Senior Bioinformatics Data Analyst with 20+ years experience

HIGHLIGHT

Certified specialist in bioinformatics, statistical software SAS9 (base and advanced programmer), NIH Clinical Research Curriculum Certificate (CRCC) and four Oracle 8i database certifications. Certified for IPA data Analysis (2024)

More than 19 years of bioinformatics experience in Genomics Core Facility and eight years of research lab experience in molecular and quantitative genetics. Genomic data administrator of NIDDK intramural program.

Technical and collaborative oriented, good communication skills and team player, willingness to assume responsibility.

WORK EXPERIENCE

2018 – present: Staff Scientist, Genomics Core Facility, NIDDK/NIH:

NIDDK Intramural Genomic Program Administrator (GPA) and secondary GPA for NIDDK Extramural program for DBGAP related issues.

Data mining for multi-omics meta datasets from publicly available data base, such as, Bio Data Banks (such as, T2TB, and Model-AD), and TCGA. The project association of GNB5 with Alzheimer’s disease revealed by genomic analysis restricted to variants impacting gene function from total 181,388 human brain subjects without and with AD is ready to be submitted.

Management of DBGAP, GSE and Microarray data repository for users in NIDDK and beyond.

Development of a novel single cell RNA sequence data analysis method in cell classifications for both experimental and meta data analysis including liver (2), Beta cell (2), Bon (1), Lung (1), Pancreas (4) and DRG (9) projects during 2022-2023 with two publications in 2023.

Bioinformatics supports for individuals or research groups at NIDDK, NIH institutes, and beyond including bioinformatics software supports, such as, IPA, FLOW, PGS, MetaCore and Genomatix and other free software, such as GSEA, Gene-set ANOVA etc.

Data analysis and bioinformatics downstream data analysis for RNA seq, Chip seq, Single cell RNA seq, Microarray including piRNA, circRNA and noncoding RNA data sets.

In 2023, mentor for NIDDK summer NIHSIP and volunteer students’ guidance for meta data (RNA seq, single cell and microarray data analysis in more than 4K human samples in Alzheimer’s disease, 5K human and mouse sample for Schizophrenia and other meta studies the O-GlcNAc gene networks, HFD, drug related studies such as, Glucosamine, Metformin and two drugs related with A3 adenosine receptor 0nly in 2023 in terms of search for gene markers and common gene pathways or networks. One of high school (HS)students entered into semifinal of national talent search. I have directly or indirectly helped HS students obtained total nine national talent search semifinals.

Collaboration with USDA scientists for the releasing web version of software for Development of software tools for semi-thermal asymmetric reverse PCR (STARP) technique through digitalization of the STARP primer design procedure by 2024.

2014 –2018: Staff Scientist, Genomics Core Facility, NIDDK/NIH:

NIDDK Intramural Genomic Data Administrator (GDA) for database DBGAP related issues.

Data mining for meta data sets (e.g., analyzed more than ten thousand patient’s data sets only between 2017-2018) from publicly available data base, such as TCGA, GSE and others based on the requests from Core Facility users and manuscript reviewers.

Development of software tools for semi-thermal asymmetric reverse PCR (STARP) technique through digitalization of the STARP primer design procedure and a JAVA based software for an e-dataset generator and its corresponding data sets.

One on one bioinformatics supports for at least 43 individuals and lab groups at NIDDK, NIH and beyond.

Administrator for three bioinformatics data servers.

December 2010 –December 2014: Biologist, Genomics Core Facility, NIDDK/NIH

Bioinformatics analysis and support for investigation of various novel technologies, including optimized designs for CRISP/CAS9 and TALEN gene target sites for several investigators.

Designed the v2.0 EDGE database for any new types of chips for CBT/NIDDK

Developed a novel miRNA sequence data set (named TB) for optimized miRNA sequence analysis.

