YEO LAB

Cellular and Molecular Medicine

 

Papers                                                                                                            


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, Khor CC

Plos One, 2014

[PDF]


Intracellular mRNA Regulation with Self-Assembled Locked Nucleic Acid Polymer Nanoparticles

Rush A, Nelles D, Blum A, Barnhill S, Tatro E, Yeo GW, Gianneschi NC

Journal of the American Chemical Society, 2014

[JACS][PDF]


Virus-Cell Interactions 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, Spector DH

Journal of Virology, 2014

[JIV][PDF]


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, Pasquinelli AE

ScienceDirect, 2014

[ScienceDirect]


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*, Chang JT*. (*co-corresponding) (+equal contribution)

Nature Immunology, 2014

[PDF][Nature Immuno]


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*, Hundley HA*. (*co-corresponding)

(+equal contribution) 

Cell Reports, 2014

[PDF][OpenAccess][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, Yeo GW.

Nature Structural and Molecular Biology, 2013

[PDF] [human fastq] [mouse fastq] [data] [hub]


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, Mercola M

Genes Dev., 2013

[PDF]


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, Ravits J.

PNAS, 2013

[PDF]


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, Kuyumcu-Martinez MN. 

The Journal of Biological Chemistry, 2013

[PDF]


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, & Gage FH.

Nature, 2013

[PDF]


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.,  Fu XD.

Molecular Cell, 2013

[PMID: 23562324][PDF]


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, Pasquinelli AE.

PLoS Genetics, 2013

[PMID: 23516374][PDF]


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,

Cleveland DW.

PNAS, 2013

[PDF]


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, Hunter T.

Develop. Growth Differ., 2012

[Dev Growth Differ][PDF]


Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome.

Andrade LN, Nathanson JL, Yeo GW, Menck CF, Muotri AR.

Human Molecular Genetics, 2012

[Hum Mol Genet][PDF]


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, Panda S.

Cell Metabolism, 2012

[Cell][PDF][Data]


Alternative Splicing of a Novel Inducible Exon Diversifies the CASK Guanylate Kinase Domain.

Dembowski JA, An P, Scoulos-Hanson M, Yeo G, Han J, Fu XD, Grabowski PJ.

Journal of Nucleic Acids, 2012

[PMID:23008758][PDF]


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, 2012

[PDF]


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 & Yeo GW.

Nature Neuroscience, 2012

[PDF] [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, Yeo GW.

Molecular Cell, 2012

[Mol Cell] [PDF][ES CLIP Clusters][293 CLIP clusters]


Misregulated RNA processing in amyotrophic lateral sclerosis.

Polymenidou M, Lagier-Tourenne C, Hutt KR, Bennett CF, Cleveland DW, Yeo GW.

Brain Research, 2012 Jun 26;1462:3-15

[PMID: 22444279]


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, Yeo GW.

Cell Reports, 2012

[Open Access] [PDF] [RNAbind]


High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection.

Stark TJ, Arnold JD, Spector DH, Yeo GW.

Journal Virology, 2012

[PMID: 22013051] [PDF]


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**, Cleveland DW** (*authors contributed

equally, **co-corresponding).

Nature Neuroscience, 2011

[PMID: 21358643] [PDF] [Data]


RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy.

Lovci MT, Li HR, Fu XD, Yeo GW.

Methods in Molecular Biology, 2011

[PDF] [EXAMPLE]


Genome-wide approaches in the study of microRNA biology.

Wilbert ML, Yeo GW.

WIREs System Biology and Medicine, 2011

[PMID: 21197653] [PDF]


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, Pasquinelli AE.

Nature Structural and Molecular Biology, 2011

[PMID: 21297634]


2010


Alternative splicing in stem cell self-renewal differentiation.

Nelles DA, Yeo GW.

The Cell Biology of Stem Cells. Meshorer E, Plath K (Eds.). Landes Biosciences, 2010

[PDF][Purchase Book]


Comprehensive discovery of endogenous argonaute binding sites in Caenorhabditis elegans.

Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang YL, Pasquinelli AE, Yeo GW.

Nature Structural and Molecular Biology, 2010

[PMID: 20062054][PDF][Data][fastq][ArrayData][UCSC Browser Track]


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, Hayek A, Pasquinelli A.

Stem Cells Dev., 2009

[PMID: 19807270] [PDF]


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 G, Black DL, Sun H, Fu XD, Zhang Y.

Molecular Cell, December 2009

[PMID: 20064465] [PDF]


Transcriptional signature and memory retention of human-induced pluripotent stem cells.

