Papers

2022

• AKT constitutes a signal-promoted alternative exon junction complext that regulates nonsense-mediated decay
  Cho H, Abshire ET, Popp MW, Proschel C, Schwartz JL, Yeo GW, Maquat LE
  Molecular Cell

• Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans
  Tang XE, Tan SX, Hoon S, Yeo GW
  Nature Medicine

• Crosstalk between CRISPR-Cas9 and the human transcriptome
  Smargon AA, Madrigal AA, Yee BA, Dong KD, Mueller JR, Yeo GW
  Nature Communications

• APEX Proximity Labeling of Stress Granule Proteins
  Elmsauri S, Markmiller S,88Yeo GW**.
  Methods in Molecular Biology

• Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing
  Martinez NM, Su A, Burns MC, Nussbacher JK, Schaenin C, Sathe S, Yeo GW§, Gilbert WV§. (§ co-corresponding)
  Molecular Cell

2021

• Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission
  Karthikeyan S, Levy J, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung Q, Cresini ES, Eisner ER, Lastrella AL, Lawrence EJ, Marotz CJ, Ngo TT, Ostrander T , Plascencia A , Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein R, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, Kingsmore SF, Lee W, Shah S, McDonald E, Zeller M, Fisch KM , Laurent L, Yeo GW, Andersen KG, Knight R. Preprint

• A multi-scale map of cell structure fusing protein images and interactions
  Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Backstrom A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi Sp, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T.
   Nature

• Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies
  Fenix AM, Miyaoka Y, Bertero A, Blue S, Spindler MJ Tan KKB, Perez-Bermejo J, Chan AH, Mayer SJ, Nguyen T, Russell CR Lizarraga P, Truong An, Po-Lin So, Kulkarni A, Chetal K, Sathe S, Sniadecki NJ, Yeo GW, Murry CE, Conklin BR, Salomonis N.
  Nature Communications

• Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce
  Keehner J, Horton LE, Binkin NJ, Laurent LC on behalf of the SEARCH Alliance Collaborators, Longhurst CA, Abeles SR, Torriani FJ.
  The New England Journal of Medicine

• Integrative RNA-omics discovers GNAS alternative splicing as a phenotypic driver of splicing factor-mutant neoplasms
  Wheeler EC, Vora S, Mayer D, Kotini AG, Olszewska M, Park S, Guccione E, Teruya-Feldstein J, Silverman L, Sunahara R, §Yeo GW, §Papapetrou EP. (§ co-corresponding)
  Cancer Discovery

• Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress
  Markmiller S, Sathe S, Server KL, Nguyen TB, Fulzele A, Cody N, Javaherian A, Broski S, Finkbeiner S, Bennett EJ, Lecuyer E, Yeo GW
  Cell Reports
  [Faculty Opinions]

• fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
  Corley M, Flynn RA, Blue SM, Yee BA, Chang HY, Yeo GW
  STAR Protocols

• Non-microRNA binding competitively inhibits LIN28 regulation.
  Tan FE§, Sathe S§, Wheeler EC, Yeo GW (§ co-first author)
  Cell Reports

• Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs
  Salido RA, Cantú VJ, Clark AE, Leibel SL, Foroughishafiei A, Saha A, Hakim A, Nouri A, Lastrella AL, Castro-Martínez A, Plascencia A, Kapadia B, Xia B, Ruiz C, Marotz CA, Maunder D, Lawrence ES, Smoot EW, Eisner E, Crescini ES, Kohn L, Franco Vargas L, Chacón M, Betty M, Machnicki M, Wu MY, Baer NA, Belda-Ferre P, De Hoff P, Seaver P, Ostrander RT, Tsai R, Sathe S, Aigner S, Morgan SC, Ngo TT, Barber T, Cheung W, Carlin AF, Yeo GW, Laurent LC, 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 AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall, M Feehan AK, Sabino-Santos Jr G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG.
   Cell

• Huntington’s disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization
  Sanchez II, Nguyen TB, England WE, Lim RG, Vu AQ, Miramontes R, Byrne LM, Markmiller S, Lau AL, Orellana I, Curtis MA, Faull RLM, Yeo GW, Fowler CD, Reidling JC, Wild EJ, Spitale RC, Thompson LM.
  J Clin Invest

• Adar and hnRNP C deficiency synergize in activating endogenous dsRNA-induced type I IFN responses
  Herzner A-M, Khan Z, Van Nostrand EL, Chan S, Cuellar T, Chen R, Pechuan-Jorge X, Komuves L, Solon M, Modrusan Z, Haley B, Yeo GW, Behrens TW, Albert ML.
  J Exp Med

• Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
  Einstein JM, Perelis M, Chaim IA, Meena JK, Nussbacher JK, Tankka AT, Yee BA, Li H, Madrigal AA, Neill NJ, Shankar A, Tyagi S, Westbrook TF, Yeo GW.
  Molecular Cell
  [Fierce Biotech] [UCSD Health News] [SciTechDaily] [Molecular Cell Preview]

• Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County
  Morgan SC§, Aigner S§, Anderson C§, Belda-Ferre P§, De Hoff P§, Marotz CA§, Sathe S§, Zeller M§, The EXCITE Team, Andersen KG&, Farnaes L&, Knight R&, Yeo GW&, Laurent LC&. (§ co-first author, & co-corresponding)
  In review

• Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes
  Brannan KW, Chaim IA, Marina RJ, Yee BA, Kofman ER, Lorenz DA, Jagannatha P, Dong KD, Madrigal AA, Underwood JG, Yeo GW.
  Nature Methods

• Emergence and rapid transmission of SARS-CoV-2B.1.1.7 in the United States
  Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Schiabor Barrett KM, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, 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 GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu C, Suchard MA, Lu JT, Lee W, Andersen KG.
   Cell

• Loss of LUCJL2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS
  Jourdain AA, Begg BE, Mick E, Shah H, Calvo SE, Skinner OS, Sharma R, Blue SM, Yeo GW, Burge CB, 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 CK, Zhang X, Han X, Cieplak P, Scott HR, Deal AK, Ghatak S, Martinez FJ, Yeo GW, Yates JR 3rd, Nakamura T, Lipton SA.
  Proceedings of the National Academy of Sciences

• A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation
  Davis AG, Einstein JM, Zheng D, Jayne ND, Fu XD, Tian B, Yeo GW, Zhang DE
  Blood Advances

• Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment
  Trujillo CA, Rice ES, Schaefer NK, Chaim IA, Wheeler EC, Madrigal AA, Buchanan J, Preissl S, Wang A, Priscilla ND, Szeto RA, Herai RH, Huseynov A, Ferraz MSA, Borges FS, Kihara AH, Byrne A, Marin M, Vollmers C, Brooks AN, Lautz JD, Semendeferi K, Shapiro B, Yeo GW, Smith SEP, Green RE, Muotri AR
  Science
  

2020

• Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression
  Okholm TLH, Sathe S, Park SS, Kamstrup AB, Rasmussen AM, Shankar A, Chua ZM, Fristrup N, Nielsen MM, Vang S, Dyrskjor L, Aigner S, Damgaard CK, Yeo GW, Pedersen JS
  Genome Medicine
  

• Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-protein Interfaces
  Corley M, Flynn RA, Lee B, Blue SM, Chang HY, Yeo GW
  Molecular Cell
  

• Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies.
  Schwartz JL, Jones KL, Yeo GW
  Critical Reviews in Biochemistry and Molecular Biology
  

• Zmat3 is a Key Splicing Regulatory in the p53 Tumor Suppression Program
  Bieging-Rolett KT, Kaiser AM, Morgens DW, Boutelle AM, Seoane JA, Van Nostrand EL, Zhu C, Houlihan SL, Mello SS, Yee BA, McClendon J, Pierce SE, Winters IP, Wang M, Connolly AJ, Lowe SW, Curtis C, Yeo GW, Winslow MM, Bassik MC, Attardi LD.
  Molecular Cell
  

• Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing
  Marina RJ, Brannan KW, Dong KD, Yee BA, Yeo GW.
  Cell Reports
  

• Base editing: advances and therapeutic opportunities
  Porto EM, Komor AC, Slaymaker IM, Yeo GW.
  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 BA, Sanchez-Hevia D, Berenguer J, Aigner S, Yeo GW, 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 JR, Schwartz S, Stern-Ginossar N, Yeo GW, Geula S, Novershtern N, Hanna JH.
  Genes & Development
  

• AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation
  Van Nostrand JL, Hellberg K, Luo E-C, Van Nostrand EL, Dayn A, Yu J, Shokhirev MN, Dayn Y, Yeo GW, Shaw RJ.
  Genes & Development
  

• The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1
  Batra R, Nelles DA, Roth DM, Krach F, Nutter CA, Tadokoro T, Thomas JD, Sznajder L, Blue SM, Gutierrez H, Liu P, Aigner S, Platoshyn O, Miyanohara A, Marsala M, Swanson MS, Yeo GW.
  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 BA, Blue SM, Chen M, Rizzeri D, Chuah C, Oehler VG, Broome HE, Sasik R, Scott-Browne J, Rao A, Yeo GW, Reya T.
  Nature Cancer
  

• Transcriptome-wide analysis of PGC-1a-binding RNAs identifies genes linked to glucagon metabolic action
  Tavares CD§, Aigner S§, Sharabi K, Sathe S, Mutli B, Yeo GW, 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 ZR, Tsai MS, Olvera JG, Omilusik K, Duong H, Kim E, Limary A, Jin W, Milner JJ, Yu BF, Patel S, Tiani L, Tysl T, Kurd N, Bortnick A, Quezada L, Kanbar J, Miralles A, Huylebroeck D, Valasek MA, Dulai P, Singh S, Lu LF, Bui J, Murre C, Sandborn WJ, Goldrath AW, Yeo GW §, Chang JT § (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 EC, Bowen K, Trost H, Aigner S, Rigo F, Yeo GW, Harel A, Svendsen CN, Sareen D, Rothstein JD.
  Neuron
  

• Conserved metabolite regulation of stress granule assembly via AdoMet
  Begovich K, Vu AQ, Yeo GW, Wilhelm JE.
  Journal of Cell Biology
  

• DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis
  Abbasi N, Long T, Li Y, Yee BA, Cho BS, Hernandez JE, Ma E, Patel PR, Sahoo D, Sayed IM, Varki N, Das S, Ghosh P, Yeo GW, Huang WJM.
  Life Science Alliance
  

• Large-scale tethered function assays identify factors that regulate mRNA stability and translation
  Luo EC, Nathanson JL, Tan FE, Schwartz JL, Schmok JC, Shankar A, Markmiller S, Yee BA, Sathe S, Pratt GA, Scaletta DB, Ha Y, Hill DE, Aigner S, Yeo GW.
  Nature Structural and Molecular Biology
  

• Perspectives on ENCODE
  ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM.
  Nature
  

• Expanded encyclopaedias of DNA elements in the human and mouse genomes
  ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z.
  Nature
  

• A large-scale binding and functional map of human RNA-binding proteins
  Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen J-Y, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu X-D, Lécuyer E, Burge CB, Graveley BR, Yeo GW.
  Nature
  5mer motifs used for eCLIP analysis

• A role for alternative splicing in circadian control of exocytosis and glucose homeostasis
  Marcheva B, Perelis M, Weidemann BJ, Taguchi A, Lin H, Omura C, Kobayashi Y, Newman MV, Wyatt EJ, McNally EM, Manning-Fox JE, Hong H, Shankar A, Wheeler EC, Ramsey KM, MacDonald PE, Yeo GW, Bass J.
  Genes & Development

• Heterogenous Populations of Tissue-Resident CD8+ T Cells Are Generated in Response to Infection and Malignancy
  Milner JJ, Toma C, He Z, Kurd NS, Nguyen QP, McDonald B, Quezada L, Widjaja CE, Witherden DA, Crowl JT, Shaw LA, Yeo GW, Chang JT, Omilusik KD, Goldrath AW.
  Immunity
  

• Early precursors and molecular determinants of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing
  Kurd NS, He Z, Louis TL, Milner JJ, Omilusik KD, Jin W, Tsai MS, Widjaja CE, Kanbar JN, Olvera JG, Tysl T, Quezada LK, Boland BS, Huang WJ, Murre C, Goldrath AW, Yeo GW, Chang JT.
  Science Immunology
  

• Pooled CRISPR screens with image-based phenotyping on microRaft arrays reveals stress granule-regulatory factors
  Wheeler EC, Vu AQ, Einstein JM, DiSalvo M, Ahmed N, Van Nostrand EL, Shiskin AA, Jin W, Allbritton NL, Yeo GW.
  Nature Methods
  

• Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
  Van Nostrand EL, Pratt GA, Yee BA, Wheeler E, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu X-D, Graveley BR, Yeo GW.
  Genome Biology

• How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms
  Corley M, Burns MC, Yeo GW.
  Molecular Cell

• RNA-targeting CRISPR systems from metagenomic discovery to transcriptomic engineering
  Smargon AA, Shi YJ, Yeo GW.
  Nat Cell Biol.

• Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
  Koga T, Chaim IA, Benitez JA, Markmiller S, Parisian AD, Hevner RF, Turner KM, Hessenauer FM, D’Antonio M, Nguyen ND, Saberi S, Ma J, Miki S, Boyer AD, Ravits J, Frazer KA, Bafna V, Chen CC, Mischel PS, Yeo GW §, Furnari FB§.(§ co-corresponding)
  Nature Communications

• The mRNA decay factor CAR-1/LSM14 regulates axon regeneration via mitochondrial calcium dynamics
  Tang NH, Kim KW, Xu S, Blazie SM, Yee BA, Yeo GW, Jin Y, Chisholm AD
  Current Biology

2019

• Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base specific resolution
  Lorenz DA, Sathe S, Einstein JM, Yeo GW
  RNA

• The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis
  Di Stefano B&, Luo EC&, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jiménez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW §, Hochedlinger K§. (§ co-corresponding)
  Cell Stem Cell

• Pervasive Chromatin-RNA binding protein interactions enable RNA-based Regulation of Transcription
  Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lécuyer E, Graveley BR, Yeo GW, Burge CB, Zhang MQ, Zhou Y, Fu XD.
   Cell

• Peptide Brush Polymers for Efficient Delivery of a Gene Editing Protein to Stem Cells
  Blum AP, Nelles DA, Hidalgo FJ, Touve MA, Sim DS, Madrigal AA, Yeo GW, Gianneschi NC.
  Angew Chem Int Ed Engl

• A protein-RNA interaction atlas of the ribosome biogenesis factor AATF
  Kaiser RWJ, Ignarski M, Van Nostrand EL, Frese CK, 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 GW, Müller RU, Fabretti F.
  Sci Rep

• Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development
  Trujillo CA, Gao R, Negraes PD, Gu J, Buchanan J, Preissl S, Wang A, Wu W, Haddard GG, Chaim IA, Domissy A, Vandenberghe M, Devor A, Yeo GW, Voytek B, Muotri AR.
  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 AQ, Javaherian A, Dowdle WE, Jolivet P, Bushway PJ, Castello NA, Baral A, Chan MY, Linsley JW, Linsley D, Mercola M, Finkbeiner S, Lecuyer E, Lewcock JW, Yeo GW.
  Neuron
  [UCSD News] [ALS News Today] [Science Daily] UCSD Health News]

• Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions
  Nussbacher JK, Tabet R, Yeo GW§, Lagier-Tourenne C§. (§ co-corresponding)
   Neuron

• Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics
  Markmiller S, Fulzele A, Higgins R, Leonard M, Yeo GW§, Bennett EJ§. (§ co-corresponding)
  Cell Reports

• Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA
  Yang E-W, Bahn JH, Hsiao EY-H, Tan BX, Sun Y, Fu T, Zhou B, Graveley BR, Burge CB, Yeo GW, Xiao X
  Nature Communications

• Regulation of RNA editing by RNA-binding proteins in human cells
  Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X.
  Commun Biol.

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 JA, Yeo GW, Gage FH, Bardy C.
  Front Mol Neurosci.

• Widespread RNA editing dysregulation in brains from autistic individuals
  Tran SS, Jun HI, Bahn JH, Azghadi A, Ramaswami G, Van Nostrand EL, Nguyen TB, Hsiao YE, Lee C, Pratt GA, Martínez-Cerdeño V, Hagerman RJ, Yeo GW, Geschwind DH, Xiao X
  Nat Neurosci.

• A Transcriptome-wide Translational Program Defined by LIN28B Expression Level
  Tan FE, Sathe S, Wheeler EC, Nussbacher JK, Peter S, Yeo GW
  Molecular Cell

• RBP-Maps enables robust generation of splicing regulatory maps
  Yee BA, Pratt GA, Graveley BR, Van Nostrand EL§, Yeo GW§ (§ co-corresponding )
  RNA

• Sequence, Structure and Context Preferences of Human RNA binding proteins
  Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB.
  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 EC, Vu AQ, Wang R, Hutt K, Rabin SJ, Baughn MW, Libby RT, Diaz‑Garcia S, Stauffer J, Pirie E, Saberi S, Rodriguez M, Madrigal AA, Kohl Z, Winner B, Yeo GW, Ravits J.
  Acta Neuropathologica

• Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9
  Huang H, Kapeli K, Jin W, Wong YP, Arumugam TV, Koh JH, Srimasorn S, Mallilankaraman K, Chua JJE, Yeo GW, Soong TW.
  Nucleic Acids Res

• Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance
  Klann JE, Kim SH, Remedios KA, He Z, Metz PJ, Lopez J, Tysl T, Olvera JG, Ablack JN, Cantor JM, Boland BS, Yeo GW, Zheng Y, Lu LF, Bui JD, Ginsberg MH, Petrich BG, Chang JT.
  J Immunol

• Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels
  Nussbacher JK, Yeo GW
  Molecular Cell

• Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules
  Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo E-C, Krach F, Yang D, Sen A, Fulzele A, Wozniak J, Gonzalez DJ, Kankel MW, Gao F-B, Bennett EJ, Lecuyer E, Yeo GW.
  Cell
  [UCSD News] [ALS Association]

• Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas.
  Roloff A, Nelles DA, Thompson MP, Yeo GW, Gianneschi NC
  Bioconjug Chem

2017

• Short poly(A) tails are a conserved feature of highly expressed genes
  Lima SA, Chipman LB, Nicholson AL, Chen YH, Yee BA, Yeo GW, Coller J, Pasquinelli AE.
  Nat Struct Mol Biol

• Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism
  Scott DD, Trahan C, Zindy PJ, Aguilar LC, Delubac MY, Van Nostrand EL, Adivarahan S, Wei KE, Yeo GW, Zenklusen D, Oeffinger M.
  Nucleic Acids Res

• The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
  Deffit SN, Yee BA, Manning AC, Rajendren S, Vadlamani P, Wheeler EC, Domissy A, Washburn MC, Yeo GW§, Hundley HA§. (§ co-corresponding )
   Elife

• Advances and challenges in the detection of transcriptome-wide protein–RNA interactions
  Wheeler EC, Van Nostrand EL, Yeo GW
  WILEY INTERDISCIPLINARY REVIEWS: RNA

• NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing
  Jiang L, Shao C, Wu QJ, Chen G, Zhou J, Yang B, Li H, Gou LT, Zhang Y, Wang Y, Yeo GW, Zhou Y, Fu XD.
  Nat Struct Mol Biol

• Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions
  Van Nostrand EL, Shishkin AA, Pratt GA, Nguyen TB, Yeo GW
   Methods

• Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9
  Batra R, Nelles DA, Pirie E, Blue SM, Marina RJ, Wang H, Chaim IA, Thomas JD, Zhang N, Nguygen V, Aigner S, Markmiller S, Xia G, Corbett KD, Swanson MS, Yeo GW.
  Cell
  [UCSD News] [The Scientist News][KPBS][PHYS.Org News]
  [The San Diego Union-Tribune News][FierceBiotech]
  [ALS Research Forum News]
  

• Robust Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).
  Van Nostrand EL, Nguyen TB, Gelboin-Burkhart C, Wang R, Blue SM, Pratt GA, Louie AL, Yeo GW.
  Methods Mol Biol.

