering research on mRNA splicing in cancer towards clinical translation
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.
-
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). Molecular Cell.
-
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation
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.
-
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes
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.
-
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues
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.
-
Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data
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.
-
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
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.
-
ePRINT: exonuclease assisted mapping of protein-RNA interactions
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.
-
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size
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.
-
Protocol to process crosslinking and immunoprecipitation data into annotated binding sites
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.
-
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 Biology.
-
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. Nucleic Acids Research.
-
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.
-
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.
-
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.
-
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
-
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.
-
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.
-
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.
-
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
-
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].
-
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].
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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].
PDF -
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].
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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
-
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.
-
RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
Illuminating RNA biology through imaging
Le P., Ahmed N., & Yeo G. W. Illuminating RNA biology through imaging. Nature Cell Biology.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
PDF
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.
-
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.
-
Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings
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
-
Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings
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.
-
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing
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.
2021
-
A multi-scale map of cell structure fusing protein images and interactions
Qin Y., Huttlin E. L., Winsnes C. F., Gosztyla M. L., Wacheul L., Kelly M. R., Blue S. M., Zheng F., Chen M., Schaffer L.V., Licon K., Backstrom A., Vaites L. P., Lee J. J., Ouyang W., Liu S. N., Zhang T., Silva E., Park J., Pitea A., Kreisberg J. F., Gygi S. P., Ma J., Harper J. W., Yeo G. W., Lafontaine D. L. J., Lundberg E., Ideker T. Nature
-
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies
Fenix A. M., Miyaoka Y., Bertero A., Blue S. M., Spindler M. J., Tan K. K. B., Perez-Bermejo J., Chan A. H., Mayer S. J., Nguyen T., Russell C. R., Lizarraga P., Truong A., So P-L., Kulkarni A., Chetal K., Sathe S., Sniadecki N. J., Yeo G. W., Murry C. E., Conklin B. R., Salomonis N. Nature Communications
-
Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce
Keehner J., Horton L. E., Binkin N. J., Laurent L.C. on behalf of the SEARCH Alliance Collaborators, Longhurst C. A., Abeles S. R., Torriani F.J. The New England Journal of Medicine
-
Integrative RNA-omics discovers GNAS alternative splicing as a phenotypic driver of splicing factor-mutant neoplasms
Wheeler E. C., Vora S., Mayer D., Kotini A. G., Olszewska M., Park S., Guccione E., Teruya-Feldstein J., Silverman L., Sunahara R., Yeo G. W.*, Papapetrou E. P.* (*co-corresponding). Cancer Discovery
-
Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress
Markmiller S., Sathe S., Server K. L., Nguyen T. B., Fulzele A., Cody N., Javaherian A., Broski S., Finkbeiner S., Bennett E. J., Lecuyer E., Yeo G. W. Cell Reports
-
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
Corley M. E., Flynn R. A., Blue S. M., Yee B. A., Chang H. Y., Yeo G. W.STAR Protocols
-
Non-microRNA binding competitively inhibits LIN28 regulation.
Tan F. E.*, Sathe S.*, Wheeler E. C., Yeo G. W. (*co-first). Cell Reports
-
Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs
Salido R. A., Cantú V. J., Clark A. E., Leibel S. L., Foroughishafiei A., Saha A., Hakim A., Nouri A., Lastrella A. L., Castro-Martínez A., Plascencia A., Kapadia B., Xia B., Ruiz C., Marotz C. A., Maunder D., Lawrence E. S., Smoot E. W., Eisner E., Crescini E. S., Kohn L., Franco Vargas L., Chacón M., Betty M., Machnicki M., Wu M. Y., Baer N. A., Belda-Ferre P., De Hoff P., Seaver P., Ostrander R. T., Tsai R., Sathe S., Aigner S., Morgan S. C., Ngo T. T., Barber T., Cheung W., Carlin A. F., Yeo G. W., Laurent L. C., Fielding-Miller R., Knight R. mSystems
-
Emergence of an early SARS-CoV-2 epidemic in the United States
Zeller M., Gangavarapu K., Anderson C., Smither A. R., Vanchiere J. A., Rose R., Snyder D. J., Dudas G., Watts A., Matteson N. L., Robles-Sikisaka R., Marshall M., Feehan A. K., Sabino-Santos Jr G., Bell-Kareem A. R., Hughes L. D., Alkuzweny M., Snarski P., Garcia-Diaz J., Scott R. S., Melnik L. I., Klitting R., McGraw M., Belda-Ferre P., DeHoff P., Sathe S., Marotz C., Grubaugh N. D., Nolan D. J., Drouin A. C., Genemaras K. J., Chao K., Topol S., Spencer E., Nicholson L., Aigner S., Yeo G. W., Farnaes L., Hobbs C. A., Laurent L. C., Knight R., Hodcroft E. B., Khan K., Fusco D. N., Cooper V. S., Lemey P., Gardner L., Lamers S. L., Kamil J. P., Garry R. F., Suchard M. A., Andersen K. G. Cell
-
Huntington’s disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization
Sanchez I. I., Nguyen T. B., England W. E., Lim R. G., Vu A. Q., Miramontes R., Byrne L. M., Markmiller S., Lau A. L., Orellana I., Curtis M. A., Faull R. L. M., Yeo G. W., Fowler C. D., Reidling J. C., Wild E. J., Spitale R. C., Thompson L. M. The Journal of Clinical Investigation
-
Adar and hnRNP C deficiency synergize in activating endogenous dsRNA-induced type I IFN responses
Herzner A.-M., Khan Z., Van Nostrand E. L., Chan S., Cuellar T., Chen R., Pechuan-Jorge X., Komuve L., Solon M., Modrusan Z., Haley B., Yeo G. W., Behrens T. W., Albert M. L. Journal of Experimental Medicine
-
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Einstein J. M., Perelis M., Chaim I. A., Meena J. K., Nussbacher J. K., Tankka A. T., Yee B. A., Li H., Madrigal A. A., Neill N. J., Shankar A., Tyagi S., Westbrook T. F., Yeo G. W. Molecular Cell
-
Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County
Morgan S. C.*, Aigner S.*, Anderson C.*, Belda-Ferre P.*, De Hoff P.*, Marotz C. A.*, Sathe S.*, Zeller M.*, The EXCITE Team, Andersen K. G.**, Farnaes L.**, Knight R.**, Yeo G. W.**, Laurent LC.** (#co-first; ##co-corresponding). medRxiv [Preprint].
