Xinghua Victor Pan M.D., Ph.D.

Associate Research Scientist in Genetics

Biographical Info

Xinghua (Victor) PAN, Ph.D., M.D.

xinghua.pan@yale.edu, xinghua.pan@gmail.com

* General Info

Associate Research Scientist, Department of Genetics, Yale University;

Member, Program in Neurodevelopment and Regeneration, Yale University;

Member, Interdepartmental Neuroscience Program, Yale University

Member, Yale CEGS, Yale University

Biography:

Dr. Xinghua (Victor) Pan earned his Ph.D. degree with Dr. CC Tan and Z Geng from the Institute of Genetics, Fudan University School of Life Science, Shanghai, China. His thesis research was on the genetic associations between HLA and SLE and myasthenia gravis. He also obtained his M.D. degree (equivalent) from the Southern Medical University (previously called First Military Medical University), Guangzhou, China. Then he got his postdoctoral training at the National Key Laboratory of Molecular Oncology, Cancer Institute, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC) with Dr. Min WU, identifying a candidate tumor suppressor gene with a grant support from the China Postdoctoral Science Foundation. Beginning in December 1994, he served as Associate Professor in Genetics in the Department of Biology, Second Military Medical University, Shanghai, China, where he earned a grant from the National Natural Science Foundation of China (NSFC), with which he established nm23 transgenic mouse and elucidated its effect on hepatocarcinoma. In addition, he studied EBV BHRF1 on nasopharyngeal carcinoma, reconstructed the phylogenetic tree for MHC genes. In 1997, Dr. Pan joined Dr. Sherman Weissman’s laboratory as a Postdoctoral Fellow in the Department of Genetics, Yale University School of Medicine, and developed an approach (GADAV) for unconditionally globally scanning of DNA mutations. From 2000 to 2004, he worked with Dr. Roger Lasken for Molecular Staging Inc. as a Research Scientist in Genomics Section and then Enzymology Leader, substantially contributed to the development of a kit for whole-genome-amplification (WGA), REPLIg, which is currently used world-wide and regarded as one of the best WGA technologies.

Dr. Pan has served for Yale School of Medicine as a research faculty since 2004, heading a group on functional genomics for single cells in Dr. Weissman laboratory, supported by grants from NIH, Connecticut stem cell grant, Yale Skin Diseases Research Core Center (YSDRCC), and other foundations. Recently he established up a bench of new approaches for single cell analysis such as WPA (Whole DNA pool amplification), SMA (semi-random primed PCR-based mRNA transcriptome amplification), PMA (Phi29 DNA polymerase-based full length mRNA transcriptome amplification), and SCT-pqPCR (single cell telomere analysis basing in multiplex pre-amplification and qPCR). More new approaches such as those for single cell DNA methylation profiling and chromatin structure analysis are ongoing and promising. These technologies combining with other advanced platforms are being applied in studies on iPS, ESC and adult stem cells (ASC, including hematopoietic stem cells, mesenchymal stem cells), neurons and cancers, and diagnosis applications. Dr. Pan is an Invited Reviewer or Editor for multiple international journals, a Committee Member for several academic conferences, and an Invited/Featured Speaker or and Section Chair in several meetings such as the Single Cell Sequencing meeting, August 2013 in Providence, RI, USA, and the Single Cell Genomics & Transcriptomics Congress, June 2013 in Singapore.

Education & Training

M.D. Southern Medical University (with its previous name as the First Military Medical University) (1985)

Ph.D. Fudan University (1993)

Postdoc. Assoc Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), (1993-1994)

Postdoc Fellow Yale University School of Medicine, Genetics (1997-1999)

Professional Services

*Editor-In-Chief, Journal of Single Cell Biology (a journal of Omics Publishing Group, 2011-), USA

*Reviewer, “Genome Medicine”, “Genome Biology”, “Current Molecular Medicine”, “Molecular Ecology Resource”, “Bioscience Biotechnology and Biochemistry”, “Translational Research”, “Theriogenology”, “BMC” journals, “Hereditas (Beijing)”, “Science in China Life Sciences” , etc.

*Technical Program Committee, The 3rd/4th/5th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2009, iCBBE2010, iCBBE2011)

*Organization Committee: the 2nd World Congress on Cell Science & Stem Cell Research Conferences, November 12-14, 2012, San Antonio, USA.

