Yuliang Wang PhD

Yuliang Wang PhD

Computational Biologist

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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Pages

Posts

Introduction to R for bioinformatics (part 1)

4 minute read

Published:

Variables, assignments, and basic arithmetic

Variable names usually begin with letters, and should be descriptive.
The assignment “<-“ operator stores value on the right hand side to the variable name on the left hand side.
You can assign values in one variable to another variable.

Bioinformatcs HOW-TOs

less than 1 minute read

Published:

This is an outline of a series of blogs that I plan to write in 2020 that will share many tools and code snippets that I find useful in Bioinformatics.

publications

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

Published in Nature Cell Biology, 2015

Integrated trancriptomic, epigenomic, and metabolomic data and discovered that NNMT, a metabolic enzyme, regulates H3K27me3 methylation levels in naive to primed transition.

Recommended citation: 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 https://www.nature.com/articles/ncb3264

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

Published in PNAS, 2017

Integrated RNA-seq, proteomic and metabolomic datasets to identify molecular signatures of positional memory in zebrafish fin regeneration

Recommended citation: 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 https://www.pnas.org/content/114/5/E717.short

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

Published in Cell Reports, 2017

Developed an algorithm to identify regulatory genes that exhibit consistent changes in mRNA level and histone methylation levels.

Recommended citation: 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 https://www.sciencedirect.com/science/article/pii/S2211124717310604

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

Published in PNAS, 2018

Integrated RNA-seq and ChIP-seq of histone marks to find genes regulated by LSD1

Recommended citation: 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 https://www.pnas.org/content/115/18/E4179.short

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

Published in Aging, 2018

Uncovered dramatic sex-specific differences in the aging process of cells of the renin lineage (progenitors for kidney podocytes).

Recommended citation: 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940125/

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

Published in Nature Communications, 2019

Integrating RNA-seq, ChIP-seq and CRISPR screens to identify regulators of naive to primed transition

Recommended citation: 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 https://www.nature.com/articles/s41467-018-08020-0

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

Published in Nucleic Acids Research, 2019

Evaluate latest the high sample throughput, low cost PIXUL-ChIP against traditional ChIP-seq

Recommended citation: 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 https://academic.oup.com/nar/article-abstract/47/12/e69/5423606

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

Published in Stem Cell Reports, 2019

Use RNA-seq to assess the effects of fatty acid on the maturation of hPSC-CM

Recommended citation: 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 https://www.sciencedirect.com/science/article/pii/S2213671119303078

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

Published in Nature Communications, 2019

scRNA-seq to discover molecular signatures of hPSC-CM maturation

Recommended citation: 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789043/

microRNAs Regulating Human and Mouse Naive Pluripotency

Published in International Journal of Molecular Sciences, 2019

Integrating multiple mRNA-seq and microRNA-seq datasets to discover important microRNAs regulating pluripotency state transitions

Recommended citation: 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 https://www.mdpi.com/1422-0067/20/23/5864