-
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes
Brannan K. W., Chaim I. A., Marina R. J., Yee B. A., Kofman E. R., Lorenz D. A., Jagannatha P., Dong K. D., Madrigal A. A., Underwood J. G., Yeo G. W. Nature Methods
-
Emergence and rapid transmission of SARS-CoV-2B.1.1.7 in the United States
Washington N. L., Gangavarapu K., Zeller M., Bolze A., Cirulli E. T., Schiabor Barrett K. M., Larsen B. B., Anderson C., White S., Cassens T., Jacobs S., Levan G., Nguyen J., Ramirez J. M., Rivera-Garcia C., Sandoval E., Wang X., Wong D., Spencer E., Robles-Sikisaka R., Kurzban E., Hughes L. D., Deng X., Wang C., Servellita V., Valentine H., De Hoff P., Seaver P., Sathe S., Gietzen K., Sickler B., Antico J., Hoon K., Liu J., Harding A., Bakhtar O., Basler T., Austin B., Isaksson M., Febbo P., Becker D., Laurent M., McDonald E., Yeo G. W., Knight R., Laurent L. C., de Feo E., Worobey M., Chiu C., Suchard M. A., Lu J. T., Lee W., Andersen K. G. Cell
-
Loss of LUCJL2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS
Jourdain A. A., Begg B. E., Mick E., Shah H., Calvo S. E., Skinner O. S., Sharma R., Blue S. M., Yeo G. W., Burge C. B., Mootha V. Molecular Cell
-
S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hIPSCs and in vivo models of ALS/FTD
Pirie E., Oh C. K., Zhang X., Han X., Cieplak P., Scott H. R., Deal A. K., Ghatak S., Martinez F. J., Yeo G. W., Yates J. R. 3rd, Nakamura T., Lipton S. A. Proceedings of the National Academy of Sciences
-
A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation
Davis A. G., Einstein J. M., Zheng D., Jayne N. D., Fu X. D., Tian B., Yeo G. W., Zhang D. E. Blood Advances
-
Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment
Trujillo C. A., Rice E. S., Schaefer N. K., Chaim I. A., Wheeler E. C., Madrigal A. A., Buchanan J., Preissl S., Wang A., Priscilla N. D., Szeto R. A., Herai R. H., Huseynov A., Ferraz M. S. A., Borges F. S., Kihara A. H., Byrne A., Marin M., Vollmers C., Brooks A. N., Lautz J. D., Semendeferi K., Shapiro B., Yeo G. W., Smith S. E. P., Green R. E., Muotri A. R. Science
2020
-
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression
Okholm T. L. H., Sathe S., Park S. S., Kamstrup A. B., Rasmussen A. M., Shankar A., Chua Z. M., Fristrup N., Nielsen M. M., Vang S., Dyrskjor L., Aigner S., Damgaard C. K., Yeo G. W., Pedersen J. S. Genome Medicine
-
Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-protein Interfaces
Corley M., Flynn R. A., Lee B., Blue S. M., Chang H. Y., Yeo G. W.Molecular Cell
-
Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies
Schwartz J. L., Jones K. L., Yeo G. W. Critical Reviews in Biochemistry and Molecular Biology
-
Zmat3 is a Key Splicing Regulatory in the p53 Tumor Suppression Program
Bieging-Rolett K. T., Kaiser A. M., Morgens D. W., Boutelle A. M., Seoane J. A., Van Nostrand E. L., Zhu C., Houlihan S. L., Mello S. S., Yee B. A., McClendon J., Pierce S. E., Winters I. P., Wang M., Connolly A. J., Lowe S. W., Curtis C., Yeo G. W., Winslow M. M., Bassik M. C., Attardi L. D. Molecular Cell
-
Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing
Marina R. J., Brannan K. W., Dong K. D., Yee B. A., Yeo G. W.Cell Reports
-
Base editing: advances and therapeutic opportunities
Porto E. M., Komor A. C., Slaymaker I. M., Yeo G. W. Nature Reviews Drug Discovery
-
The Thermus thermophilus DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism
Donsbach P., Yee B. A., Sanchez-Hevia D., Berenguer J., Aigner S., Yeo G. W., Klostermeier D. RNA
-
Context-dependent functional compensation between Ythdf m6a reader proteins
Lasman L., Krupalnik V., Viukov S., Mor N., Aguilera-Castrejon A., Schneir D., Bayerl J., Mizrahi O., Peles S., Tawil S., Sathe S., Nachshon A., Shani T., Zerbib M., Kilimnik I., Aigner S., Shankar A., Mueller J. R., Schwartz S., Stern-Ginossar N., Yeo G. W., Geula S., Novershtern N., Hanna J. H Genes & Development
-
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation
Van Nostrand J. L., Hellberg K., Luo E.-C., Van Nostrand E. L., Dayn A., Yu J., Shokhirev M. N., Dayn Y., Yeo G. W., Shaw R. J. Genes & Development
-
The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1
Batra R., Nelles D. A., Roth D. M., Krach F., Nutter C. A., Tadokoro T., Thomas J. D., Sznajder L., Blue S. M., Gutierrez H., Liu P., Aigner S., Platoshyn O., Miyanohara A., Marsala M., Swanson M. S., Yeo G. W. Nature Biomedical Engineering
-
An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia
Bajaj J., Hamilton M., Shima Y., Chambers K., Spinler K., Van Nostrand E., Yee B. A., Blue S. M., Chen M., Rizzeri D., Chuah C., Oehler V. G., Broome H. E., Sasik R., Scott-Browne J., Rao A., Yeo G. W., Reya T. Nature Cancer
-
Transcriptome-wide analysis of PGC-1a-binding RNAs identifies genes linked to glucagon metabolic action
Tavares C. D. §, Aigner S. §, Sharabi K., Sathe S., Mutli B., Yeo G. W., Puigserver P. (§ co-first author) Proceedings of the National Academy of Sciences
-
Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses
Boland B., He Z. R., Tsai M. S., Olvera J. G., Omilusik K., Duong H., Kim E., Limary A., Jin W., Milner J. J., Yu B. F., Patel S., Tiani L., Tysl T., Kurd N., Bortnick A., Quezada L., Kanbar J., Miralles A., Huylebroeck D., Valasek M. A., Dulai P., Singh S., Lu L. F., Bui J., Murre C., Sandborn W. J., Goldrath A. W., Yeo G. W. §, Chang J. T. § (§ co-corresponding) Science Immunology