*Organization Committee: the 2nd International Conference on Genetic Engineering & Genetically Modified Organisms. August 12-14, 2013, Raleigh-North Carolina, USA.

*Chief Consultant of the Academic Committee, The Jiangxi Province Key Laboratory for Systems Biological Medicine, China (2011-)

* Adjunct Professor: Jiujiang University, China (2007-)

*Vice President: the Chinese Association for Science and Technology in USA (CAST- USA), in USA (2012, 2013).

Honors and Awards

1993-1994 Fellowship award on “Isolation, Identification and Characterization of the YAC Clones for the Full Length of RA538 - a Putative Tumor-Suppressor Gene”, by China Postdoctoral Science Foundation.

1994UICC (International Union Against Cancer) scholarship, for 15th UICC Training Course on “Molecular Biology of Cancer”, in Ludwig Institute for Cancer Research & Melbourne University Melbourne, Australia.

1995Cold Spring Harbor Laboratory (CSHL) scholarship for training course on “Analysis and Genetic Manipulation of Yeast Artificial Chromosomes”, NY, USA.

1996-1998 NSFC grant (No. 39500171) for “Establishment of Transgenic Mice for nm23 Gene and Its Effect Related to Tumor Formation & Metastasis” awarded by the National Natural Science Foundation of China (NSFC), as PI.

1998-1999 Fellowship for “Use of MutS and MutL to Scan Mutations in cDNA” by PolyGenomics, Inc., USA, awarded as PI.

2003-2005 NIH grant (R21 AI055713-01) for “Global Scanning for Resistance Mutation in H. pylori“, awarded as co-PI (with Dr. Sherman M. Weissman - PI).

2007-2008 NIH grant (NIH5 P30 AR041942-14) for its pilot grant (YSDRCC PF) “Genome-wide analysis of minute amounts of DNAs from melanocytic lesions” awarded as PI, supported via Yale Skin Diseases Research Core Center.

2010-2012 NIH grant (1R21HD066457-01) for “Transcription and Methylome Analysis of Single Cells”, playing the role as the executive leader working with Dr. Weissman (PI).

2011-2013 CT stem cell grant: S01514 MPROG Stem Cell Center 690888. “Single Cell Molecular Signatures for Hematopoietic Differentiation of Human Embryonic Stem Cells” (PI: Rong Fan, Sherman Weissman), as the project leader.

2011-2016 NIGMS P01 grant (1P01GM099130-01) for “Genomic Scale Analysis of Reprogramming Processes in Fibroblasts” (PI: Michael Snyder, from Stanford University, and Co-PI: Sherman Weissman), as a Key Personnel.

Research Interests

Dr. Pan’s main interest is functional genomics, focusing on the development and application of functional genomics technologies for analysis of single cells and low quantity of cells. These approaches include whole DNA pool amplification, whole mRNA transcriptome amplification, CpG methylation pattern scanning, DNase hypersensitive and resistant sites profiling, and telomere size analysis. Combining these technologies with second generation sequencing and microfluidic platform, and collaborating with other research teams, his group explores the genomic and epigenomic mechanism for reprogramming and transdifferentiation of human induced pluripotent stem cells (iPS), differentiation of embryo stem cells (ESCs) and adult stem cells (ASC, including hematopoietic stem cells, mesenchymal stem cells), molecular regulation underlying sensory neurons, embryo development and carcinogenesis and translational medicine.

Selected Recent Publications

1. Tanaka Y, Kim KY, Hysolli E, Zhong M, Pan X, Weissman SM, and Park I-H. Transcriptome Analysis of iPS cells from Rett syndrome patients shows novel functional roles of MeCP2 in undifferentiated cells. Human Molecular Genetics (in reversion).

2. Zuo L, Pan X, …Luo X. Common PTP4A1-PHF3-EYS variants are specific for alcohol dependence. American Journal on Addictions (accepted for publication on August 19, 2013).

3. Wang Y, Yang F, Zhang HX, Zi XY, Pan XH, Chen F, Luo WD, Li JX, Zhu HY, Hu YP. (2013) Cuprous oxide nanoparticles inhibit the growth and metastasis of melanoma by targeting mitochondria. Cell Death and Disease 4,e783; doi:10.1038/cddis.2013.314.