Marchetto MC, Yeo GW,Kainohana O, Marsala M, Gage FH, Muotri AR.

PLoS One, 2009

[PMID: 19763270] [PDF]


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, Gage FH.

Nature, 2009

[PMID: 19657334] [PDF]


Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice.

Thuret S, Toni N, Aigner S, Yeo GW, Gage FH.

Hippocampus, 2009

[PDF]


Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea.

Lu Y-C, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW*, Graveley BR* (*co-corresponding)

RNA, 2009

[PMID: 19553344] [PDF]


A 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*, Gage, FH* (*co-corresponding)

Nature Structural and Molecular Biology, 2009

[PMID: 19136955] [PDF] [fasta] [Data] [UCSC Browser Track] Cell’s Leading Edge: RNA Select [PDF]


2008


Evolutionarily conserved intronic splicing regulatory elements in the human genome.

Van Nostrand E and Yeo GW

Encyclopedia of Life Sciences, 2008

[PDF]


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*, Yeo GW* (*co-corresponding)

PNAS, 2008

[PMID: 19088194] [PDF] [Data]


Divergent transcription from active promoters. 

Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.

Science, 2008

[PMID: 19056940] [PDF]


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*, Graveley BR* (*co-corresponding)

RNA, 2008 

[PMID: 18456843] [PDF]


2007


RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells.

Calabrese JM, Seila AC, Yeo GW, Sharp PA.

PNAS. 2007

[PMID: 17989215] [PDF]


A regulator of dscam mutually exclusive splicing fidelity. 

Olson S, Blanchette M, Park J, Savva Y, Yeo G, Yeakley J, Rio D, Graveley B.

Nature Structural and Molecular Biology, 2007

[PMID: 18059285] [PDF]


Alternative events identified in human embryonic stem cells and neural progenitors. 

Yeo G*, Xiang-dong X, Liang YT, Muotri AM, Carson C, Coufal N, Gage FH* (*co-corresponding)

PLoS Computational Biology, 2007

[PMID: 17967047] [PDF] [Data]


Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements in mammalian

genomes.

Yeo G, Van Nostrand E, Liang Y.T.

PLoS Genetics, 2007

[PMID: 17530930] [Data] [PDF]


Immunoglobulin light chains in zebrafish: genomic configurations and inversional rearrangements between

(V(L)-J(L)C(L)) gene clusters. 

Zimmerman AM, Yeo G, Howe K, Maddox BJ, Steiner

LA Dev. Computational Immunology, 2007

[PMID: 18022691] [PDF]


The EJC factor eIFAIII modulates synaptic strength and neuronal protein expression. 

Giorgi. C, Yeo, G, Stone, ME, Katz, DB, Burge C, Turrigiano, C, Moore, MJ.

Cell, 2007

[PMID: 17632064]


2006


Inference of splicing regulatory activities by sequence neighborhood analysis. 

Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, Burge CB

PLoS Genetics, 2006

[PMID: 17121466]


2005


Combinatorial code for splicing silencing: UAGG and GGGG motifs. 

Han K, Yeo G, An P, Burge CB and Grabowski P.

PLoS Biology,  2005

[PMID: 15828859]


Identification and analysis of alternative splicing events conserved in human and mouse. 

Yeo G*, Van Nostrand, E Holste, D Poggio T, and Burge CB* (*co-corresponding)

PNAS, 2005

[PMID: 15708978]


2004


Systematic identification and analysis of exonic splicing silencers.

Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, and Burge C.B.

Cell, 2004

[PMID: 15607979]


Variation in alternative splicing across human tissues. 

Yeo G, Holste D, Kreiman G, and Burge C.B.

Genome Biology, 2004

[PMID: 15461793]


Variation in the splicing regulatory elements and their organization in vertebrate genomes. 

Yeo G, Hoon S, Venkatesh B, and Burge C.B.

PNAS, 2004

[PMID: 15505203]


RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. 

Fairbrother WG, Yeo G, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB.

Nucleic Acids Res., 2004

[PMID: 15215377]


Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. 

Yeo G and Burge,C.

Journal of Computational Biology, 2004

[PDF]


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, Tanouye R, Drk T, Burge C.B, and Gatti R.A.

Human Mutation, 23(1), 67-76, 2004

[PMID:14695534]


2003


Regularized least-squares classification. 

Rifkin R, Yeo G, and Poggio, T. 

Advances in Learning Theory: Methods, Model and Applications, NATO Science Series III:  Computer and

System Sciences, Vol. 190, ISO Press, Amsterdam 2003

[PDF]