-
G4C2 Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD
Coyne A., Zaepfel B., Hayes L., Fitchman B., Salzberg Y., Luo E. C., Bowen K., Trost H., Aigner S., Rigo F., Yeo G. W., Harel A., Svendsen C. N., Sareen D., Rothstein J. D. Neuron
-
Conserved metabolite regulation of stress granule assembly via AdoMet
Begovich K., Vu A. Q., Yeo G. W., Wilhelm J. E. Journal of Cell Biology
-
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis
Abbasi N., Long T., Li Y., Yee B. A., Cho B. S., Hernandez J. E., Ma E., Patel P. R., Sahoo D., Sayed I. M., Varki N., Das S., Ghosh P., Yeo G. W., Huang W. J. M. Life Science Alliance
-
Large-scale tethered function assays identify factors that regulate mRNA stability and translation
Luo E. C., Nathanson J. L., Tan F. E., Schwartz J. L., Schmok J. C., Shankar A., Markmiller S., Yee B. A., Sathe S., Pratt G. A., Scaletta D. B., Ha Y., Hill D. E., Aigner S., Yeo G. W.Nature Structural and Molecular Biology
-
Perspectives on ENCODE
ENCODE Project Consortium, Snyder M. P., Gingeras T. R., Moore J. E., Weng Z., Gerstein M. B., Ren B., Hardison R. C., Stamatoyannopoulos J. A., Graveley B. R., Feingold E. A., Pazin M. J., Pagan M., Gilchrist D. A., Hitz B. C., Cherry J. M., Bernstein B. E., Mendenhall E. M., Zerbino D. R., Frankish A., Flicek P., Myers R. M. Nature
-
Expanded encyclopaedias of DNA elements in the human and mouse genomes
ENCODE Project Consortium, Moore J. E., Purcaro M. J., Pratt H. E., Epstein C. B., Shoresh N., Adrian J., Kawli T., Davis C. A., Dobin A., Kaul R., Halow J., Van Nostrand E. L., Freese P., Gorkin D. U., Shen Y., He Y., Mackiewicz M., Pauli-Behn F., Williams B. A., Mortazavi A., Keller C. A., Zhang X. O., Elhajjajy S. I., Huey J., Dickel D. E., Snetkova V., Wei X., Wang X., Rivera-Mulia J. C., Rozowsky J., Zhang J., Chhetri S. B., Zhang J., Victorsen A., White K. P., Visel A., Yeo G. W., Burge C. B., Lécuyer E., Gilbert D. M., Dekker J., Rinn J., Mendenhall E. M., Ecker J. R., Kellis M., Klein R. J., Noble W. S., Kundaje A., Guigó R., Farnham P. J., Cherry J. M., Myers R. M., Ren B., Graveley B. R., Gerstein M. B., Pennacchio L. A., Snyder M. P., Bernstein B. E., Wold B., Hardison R. C., Gingeras T. R., Stamatoyannopoulos J. A., Weng Z. Nature
-
A large-scale binding and functional map of human RNA-binding proteins
Van Nostrand E. L., Freese P., Pratt G. A., Wang X., Wei X., Xiao R., Blue S. M., Chen J.-Y., Cody N. A. L., Dominguez D., Olson S., Sundararaman B., Zhan L., Bazile C., Bouvrette L. P. B., Bergalet J., Duff M. O., Garcia K. E., Gelboin-Burkhart C., Hochman M., Lambert N. J., Li H., Nguyen T. B., Palden T., Rabano I., Sathe S., Stanton R., Su A., Wang R., Yee B. A., Zhou B., Louie A. L., Aigner S., Fu X.-D., Lécuyer E., Burge C. B., Graveley B. R., Yeo G. W.Nature
-
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis
Marcheva B., Perelis M., Weidemann B. J., Taguchi A., Lin H., Omura C., Kobayashi Y., Newman M. V., Wyatt E. J., McNally E. M., Manning-Fox J. E., Hong H., Shankar A., Wheeler E. C., Ramsey K. M., MacDonald P. E., Yeo G. W., Bass J. Genes & Development
-
Heterogenous Populations of Tissue-Resident CD8+ T Cells Are Generated in Response to Infection and Malignancy
Milner J. J., Toma C., He Z., Kurd N. S., Nguyen Q. P., McDonald B., Quezada L., Widjaja C. E., Witherden D. A., Crowl J. T., Shaw L. A., Yeo G. W., Chang J. T., Omilusik K. D., Goldrath A. W. Immunity
-
Early precursors and molecular determinants of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing
Kurd N. S., He Z., Louis T. L., Milner J. J., Omilusik K. D., Jin W., Tsai M. S., Widjaja C. E., Kanbar J. N., Olvera J. G., Tysl T., Quezada L. K., Boland B. S., Huang W. J., Murre C., Goldrath A. W., Yeo G. W., Chang J. T. Science Immunology
-
Pooled CRISPR screens with image-based phenotyping on microRaft arrays reveals stress granule-regulatory factors
Wheeler E. C., Vu A. Q., Einstein J. M., DiSalvo M., Ahmed N., Van Nostrand E. L., Shiskin A. A., Jin W., Allbritton N. L., Yeo G. W. Nature Methods
-
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
Van Nostrand E. L., Pratt G. A., Yee B. A., Wheeler E., Blue S. M., Mueller J., Park S. S., Garcia K. E., Gelboin-Burkhart C., Nguyen T. B., Rabano I., Stanton R., Sundararaman B., Wang R., Fu X.-D., Graveley B. R., Yeo G. W. Genome Biology
-
How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms
Corley M., Burns M. C., Yeo G. W. Molecular Cell Review
-
RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering
Smargon A. A., Shi Y. J., Yeo G. W. Nature Cell Biology
-
Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
Koga T., Chaim I. A., Benitez J. A., Markmiller S., Parisian A. D., Hevner R. F., Turner K. M., Hessenauer F. M., D’Antonio M., Nguyen N. D., Saberi S., Ma J., Miki S., Boyer A. D., Ravits J., Frazer K. A., Bafna V., Chen C. C., Mischel P. S., Yeo G. W. §, Furnari F. B. §. (§ co-corresponding) Nature Communications
-
The mRNA decay factor CAR-1/LSM14 regulates axon regeneration via mitochondrial calcium dynamics