• Genetic mutations in RNA‐binding proteins and their roles in ALS
  Kapeli K, Martinez FJ, Yeo GW
  Human Genetics

• Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation
  Song Y, Botvinnik OB, Lovci MT, Kakaradov B, Liu PL, Xu JL,Yeo GW
  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 AC, Huising MO, Shirihai OS, Yeo GW, 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 AD, D’Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson B, Harismendy O, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, McGarry TJ, Matsui H, Reyna J, Aguirre A, Rao F, O’Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller F-J, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D’Antonio-Chronowska A, Smith EN, and Frazer KA.
  Stem Cell Reports

• High-throughput and cost-effective characterization of induced pluripotent stem cells
  D’Antonio M, Woodruff G, Nathanson JL, D’Antonio-Chronowska A, Arias A, Matsui H, Williams R, Herrera C, Reyna SM, Yeo GW, Goldstein LSB, Panopoulos AD, and Frazer KA.
  Stem Cell Reports

• Interaction landscape of inherited polymorphisms with somatic events in cancer
  Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, and Ideker T.
  Cancer Discovery

• Biallelic mutations in the 3′ exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing
  Lardelli RM, Schaffer AE, Eggens VR, Zaki MS, Grainger S, Sathe S, Van Nostrand EL, Schlachetzki Z, Rosti B, Akizu N, Scott E, Silhavy JL, Heckman LD, Rosti RO, Dikoglu E, Gregor A, Guemez-Gamboa A, Musaev D, Mande R, Widjaja A, Shaw TL, Markmiller S, Marin-Valencia I, Davies JH, de Meirleir L, Kayserili H, Altunoglu U, Freckmann ML, Warwick L, Chitayat D, Blaser S, Çağlayan AO, Bilguvar K, Per H, Fagerberg C, Christesen HT, Kibaek M, Aldinger KA, Manchester D, Matsumoto N, Muramatsu K, Saitsu H, Shiina M, Ogata K, Foulds N, Dobyns WB, Chi NC, Traver D, Spaccini L, Bova SM, Gabriel SB, Gunel M, Valente EM, Nassogne MC, Bennett EJ, Yeo GW, Baas F, Lykke-Andersen J, Gleeson JG.
  Nature Genetics

• Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing
  Kakaradov B , Arsenio J, Widjaja CE, He Z, Aigner S, Metz PJ, Yu B, Wehrens EJ, Lopez J, Kim SH, Zuniga EI, Goldrath AW, Chang JT§, and Yeo GW§. (§ 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 EL, Gelboin-Burkhart C, Wang R, Pratt GA, Blue SM, and Yeo GW. (Edited by Yael Mandel-Gutfreund).
   Methods

• MicroRNA-101 regulates multiple developmental programs to constrain excitation in adult network networks
  Lippi G§, Fernandes CC, Ewell LA, John D, Romoli B, Curia G, Taylor SR, Frady EP, Jensen AB, Liu JC, Chaabane MM, Belal CC, Nathanson JL, Zoli M, Leutgeb JK, Biagini G, Yeo GW, and Berg DK§. (§ co-corresponding )
   Neuron

• Making the cut in the dark genome
  Einstein JM and Yeo GW.
   Science

• From Protein-RNA Predictions toward a Peptide-RNA Code
  Brannan KW and Yeo GW.
  Molecular Cell

• RNA-binding protein CPEB1 remodels host and viral RNA landscapes
  Batra R, Stark TJ, Clark E, Belzile JP, Wheeler EC, Yee BA, Huang H, Gelboin-Burkhart C, Huelga SC, Aigner S, Roberts BT, Bos TJ, Sathe S, Donohue JP, Rigo F, Ares M Jr, Spector DH, and Yeo GW.
  Nature Structural and Molecular Biology
  [UCSD News] [Quanta Magazine] [Infection Control Today News] [Drug Discovery Today News] [Kaiser Health News] [The Medical News]

• Protein-RNA networks regulated by normal and ALS-associated mutant HNRNPA2B1 in the nervous system
  Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang H, Nussbacher JK, Broski, SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett F, Ares M, Burge CB, Taylor JP, Rigo F, and Yeo GW.
  Neuron
  [Video]
  [UCSD News] [Science Daily News] [Healthcanal News]

• Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts
  Verma SK, Deshmukh V, Nutter CA, Jaworski E, Jin W, Wadhwa L, Abata J, Ricci M, Lincoln J, Martin JF, Yeo GW, and Kuyumcu-Martinez MN.
  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 GW§, and Gage FH§. (§ co-corresponding)
  Molecular Psychiatry

• SONAR discovers RNA-binding proteins from analysis of large-scale protein-protein interactomes
  Brannan KW, Jin W, Huelga SC,Banks CA,Gilmore JM, Florens L, Washburn MP, Nostrand EV,Pratt GA, Schwinn MK, Daniels DL, and Yeo GW
  Molecular Cell
  [UCSD News] [ACS Spotlight]

• Pairing beyond the seed supports microRNA targeting specificity
  Broughton JP,Lovci MT, Huang JL, Yeo GW, and Pasquinelli AE
  Molecular Cell

• Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model
  Grabole N, Zhang JD, Aigner S, Ruderisch N, Costa V, Weber FC, Theron M, Berntenis N, Spleiss O, Ebeling M, Yeo GW, Jagasia R, and Kiialainen A.
  Genome Medicine

• Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses
  Kapeli K, Pratt GA , Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Freese P, Lambert NJ, Huelga SC, Chun S, Liang TY, Chang J, Donohue JP, Shiue L, Zhang J, Zhu H, Cambi F, Kasarskis E, Ares M, Burge CB, Rigo F, and Yeo GW.
  Nature Communications

• Dysregulation of RBFOX2 is an early event in cardiac pathogenesis of diabetes
  Nutter CA, Jaworski EA, Verma SK, Deshmukh V, Wang Q, Botvinnik OB, Lozano MJ, Abass IJ, Ijaz T, Brasier AR, Garg NJ, Wehrens XH, and Yeo GW, and Kuyumcu-Martinez MN.
  Cell Reports

• Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells
  Rentas S, Holzapfel NT, Belew MS, Pratt GA, Voisin V, Wilhelm BT, Bader GD, Yeo GW§, and Hope KJ. (§ co-corresponding)
  Nature
  [Phys.Org News]

• Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival
  Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL§, and Yeo GW§. ( § co-corresponding)
  Cell Reports
  [UCSD News]

• Programmable RNA tracking in live cells with CRISPR/Cas9
  Nelles DA, Fang M, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, and Yeo GW.
  Cell
  [Video] [UCSD News] [Highlight in Nature Reviews Genetics] [Highlight in Nature Methods] [METHOD TO WATCH in Nature Methods] [ TOP 100 STORIES OF 2016 in Discover Magazine]

• Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
  Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang M, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, and Yeo GW.
  Nature Methods
  [UCSD News] [Biotechniques News] [Technology Preview in Molecular Cell]

• 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 EL, Huelga SC, Smalec BM, Wang X, Hong EL, Davidson JM, Lecuyer E, Graveley BR§, and Yeo GW§. (§ co-corresponding)
  Molecular Cell
  [Highlight in Nature Reviews Genetics]

• A small RNA-catalytic Argonaute pathway tunes germline transcript levels to ensure embryonic divisions
  Gerson-Gurwitz A, Wang S, Sathe S, Green R, Yeo GW, 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 AS, Pineda VV, Tsunemi T, Liu PP, Miranda HC, Gilmore-Hall SK, Lomas N, Sampat KR, Buttgereit A, Torres MM, Flores AL, Arreola M, Arbez N, Akimov SS, Gaasterland T, Lazarowski ER, Ross CA, Yeo GW, Sopher BL, Magnuson GK, Pinkerton AB, Masliah E, and La Spada AR.
  Nature Medicine
  

• A gene regulatory network cooperatively controlled by Pdx1 and Sox9 governs lineage allocation of foregut progenitor cells
  Shih HP, Seymour PA, Patel NA, Xie R, Wang A, Liu PP, Yeo GW, Magnuson MA, and Sander M.
  Cell Reports

• The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression
  Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, Graham RR, Ortmann W, Criswell LA, Yeo GW§, and Behrens T§. (§ co-corresponding)
  Science

• Target discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity
  Lee SR, Pratt GA, Martinez FJ, Yeo GW§, and Lykke-Anderson J§. (§ co-corresponding)
  Molecular Cell

• Applications of Cas9 as an RNA-programmed RNA-binding protein
  Nelles DA, Fang MY, Aigner S, and Yeo GW.
  Bioessays

• The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion
  Singh G, Pratt GA, Yeo GW, and Moore MJ.
  Annual Review of Biochemistry

• Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects
  Concepcion D, Ross KD, Hutt KR, Yeo GW, and Hamilton BA.
  PLoS Genetics

• RNA-binding proteins in neurodegeneration: Seq and you shall receive
  Nussbacher JK, Batra R, Lagier-Tourenne C, and Yeo GW.
  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 CP, Zhou Y, Tokunaga S, Li H, Qiu H, Bui A, Yeo GW, Huang EJ, Eggan K, Zhou H, Fu X-D, Lagier-Tourenne C, and Cleveland DW.
  Nature Communications

• Regulation of asymmetric division and CD8+ T lympocyte fate specification by protein kinase Ceta and protein kinase C lambda
  Metz PJ, Arsenio J, Kakaradov B, Kim SH, Remedios KA, Oakley K, Akimoto K, Ohno S, Yeo GW, and Chang JT.
  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 MN, Nelles D, Esteban CR, Campistol J, Yeo GW, and Belmonte JCI.
  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 JN, Vu A, Azim S, Silver DL, Mansoor A, Tay SKH, Abbasi S, Hashmi AH, Janjua J, Khalid S, Tai ES, Yeo GW, and Khor CC.
  PLOS ONE

• Intracellular mRNA Regulation with Self-Assembled Locked Nucleic Acid Polymer Nanoparticles]
  Rush AM, Nelles DA, Blum AP, Barnhill SA, Tatro ET, Yeo GW, and Gianneschi NC.
  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 JP, Stark TJ, Yeo GW, and Spector DH.
  Journal of Virology