NGS data sets services for ChIP-Seq, miRNA sequences, non-coding RNA and RNA-seq data analysis

Provided services to support clinical informatics: database search for TCGA, OMIM, and HGMD; big data mining for data match by comparison of data generated from a mouse model with the integration of the published human data sets in GEO; correlation of any understudied gene to the clinical phenotypes by bioinformatics tools based on the clinical database search.

Microarray data statistical analysis generated from a total of 1257 chips involved in 94 projects from 32 PIs (NIDDK) and from 366 chips involved in 46 projects from 14 non-NIDDK PIs; analysis of more than 1000 chips from GEO database based on the record before 2014 only.

Regular consultation services and provide constructive recommendations for researchers (e.g., at least 7-10 interactions/week) including but is not limited to, a) data explanations; b) experimental designs; c) downstream bioinformatics data analysis and verification of related issues; d) Q & A in generals; e) discussion of issues related to manuscripts raised by reviewers f) EDGE database daily data uploading and other bioinformatics software usage related issues; g) helping the GEO data submissions; h) training for the application of various bioinformatics software

Bioinformatics Specialist (Kelly scientific service contractor)

1.Genomic Core Facility, NIDDK/NIH: April 2005-December 2010

Statistical data analyses and experimental designs for microarray users at NIDDK and beyond with over 3,000 chips involved in a total of 272 projects from 74 PIs at NIH. NGS sequence data analysis and its correlation with gene expression

In collaboration with more than 50 PIs at NIDDK to provide bioinformatics support including 1) gene ontology enrichment and gene pathway analyses, 2) transcription binding analysis, 3) optimal design of siRNAs/RNAi, 4) similarity searching across profiles and NCBI database via power scripting, and 5) statistical data mining, etc.

Daily consult for postdoctoral and scientists at NIDDK and other Institutions at the NIH

Administrator of software servers for GeneSpring, Partek, and EDGE (oracle11g) microarray database

Design and teach EDGE training classes; coordinate various microarray/bioinformatics related seminars and training classes at the NIH

Technical supports for the following tools and software: Partek, SAS, BRB, Insightful miner, S-plus, R, GeneSpring, Genomatix, Genepathway studios, GeneGo/Meta-core, PowerArray, Array Assist, GoMiner, CLC, and Oracle 11g (total 19 manuscripts published for the contract positions as one of the coauthors)

2.Bioinformatics Unit at National Institute of Aging (NIA)/NIH: July 2004 – April 2005

cDNA & protein microarray data analysis for users at NIA

Experimental designs and statistical analysis of the data collected from a clinical trial for the treatment of osteoarthritis.

2002-2004: Post-Doctoral IRTA Fellow

Laboratory of Mechanisms of Ocular Diseases of National Eye Institute (NEI)/NIH

Study the relationship between the mRNA secondary structures and gene silencing ratios by siRNA.

Statistical data mining for the optimal design of siRNAs via my own Perl scripts

Knock down gene expression via siRNA/RNAi in cell lines and transgenic mice.

2000 - 2001: DBA Lead

Internet Solution Center of Cable & Wireless USA, Reston, VA

Installation, creation, and management of approximately 300 customer Oracle & SQL databases in the DBA team

Attention to details leading to a saving of about $160 000.00 per year for the company.

1998-2000: Post-Doctoral IRTA Fellow

Metabolic Disease Branch of NIDDK/NIH

Genetically imprinting studies on mouse gene Gnas products in knockout mice

DNA sequencing annotation and screening mice genomic and cDNA libraries

EDUCATION

PhD. 1997 Zoology/Genetics Iowa State University, U.S.A.

MSc. 1985 Conservation, Utilization & Evaluation of Plant Genetics Resources University of Birmingham, Birmingham, U.K.

Bsc. 1982 Genetics Wuhan University, Wuhan, P. R. China

AWARDS

2008: Distinguish Performance Award. Kelly Services

2017: NIDDK Director Awards: Citation: You made a difference

2022: NIDDK Director Awards: Scientific

SELECTED PUBLICATIONS (NO ABSTRACTS)

1.Zhang J, Mritunjay Pandey M, Awe A, Lue N, Kittock C, Fikse E, Degner K, Staples J, Mokhasi N, Chen W, Yang Y, Adikaram P, Jacob N, Allen E, Thomas R, Bomeny L, Zhang Y, Petros T, Wang X, Li Y, and Simonds W*. The association of GNB5 with Alzheimer’s disease revealed by genomic analysis restricted to variants impacting gene function. 2024 The American Journal of Human Genetics 111, 1–14.

