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 mechanisms 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 exciting emerging field of genomics and bioinformatics, which advance 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 look for highly motivated and hard working graduate students either from a biological field with a 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.)
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
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
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)
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)
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.
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.
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.
Amed M, Liang P. Transposable elements are a significant contributor to tandem repeats in the human genome. Comp Funct Genomics 2012, Article 947089, 2012.
Ahmed M, Li W, Liang P. Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements. Mobile DNA 4:25, 2013.
Ahmed M, Liang P. Study of modern human evolution via comparative analysis with the Neanderthal genome. Genomics Inform. 11:230-238, 2013.
doi: 10.1093/dnares/dsy022. (Open access), , , , Liang P. Contribution of mobile elements to the uniqueness of human genome with more than 15,000 human-specific insertions. DNA Res. 25(5):521-533.
- Tang W, Liang P. Comparative genomics analysis reveals high levels of differential DNA transposition among primates. (available as pre-print at BioRxiv on Jan 14, 2019)
- 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
- Liang P, and M. Riley. Comparative genomics approach for studying ancestral proteins and evolution. Adv Appl Microbiol 50: 39-72, 2001. PubMed Abstract
- Liang P, LabedanB, Riley M. Physiological genomics of E. coli protein families. Physiol Genomics 9:15-26, 2002. PubMed Abstract, PDF
- 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
- Wang J, Liang P. Digi-Northern digital expression analysis of query genes based on ESTs. Bioinformatics 19:653-654, 2003. PubMed Abstract, PDF
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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
- 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: 2011. Publisher’s full text
- 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.
- 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.
- 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)
- Bering AH, Pickering G, Liang P. TAS2R38 Single Nucleotide Polymorphisms Are Associated with PROP—but Not Thermal—Tasting: a Pilot Study. Chemosensory Perception 7:23-30. 2014.
- Xie P, Sun Y, Ouyang Q, Hu L, Tan Y, Zhou X, Xiong B, Zhang Q, Yuan D, Pan Y, Liu T, Liang P, Lin G, Lu G. Physiological Oxygen Prevents Frequent Silencing of DLK1-DIO3 Cluster During Human Embryonic Stem Cells Culture. Stem Cells 32:391-401, 2014.
- Zhang L, Meng K, Jiang X, Liu C, Pao A, Belichenko PV, Kleshevnikov AM, Josselyn S, Liang P, Ye P, Mobley WC, Yu YE. Human chromosome 21 orthologous region on mouse chromosome 17 is a major determinant of Down syndrome-related developmental cognitive deficits. Hum Mol Genet 23:578-89, 2014.
- Belyea BC, Xu F, Pentz ES, Medrano S, Li M, Hu Y, Turner S, Legallo R, Jones CA, Tario JD, Liang P, Gross KW, Sequeira-Lopez MLS, Gomez RA. Renin Progenitors in the Bone Marrow: A Novel Origin for B-Cell Leukemia. Nat Commun 5:3273, 2014.
- Fujiwara L, Ghosh S, Liang P, Morien E, Masayoshi Soma, Nagase N. Genome-wide screening of aberrant DNA methylation which associated with gene expression in mouse skin cancers. Mol Carcinogen 54:178-88, 2015.
- Sjaarda C, Patrick Hecht P, McNaughton A, Audrina Zhou A, Hudson M, Liang P, Chen N, Ayub M, Beversdorf D, Liu X. Interplay between maternal Slc6a4 mutation and prenatal stress: a possible mechanism for autistic behaviour development. Scientific Reports (accepted on June 25, 2017).
- Tan Y, Tu C, Meng L, Yuan S, Sjaarda C, Luo A, Du J, Li W, Gong F, Zhong C, Deng HX, Lu G, Liang P*, Lin G*. Loss-of-function mutations TDRD7 lead to a rare novel syndrome combining congenital cataract and non-obstructive azoospermia in humans. Genetics in Medicine (accepted on June 20, 2017) (*co-corresponding authors).
- Yuan S, Meng L, Zhang Y, Tu C, Du J, Wen Li, Liang P, Lu G, Tan Y. Genotype-phenotype correlation and identification of two novel SRD5A2 mutations in 33 Chinese patients with hypospadias. Steroids (accepted on June 22, 2017)
- He W, Lin G, Liang P, Cheng D, Li W. Genetic analysis of three families affected with split-hand/split-foot malformation. Chinese Journal of Medical Genetics 34:476-480, 2017. (in Chinese)
- Qu Y, Thamm AMK, Czerwinski M, Masada S; Kim KH, Jones G, Liang P, De Luca V. Identification and biochemical description of geissoschizine synthase, the gateway enzyme controlling flux for the formation of iboga and aspidosperma monoterpenoid indole alkaloids in Catharanthus roseus”. Planta 247:625-634, 2018.
- Aida AM, Sarker LS, Malli RPN, Liang P, Mahmoud S. Discovery of novel structural and regulatory terpenoid biosynthetic genes in Lavandula through RNA-Seq. Planta (accepted on June 2, 2018).
- Malli RNP, Adal AM, Saker LS, Liang P*, Mahmoud S*. De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production. Planta (accepted on Sept 15, 2018). (*corresponding authors). Advanced online version available at ReadCube.
- A new manuscript titled “Comparative genomics analysis reveals high levels of differential DNA transposition among primates” as part of Daniel Tang’s PhD thesis has been published as a pre-print at BioRxiv on Jan 14, 2019. Among many new findings from this study, we demonstrated that crab-eating macaque genome has an extremely low level of DNA transposition, while the human genome was shown to be a very young and actively evolving genome by DNA transposition among the eight primate genomes we examined for the great ape and old world monkey groups of primates.
- Our work (Part of Radesh’s PhD thesis) in sequencing the lavender genome was recently accepted for publication in journal, Planta, with its online version of the paper available at here and via ReadCube. Paper title: “De novo sequencing of the Lavandula angustifolia genome reveals highly duplicated and optimized features for essential oil production”.
- A success story about Jina in our lab at https://brocku.ca/brock-news/2018/06/the-road-to-becoming-a-physician-scientist/
- A paper titled “Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase” was accepted on June 20, 2018 and is now available for reading at DNA Research. This paper is based on Daniel W. Tang’s MSc thesis work. In addition to the main discoveries reported in the paper, we also revised the content of transposable elements in the human reference genome from originally reported 49% to 52%.
- In the 2018 Spring Convocation, we had three graduates completing their programs: Jinadari (Jina) Nanayakkara, BSc with Honours in first class standing; Aditya Joshi, MSc in Biotechnology; Robert Baldwin, MSc in Biotechnology. Congratulations to them!!!
- Jina and Zakia’s video “DNA: A Mobile Molecule” for NSERC’s Science, Action competition got into the top 15!!!