CV

Education

• B.S. in Bioengineering, Tianjin University, 2009
• M.S. in Applied Statistics, University of Illinois at Urbana-Champaign, 2013
• Ph.D in Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, 2013

Work experience

• 08/2009-10/2013, Graduate Research Assistant
  • University of Illinois at Urbana-Champaign
  • Advisor: Dr. Nathan Price
• 11/2013-06/2014, Postdoctoral researcher
  • Sage Bionetworks
  • Advisor: Dr. Adam Margolin
• 06/2014-07/2016, Senior Research Associate
  • Computational Biology Program, Oregon Health & Science University
  • Advisor: Dr. Adam Margolin

Awards

• Jaconette L. Tietze Young Scientist Award, 2020
• University of Washington Royalty Research Fund Award, 2018

Skills

• RNA-seq
  • Batch effects correction
  • Differential expression, PCA, pathway enrichment, network analysis
  • Alternative splicing
  • Single cell RNA-seq
  • Spatial transcriptomics
• ChIP-seq
  • Peak calling
  • Peak enrichment
  • Differential binding
  • Visualization
  • Integration with RNA-seq
• Metabolic network analysis
  • Cell type-specific metabolic network inference
  • Cancer metabolic network

Select publications

For a full list of publications, please check my Google Scholar page.

Molecular signatures from omics data: From chaos to consensus

Sung J, Wang Y, Chandrasekaran S, Witten DM, Price ND: Molecular signatures from omics data: From chaos to consensus. Biotechnology journal. 7:946-957, 2012

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

Wang Y, Eddy JA, Price ND: Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol. 6:153-153, 2012

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin AA, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H: The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition. Nat Cell Biol. 17:1523-1535, 2015

Metabolic remodeling in early development and cardiomyocyte maturation

Ellen Kreipke R, Wang Y, Miklas JW, Mathieu J, Ruohola-Baker H: Metabolic remodeling in early development and cardiomyocyte maturation. Semin Cell Dev Biol. 52:84-92, 2016

Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish

Rabinowitz JS, Robitaille AM, Wang Y, Ray CA, Thummel R, Gu H, Djukovic D, Raftery D, Berndt JD, Moon RT: Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish. Proc Natl Acad Sci U S A. 114:E717-E726, 2017

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis

Palpant NJ, Wang Y, Hadland B, Zaunbrecher RJ, Redd M, Jones D, Pabon L, Jain R, Epstein J, Ruzzo WL, Zheng Y, Bernstein I, Margolin A, Murry CE: Chromatin and transcriptional analysis of mesoderm progenitor cells identifies HOPX as a regulator of primitive hematopoiesis. Cell Rep. 20:1597-1608, 2017

LSD1 activates a lethal prostate cancer gene network independently of its demethylase function

Sehrawat A, Gao L, Wang Y, Bankhead A, McWeeney SK, King CJ, Schwartzman J, Urrutia J, Bisson WH, Coleman DJ, Joshi SK, Kim DH, Sampson DA, Weinmann S, Kallakury BVS, Berry DL, Haque R, Van Den Eeden, S K, Sharma S, Bearss J, Beer TM, Thomas GV, Heiser LM, Alumkal JJ: LSD1 activates a lethal prostate cancer gene network independently of its demethylase function. Proc Natl Acad Sci U S A. 115:E4179-E4188, 2018

Sex differences in transcriptomic profiles in aged kidney cells of renin lineage.

Wang Y, Eng DG, Pippin JW, Gharib SA, McClelland A, Gross KW, Shankland SJ: Sex differences in transcriptomic profiles in aged kidney cells of renin lineage. Aging (Albany NY). 10:606-621, 2018

DNA methylation yields epigenetic clues into the diabetic nephropathy of Pima Indians

Bomsztyk K, Denisenko O, Wang Y: DNA methylation yields epigenetic clues into the diabetic nephropathy of pima indians. Kidney Int. 93:1272-1275, 2018

Transforming Endothelium with Platelet_Rich Plasma in Engineered Microvessels

Nagao RJ, Marcu R, Wang Y, Wang L, Arakawa C, DeForest C, Chen J, Lopez JA, Zheng Y: Transforming endothelium with platelet-rich plasma in engineered microvessels. Adv Sci (Weinh). 6:1901725, 2019

Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency

Mathieu J, Detraux D, Kuppers D, Wang Y, Cavanaugh C, Sidhu S, Levy S, Robitaille AM, Ferreccio A, Bottorff T, McAlister A, Somasundaram L, Artoni F, Battle S, Hawkins RD, Moon RT, Ware CB, Paddison PJ, Ruohola-Baker H: Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency. Nature communications. 10:632, 2019

PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies

Bomsztyk K, Mar D, Wang Y, Denisenko O, Ware C, Frazar CD, Blattler A, Maxwell AD, MacConaghy BE, Matula TJ: PIXUL-ChIP: Integrated high-throughput sample preparation and analytical platform for epigenetic studies. Nucleic Acids Res. 47:e69, 2019

Genome-bound enzymes as epigenetic drug targets in cancer

Bomsztyk K, Wang Y: Genome-bound enzymes as epigenetic drug targets in cancer. Epigenomics. 11:1463-1467, 2019

Fatty Acids Enhance the Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells

Yang X, Rodriguez ML, Leonard A, Sun L, Fischer KA, Wang Y, Ritterhoff J, Zhao L, Kolwicz SC, Pabon L, Reinecke H, Sniadecki NJ, Tian R, Ruohola-Baker H, Xu H, Murry CE: Fatty acids enhance the maturation of cardiomyocytes derived from human pluripotent stem cells. Stem Cell Reports. 13:657-668, 2019

TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes

Miklas JW, Clark E, Levy S, Detraux D, Leonard A, Beussman K, Showalter MR, Smith AT, Hofsteen P, Yang X, Macadangdang J, Manninen T, Raftery D, Madan A, Suomalainen A, Kim DH, Murry CE, Fiehn O, Sniadecki NJ, Wang Y, Ruohola-Baker H: TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes. Nat Commun. 10:4671-1, 2019

microRNAs Regulating Human and Mouse Naive Pluripotency

Wang Y, Hussein AM, Somasundaram L, Sankar R, Detraux D, Mathieu J, Ruohola-Baker H: microRNAs regulating human and mouse naive pluripotency. Int J Mol Sci. 20:10.3390/ijms20235864, 2019

Metabolic Control over mTOR-Dependent Diapause-like State

Hussein AM, Wang Y, Mathieu J, et al. Metabolic Control over mTOR-Dependent Diapause-like State. Dev Cell. 2020;52(2):236-250

talklr uncovers ligand-receptor mediated intercellular crosstalk

Yuliang Wang, talklr uncovers ligand-receptor mediated intercellular crosstalk, bioRxiv 2020.02.01.930602

Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities

Wang, Y., Ma, S. & Ruzzo, W.L. Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities. Sci Rep 10, 3490 (2020).