• The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans
  Van Wynsberghe PM, Finnegana EF, Stark TJ, Angelus EP, Homan KE, Yeo GW, and Pasquinelli AE.
  Developmental Biology

• Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene expression analyses
  Arsenio J+, Kakaradov B+, Metz PJ, Kim SH, Yeo GW§, and Chang JT§. (§ 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 MC+, Kakaradov B, Sundararaman B, Wheeler E, Hoon S, Yeo GW§, and Hundley HA§. (§ co-corresponding)
  Cell Reports
  [Data]

2013

• Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges
  Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Pratt GA, Black DL, Gray JW, Conboy JG, and Yeo GW.
  Nature Structural and Molecular Biology
  
  [Identification of RNA bridges]
  [Human fasta] [Mouse fasta]

• Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment
  Cai W, Albini S, Wei K, Willems E, Guzzo RM, Tsuda M, Giordani L, Spiering S, Kurian L, Yeo GW, Puri PL, and Mercola M.
  Genes & Development

• 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 HR, Jiang J, Watt AT, Chun S, Katz M, Qiu J, Sun Y, Ling SC, Zhu Q, Polymenidou M, Drenner K, Artates JW, McAlonis-Downes M, Markmiller S, Hutt KR, Pizzo DP, Cady J, Harms MB, Baloh RH, Vandenberg SR, Yeo GW, Fu XD, Bennett CF, Cleveland DW, and Ravits J.
  Proceedings of the National Academy of Sciences USA

• Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling
  Verma SK, Deshmukj V, Liu P, Nutter CA, Espejo R, Hung M-L, Wang G-S, Yeo GW, and Kuyumcu-Martinez MN.
  Journal of Biological Chemistry

• Differential L1 regulation in pluripotent stem cells of humans and apes
  Marchetto MCN, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola ACM, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, and Gage FH.
  Nature

• Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing
  Pandit S, Zhou Y, Shiue L, Coutinho-Mansfield G, Li H, Qiu J, Huang J, Yeo GW, Ares M Jr, and Fu XD.
  Molecular Cell

• Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans
  Hunter SE, Finnegan EF, Zisoulis DG, Lovci MT, Melnik-Martinez KV, Yeo GW, and Pasquinelli AE.
  PLoS Genetics

• ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43
  Arnold ES, Ling SC, Huelga SC, Lagier-Tourenne C, Polymenidou M, Ditsworth D, Kordasiewicz HB, McAlonis-Downes M, Platoshyn O, Parone PA, Da Cruz S, Clutario KM, Swing D, Tessarollo L, Marsala M, Shaw CE, Yeo GW, and Cleveland DW.
  Proceedings of the National Academy of Sciences USA

2012

• Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration
  Zhu W, Kuo D, Nathanson J, Satoh A, Pao GM, Yeo GW, Bryant SV, Voss SR, Gardiner DM, and Hunter T.
  Development, Growth & Differentiation

• Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome
  Andrade LN, Nathanson JL, Yeo GW, Menck CF, and Muotri AR.
  Human Molecular Genetics

• Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome
  Vollmers C, Schmitz RJ, Nathanson J, Yeo GW, Ecker JR, and Panda S.
  Cell Metabolism
  [Data]

• Alternative splicing of a novel inducible exon diversifies the CASK guanylate kinase domain
  Dembowski JA, An P, Scoulos-Hanson M, Yeo GW, Han J, Fu XD, and Grabowski PJ.
  Journal of Nucleic Acids

• Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases
  Kapeli K and Yeo GW.
  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 KR, Vu AQ, Baughn M, Huelga SC, Clutario KM, Ling SC, Liang TY,Mazur C, Wancewicz E, Kim AS, Watt A, Freier S, Hicks GG, Donohue JP, Shiue L, Bennett CF, Ravits J, Cleveland DW and Yeo GW.
  Nature Neuroscience
  [News&Views]

• LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance
  Wilbert MW, Huelga SC, Kapeli K, Stark TJ, Liang TY, Chen SX, Yan BY, Nathanson JL, Hutt KR, Lovci MT, Kazan H, Vu AQ, Massirer KB, Morris Q, Hoon S, and Yeo GW.
  Molecular Cell
  
  [ES CLIP Clusters] [293 CLIP clusters]

• Misregulated RNA processing in amyotrophic lateral sclerosis
  Polymenidou M, Lagier-Tourenne C, Hutt KR, Bennett CF, Cleveland DW, and Yeo GW.
  Brain Research

• Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins
  Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, Ares M, and Yeo GW.
  Cell Reports
  [RNAbind]

• High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection
  Stark TJ, Arnold JD, Spector DH, and Yeo GW.
  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 KR * , Huelga SC, Moran J, Liang TY, Ling SC, Sun E, Wancewicz E, Mazur C, Kordasiewicz H, Sedaghat Y, Donohue JP, Shiue L, Bennett CF, Yeo GW§, and Cleveland DW§ ( * co-first authors; § co-corresponding)
  Nature Neuroscience
  
  [Data]

• RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy
  Lovci MT, Li HR, Fu XD, and Yeo GW.
  Methods in Molecular Biology
  [Example]