2.Gao, Z Chen W, Gao R, Li J, Tosh D, Hanover J, Jacobson K. Genetic and functional modulation by agonist MRS5698 and allosteric enhancer LUF6000 at the native A3 adenosine receptor in HL-60 cells. 2024 Purinergic Signalling. © Springer Nature B.V. 2024 Accepted: 12 February 2024

3.Wang S, Zha L, Cui X, Yeh YT, Liu R, Jing J, Shi H, Chen W, Hanover J, Yin J, Yu L, Xue B, Shi H. Epigenetic Regulation of Hepatic Lipid Metabolism by DNA Methylation. Adv Sci 2023 Jul;10(20): e2206068.

4.Li H, Chaitankar V, Cui L, Chen W, Chin K, Zhu J, Liu W, Rodgers GP. Characterization of olfactomedin 4+ cells in prostate and urethral-tube epithelium during murine postnatal development and in adult mice. Sci Rep. 2023 Jun 25;13(1):10290.

5.Zhang J, Chen W, Chen G, Flannick J, Fikse E, Smerin G, Degner K, Yang Y, Xu C, Li Y, Hanover JA, Simonds WF. Ancestry-specific high-risk gene variant profiling unmasks diabetes-associated genes. Hum Mol Genet. 2022

6.Mathur M, Yeh YT, Arya RK, Jiang L, Pornour M, Chen W, Ma Y, Gao B, He L, Ying Z, Xue B, Shi H, Choi Y, Yu L. Adipose lipolysis is important for ethanol to induce fatty liver in the National Institute on Alcohol Abuse and Alcoholism murine model of chronic and binge ethanol feeding. Hepatology. 2023 May 1;77(5):1688-1701.

7.Yu Y, Dai M, Huang L, Chen W, Yu E, Mendoza A, Michael H, Khanna C, Bosenberg M, McMahon M, Merlino G. PTEN phosphatase inhibits metastasis by negatively regulating the Entpd5/IGF1R pathway through ATF6. iScience. 2023 Feb 17;26(2):106070.

8. Kökény G, Németh Á, Kopp JB, Chen W, Oler AJ, Manzéger A, Rosivall L, Mózes MM. Susceptibility to kidney fibrosis in mice is associated with early growth response-2 protein and tissue inhibitor of metalloproteinase-1 expression. Kidney Int. 2022 Aug;102(2):337-354

9.Liu A, Zhu Y, Chen W, Merlino G, Yu Y. PTEN Dual Lipid- and Protein-Phosphatase Function in Tumor Progression. Cancers (Basel). 2022 Jul 28;14(15).

10.Hartono AB, Kang HJ, Shi L, Phipps W, Ungerleider N, Giardina A, Chen W, Spraggon L, Somwar R, Moroz K, Drewry DH, Burow ME, Flemington E, Ladanyi M, Lee SB. Salt-Inducible Kinase 1 is a potential therapeutic target in Desmoplastic Small Round Cell Tumor. Oncogenesis. 2022 Apr 20;11(1):18.

11.Qiu P, Hou W, Wang H, Lei K, Wang S, Chen W, Pardeshi LA, Prothro K, Shukla Y, Su SSM, Schrump DS, Chen Q, Deng CX, Xu X, Wang R. Sirt1 deficiency upregulates glutathione metabolism to prevent hepatocellular carcinoma initiation in mice. Oncogene. 2021 Oct;40(41):6023-6033.

12.Hou W, Chen Q, Wang H, Qiu P, Lyu X, Chen W, Chua MLK, Chinn YE, Deng CX, Wang R. The metabolic footprint during adipocyte commitment highlights ceramide modulation as an adequate approach for obesity treatment. EBioMedicine. 2020 Jan; 51:102605.

