Yichuan (Ed) Liu

Yichuan (Edward) Liu is a Bioinformatics Scientist at CAG. He joined us in 2013, and is engaged in a range of projects, including copy number variation (CNV) analysis for children's rare diseases, next generation sequencing (NGS) for Congenital Heart Defects (CHD), especially for clinical subtypes of CHD.

Before joining CAG, Ed was a Postdoctoral Fellow at the University of Pennsylvania School of Medicine, where his primary research focus was on RNA-seq of human cardimetabolic diseases. He has a doctoral degree in Biomedical Engineering from Drexel University School of Biomedical Engineering, Science & Public Health System. He has a Bachelor of Computer Science from the University of Waterloo with computer science/molecular biology major.


CAG Publications

An updated list of publications is available at My NCBI Collections.
Relevant papers include:

Modular composition predicts kinase/substrate interactions.
Liu Y, Tozeren A.
BMC Bioinformatics. 2010 Jun 25;11:349. doi: 10.1186/1471-2105-11-349.

Domain altering SNPs in the human proteome and their impact on signaling pathways.
Liu Y, Tozeren A.
PLoS One. 2010 Sep 23;5(9):e12890. doi: 10.1371/journal.pone.0012890.

Evaluating the impact of sequencing depth on transcriptome profiling in human adipose.
Liu Y, Ferguson JF, Xue C, Silverman IM, Gregory B, Reilly MP, Li M.
PLoS One. 2013 Jun 24;8(6):e66883. doi: 10.1371/journal.pone.0066883. Print 2013.

Testing genetic association with rare variants in admixed populations.
Mao X, Li Y, Liu Y, Lange L, Li M.
Genet Epidemiol. 2013 Jan;37(1):38-47. doi: 10.1002/gepi.21687. Epub 2012 Oct 2.

Mapping Splicing Quantitative Trait Loci in RNA-Seq.
Jia C, Hu Y, Liu Y, Li M.
Cancer Inform. 2014;13(Suppl 4):35-43. doi: 10.4137/CIN.S13971.

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.
Hu Y, Liu Y, Mao X, Jia C, Ferguson JF, Xue C, Reilly MP, Li H, Li M.
Nucleic Acids Res. 2014 Feb;42(3):e20. doi: 10.1093/nar/gkt1304. Epub 2013 Dec 20.

Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases.
Liu Y, Ferguson JF, Xue C, Ballantyne RL, Silverman IM, Gosai SJ, Serfecz J, Morley MP, Gregory BD, Li M, Reilly MP.
Arterioscler Thromb Vasc Biol. 2014 Apr;34(4):902-12. doi: 10.1161/ATVBAHA.113.303123. Epub 2014 Feb 6.

Comprehensive analysis of gene expression in human retina and supporting tissues.
Li M, Jia C, Kazmierkiewicz KL, Bowman AS, Tian L, Liu Y, Gupta NA, Gudiseva HV, Yee SS, Kim M, Dentchev T, Kimble JA, Parker JS, Messinger JD, Hakonarson H, Curcio CA, Stambolian D.
Hum Mol Genet. 2014 Aug 1;23(15):4001-14. doi: 10.1093/hmg/ddu114. Epub 2014 Mar 14.

A functional synonymous coding variant in the IL1RN gene is associated with survival in septic shock.
Meyer NJ, Ferguson JF, Feng R, Wang F, Patel PN, Li M, Xue C, Qu L, Liu Y, Boyd JH, Russell JA, Christie JD, Walley KR, Reilly MP.
Am J Respir Crit Care Med. 2014 Sep 15;190(6):656-64. doi: 10.1164/rccm.201403-0586OC.

Mapping Splicing Quantitative Trait Loci in RNA-Seq.
Jia C, Hu Y, Liu Y, Li M.
Cancer Inform. 2015;14(Suppl 1):45-53. doi: 10.4137/CIN.S24832.

RNA-Seq identifies novel myocardial gene expression signatures of heart failure.
Liu Y, Morley M, Brandimarto J, Hannenhalli S, Hu Y, Ashley EA, Tang WH, Moravec CS, Margulies KB, Cappola TP, Li M; MAGNet consortium.
Genomics. 2015 Feb;105(2):83-9. doi: 10.1016/j.ygeno.2014.12.002. Epub 2014 Dec 17.

Integrative genomics identifies 7p11.2 as a novel locus for fever and clinical stress response in humans.
Ferguson JF, Meyer NJ, Qu L, Xue C, Liu Y, DerOhannessian SL, Rushefski M, Paschos GK, Tang S, Schadt EE, Li M, Christie JD, Reilly MP.
Hum Mol Genet. 2015 Mar 15;24(6):1801-12. doi: 10.1093/hmg/ddu589. Epub 2014 Nov 20.