• Genome-wide approaches in the study of microRNA biology
  Wilbert ML and Yeo GW.
  WIREs System Biology and Medicine

• LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans
  Van Wynsberghe PM, Kai ZS, Massirer KB, Burton VH, Yeo GW, and Pasquinelli AE.
  Nature Structural and Molecular Biology

2010

• Alternative splicing in stem cell self-renewal differentiation
  Nelles DA and Yeo GW.
  The Cell Biology of Stem Cells. Meshorer E, Plath K (Eds.). Landes Biosciences

• Comprehensive discovery of endogenous argonaute binding sites in Caenorhabditis elegans
  Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang YL, Pasquinelli AE, and Yeo GW.
  Nature Structural and Molecular Biology
  [Fasta] [Data] [Array Data]

• A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells.
  Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, Mu Y, Chen G, Gage FH, and Muotri AR.
  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 GW, Hayek A, and 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 YS, Zhang C, Yeo GW, Black DL, Sun H, Fu XD, and Zhang Y.
  Molecular Cell

• Transcriptional signature and memory retention of human-induced pluripotent stem cells
  Marchetto MC, Yeo GW, Kainohana O, Marsala M, Gage FH, and Muotri AR.
  PLOS ONE

• L1 retrotransposition in human neural progenitor cells
  Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Maria M, O’Shea KS, Moran JV, and Gage FH.
  Nature

• Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice.
  Thuret S, Toni N, Aigner S, Yeo GW, and Gage FH.
  Hippocampus

• Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea
  Lu Y-C, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW§, and Graveley BR§ (§ co-corresponding)
  RNA

• An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
  Yeo GW, Coufal NG, Liang TY, Peng GE Fu X-D, and Gage FH.
  Nature Structural and Molecular Biology
  [RNA select in Cell]
  [Fasta] [BED file]

2008

• Evolutionarily conserved intronic splicing regulatory elements in the human genome
  Van Nostrand EL and Yeo GW
  Encyclopedia of Life Sciences

• Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model
  Li H, Lovci MT, Kwon Y-S, Rosenfeld MG, Fu, X-D§, and Yeo GW§. (§ co-corresponding)
  Proceedings of the National Academy of Sciences USA
  [Fasta]

• Divergent transcription from active promoters
  Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.
  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§, and Graveley BR§ (§ co-corresponding)
  RNA

2007

• RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells
  Calabrese JM, Seila AC, Yeo GW, and Sharp PA.
  Proceedings pf the Natioanl Academy of Sciences USA

• A regulator of dscam mutually exclusive splicing fidelity
  Olson S, Blanchette M, Park J, Savva Y, Yeo GW, Yeakley J, Rio D, Graveley B.
  Nature Structural and Molecular Biology

• Alternative events identified in human embryonic stem cells and neural progenitors
  Yeo GW§ , Xiang-dong X, Liang YT, Muotri AM, Carson C, Coufal N, and Gage FH§. (§ co-corresponding)
  PLoS Computational Biology
  [Data]

• Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements in mammalian genomes
  Yeo GW§, Van Nostrand EL, and Liang YT. (§ corresponding)
  PLoS Genetics
  [Data]

• Immunoglobulin light chains in zebrafish: genomic configurations and inversional rearrangements between (V(L)-J(L)C(L)) gene clusters
  Zimmerman AM, Yeo GW, Howe K, Maddox BJ, and Steiner LA.
  Developmental and Comparative Immunology

• The EJC factor eIFAIII modulates synaptic strength and neuronal protein expression
  Giorgi. C, Yeo GW, Stone, ME, Katz, DB, Burge C, Turrigiano, C, and Moore, MJ.
  Cell

2006

• Inference of splicing regulatory activities by sequence neighborhood analysis
  Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, and Burge CB.
  PLoS Genetics
  

2005

• A Combinatorial code for splicing silencing: UAGG and GGGG motifs
  Han K§, Yeo GW§, An P, Burge CB and and Grabowski P. (§ co-first authors)
  PLoS Biology

• Identification and analysis of alternative splicing events conserved in human and mouse
  Yeo GW§, Van Nostrand EL, E Holste, D Poggio T, and Burge CB§. (§ co-corresponding)
  Proceedings of the National Academy of Sciences USA

2004

• Systematic identification and analysis of exonic splicing silencers
  Wang Z, Rolish ME, Yeo GW, Tung V, Mawson M, and Burge CB.
  Cell

• Variation in alternative splicing across human tissues
  Yeo GW, Holste D, Kreiman G, and Burge CB.
  Genome Biology

• Variation in the splicing regulatory elements and their organization in vertebrate genomes
  Yeo GW, Hoon S, Venkatesh B, and Burge CB.
  Proceedings of the National Academy of Sciences USA

• RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
  Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, and Burge CB.
  Nucleic Acids Research

• Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
  Yeo GW and Burge CB.
  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 GW, Tanouye R, Drk T, Burge CB, and Gatti RA.
  Human Mutation

2003

• Regularized least-squares classification
  Rifkin R, Yeo GW, and Poggio, T.
  Advances in Learning Theory: Methods, Model and Applications, NATO Science Series III: Computer and System Sciences, Vol. 190, ISO Press, Amsterdam