13.Zhang X, Liu T, Li Z, Feng Y, Corpe C, Liu S, Zhang J, He X, Liu F, Xu L, Shen L, Li S, Xia Q, Peng X, Zhou X, Chen W, Zhang X, Xu J, Wang J. Hepatomas are exquisitely sensitive to pharmacologic ascorbate (P-AscH-). Theranostics. 2019;9(26):8109-8126.

14.Xia Q, Li Z, Zheng J, Zhang X, Di Y, Ding J, Yu D, Yan L, Shen L, Yan D, Jia N, Chen W, Feng Y, Wang J. Identification of novel biomarkers for hepatocellular carcinoma using transcriptome analysis. J Cell Physiol. 2019 Apr;234(4):4851-4863.

15.Xu X, Chen E, Mo L, Zhang L, Shao F, Miao K, Liu J, Su SM, Valecha M, Chan UI, Zheng H, Chen M, Chen W, Chen Q, Fu H, Aladjem MI, He Y, Deng CX. BRCA1 represses DNA replication initiation through antagonizing estrogen signaling and maintains genome stability in parallel with WEE1-MCM2 signaling during pregnancy. Hum Mol Genet. 2019 Mar 1;28(5):842-857.

16.Xia Y, Cheng X, Li Y, Valdez K, Chen W, Liang TJ. Hepatitis B Virus Deregulates the Cell Cycle To Promote Viral Replication and a Premalignant Phenotype. J Virol. 2018 Oct 1;92(19).

17. Wankhade UD, Lee JH, Dagur PK, Yadav H, Shen M, Chen W, Kulkarni AB, McCoy JP, Finkel T, Cypess AM, Rane SG. TGF-β receptor 1 regulates progenitors that promote browning of white fat. Mol Metab. 2018 Oct;16:160-171.

18.Zheng J, Wang L, Cheng Z, Pei Z, Zhang Z, Li Z, Zhang X, Yan D, Xia Q, Feng Y, Song Y, Chen W, Zhang X, Xu J, Wang J. Molecular Changes of Lung Malignancy in HIV Infection. Sci Rep. 2018 Sep 3;8(1):13128.

19.Quan XX, Hawk NV, Chen W, Coupar J, Lee SK, Petersen DW, Meltzer PS, Montemarano A, Braun M, Chen Z, Van Waes C. Targeting Notch1 and IKKα Enhanced NF-κB Activation in CD133+ Skin Cancer Stem Cells. Mol Cancer Ther. 2018 Sep;17(9):2034-2048.

20.Hanover JA, Chen W, Bond MR. O-GlcNAc in cancer: An Oncometabolism-fueled vicious cycle. J Bioenerg Biomembr. 2018 Jun;50(3):155-173.

21.Dong K, Guo X, Chen W, Hsu AC, Shao Q, Chen JF, Chen SY. Mesenchyme homeobox 1 mediates transforming growth factor-β (TGF-β)-induced smooth muscle cell differentiation from mouse mesenchymal progenitors. J Biol Chem. 2018 Jun 1;293(22):8712-8719.

22.Shan M, Xia Q, Yan D, Zhu Y, Zhang X, Zhang G, Guo J, Hou J, Chen W, Zhu T, Zhang X, Xu J, Wang J, Ding T, Zheng J. Molecular analyses of prostate tumors for diagnosis of malignancy on fine-needle aspiration biopsies. Oncotarget. 2017 Dec 1;8(62):104***-******.

23.Pei Z, Liu SM, Huang JT, Zhang X, Yan D, Xia Q, Ji C, Chen W, Zhang X, Xu J, Wang J. Clinically relevant circulating microRNA profiling studies in pancreatic cancer using meta-analysis. Oncotarget. 2017 Apr 4;8(14):226**-*****.