Tang N. H., Kim K. W., Xu S., Blazie S. M., Yee B. A., Yeo G. W., Jin Y., Chisholm A. D. Current Biology
2019
-
Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base specific resolution
Lorenz D. A., Sathe S., Einstein J. M., Yeo G. W. RNA
-
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis
Di Stefano B. §, Luo E. C. §, Haggerty C., Aigner S., Charlton J., Brumbaugh J., Ji F., Rabano Jiménez I., Clowers K. J., Huebner A. J., Clement K., Lipchina I., de Kort M. A. C., Anselmo A., Pulice J., Gerli M. F. M., Gu H., Gygi S. P., Sadreyev R. I., Meissner A., Yeo G. W. §, Hochedlinger K. §. (§ co-corresponding) Cell Stem Cell
-
Pervasive Chromatin-RNA binding protein interactions enable RNA-based Regulation of Transcription
Xiao R., Chen J. Y., Liang Z., Luo D., Chen G., Lu Z. J., Chen Y., Zhou B., Li H., Du X., Yang Y., San M., Wei X., Liu W., Lécuyer E., Graveley B. R., Yeo G. W., Burge C. B., Zhang M. Q., Zhou Y., Fu X. D. Cell
-
Peptide Brush Polymers for Efficient Delivery of a Gene Editing Protein to Stem Cells
Blum A. P., Nelles D. A., Hidalgo F. J., Touve M. A., Sim D. S., Madrigal A. A., Yeo G. W., Gianneschi N. C. Angewandte Chemie International Edition
-
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF
Kaiser R. W. J., Ignarski M., Van Nostrand E. L., Frese C. K., Jain M., Cukoski S., Heinen H., Schaechter M., Seufert L., Bunte K., Frommolt P., Keller P., Helm M., Bohl K., Höhne M., Schermer B., Benzing T., Höpker K., Dieterich C., Yeo G. W., Müller R. U., Fabretti F. Scientific Reports Nature Research
-
Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development
Trujillo C. A., Gao R., Negraes P. D., Gu J., Buchanan J., Preissl S., Wang A., Wu W., Haddard G. G., Chaim I. A., Domissy A., Vandenberghe M., Devor A., Yeo G. W., Voytek B., Muotri A. R. Cell Stem Cell
-
Small-Molecule Modulation of TDP-43 Recruitment to Stress Granules Prevents Persistent TDP-43 Accumulation in ALS/FTD
Fang M., Markmiller S., Vu A. Q., Javaherian A., Dowdle W. E., Jolivet P., Bushway P. J., Castello N. A., Baral A., Chan M. Y., Linsley J. W., Linsley D., Mercola M., Finkbeiner S., Lecuyer E., Lewcock J. W., Yeo G. W. Neuron
-
Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions
Nussbacher J. K., Tabet R., Yeo G. W. §, Lagier-Tourenne C. §. (§ co-corresponding) Neuron Review
-
Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics
Markmiller S., Fulzele A., Higgins R., Leonard M., Yeo G. W.§, Bennett E. J.§. (§ co-corresponding) Cell Reports
-
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA
Yang E.-W., Bahn J. H., Hsiao E. Y.-H., Tan B. X., Sun Y., Fu T., Zhou B., Graveley B. R., Burge C. B., Yeo G. W., Xiao X. Nature Communications
-
Regulation of RNA editing by RNA-binding proteins in human cells
Quinones-Valdez G., Tran S. S., Jun H. I., Bahn J. H., Yang E. W., Zhan L., Brümmer A., Wei X., Van Nostrand E. L., Pratt G. A., Yeo G. W., Graveley B. R., Xiao X. Communications Biology
2018
-
Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells
van den Hurk M., Erwin J. A., Yeo G. W., Gage F. H., Bardy C. Frontiers in Molecular Neuroscience
-
Widespread RNA Editing Dysregulation in Brains From Autistic Individuals
Tran S. S., Jun H. I., Bahn J. H., Azghadi A., Ramaswami G., Van Nostrand E. L., Nguyen T. B., Hsiao Y. E., Lee C., Pratt G. A., Martínez-Cerdeño V., Hagerman R. J., Yeo G. W., Geschwind D. H., Xiao X. Nature Neuroscience
-
A Transcriptome-wide Translational Program Defined by LIN28B Expression Level
Tan F. E., Sathe S., Wheeler E. C., Nussbacher J. K., Peter S., Yeo G. W. Molecular Cell
-
RBP-Maps enables robust generation of splicing regulatory maps
Yee B. A., Pratt G. A., Graveley B. R., Van Nostrand E. L. §, Yeo G. W. § (§ co-corresponding) RNA
-
Sequence, Structure and Context Preferences of Human RNA binding proteins
Dominguez D., Freese P., Alexis M. S., Su A., Hochman M., Palden T., Bazile C., Lambert N. J., Van Nostrand E. L., Pratt G. A., Yeo G. W., Graveley B. R., Burge C. B. Molecular Cell
-
Transcriptome–pathology correlation identifies interplay between TDP‑43 and the expression of its kinase CK1E in sporadic ALS
Krach F., Batra R., Wheeler E. C., Vu A. Q., Wang R., Hutt K., Rabin S. J., Baughn M. W., Libby R. T., Diaz‑Garcia S., Stauffer J., Pirie E., Saberi S., Rodriguez M., Madrigal A. A., Kohl Z., Winner B., Yeo G. W., Ravits J. Acta Neuropathologica
-
Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9
Huang H., Kapeli K., Jin W., Wong Y. P., Arumugam T. V., Koh J. H., Srimasorn S., Mallilankaraman K., Chua J. J. E., Yeo G. W., Soong T. W. Nucleic Acids Research
-
Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance
Klann J. E., Kim S. H., Remedios K. A., He Z., Metz P. J., Lopez J., Tysl T., Olvera J. G., Ablack J. N., Cantor J. M., Boland B. S., Yeo G. W., Zheng Y., Lu L. F., Bui J. D., Ginsberg M. H., Petrich B. G., Chang J. T. The Journal of Immunology
-
Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels
Nussbacher J. K., Yeo G. W. Molecular Cell
-
Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules
Markmiller S., Soltanieh S., Server K. L., Mak R., Jin W., Fang M. Y., Luo E.-C., Krach F., Yang D., Sen A., Fulzele A., Wozniak J., Gonzalez D. J., Kankel M. W., Gao F.-B., Bennett E. J., Lecuyer E., Yeo G. W. Cell
