Ping Liang

Department of Biological Sciences




Ping Liang

Associate Professor

Office: MC F236
Phone: ext 5922
E-mail: pliang at brocku.ca
Additional lab website
dbRIP database

Understanding the mechanism of genetic diversity and their contribution to phenotype via bioinformatics and genomics approaches

Research Interest:

My lab is interested in studying the mechanisms of inter- and intra-species genetic diversity and their contribution to the diversity of biological traits, using an integrated approach combining the use of computational and experimental comparative and functional genomics technologies.

Genetic variation underlies the vivid diversity of our own human species and of all other organisms on Earth.  Understanding the mechanisms of genetic diversity and how they lead to phenotype variations continues to be an intriguing and fundamental question in life science research, and it has invaluable implications in medicine and agriculture. The advent of high throughput genome sequencing and functional genomics technologies and the availability of genome sequences for an ever increasing number of species have brought in a golden age for genetics research. By means of computational and experimental comparative genomics approaches, a comprehensive survey of inter- and intra-species genetic diversity now becomes possible, and their functional impacts can be assessed using functional genomics methodologies.

Among the many types of genetic polymorphisms, we are currently focusing on a class of genetic components called transposable elements, which exist very abundantly and evolve actively in the genomes of most organisms, including humans. Our past work includes the development of several computational comparative genomics methodologies for the identification of retrotransposon insertion polymorphisms and retrotransposon-derived genome rearrangements, as well as the development of the database of Retrotransposon Insertion Polymorphisms in humans (dbRIP). In our current research, we are utilizing newly available individual human genome sequences generated by the next-generation sequencing technologies, such as 454 and Illumina, for more comprehensive surveys and documentation of genetic diversity derived from transposable elements. We are also extending our attention to the mechanism and identification of other types of structural variations, such as copy number variations. We will then start to examine the impact of these genetic variations on gene function and phenotype, including human disease susceptibility and tasting variation.

In addition to those above research activities, we also collaborate with a large number of investigators within and outside Brock campus by providing our bioinformatics expertise. Outside the biology-oriented research, we are also interested in developing novel bioinformatics and genomics analytic tools.
  
My research lab provides an ideal environment for students who have interest in the emerging field of genomics and bioinformatics, an exciting field, which advances essentially on a daily-basis. Within this group, students have the opportunity to learn and apply computational skills, as well as advanced genomics and molecular techniques. I am currently looking for highly motivated and hard working graduate students either from a biological field with certain level of computer programming skills or from a computer science background with a minor degree in biology. (Note: Students with interests only for bench research and those with no prior trainings or skills in computer programming will not be considered.)

 
Courses offered:
Bioinformatics (BIOL 4P06BCHM 4P06BTEC 4P06)
Human Molecular Biology (BIOL 4P41BCHM 4P41BTEC 4P41CHSC 4P41)
Protein Structure and Function (BCHM3P02)
 
Graduate students:
Supervised: Sami Azrak (PhD, graduated), Musaddeque Ahmed (PhD), Amanda Bering (MSc), Scott Golem (MSc), Wangxiangfu Tang (MSc, graduated), Joseph Zelic (MSc)
Co-supervised: Xuemei Luo (PhD, Carlton, graduated), Darren Peters (MSc, Brock, graduated)
 