24.Chen Q, Hao W, Xiao C, Wang R, Xu X, Lu H, Chen W, Deng CX. SIRT6 Is Essential for Adipocyte Differentiation by Regulating Mitotic Clonal Expansion. Cell Rep. 2017 Mar 28;18(13):3155-3166.

25.Chisholm CL, Wang H, Wong AH, Vazquez-Ortiz G, Chen W, Xu X, Deng CX. Ammonium tetrathiomolybdate treatment targets the copper transporter ATP7A and enhances sensitivity of breast cancer to cisplatin. Oncotarget. 2016 Dec 20;7(51):844**-*****.

26.Lui JC, Garrison P, Nguyen Q, Ad M, Keembiyehetty C, Chen W, Jee YH, Landman E, Nilsson O, Barnes KM, Baron J. EZH1 and EZH2 promote skeletal growth by repressing inhibitors of chondrocyte proliferation and hypertrophy. Nat Commun. 2016 Nov 29;7:13685.

27.Liu W, Li H, Hong SH, Piszczek GP, Chen W, Rodgers GP. Olfactomedin 4 deletion induces colon adenocarcinoma in ApcMin/+ mice. Oncogene. 2016 Oct 6;35(40):5237-5247.

28.Wang RH, Zhao T, Cui K, Hu G, Chen Q, Chen W, Wang XW, Soto-Gutierrez A, Zhao K, Deng CX. Negative reciprocal regulation between Sirt1 and Per2 modulates the circadian clock and aging. Sci Rep. 2016 Jun 27;6:28633.

29.Taguchi Y, Allende ML, Mizukami H, Cook EK, Gavrilova O, Tuymetova G, Clarke BA, Chen W, Olivera A, Proia RL. Sphingosine-1-phosphate Phosphatase 2 Regulates Pancreatic Islet β-Cell Endoplasmic Reticulum Stress and Proliferation. J Biol Chem. 2016 Jun 3;291(23):12029-38.

30.Li H, Liu W, Chen W, Zhu J, Deng CX, Rodgers GP. Olfactomedin 4 deficiency promotes prostate neoplastic progression and is associated with upregulation of the hedgehog-signaling pathway. Sci Rep. 2015 Nov 19;5:16974.

31.Chattopadhyay MK, Keembiyehetty CN, Chen W, Tabor H. Polyamines Stimulate the Level of the σ38 Subunit (RpoS) of Escherichia coli RNA Polymerase, Resulting in the Induction of the Glutamate Decarboxylase-dependent Acid Response System via the gadE Regulon. J Biol Chem. 2015 Jul 17;290(29):178**-*****.

32.Gorrepati L, Krause MW, Chen W, Brodigan TM, Correa-Mendez M, Eisenmann DM. Identification of Wnt Pathway Target Genes Regulating the Division and Differentiation of Larval Seam Cells and Vulval Precursor Cells in Caenorhabditis elegans. G3 (Bethesda). 2015 Jun 5;5(8):1551-66.

33.Lui JC, Chau M, Chen W, Cheung CS, Hanson J, Rodriguez-Canales J, Nilsson O, Baron J. Spatial regulation of gene expression during growth of articular cartilage in juvenile mice. Pediatr Res. 2015 Mar;77(3):406-15.

34.Li Y, Hong N, Zhang A, Chen W, Wang RH, Xu XL, Deng CX. Enhancing mammary differentiation by overcoming lineage-specific epigenetic modification and signature gene expression of fibroblast-derived iPSCs. Cell Death Dis. 2014 Dec 4;5:e1550.

35. Ichii O, Otsuka-Kanazawa S, Nakamura T, Ueno M, Kon Y, Chen W, Rosenberg AZ, Kopp JB. Podocyte injury caused by indoxyl sulfate, a uremic toxin and aryl-hydrocarbon receptor ligand. PLoS One. 2014;9(9):e108448.

36.Vassilopoulos A, Xiao C, Chisholm C, Chen W, Xu X, Lahusen TJ, Bewley C, Deng CX. Synergistic therapeutic effect of cisplatin and phosphatidylinositol 3-kinase (PI3K) inhibitors in cancer growth and metastasis of Brca1 mutant tumors. J Biol Chem. 2014 Aug 29;289(35):24202-14.