-
Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas
Roloff A., Nelles D. A., Thompson M. P., Yeo G. W., Gianneschi N. C. Bioconjugate Chemistry
2017
-
Short poly(A) tails are a conserved feature of highly expressed genes
Lima S. A., Chipman L. B., Nicholson A. L., Chen Y. H., Yee B. A., Yeo G. W., Coller J., Pasquinelli A. E. Nature Structural & Molecular Biology
-
Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism
Scott D. D., Trahan C., Zindy P. J., Aguilar L. C., Delubac M. Y., Van Nostrand E. L., Adivarahan S., Wei K. E., Yeo G. W., Zenklusen D., Oeffinger M. Nucleic Acids Research
-
The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
Deffit S. N., Yee B. A., Manning A. C., Rajendren S., Vadlamani P., Wheeler E. C., Domissy A., Washburn M. C., Yeo G. W.§, Hundley H. A.§. (§ co-corresponding) eLife
-
Advances and challenges in the detection of transcriptome-wide protein–RNA interactions
Wheeler E. C., Van Nostrand E. L., Yeo G. W. WILEY INTERDISCIPLINARY REVIEWS: RNA
-
NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing
Jiang L., Shao C., Wu Q. J., Chen G., Zhou J., Yang B., Li H., Gou L. T., Zhang Y., Wang Y., Yeo G. W., Zhou Y., Fu X. D. Nature Structural & Molecular Biology
-
Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions
Van Nostrand E. L., Shishkin A. A., Pratt G. A., Nguyen T. B., Yeo G. W. Methods
-
Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9
Batra R., Nelles D. A., Pirie E., Blue S. M., Marina R. J., Wang H., Chaim I. A., Thomas J. D., Zhang N., Nguygen V., Aigner S., Markmiller S., Xia G., Corbett K. D., Swanson M. S., Yeo G. W.Cell
-
Robust Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP)
Van Nostrand E. L., Nguyen T. B., Gelboin-Burkhart C., Wang R., Blue S. M., Pratt G. A., Louie A. L., Yeo G. W. Methods in Molecular Biology
-
Genetic mutations in RNA‐binding proteins and their roles in ALS
Kapeli K., Martinez F. J., Yeo G. W. Human Genetics
-
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation
Song Y., Botvinnik O. B., Lovci M. T., Kakaradov B., Liu P. L., Xu J. L., Yeo G. W. Molecular Cell
-
Pseudotemporal ordering of single cells reveals metabolic control of postnatal beta-cell proliferation
Zeng C., Mulas F., Sui Y., Guan T., Miller N., Tan Y., Liu F., Jin W., Carrano A. C., Huising M. O., Shirihai O. S., Yeo G. W., and Sander M. Cell Metabolism
-
iPSCORE: A resource of 222 iPSC lines enabling functional characterization of genetic variation across a variety of cell types
Panopoulos A. D., D’Antonio M., Benaglio P., Williams R., Hashem S. I., Schuldt B. M., DeBoever C., Arias A. D., Garcia M., Nelson B., Harismendy O., Grinstein J. D., Drees F., Okubo J., Diffenderfer K. E., Hishida Y., Modesto V., Dargitz C. T., Feiring R., Zhao C., McGarry T. J., Matsui H., Reyna J., Aguirre A., Rao F., O’Connor D. T., Yeo G. W., Evans S. M., Chi N. C., Jepsen K., Nariai N., Müller F.-J., Goldstein L. S. B., Izpisua Belmonte J. C., Adler E., Loring J. F., Berggren W. T., D’Antonio-Chronowska A., Smith E. N., and Frazer K. A. Stem Cell Reports
-
High-throughput and cost-effective characterization of induced pluripotent stem cells
D’Antonio M., Woodruff G., Nathanson J. L., D’Antonio-Chronowska A., Arias A., Matsui H., Williams R., Herrera C., Reyna S. M., Yeo G. W., Goldstein L. S. B., Panopoulos A. D., and Frazer K. A. Stem Cell Reports
-
Interaction landscape of inherited polymorphisms with somatic events in cancer
Carter H., Marty R., Hofree M., Gross A. M., Jensen J., Fisch K. M., Wu X., DeBoever C., Van Nostrand E. L., Song Y., Wheeler E., Kreisberg J. F., Lippman S. M., Yeo G. W., Gutkind J. S., and Ideker T. Cancer Discovery
-
Biallelic mutations in the 3′ exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing
Lardelli R. M., Schaffer A. E., Eggens V. R., Zaki M. S., Grainger S., Sathe S., Van Nostrand E. L., Schlachetzki Z., Rosti B., Akizu N., Scott E., Silhavy J. L., Heckman L. D., Rosti R. O., Dikoglu E., Gregor A., Guemez-Gamboa A., Musaev D., Mande R., Widjaja A., Shaw T. L., Markmiller S., Marin-Valencia I., Davies J. H., de Meirleir L., Kayserili H., Altunoglu U., Freckmann M. L., Warwick L., Chitayat D., Blaser S., Çağlayan A. O., Bilguvar K., Per H., Fagerberg C., Christesen H. T., Kibaek M., Aldinger K. A., Manchester D., Matsumoto N., Muramatsu K., Saitsu H., Shiina M., Ogata K., Foulds N., Dobyns W. B., Chi N. C., Traver D., Spaccini L., Bova S. M., Gabriel S. B., Gunel M., Valente E. M., Nassogne M. C., Bennett E. J., Yeo G. W., Baas F., Lykke-Andersen J., Gleeson J. G. Nature Genetics
-
Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing
Kakaradov B., Arsenio J., Widjaja C. E., He Z., Aigner S., Metz P. J., Yu B., Wehrens E. J., Lopez J., Kim S. H., Zuniga E. I., Goldrath A. W., Chang J. T.§, & Yeo G. W. §. (§ co-corresponding) Nature Immunology
2016
-
CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. Special issue “Protein-RNA: Structure function and recognition
Van Nostrand E. L., Gelboin-Burkhart C., Wang R., Pratt G. A., Blue S. M., and Yeo G. W. (Edited by Yael Mandel-Gutfreund). Methods
-
MicroRNA-101 regulates multiple developmental programs to constrain excitation in adult network networks
