Perl/Python/R scripts writing, NGSdata analysis,SQLite, IGV

WANFENG YU

*******@*****.***

617-***-****

** ******* ******, ********, ** 02135

MS in Bioinformatics, PhD in Biology, permanent resident in United States. Hands on experience in NGS data analysis, RNA library prep, and cancer genomic research. Good understanding of Python/Perl scripts, ability of data management and statistical application. Highly productive experimentalist in human genetic diseases, experience on CRISPR-Cas9 in vitro DNA digestion.

EXPERIENCE Intern

New England Biolabs Inc., Ipswich, MA

2017.1-present

Designed and screened effective sgRNAs; Applied a CRISPR-Cas9 based method for removal of unwanted transcripts during RNA library preparation; RNAseq analysis by Galaxy

Research Associate

Cleveland Clinic, Cleveland, OH

2012.5-2016.1

Identified functional consequences associated with specific SDH mutations in thyroid cancer; Discovered a novel mechanism of SMAD9 V90M mutation in colon cancer development; Published four high impact research papers; Trained two summer students Research Fellow

Harvard Medical School, Boston, MA

2007.11-2012.5

Identified novel regulation of PC-1 on Galpha12/JNK apoptosis signaling pathway in Polycystic Kidney Disease; Discovered a new signaling pathway of Galpha12 activation in Acute Renal Failure; Trained three undergraduate students; Published seven high impact research papers

SKILLS

programming:

- Bioinformatics: Perl, Python and Shell (parse data from varieties of sources, sequence alignment, deferential gene expression analysis, annotation and data visualization)

- Statistics: RStudio (data collecting and cleaning, statistic inference, simulations, regression model)

Data analysis and database:

- Next Generation Sequencing: GALAXY, ALLPATHS-LG, SOAPdenovo, IGV et al Image Processing: Adobe Illustrator, ImageJ, Prism

- Databases: SQLite, GenBank, Uniprot, NCBI, Gene Ontology

Molecular biology:

CRISPR, Real-time PCR, RNA library preparation, construction of lentiviral vectors, molecular cloning, mutagenesis, DNA and RNA purification, miRNA assay, Western-blot, ELISA, CHIP

• Cell biology:

Gene knockout and transgene expression in human cell cultures, gene delivery (transfection, lentiviral transduction, electroporation), cell-based assays(FACS, plate based luciferase/fluorescence assay), Seahorse (OCR, ECAR)

Ex vivo and In vivo models:

Patient samples: measuring PTEN oxidation, tyrosine kinase activity and apoptosis rate in lymphoblasts from Cowden Syndrome patients.

Mouse model: Mouse bilateral kidney ischemia-reperfusion and unilateral ureteral obstruction surgery, renal injury histology analysis EDUCATION Northeastern University

2016.1-Present

MS Bioinformatics

University of Alabama at Birmingham

2002.8-2007.5

PhD Cell Biology

Wuhan University

1996.9-2000.6

BS Biochemistry

SELECTED PUBLICATIONS

1. Yu W, Ni Y, Ringel MD, Jaini R, Eng C. Cowden syndrome-associated succinate dehydrogenase complex subunit D (SDHD) variants cause PTEN-mediated down-regulation of autophagy in thyroid cancer cells. Hum Mol Genet, 2017 Feb 6 2. Wu Y, Yu W et al. Gα12 is required for renal cystogenesis induced by Pkd1 inactivation. J Cell Sci. 2016 129(19):3675-3684

3. Ngeow J, Yu W, Yehia L, Niazi F et al. Germline SMAD9 Mutation Destabilizes PTEN: Exome Sequencing Reveals a Novel Susceptibility Gene For Hamartomatous Polyposis and Gastrointestinal Ganglioneuromas. Gastroenterology, 2015 149(4):886-889 4. Yu W, He X, Ni Y, Ngeow J, Eng C. Cowden syndrome-associated germiline SDHD variants alter PTEN nuclear translocation through SRC-induced PTEN oxidation. Hum Mol Genet, 2015 24(1):142-153

5. Tilot AK, Gaugler MK, Yu Q, Romigh T, Yu W, Miller RH, Grazier TW 2nd, Eng C. Germline disruption of Pten localization causes enhanced sex-dependent social motivation and increased glial production. Hum Mol Genet, 2014 23(12):3212-3227 6. Yu W, Beaudry S, Negoro H, Boucher I, Denker BM. In vitro and in vivo studies of Gα12 in reactive oxygen species mediated epithelial cell injury. Proc Natl Acad Sci U S A, 2012 109(17):6680-6685

7. Boucher I, Yu W, Beaudry S, Negoro H, Tran M, Pollak M, Henderson J, Denker BM. Gα12 activation in Podocytes leads to age-dependent changes in Glomerular collagen expression, proteinuria and Glomerulosclerosis. Lab Investigation, 2011.198 8. Yu W, Ritchie BJ, Su X, Zhou J, Meigs TE, Denker BM. Identification of polycystin-1 and Gα12 binding regions necessary for regulation of apoptosis. Cell Signal. 2011 23(1): 213-221 9. Yu W, Kong T, Beaudry S, Tran M, Negoro H, Yanamadala V, Denker BM. Polycystin-1 protein level determines activity of the Gα12/JNK apoptosis pathway. J Biol Chem, 2010 285(14): 102**-*****.

10. Kong T, Xu D, Yu W, Takakura A, Boucher I, Tran M, Kreidberg JA, Shah J, Zhou J, Denker BM. G alpha12 Inhibits alpha2beta1 integrin-mediated Madin-Darby canine kidney cell attachment and migration on collagen-I and blocks tubulogenesis. Mol Biol Cell. 2009: 20(21): 4596-610.

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