37.Kang HJ, Park JH, Chen W, Kang SI, Moroz K, Ladanyi M, Lee SB. EWS-WT1 oncoprotein activates neuronal reprogramming factor ASCL1 and promotes neural differentiation. Cancer Res. 2014 Aug 15;74(16):4526-35.

38.Chen YP, Pettis JS, Corona M, Chen W, Li CJ, Spivak M, Visscher PK, DeGrandi-Hoffman G, Boncristiani H, Zhao Y, vanEngelsdorp D, Delaplane K, Solter L, Drummond F, Kramer M, Lipkin WI, Palacios G, Hamilton MC, Smith B, Huang SK, Zheng HQ, Li JL, Zhang X, Zhou AF, Wu LY, Zhou JZ, Lee ML, Teixeira EW, Li ZG, Evans JD. Israeli acute paralysis virus: epidemiology, pathogenesis and implications for honey bee health. PLoS Pathog. 2014 Jul;10(7):e1004261.

39.Liu SM, Chen W, Wang J. Distinguishing between cancer cell differentiation and resistance induced by all-trans retinoic acid using transcriptional profiles and functional pathway analysis. Sci Rep. 2014 Jul 4;4:5577.

40.Delaney A, Padmanabhan V, Rezvani G, Chen W, Forcinito P, Cheung CS, Baron J, Lui JC. Evolutionary conservation and modulation of a juvenile growth-regulating genetic program. J Mol Endocrinol. 2014 Jun;52(3):269-77.

41.Bettahi I, Sun H, Gao N, Wang F, Mi X, Chen W, Liu Z, Yu FS. Genome-wide transcriptional analysis of differentially expressed genes in diabetic, healing corneal epithelial cells: hyperglycemia-suppressed TGFβ3 expression contributes to the delay of epithelial wound healing in diabetic corneas. Diabetes. 2014 Feb;63(2):715-27.

42. Olivera A, Kitamura Y, Wright LD, Allende ML, Chen W, Kaneko-Goto T, Yoshihara Y, Proia RL, Rivera J. Sphingosine-1-phosphate can promote mast cell hyper-reactivity through regulation of contactin-4 expression. J Leukoc Biol. 2013 Nov;94(5):1013-24.

43.Gao N, Sang Yoon G, Liu X, Mi X, Chen W, Standiford TJ, Yu FS. Genome-wide transcriptional analysis of differentially expressed genes in flagellin-pretreated mouse corneal epithelial cells in response to Pseudomonas aeruginosa: involvement of S100A8/A9. Mucosal Immunol. 2013 Sep;6(5):993-1005.

44.Allende ML, Sipe LM, Tuymetova G, Wilson-Henjum KL, Chen W, Proia RL. Sphingosine-1-phosphate phosphatase 1 regulates keratinocyte differentiation and epidermal homeostasis. J Biol Chem. 2013 Jun 21;288(25):18381-91.

45.Lee GS, He Y, Dougherty EJ, Jimenez-Movilla M, Avella M, Grullon S, Sharlin DS, Guo C, Blackford JA Jr, Awasthi S, Zhang Z, Armstrong SP, London EC, Chen W, Dean J, Simons SS Jr. Disruption of Ttll5/stamp gene (tubulin tyrosine ligase-like protein 5/SRC-1 and TIF2-associated modulatory protein gene) in male mice causes sperm malformation and infertility. J Biol Chem. 2013 May 24;288(21):15167-80.

46.Chattopadhyay MK, Chen W, Tabor H. Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression. FEMS Microbiol Lett. 2013 Jan;338(2):132-40.