Publications: (selected from a total of 64 of peer –reviewed papers)
Papers related to retrotransposons and the associated genomic variations in humans
  1. Callinan PA*, Wang J*, Herke SW*, Garber RK, Liang P, Batzer MA. Alu retrotransposition-mediated deletion. J Mol Biol 348:791-800, 2005. (*co-first authors). PubMed Abstract, PDF, Supplemental Materials.
  2. Wang J*, Song L*, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365:11-20, 2006. PubMed Abstract, , PDF, Supplemental Data (*co-first authors)
  3. Han K*, Sen SK*, Wang J*, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res 33:4040-4052, 2005. (*co-first authors) PubMed Abstract; Supplemental Data1; Supplemental Data2
  4. Charbonnier F, Baert-Desurmont S, Liang P, Di Fiore F, Martin C, Frerot S, Olschwang S, Wang Q, Buisine MP, Gilbert B, Nilbert M, Lindblom A, Frebourg T. The 5' region of the MSH2 gene involved in hereditary non-polyposis colorectal cancer contains a high density of recombinogenic sequences. Hum Mutat 26:255-261, 2005. PubMed Abstract, PDF
  5. Wang, J.*, L. Song*, D. Grover*, S. Azrak, M. A. Batzer, Liang P. dbRIP: A Highly Integrated Database of Retrotransposon Insertion Polymorphism in Human. Human Mutat 27:323-329,2006. PubMed Abstract; PDF (*co-first authors).
  6. Li L, McVety S, Younan R, Liang P, DuSart D, Gordon P, Hutter P, Hogervorst FB, Chong G, and Foulkes WD. Distinct patterns of Germ-Line Deletions in MLH1 and MSH2 in hereditary non-polyposiscolorectal cancer families: the role of Alu sequences. Human Mutat 27:388, 2006. PubMed Abstract
  7. Sen SK*, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA.Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet 79:41-53, 2006. PubMed Abstract , PDF
  8. Lee, J, Cordaux R, Han K, Wang J, Hedges DJ, Batzer MA*, Liang P*. Different evolutionary fates of recently integrated human and chimpanzee LI NE-1 retrotransposons. Gene 390:18-27, 2007. PubMed Abstract. (*co-senior authors)
  9. Konkel M*, Wang J*, Liang P, Batzer MA. Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two Human genome sequence assemblies. Gene 390:28-38, 2007. PubMed Abstract (*co-first authors)
  10. Han K, Lee J, Meyer TJ, Wang J, Sen SK, Srikanta D, Liang P, Batzer MA. Chimpanzee-specific structural variation deriv ed from Alu recombination-mediated deletions. PLOS Genetics 3:1939-1949, 2007. Open Access at PLOS Genetics.
  11. Liang P and Wang T. Database documentation of retrotransposon insertion polymorphisms. In “Mobile DNAs in Mammalian Genomes” in Encyclopedia of Bioscience, Frontiers in Bioscience E4,1542-1555, 2012.

  12. Luo X, Dehne F, Liang P. Identification of Transposon Insertion Polymorphisms (TIPs) by computational comparative analysis of next generation personal genome data. AIP Proceedings of the AMMCS-2011 Conference. (Accepted on September 27, 2011.
  13. Amed M, Liang P. Transposable elements are a significant contributor to tandem repeats in the human genome. Comp Funct Genomics 2012, Article 947089, 2012.