4. Wang F, Pan X, Kalmbach K, Seth-Smith ML, Ye X, Antumes DM, Yin Y, Liu L, Keefe DL, Weissman SM. (2013) Robust measurement of telomere length in single cells. Proc Natl Acad Sci U S A. 110 (21): E1906–E1912. PMID: 23661059 March 9th (a corresponding author). It is shown in PNAS comments: New ruler for telomere length, May 10, 2013 by Sarah CP Williams; highlighted in “This week in PNAS - In this Issue”: May 21, 2013 by C.R.; and highlighted as “Telomere length measurement in single cells” by Hannah Stower published in Nature Reviews Genetics, 14, 444, (2013), doi:10.1038/nrg3529, June 18, 2013.

5. Zhang Y, Schulz V, Reed B, Wang Z, Pan X, Mariani J, Euskirchenc G, Snyder M, Vaccarino FM, Ivanova N, Weissman SM, Szekely AM. (2013). Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neuodeeneration. Proc Natl Acad Sci U S A. 2013, July 8 [Epub ahead of print]; PMID: 23836664.

6. Zuo L, Wang K, Zhang X, Pan X, Wang G, Krystal JK, Zhang H, Luo X. (2013). Sex chromosome-wide association analysis suggested male-specific risk genes for alcohol dependence. Psychiatric Genetics. 2013 Jul 31. [Epub ahead of print]. PMID: 23907288.

7. Zuo L, Wang K, Zhang X-Y, Pan X, Wang G, Tan Y, Zhong C, Krystal JH, State M, Zhang H, Luo X. (2013). Association between common alcohol dehydrogenase gene (ADH) variants and schizophrenia and autism. Human Genetics, 2013 Mar 7. [Epub ahead of print]. PMID: 23468174.

8. Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, Lamotte RH, Park IH, Snyder MP, Mason CE, Weissman SM. (2013). Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A. 110(2):594-9. PMID: 23267071(a corresponding author).

9. Qu L, Li Y, Pan X, Zhang P, LaMotte RH and Ma C. (2012). Transient receptor potential canonical 3 (TRPC3) is required for IgG immune complex-induced excitation of dorsal root ganglion neurons. The Journal of Neuroscience. 32(28):9554-62. PMID: 22787041.

10. Wang F, Yin Y, Ye Xiaoying, Liu K, Zhu H, Wang L, Chiourea M, Okuka M, Jia G, Dan, J, Zuo B, Li M, Zhang Q, Liu N, Chen L, Pan X, Gagos S, Keefee D, and Lin L. (2012). Molecular insights into the heterogeneity of telomere reprogramming in induced pluripotent stem cells (iPSCs). Cell Research. 22:757–768, PMID: 22184006.

11. Pan XH, Zhu HY, Marjani SL. (2011). Technological advances in single-cell genomic analyses. Hereditas (appeared in Pubmed as YiChuan) , 33(1): 17-24. PMID: 21377954 (review, the corresponding author).

12. Liu Z, Hu Z, Pan X, Li M, Togun TA, Tuck D, Pelizzola M, Huang J, Ye X, Yin Y, Liu M, Li C, Chen Z, Wang F, Zhou L, Chen L, Keefe DL, Liu L. (2011). Germline competency of parthenogenetic embryonic stem cells from immature oocytes of adult mouse ovary. Hum Mol Genet. 20(7):1339-52. PMID:21239471.

13. Yasukochia Y, Maruyamab O, Mahajana MC, Paddenc C, Euskirchend GM, Schulze V, Hirakawaf H, Kuharag S, Pan XH, Newburgerc PE, Snyder M, Weissmana SM. (2010). X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. Proc Natl Acad Sci U S A. 107(8): 3704-3709. PMID: 20133578.

14. Pan X, Urban AE, Dean P, Vincent S, Grubbert F, Hu Y, Snyder M, Weissman SM. (2008) A procedure for highly specific, hypersensitive and unbiased whole genome amplification. Proc Natl Acad Sci U S A. 105(40):15499-504. PMID: 18832167 (a corresponding author).

15. Pan X, Weissman SM. (2002) An approach for global scanning of single nucleotide variations. Proc Natl Acad Sci U S A. 99(14):9346-51. PMID: 12093903.


Education & Training

M.D.
First Military Medical University (1985)
Ph.D.
Fudan University (1993)

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