47.Chen G, Yuan A, Zhou Y, Bentley AR, Zhou J, Chen W, Shriner D, Adeyemo A, Rotimi CN. Simultaneous Analysis of Common and Rare Variants in Complex Traits: Application to SNPs (SCARVAsnp). Bioinform Biol Insights. 2012;6:177-85

48.Zhu BM, Kang K, Yu JH, Chen W, Smith HE, Lee D, Sun HW, Wei L, Hennighausen L. Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes. Nucleic Acids Res. 2012 May;40(10):4461-72.

49.Thomas E, Gonzalez VD, Li Q, Modi AA, Chen W, Noureddin M, Rotman Y, Liang TJ. HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons. Gastroenterology. 2012 Apr;142(4):978-88.

50.Zhang JH, Pandey M, Seigneur EM, Panicker LM, Koo L, Schwartz OM, Chen W, Chen CK, Simonds WF. Knockout of G protein β5 impairs brain development and causes multiple neurologic abnormalities in mice. J Neurochem. 2011 Nov;119(3):544-54.

51.Yadav H, Quijano C, Kamaraju AK, Gavrilova O, Malek R, Chen W, Zerfas P, Zhigang D, Wright EC, Stuelten C, Sun P, Lonning S, Skarulis M, Sumner AE, Finkel T, Rane SG. Protection from obesity and diabetes by blockade of TGF-β/Smad3 signaling. Cell Metab. 2011 Jul 6;14(1):67-79.

52.Allende ML, Bektas M, Lee BG, Bonifacino E, Kang J, Tuymetova G, Chen W, Saba JD, Proia RL. Sphingosine-1-phosphate lyase deficiency produces a pro-inflammatory response while impairing neutrophil trafficking. J Biol Chem. 2011 Mar 4;286(9):7348-58.

53.Wang Q, Shinkre BA, Lee JG, Weniger MA, Liu Y, Chen W, Wiestner A, Trenkle WC, Ye Y. The ERAD inhibitor Eeyarestatin I is a bifunctional compound with a membrane-binding domain and a p97/VCP inhibitory group. PLoS One. 2010 Nov 12;5(11):e15479.

54.Yu JH, Zhu BM, Wickre M, Riedlinger G, Chen W, Hosui A, Robinson GW, Hennighausen L. The transcription factors signal transducer and activator of transcription 5A (STAT5A) and STAT5B negatively regulate cell proliferation through the activation of cyclin-dependent kinase inhibitor 2b (Cdkn2b) and Cdkn1a expression. Hepatology. 2010 Nov;52(5):1808-18.

55.Kimura 木村丹香子 A, Martin C, Robinson GW, Simone JM, Chen W, Wickre MC, O'Shea JJ, Hennighausen L. The gene encoding the hematopoietic stem cell regulator CCN3/NOV is under direct cytokine control through the transcription factors STAT5A/B. J Biol Chem. 2010 Oct 22;285(43):327**-*****.

56.Lui JC, Chen W, Barnes KM, Baron J. Changes in gene expression associated with aging commonly originate during juvenile growth. Mech Ageing Dev. 2010 Oct;131(10):641-9.

57.Zhang JH, Panicker LM, Seigneur EM, Lin L, House CD, Morgan W, Chen W, Mehta H, Haj-Ali M, Yu ZX, Simonds WF. Cytoplasmic polyadenylation element binding protein is a conserved target of tumor suppressor HRPT2/CDC73. Cell Death Differ. 2010 Oct;17(10):1551-65.

58.Lui JC, Forcinito P, Chang M, Chen W, Barnes KM, Baron J. Coordinated postnatal down-regulation of multiple growth-promoting genes: evidence for a genetic program limiting organ growth. FASEB J. 2010 Aug;24(8):3083-92.

59.Lui JC, Andrade AC, Forcinito P, Hegde A, Chen W, Baron J, Nilsson O. Spatial and temporal regulation of gene expression in the mammalian growth plate. Bone. 2010 May;46(5):1380-90.

60.Bektas M, Allende ML, Lee BG, Chen W, Amar MJ, Remaley AT, Saba JD, Proia RL. Sphingosine 1-phosphate lyase deficiency disrupts lipid homeostasis in liver. J Biol Chem. 2010 Apr 2;285(14):10880-9.