Selected papers related to genetic and bioinformatics data analysis and development of bioinformatics tools
  1. Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S. Genome sequence of a genetically tractable and extremely halophilic archaeon. PNAS 97: 11677-12388, 2000. PubMed Abstract , PDF
  2. Liang P, and M. Riley. Comparative genomics approach for studying ancestral proteins and evolution. Adv Appl Microbiol 50: 39-72, 2001. PubMed Abstract
  3. Liang P, LabedanB, Riley M. Physiological genomics of E. coli protein families. Physiol Genomics 9:15-26, 2002. PubMed Abstract, PDF
  4. Serres M, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M. A functional update of the Escherichia coli K-12 genome. Genome Biol 2: Research0035.1-7,2002. PubMed Abstract, PDF
  5. Wang J, Liang P. Digi-Northern digital expression analysis of query genes based on ESTs. Bioinformatics 19:653-654, 2003. PubMed Abstract, PDF
  6. Zhang Q, Zhao B, Li W, Oiso N, Novak EK, Rusiniak ME, Gautam R, Chintala S, O'Brien EP, Zhang Y, Roe BA, Elliott RW, Eicher EM, Liang P, Kratz C, Legius E, Spritz RA, O'Sullivan TN, Copeland NG, Jenkins NA, Swank RT. Ru2 and Ru encode mouse orthologs of the genes mutated in human Hermansky-Pudlak syndromes type 5 and 6. Nature Genet 33:145-153, 2003. PubMed Abstract, PDF
  7. Shankar G, Rossi1 MR, McQuaid DE, Conroy JM, Gaile DP, Cowell JK, Nowak NJ, Liang P. 2006. aCGHViewer: a generic visualization tool for aCGH data. Cancer Informatics 2:36-43, 2006.
  8. Lo K, Shankar G, Rossi M, Burkhardt T, Liang P, Cowell JK. 2007. Overlay tool for aCGHViewer: an analysis module built for aCGHViewer used to combine different microarray platforms for visualization. Cancer Informatics 3:309-319, 2007.
  9. Song F, Mahmood S, Ghosh S, Liang P, Smiraglia DJ, Nagase N, Held WA. Tissue specific differentially methylated regions (TDMR): changes in DNA methylation during development. Genomics 93,130-139, 2009.
  10. Safina AF, Varga AE, Bianchi A, Zheng Q, Kunnev D, Liang P, Bakin AV. Ras alters epithelial-mesenchymal transition in response to TGFβ by reducing actin fibers and cell-matrix adhension. Cell Cycle 8:284-298, 2009.
  11. Hall BM, Ma CX, Liang P, Singh KK. Fluctuation AnaLysis CalculatOR (FALCOR): a web tool for the determination of mutation rate using Luria-Delbrück fluctuation analysis. Bioinformatics 25:1564-1565, 2009.
  12. Marella N, Malyavantham, K, Wang J, Matsui S, Liang P, Berezney R. Cytogenetic and cDNA Microarray Expression Analysis of MCF10A Human Breast Cancer Progression Cell Lines. Cancer Res 69: 5946-5953, 2009.
  13. Sood AK, Wang J, Mhawech-Fauceglia P, Jana B, Liang P, Geradts J. Sam-pointed domain containing Ets transcription factor in luminal breast cancer pathogenesis. Cancer Epidemiol Biomarkers Prev. 18:1899-903, 2009.
  14. Huang J, Okuka M, Wang F, Zuo B, Liang P, Kalmbach K, Liu L, Keefe DL. Generation of pluripotent stem cells from eggs of aging mice.  Aging Cell 9:113-125, 2010.
  15. Huang J, Wang F, Okuka M, Liu N, Ji G, Ye X, Zuo B, Li M, Liang P, Ge WW, Tsibris JC, Keefe DL, Liu L.  Association of telomere length with authentic pluripotency of ES/iPS cells. Cell Res. 21,779-92, 2011.
  16. Liu N, Enkenann SA, Liang P, Hesmus R, Zanazzi, C, Huang J, Wu C, Chen, Z, Looijenqa, LHJ, Keefe DL, Liu L. Genome-wide gene expression profiling reveals novel signaling pathways associated with early parthenogenesis. J Mol Cell Biol 2:333-344, 2010.    
  17. Huang J, Wang F, Okuka M, Liu N, Ji G, Ye X, Zuo B, Li M, Liang P, Ge WW, Tsibris JC, Keefe DL, Liu L.  Association of telomere length with authentic pluripotency of ES/iPS cells. Cell Res. 21,779-92, 2011. Publisher's full text
  18. Liu C, Morishima M, Yu T, Pao A, Matsui S, Zhang L, Fu D, Parmacek MS, Liang P,  Baldini A, Yu YE. Genetic analysis of Down syndrome-associated heart defects in mice.  Hum Genet.  130: 623-32, 2011. Free access at PMC
  19. Zhang L, Fu D, Belichenko PV, Liu C,  Kleschevnikov AM, Pao A, Liang P, Clapcote SJ, Mobley WC, Yu YE. Genetic analysis of Down syndrome facilitated by mouse chromosome engineering. Bioengineered Bugs. 3(1), 2011. Publisher's full text
  20. Liang P*#, Song F*, Ghosh S, Morien E, Qin M, Mahmood S, Fujiwara K, Igarashi J, Nagase H#,  Held WA. Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics 12, 231, 2011. (*: co-first author, #: corresponding author; highly accessed article). Open access at the journal.
  21. Stuart JA, Liang P, Luo X, Page MM, Gallagher EJ, Robb EL. A comparative cellular and molecular biology of longevity database. Age (advanced online publication on July 27, 2012). Link to PubMed.
  22. Peters D, Luo X, Qiu K, Liang P. Speeding up large-scale next generation sequencing data analysis with pBWA.  J. Biocomput. (accepted on Nov 23, 2012)

(Last update: 2012-12-19)