NAME eRA COMMONS USER NAME geneyeo
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
Yeo, Eugene Wei-Ming
POSITION TITLE
Associate Professor
Dept of Cellular and Molecular Medicine
Scientific Director, Sanford Genomics Core
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
University of Illinois, Urbana-Champaign, Illinois
University of Illinois, Urbana-Champaign, Illinois
DEGREE
(if applicable)
B.A.
B.Sc
YEAR(s)
1997
1997
FIELD OF STUDY
Economics
Chemical Engineering
Massachusetts Institute of Technology, Cambridge
University of California, San Diego
Ph.D.
MBA
2005
Computational
Neuroscience
2006-2008 Management
The Salk Institute, La Jolla, CA Postdoc 2005-2008 Stem Cells
A. Personal Statement
I lead a multidisciplinary team that uses high-throughput genomics and systems biology approaches, engineering, statistical and machine learning methods, as well as biochemical, molecular and cell biology methods to solve problems in RNA processing, gene expression and systems biology. My expertise in both computational and experimental methods is evident from my graduate and postdoctoral training. My work as a graduate student under the co-supervision of Drs Tomaso Poggio (MIT) and Christopher Burge (MIT) provided me with an exceptional foundation in machine learning and statistics (Poggio lab), and computational biology/genomics applied to RNA processing (Burge lab). As a Junior Fellow at the Crick-Jacobs Center at the
Salk Institute under the mentorship of Senior Fellows Sean Eddy (Janelia Farms) and Fred Gage (Salk
Institute), I strengthened my experimental skills in biochemistry, cellular and molecular biology, working on embryonic/induced pluripotent stem cells and neuronal differentiation. My lab is an expert in the application of high-throughput genomics technologies (CHIP-seq, CLIP-seq, RNA-seq) to studying the systems biology of
RNA processing and gene regulatory networks in eukaryotic cells. We are one of the pioneers in the genomewide identification of protein-RNA interaction sites in human cells and whole organisms. Since starting my lab in late 2008, we have led the field in genome-wide analyses of protein-RNA interactions. Since 2008, we have published the identification of FOX2 targets in human embryonic stem cells in Nature Structural Molecular
Biology (NSMB) in 2009, the analysis of PTB-mRNA binding sites in human cells in 2009, the identification of
Argonaute binding sites in vivo in C. elegans in 2010, a compendium of hnRNP functional splicing targets in
Cell Reports in 2012, targets of the cancer-enriched protein LIN28 in Molecular Cell in 2012 and a new mode for RBFOX target regulation in the brain in NSMB in 2013.
My lab is also at the forefront of studying RNA targets of neurodegenerative (ALS) disease-associated RBPs TDP-43 and FUS/TLS, with publications in
Nature Neuroscience in 2011 and 2012. I maintain a mixture of computational and experimental training for my students and postdocs, most of which have leveraged their unique training for the next stage of their careers.
Of the 5 postdocs that have completed their training in my lab, 3 have obtained independent faculty positions in
Germany, Brazil and California. Of the 6 graduate students that have obtained their PhDs, all are either postdocs or in excellent positions in biotech/pharma companies. The lab currently consists of 1 project scientist, 10 postdocs, 7 Ph.D. students, and 8 technicians, all of whom present in lab meetings and participate in international and national conferences.

B. Positions and Honors
Positions and Employment
1997 Research Technician, Affymetrix, Santa Clara, CA
2000
2001
2001
2005
Research Technician, Chiron R&D, Emeryville, CA
Instructor, Northeastern University, Bioinformatics Essentials Graduate Course
Bioinformatics Researcher, Millennium Pharmaceuticals, Cambridge, MA
Bioinformatics Consultant, Neuron Systems, Cambridge, MA
2001-2005 Graduate student, Massachusetts Institute of Technology, Burge and Poggio lab
2005-2008 Fellow, Crick-Jacobs Center for Theoretical and Computational Biology, Salk Institute
Laboratory of Genetics, Salk Institute
2008-2014 Assistant Professor, Department of Cellular and Molecular Medicine, UCSD
2014-present Associate Professor with tenure, Department of Cellular and Molecular Medicine, UCSD
Other Experience and Professional Memberships
2008,2009 Ad hoc Reviewer for NIH/NSF, CRCNS
2010 Ad hoc Reviewer for NIH, GCAT
2010
2011
Ah hoc Reviewer for NIH, ZRG1 MOSS Special Emphasis Panel
Guest Editor, PLoS Genetics
2011
2012
2012
2013
Editorial Board, Cell Reports
Ad hoc Reviewer for NIH, NHLBI SBIR grants
Ad hoc Reviewer for NIH study sections (MNG and GCAT)
Grant reviewer for NIH MNG study section, NIH K99 awards, American Heart Association, Israel
2014
2014
Honors
Science foundation and CIRM fellowships
Permanent study section member for NIH MNG study section, NIH GGG study section
Editorial Board, Cell Research
1996
1996
Hauser Chemical Engineering Scholarship for research
A.T. Widiger Chemical Engineering Scholarship for outstanding scholarship in Chemical
Engineering
1996-1998 James Scholar, College of Liberal Arts and Sciences, University of Illinois, Urbana-Champaign
2000-2005 Lee Kuan Yew Graduate Scholar, by the Lee Kuan Yew Foundation, Singapore
2005 Crick-Jacobs Junior Fellowship, Salk Institute
2011-2013 Alfred P. Sloan Foundation Sloan Research Fellow
C. Selected Relevant Peer-Reviewed Publications (in chronological order, out of 67)
1. Yeo G and Burge C. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. Journal of Computational Biology , 2004; 11(2-3):377-94. PMID: 15285897
2. Yeo G , Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome
Biol.
2004; 5(10):R74. PMID: 15461793
3. Yeo G , Hoon S, Venkatesh B, Burge CB. Variation in the splicing regulatory elements and their organization in vertebrate genomes. Proceedings of the National Academy of Sciences, USA . 2004.
Nov 2; 101 (44):15700-5. PMID: 15505203
4. Yeo GW *, Van Nostrand E, Holste D, Poggio T, Burge CB*. Identification and analysis of alternative splicing events conserved in human and mouse. Proceedings of the National Academy of Sciences,
USA.
2005. Feb 22; 102(8):2850-5. ( *co-corresponding ) PMID: 15708978
5. Yeo G* , Van Nostrand EL, Liang TY. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements in mammalian genomes. PLoS Genetics . 2007(* corresponding ) PMID: 17530930