61.Kimura A, Rieger MA, Simone JM, Chen W, Wickre MC, Zhu BM, Hoppe PS, O'Shea JJ, Schroeder T, Hennighausen L. The transcription factors STAT5A/B regulate GM-CSF-mediated granulopoiesis. Blood. 2009 Nov 19;114(21):4721-8.

62.Yamaji D, Na R, Feuermann Y, Pechhold S, Chen W, Robinson GW, Hennighausen L. Development of mammary luminal progenitor cells is controlled by the transcription factor STAT5A. Genes Dev. 2009 Oct 15;23(20):2382-7.

63.Chattopadhyay MK, Chen W, Poy G, Cam M, Stiles D, Tabor H. Microarray studies on the genes responsive to the addition of spermidine or spermine to a Saccharomyces cerevisiae spermidine synthase mutant. Yeast. 2009 Oct;26(10):531-44.63.

64.Klover P, Chen W, Zhu BM, Hennighausen L. Skeletal muscle growth and fiber composition in mice are regulated through the transcription factors STAT5a/b: linking growth hormone to the androgen receptor. FASEB J. 2009 Sep;23(9):3140-8.

65.Wojtanik KM, Edgemon K, Viswanadha S, Lindsey B, Haluzik M, Chen W, Poy G, Reitman M, Londos C. The role of LMNA in adipose: a novel mouse model of lipodystrophy based on the Dunnigan-type familial partial lipodystrophy mutation. J Lipid Res. 2009 Jun;50(6):1068-79.

66.Wang Q, Mora-Jensen H, Weniger MA, Perez-Galan P, Wolford C, Hai T, Ron D, Chen W, Trenkle W, Wiestner A, Ye Y. ERAD inhibitors integrate ER stress with an epigenetic mechanism to activate BH3-only protein NOXA in cancer cells. Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2200-5.

67.Wang RH, Zheng Y, Kim HS, Xu X, Cao L, Luhasen T, Lee MH, Xiao C, Vassilopoulos A, Chen W, Gardner K, Man YG, Hung MC, Finkel T, Deng CX. Interplay among BRCA1, SIRT1, and Survivin during BRCA1-associated tumorigenesis. Mol Cell. 2008 Oct 10;32(1):11-20.

68.Feld JJ, Nanda S, Huang Y, Chen W, Cam M, Pusek SN, Schweigler LM, Theodore D, Zacks SL, Liang TJ, Fried MW. Hepatic gene expression during treatment with peginterferon and ribavirin: Identifying molecular pathways for treatment response. Hepatology. 2007 Nov;46(5):1548-63.

69.Cui Y, Hosui A, Sun R, Shen K, Gavrilova O, Chen W, Cam MC, Gao B, Robinson GW, Hennighausen L. Loss of signal transducer and activator of transcription 5 leads to hepatosteatosis and impaired liver regeneration. Hepatology. 2007 Aug;46(2):504-13.

70.Russell P, Walsh E, Chen W, Goldwich A, Tamm ER. The effect of temperature on gene silencing by siRNAs: implications for silencing in the anterior chamber of the eye. Exp Eye Res. 2006 Jun;82(6):1011-6.

71.Chen W, Wu D, Zha W, Russel P. Identification of highly significant sequence patterns in siRNAs for the optimal design of siRNA. 2004.Proceedings of the IEEE Symposium on Computer-Based Medical Systems. DOI: 10.1109/CBMS.2004.1311738

72.Chen W, Zha W, Cox T, Zhao X, Russell P. 3Si: a computer program for the optimal design of short interfering RNA (siRNA) for gene silencing. July 2004 Proceedings of the IEEE Symposium on Computer-Based Medical Systems 17:335- 342 DOI: 10.1109/CBMS.2004.1311737

73.Liu J, Yu S, Litman D, Chen W, Weinstein LS. Identification of a methylation imprint mark within the mouse Gnas locus. Mol Cell Biol. 2000 Aug;20(16):5808-17.

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