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Raj Chari, PhD

Current position: Postdoctoral fellow in the George Church lab, Department of Genetics, Harvard Medical School

rchari@bccrc.ca   675 West 10th Avenue, Vancouver, B.C., V5Z 1L3, Canada 

| BCCA | BCCRC | Integrative Oncology | Cancer Genetics | Wan Lam Lab | Raj Chari |


Raj Chari1  


Training 

BSc (Biochemistry), University of British Columbia, 2001
BSc (Computer Science), University of British Columbia, 2004

PhD (Pathology and Laboratory Medicine), University of British Columbia, 2010


Research Interests

With a background in both the computational and biological sciences, my interests are diverse. My focus currently is looking at data mining and analysis techniques for array Comparative Genomic Hybridization (CGH), genome sequencing as well high throughput gene expression. Some of the biological questions I am interested in are involved with lung cancer progression, cross-comparative analysis of different types and sub-types of cancers, as well as the development of tools for integrative genomics analysis. 

I am also interested in technology development, with respect to both synthetic biology and genome engineering as well as novel applications of high-throughput sequencing.


Scholarships and Awards 

BC Cancer Agency Lloyd Skarsgard Research Excellence Prize (2010)

Michael Smith Foundation for Health Research, Senior Graduate Studentship (2007-2010)

Canadian Institutes of Health Research, Frederick Banting and Charles Best Canada Graduate Scholarship - Doctoral Award (2007-2010)

Canadian Cancer Society Research Institute Travel Award (2009)

Marie Curie Genome Architecture in Relation to Disease (MC-GARD) Bioinformatic Techniques Workshop - European Union Travel Grant (2008)

Human Genome Organisation 12th Human Genome Meeting, 2nd place poster award competition (2007)

Human Genome Organisation 12th Human Genome Meeting, Genome Canada Student Sponsorship (2007)

BC Cancer Agency Betty Rice Award for Lung Cancer Research (2006)

11th Annual Conference Advancing Practice, Instruction, and Innovation through Informatics, Best Presentation - Bioinformatics (2006)

Natural Sciences and Engineering Research Council Summer Studentship (2003)