Lippi G. §, Fernandes C. C., Ewell L. A., John D., Romoli B., Curia G., Taylor S. R., Frady E. P., Jensen A. B., Liu J. C., Chaabane M. M., Belal C. C., Nathanson J. L., Zoli M., Leutgeb J. K., Biagini G., Yeo G. W., and Berg D. K. §. (§ co-corresponding) Neuron
-
Making the cut in the dark genome
Einstein J. M., and Yeo G. W. Science
-
From Protein-RNA Predictions toward a Peptide-RNA Code
Brannan K. W., and Yeo G. W.Molecular Cell
-
RNA-binding protein CPEB1 remodels host and viral RNA landscapes
Batra R., Stark T. J., Clark E., Belzile J. P., Wheeler E. C., Yee B. A., Huang H., Gelboin-Burkhart C., Huelga S. C., Aigner S., Roberts B. T., Bos T. J., Sathe S., Donohue J. P., Rigo F., Ares M. Jr., Spector D. H., and Yeo G. W. Nature Structural and Molecular Biology
-
Protein-RNA networks regulated by normal and ALS-associated mutant HNRNPA2B1 in the nervous system
Martinez F. J., Pratt G. A., Van Nostrand E. L., Batra R., Huelga S. C., Kapeli K., Freese P., Chun S. J., Ling K., Gelboin-Burkhart C., Fijany L., Wang H., Nussbacher J. K., Broski S. M., Kim H. J., Lardelli R., Sundararaman B., Donohue J. P., Javaherian A., Lykke-Andersen J., Finkbeiner S., Bennett F., Ares M., Burge C. B., Taylor J. P., Rigo F., and Yeo G. W. Neuron
-
Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts
Verma S. K., Deshmukh V., Nutter C. A., Jaworski E., Jin W., Wadhwa L., Abata J., Ricci M., Lincoln J., Martin J. F., Yeo G. W., & Kuyumcu-Martinez M. N. Scientific Reports
-
Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology
Bardy C.§, Hurk M., Kakaradov B., Erwin J., Jaeger B., Hernandez R., Eames T., Paucar A., Gorris M., Marchand C., Jappelli R., Barron J., Bryant A., Kellogg M., Lasken R., Rutten B., Steinbusch H., Yeo G. W. §, and Gage F. H. §. (§ co-corresponding) Molecular Psychiatry
-
SONAR discovers RNA-binding proteins from analysis of large-scale protein-protein interactomes
Brannan K. W., Jin W., Huelga S. C., Banks C. A., Gilmore J. M., Florens L., Washburn M. P., Nostrand E. V., Pratt G. A., Schwinn M. K., Daniels D. L., & Yeo G. W.Molecular Cell
-
Pairing beyond the seed supports microRNA targeting specificity
Broughton J. P., Lovci M. T., Huang J. L., Yeo G. W., and Pasquinelli A. E. Molecular Cell
-
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model
Grabole N., Zhang J. D., Aigner S., Ruderisch N., Costa V., Weber F. C., Theron M., Berntenis N., Spleiss O., Ebeling M., Yeo G. W., Jagasia R., & Kiialainen A. Genome Medicine
-
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses
Kapeli K., Pratt G. A., Vu A. Q., Hutt K. R., Martinez F. J., Sundararaman B., Freese P., Lambert N. J., Huelga S. C., Chun S., Liang T. Y., Chang J., Donohue J. P., Shiue L., Zhang J., Zhu H., Cambi F., Kasarskis E., Ares M., Burge C. B., Rigo F., and Yeo G. W. Nature Communications
-
Dysregulation of RBFOX2 is an early event in cardiac pathogenesis of diabetes
Nutter C. A., Jaworski E. A., Verma S. K., Deshmukh V., Wang Q., Botvinnik O. B., Lozano M. J., Abass I. J., Ijaz T., Brasier A. R., Garg N. J., Wehrens X. H., Yeo G. W., & Kuyumcu-Martinez M. N. Cell Reports
-
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells
Rentas S., Holzapfel N. T., Belew M. S., Pratt G. A., Voisin V., Wilhelm B. T., Bader G. D., Yeo G. W. §, & Hope K. J. (§ co-corresponding) Nature
-
Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival
Conway A. E., Van Nostrand E. L., Pratt G. A., Aigner S., Wilbert M. L., Sundararaman B., Freese P., Lambert N. J., Sathe S., Liang T. Y., Essex A., Landais S., Burge C. B., Jones D. L. §, & Yeo G. W. §. ( § co-corresponding) Cell Reports
-
Programmable RNA tracking in live cells with CRISPR/Cas9
Nelles D. A., Fang M., O’Connell M. R., Xu J. L., Markmiller S. J., Doudna J. A., & Yeo G. W. Cell
-
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Van Nostrand E. L., Pratt G. A., Shishkin A. A., Gelboin-Burkhart C., Fang M., Sundararaman B., Blue S. M., Nguyen T. B., Surka C., Elkins K., Stanton R., Rigo F., Guttman M., & Yeo G. W.Nature Methods
-
Resources for the comprehensive discovery of functional RNA elements
Sundararaman B., Zhan L., Blue S., Stanton R., Elkins K., Olson S., Wei X., Van Nostrand E. L., Huelga S. C., Smalec B. M., Wang X., Hong E. L., Davidson J. M., Lecuyer E., Graveley B. R. §, & Yeo G. W. §. (§ co-corresponding) Molecular Cell
-
A small RNA-catalytic Argonaute pathway tunes germline transcript levels to ensure embryonic divisions
Gerson-Gurwitz A., Wang S., Sathe S., Green R., Yeo G. W., Oegema K., and Desai A. Cell
2015
-
PPAR-δ is repressed in Huntington’s disease, is required for normal neuronal function and can be targeted therapeutically
Dickey A. S., Pineda V. V., Tsunemi T., Liu P. P., Miranda H. C., Gilmore-Hall S. K., Lomas N., Sampat K. R., Buttgereit A., Torres M. M., Flores A. L., Arreola M., Arbez N., Akimov S. S., Gaasterland T., Lazarowski E. R., Ross C. A., Yeo G. W., Sopher B. L., Magnuson G. K., Pinkerton A. B., Masliah E., and La Spada A. R. Nature Medicine
-
A gene regulatory network cooperatively controlled by Pdx1 and Sox9 governs lineage allocation of foregut progenitor cells
Shih H. P., Seymour P. A., Patel N. A., Xie R., Wang A., Liu P. P., Yeo G. W., Magnuson M. A., & Sander M. Cell Reports
-