6. Yeo, G* , Xiang-dong X., Liang, Y.T., Muotri. A.M., Carson, C., Coufal, N, Gage, F.H*. Alternative events
Identified in Human embryonic stem cells and neural progenitors. PLoS Computational Biology , 2007.
(* co-corresponding ) PMID: 17967047
7. Li H, Lovci, MT, Kwon YS, Rosenfeld MG, Fu, XD, Yeo GW . Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model Proceedings of the National Academy of Sciences, USA . 2008. Dec 23;105(51):20179-84. (* corresponding ). PMID:
19088194; PMC2603435
8. Yeo GW *, Coufal NG, Liang TY, Peng GE, Fu XD*, Gage FH* An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nature Structural & Molecular
Biology , 2009. Feb;16(2):130-7. PMID: 19136955 (* co-corresponding ). PMID: 19136955; PMC2735254
9. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang YL, Pasquinelli AE, Yeo GW. Comprehensive discovery of endogenous Argonaute binding sites in C. elegans. Nature Structural & Molecular Biology , 2010.
Feb;17(2):173-9. PMID: 20062054. PMC2834287
10. Polymenidou M, Lagier-Tourenne C, Hutt KR, Huelga SC, Moran J, Liang TY, Ling S-C, Sun E,
Wancewicz, E, Mazur C, Kordasiewicz H, Sedaghat Y, Donohue JP, Shiue L, Bennett FC, Yeo GW *,
Cleveland DW*. Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nature Neuroscience , 2011. Apr;14(4):459-68. PMID: 21358643 (* co-corresponding ).
PMID: 21358643; PMC3094729
11. Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner B, Ares
M, Yeo GW . Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Reports , 2012. PMID: 22574288; PMC3345519
12. Wilbert ML, 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 . LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Molecular Cell , 2012. PMID: 22959275; PMC3483422
13. Lagier-Tourenne C, Polymenidou M, Hutt KR, Vu AQ, Baughn M, Huelga SC, Clutario KM, Ling S-C, 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 . Divergent roles of ALS-linked proteins FUS/TLS and TDL-43 intersect in processing long pre-mRNAs. Nature Neuroscience , 2012. PMID: 23023293, PMC3586380
14. Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark T, Gehman LT, Hoon S, Massirer
K, Pratt GA, Black DL, Gray J, Conboy JG, Yeo GW . Distal RBFOX binding sites control alternative splicing via conserved RNA-RNA interactions. Nature Structural and Molecular Biology , 2013. PMID:
24213538, PMC3918504
15. Arsenio J, Kakaradov B, Metz PJ, Kim SH, Yeo GW* , Chang JT*. Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene expression analyses. Nature Immunology ,
2014 (* co-corresponding ). PMID: 24584088, PMC3968536
D. Research Support (Selected)
Ongoing
5 R01 NS075449-03 Yeo (PI) 02/15/2012-01/31/2017
NIH/NINDS
Defining the messenger RNP code in the brain
In this project, we will discover cisregulatory elements recognized by RNA binding proteins in the mammalian brain, and combined with multiple functional genome-wide assays, we will identify the RNAs regulated by direct
RBP-RNA interactions. This information will enable us to build predictive models of the RNA life cycle in the brain.
5 U54 HG007005-03 Yeo (co-PI) 09/01/2012-8/31/2016
NIH/NIHGRI
Comprehensive analysis of functional RNA elements encoded in the human genome

In this multi-PI ENCODE project with the Burge, Graveley and Fu laboratories, my lab is responsible for performing CLIP-seq and associated analyses in duplicates for 250 RNA binding proteins in K562 and
MCF7 cells to identify their binding sites in a genome-wide fashion.

5 R01 HG004659-07
NIH/NHGRI
Yeo (co-PI) 06/01/2008-06/30/2017
Functional RNA elements in the human genome
In this multi-PI project with the Fu lab at UCSD, we will develop experimental and computational methods to study splicing factors in human 293T cells using CLIP-seq, siRNA depletion and splicing arrays.
Completed
R01 GM084317-05 Yeo (co-PI) 01/01/2009-12/31/2012
NIH/NIGMS
Genomic measurement of alternative splicing
In this multi-PI project, we focused on the development and application of alternative splicing DNA microarrays that allow medium to high-throughput parallel detection and analysis of multiple alternative splicing patterns.