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression
Hung T., Pratt G. A., Sundararaman B., Townsend M. J., Chaivorapol C., Bhangale T., Graham R. R., Ortmann W., Criswell L. A., Yeo G. W. §, & Behrens T. §. (§ co-corresponding) Science
-
Target discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity
Lee S. R., Pratt G. A., Martinez F. J., Yeo G. W. §, & Lykke-Anderson J. §. (§ co-corresponding) Molecular Cell
-
Applications of Cas9 as an RNA-programmed RNA-binding protein
Nelles D. A., Fang M. Y., Aigner S., & Yeo G. W. Bioessays
-
The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion
Singh G., Pratt G. A., Yeo G. W., & Moore M. J. Annual Review of Biochemistry
-
Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects
Concepcion D., Ross K. D., Hutt K. R., Yeo G. W., & Hamilton B. A. PLoS Genetics
-
RNA-binding proteins in neurodegeneration: Seq and you shall receive
Nussbacher J. K., Batra R., Lagier-Tourenne C., & Yeo G. W. Trends in Neurosciences
-
ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1 snRNP
Sun S., Ling S.-C., Qiu J., Albuquerque C. P., Zhou Y., Tokunaga S., Li H., Qiu H., Bui A., Yeo G. W., Huang E. J., Eggan K., Zhou H., Fu X.-D., Lagier-Tourenne C., & Cleveland D. W. Nature Communications
-
Regulation of asymmetric division and CD8+ T lymphocyte fate specification by protein kinase Ceta and protein kinase C lambda
Metz P. J., Arsenio J., Kakaradov B., Kim S. H., Remedios K. A., Oakley K., Akimoto K., Ohno S., Yeo G. W., & Chang J. T. Journal of Immunology
-
Identification of novel long non-coding RNAs underlying vertebrate cardiovascular development
Kurian L., Aguirre A., Sancho-Martinez I., Benner C., Hishida T., Nguyen T., Reddy P., Nivet E., Krause M. N., Nelles D., Esteban C. R., Campistol J., Yeo G. W., & Belmonte J. C. I. Circulation
2014
-
A Novel Splice-Site Mutation in ALS2 Establishes the Diagnosis of Juvenile Amyotrophic Lateral Sclerosis in a Family with Early Onset Anarthria and Generalized Dystonias
Siddiqi S., Foo J. N., Vu A., Azim S., Silver D. L., Mansoor A., Tay S. K. H., Abbasi S., Hashmi A. H., Janjua J., Khalid S., Tai E. S., Yeo G. W., & Khor C. C. PLOS ONE
-
Intracellular mRNA Regulation with Self-Assembled Locked Nucleic Acid Polymer Nanoparticles
Rush A. M., Nelles D. A., Blum A. P., Barnhill S. A., Tatro E. T., Yeo G. W., & Gianneschi N. C. Journal of the American Chemical Society
-
Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA
Belzile J. P., Stark T. J., Yeo G. W., & Spector D. H. Journal of Virology
-
The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans
Van Wynsberghe P. M., Finnegana E. F., Stark T. J., Angelus E. P., Homan K. E., Yeo G. W., & Pasquinelli A. E. Developmental Biology
-
Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene expression analyses
Arsenio J.+, Kakaradov B.+, Metz P. J., Kim S. H., Yeo G. W.§, & Chang J. T.§. (§ co-corresponding) Nature Immunology
-
The dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome
Washburn M. C.+, Kakaradov B., Sundararaman B., Wheeler E., Hoon S., Yeo G. W.§, & Hundley H. A.§. (§ co-corresponding) Cell Reports
2013
-
Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans
Hunter S. E., Finnegan E. F., Zisoulis D. G., Lovci M. T., Melnik-Martinez K. V., Yeo G. W., Pasquinelli A. E. PLoS Genet
-
Genome-wide Analysis Reveals SR ProteinCooperation and Competition in Regulated Splicing
Pandit S., Zhou Y., Shiue L., Coutinho-Mansfield G., Li H., Qiu J., Huang J., Yeo G. W., Ares M. Jr., Fu X. D. Mol Cell
-
Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment
Cai W., Albini S., Wei K., Willems E., Guzzo R. M., Tsuda M., Giordani L., Spiering S., Kurian L., Yeo G. W., Puri P. L., Mercola M. Genes Dev
-
Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling
Verma S. K., Deshmukh V., Liu P., Nutter C. A., Espejo R., Hung M. L., Wang G. S., Yeo G. W., Kuyumcu-Martinez M. N. J Biol Chem
-
Differential L1 regulation in pluripotent stem cells of humans and apes
Marchetto M. C. N., Narvaiza I., Denli A. M., Benner C., Lazzarini T. A., Nathanson J. L., Paquola A. C. M., Desai K. N., Herai R. H., Weitzman M. D., Yeo G. W., Muotri A. R., Gage F. H. Nature
-
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges
Lovci M. T., Ghanem D., Marr H., Arnold J., Gee S., Parra M., Liang T. Y., Stark T. J., Gehman L. T., Hoon S., Massirer K. B., Pratt G. A., Black D. L., Gray J. W., Conboy J. G., Yeo G. W. Nat Struct Mol Biol
-
Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration
Lagier-Tourenne C., Baughn M., Rigo F., Sun S., Liu P., Li H. R., Jiang J., Watt A. T., Chun S., Katz M., Qiu J., Sun Y., Ling S. C., Zhu Q., Polymenidou M., Drenner K., Artates J. W., McAlonis-Downes M., Markmiller S., Hutt K. R., Pizzo D. P., Cady J., Harms M. B., Baloh R. H., Vandenberg S. R., Yeo G. W., Fu X. D., Bennett C. F., Cleveland D. W., Ravits J. Proc Natl Acad Sci U S A
-
ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43
Arnold E. S., Ling S. C., Huelga S. C., Lagier-Tourenne C., Polymenidou M., Ditsworth D., Kordasiewicz H. B., McAlonis-Downes M., Platoshyn O., Parone P. A., Da Cruz S., Clutario K. M., Swing D., Tessarollo L., Marsala M., Shaw C. E., Yeo G. W., Cleveland D. W. Proc Natl Acad Sci U S A
2012
-
Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration
Zhu W., Kuo D., Nathanson J., Satoh A., Pao G. M., Yeo G. W., Bryant S. V., Voss S. R., Gardiner D. M., & Hunter T. Development, Growth & Differentiation
-
Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome
Andrade L. N., Nathanson J. L., Yeo G. W., Menck C. F., & Muotri A. R. Human Molecular Genetics
-
Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome
Vollmers C., Schmitz R. J., Nathanson J., Yeo G. W., Ecker J. R., & Panda S. Cell Metabolism
-
Alternative splicing of a novel inducible exon diversifies the CASK guanylate kinase domain
Dembowski J. A., An P., Scoulos-Hanson M., Yeo G. W., Han J., Fu X. D., & Grabowski P. J. Journal of Nucleic Acids
-
Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases
Kapeli K. & Yeo G. W. Frontiers in Neuroscience
-
Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs
Lagier-Tourenne C., Polymenidou M., Hutt K. R., Vu A. Q., Baughn M., Huelga S. C., Clutario K. M., Ling S. C., Liang T. Y., Mazur C., Wancewicz E., Kim A. S., Watt A., Freier S., Hicks G. G., Donohue J. P., Shiue L., Bennett C. F., Ravits J., Cleveland D. W., & Yeo G. W. Nature Neuroscience
-
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance
Wilbert M. W., Huelga S. C., Kapeli K., Stark T. J., Liang T. Y., Chen S. X., Yan B. Y., Nathanson J. L., Hutt K. R., Lovci M. T., Kazan H., Vu A. Q., Massirer K. B., Morris Q., Hoon S., & Yeo G. W. Molecular Cell
-
Misregulated RNA processing in amyotrophic lateral sclerosis
Polymenidou M., Lagier-Tourenne C., Hutt K. R., Bennett C. F., Cleveland D. W., & Yeo G. W. Brain Research
-
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins
Huelga S. C., Vu A. Q., Arnold J. D., Liang T. Y., Liu P. P., Yan B. Y., Donohue J. P., Shiue L., Hoon S., Brenner S., Ares M., & Yeo G. W. Cell Reports
-
High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection
Stark T. J., Arnold J. D., Spector D. H., & Yeo G. W. Journal Virology
2011
-
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43
Polymenidou M.* , Lagier-Tourenne C.* , Hutt K. R.* , Huelga S. C., Moran J., Liang T. Y., Ling S. C., Sun E., Wancewicz E., Mazur C., Kordasiewicz H., Sedaghat Y., Donohue J. P., Shiue L., Bennett C. F., Yeo G. W.§, & Cleveland D. W. § ( *co-first authors; § co-corresponding) Nature Neuroscience
-
RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy
Lovci M. T., Li H. R., Fu X. D., & Yeo G. W. Methods in Molecular Biology
-
Genome-wide approaches in the study of microRNA biology
Wilbert M. L., & Yeo G. W. WIREs System Biology and Medicine
-
LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans
Van Wynsberghe P. M., Kai Z. S., Massirer K. B., Burton V. H., Yeo G. W., & Pasquinelli A. E. Nature Structural and Molecular Biology
2010
-
Alternative splicing in stem cell self-renewal differentiation
Nelles D. A., & Yeo G. W. The Cell Biology of Stem Cells. Meshorer E, Plath K (Eds.). Landes Biosciences
-
Comprehensive discovery of endogenous argonaute binding sites in Caenorhabditis elegans
Zisoulis D. G., Lovci M. T., Wilbert M. L., Hutt K. R., Liang Y. L., Pasquinelli A. E., & Yeo G. W. Nature Structural and Molecular Biology
-
A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells.
Marchetto M. C., Carromeu C., Acab A., Yu D., Yeo G. W., Mu Y., Chen G., Gage F. H., & Muotri A. R. Cell
2009
-
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells
Hinton A., Afrikanova I., Wilson M., King C., Maurer B., Yeo G. W., Hayek A., & Pasquinelli A. Stem Cells and Development
-
Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping
Xue Y., Zhou Y., Wu T., Zhu T., Ji X., Kwon Y. S., Zhang C., Yeo G. W., Black D. L., Sun H., Fu X. D., & Zhang Y. Molecular Cell
-
Transcriptional signature and memory retention of human-induced pluripotent stem cells
Marchetto M. C., Yeo G. W., Kainohana O., Marsala M., Gage F. H., & Muotri A. R. PLOS ONE
-
L1 retrotransposition in human neural progenitor cells
Coufal N. G., Garcia-Perez J. L., Peng G. E., Yeo G. W., Mu Y., Lovci M. T., Maria M., O’Shea K. S., Moran J. V., & Gage F. H. Nature
-
Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice
Thuret S., Toni N., Aigner S., Yeo G. W., & Gage F. H. Hippocampus
-
Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea
Lu Y.-C., Smielewska M., Palakodeti D., Lovci M. T., Aigner S., Yeo G. W.§, & Graveley B. R.§ (§ co-corresponding) RNA
-
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
Yeo G. W., Coufal N. G., Liang T. Y., Peng G. E., Fu X.-D., & Gage F. H. Nature Structural and Molecular Biology
2008
-
Evolutionarily conserved intronic splicing regulatory elements in the human genome
Van Nostrand E. L., & Yeo G. W. Encyclopedia of Life Sciences
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
Variation in alternative splicing across human tissues
Yeo G. W., Holste D., Kreiman G., & Burge C. B. Genome Biology
-
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
-
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
-
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signalsSell it.
Yeo G. W., & Burge C. B. Journal of Computational Biology
-
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
-
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