Publications 

  1. Vucic, EA*, Thu KL*, Robison K, Rybaczyk L, Chari R, Alvarez CE, Lam WL (2012) Translating cancer omics to outcomes. Genome Research 22:188-95. [PMID: 22301133]
  2. Enfield KSS, Stewart GL, Pikor LA, Alvarez CE, Lam S, Lam WL, Chari R (2011) MircroRNA gene dosage alterations and drug response in lung cancer. Journal of Biomedicine and Biotechnology.  Accepted.
  3. Starczynowski DT, Morin R, McPherson A, Lam J, Chari R, Wegrzyn J, Kuchenbauer F, Hirst M, Tohyama K, Humphries RK, Lam WL, Marra M, Karsan A (2011) Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations. Blood. In press. [2010 Oct 20. Epub ahead of print]
  4. Gibb EA, Enfield KSS, Tsui IFL, Chari R, Lam, S, Alvarez CE, Lam WL (2011) Deciphering squamous cell carcinoma using multi-dimensional genomic approaches. Journal of Skin Cancer 2011: 1-16.
  5. Chari R, Lonergan KM, Pikor LA, Coe BP, Zhu CQ, Chan THW, MacAulay C, Tsao MS, Lam S, Ng RT, Lam WL (2010) A sequence-based approach to identify reference genes for gene expression analysis.  BMC Medical Genomics 3:32, 1-11. 
  6. Lockwood WW, Chari R, Coe BP, Thu KL, Garnis C, Malloff CA, Campbell JM, Williams AC, Hwang D, Chang QZ, Buys TPH, Yee J, English J, MacAulay C, Tsao MS, Gazdar AF, Minna JD, Lam S, Lam WL (2010) Integrative genomic analyses identify BRF2 as a novel lineage specific oncogene in lung squamous cell carcinoma. PLoS Medicine 7(7): e1000315, 1-14.
  7. Coe BP, Chari R, MacAulay C, Lam WL (2010) FACADE: A fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data. Nucleic Acids Research. 38: e157, 1-7.
  8. Chari R, Coe BP, Vucic EA, Lockwood WW, Lam WL (2010) An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. BMC Systems Biology 4: 67, 1-14.
  9. Chari R, Thu KL, Wilson IM, Lockwood WW, Lonergan KM, Coe BP, Malloff CA, Gazdar AF, Lam S, Garnis C, MacAulay CE, Alvarez CE, Lam WL (2010) Integrating the multiple dimensions of genomic and epigenomic lanscapes of cancer. Cancer and Metastasis Reviews 29: 73-93.
  10. Lonergan, KM, Chari R, Coe BP, Wilson IM, Tsao MS, Ng RT, MacAulay C, Lam S, Lam WL (2010) Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE. PLoS ONE 5: e9162, 1-22.
  11. Soh J*, Okumura N*, Lockwood WW, Yamamoto H, Shigematsu H, Zhang W, Chari R, Shames D, Tang X, MacAulay C, Varella-Garcia M, Vooder T, Wistuba II, Lam S, Brekken R, Toyooka S, Minna JD, Lam WL, Gazdar AF (2009) Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells. PLoS ONE 4: e7464, 1-13.
  12. Garnis C, Chari R, Buys TPH, Zhang L, Ng RT, Rosin MP, Lam WL (2009) Genomic imbalances in precancerous tissues signal oral cancer risk. Molecular Cancer 8: 50, 1-7.
  13. Coe BP, Lockwood WW, Chari R, Lam WL (2009) Comparative genomic hybridization on BAC arrays. Methods in Molecular Biology 556: 7-19.
  14. Chari R, Coe BP, Wedseltoft C, Benetti M, Wilson IM., Vucic EA., MacAulay C, Ng RT, Lam WL (2008) SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. BMC Bioinformatics 9:422, 1-12.
  15. Campbell JM*, Lockwood WW*, Buys THP, Chari R, Coe BP, Lam S, Lam WL (2008) Integrative genomic and gene expression analysis of chromosome 7 identified novel oncogene loci in non-small cell lung cancer. Genome 51: 1032-9.
  16. Coe BP, Chari R, Lockwood WW, Lam WL (2008) Evolving strategies for global gene expression analysis of cancer. Journal of Cellular Physiology 217: 590-7.
  17. Lee EHL*, Chari R*, Lam A, Ng RT, Yee J, English J, Evans KG, MacAulay C, Lam S, Lam WL (2008) Disruption of the non-canonical Wnt pathway in lung squamous cell carcinoma. Clinical Medicine: Oncology 2: 169-79. *these authors contributed equally
  18. Lockwood WW, Chari R, Coe BP, Girard L, MacAulay C, Lam S, Gazdar AF, Minna JD, Lam WL (2008) DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers. Oncogene 27: 4615-4624.
  19. Shadeo A, Chari R, Lonergan KM, Pusic A, Miller D, Ehlen T, Van Niekerk D, Matisic J, Richards-Kortum R, Follen M, Guillaud M, Lam WL*, MacAulay C* (2008) Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia. BMC Genomics 9: 64, 1-14.
  20. Tsui IFL, Chari R, Buys TPH, Lam WL (2007) Public databases and software for the pathway analysis of cancer genomes. Cancer Informatics 3, 389-407.
  21. Buys TPH, Chari R, Lee E, Zhang M, MacAulay C, Lam S, Lam WL, Ling V (2007) Genetic changes in the evolution of multidrug resistance for cultured human ovarian cancer cells. Genes Chromosomes and Cancer 46(12):1069-79.
  22. Chari R, Lonergan KM, Ng RT, MacAulay C, Lam S, Lam WL (2007) Effect of active smoking on the bronchial epithelial transcriptome. BMC Genomics 8(1):297, 1-13.
  23. Shadeo A, Chari R, Vatcher G, Campbell J, Lonergan KM, Matisic J, van NieKerk D, Ehlen T, Miller D, Follen M, Lam WL, MacAulay C (2007) Comprehensive serial analysis of gene expression of the cervical transcriptome. BMC Genomics 8(1):142, 1-11.
  24. deLeeuw RJ, Zettl A, Klinker E, Haralambieva E, Trottier M, Chari R, Ge Y, Gascoyne RD, Chott A, Muller-Hermelink HK, Lam WL (2007) Whole genome analysis and HLA haplotyping of enteropathy-type T-cell lymphoma reveals two distinct lymphoma subtypes. Gastroenterology 132(5):1902-11.
  25. Chari R, Lockwood WW, Coe BP, Chu A, Macey D, Thomson A, Davies JJ, MacAulay C, Lam WL (2006) SIGMA: A system for the integrative genomic microarray analysis of cancer genomes. BMC Genomics 7(1):324, 1-11. **Highly accessed article, over 500+ accesses in first two weeks**
  26. Lonergan KM, Chari R, deLeeuw RJ, Shadeo A, Chi B, Tsao M, Jones S, Marra M, Ng R, MacAulay C, Lam S, Lam WL (2006) Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression. American Journal of Respiratory Cell and Molecular Biology 35(6):651-61.
  27. Coe BP, Lockwood WW, Girard L, Chari R, Minna JD, MacAulay C, Lam S, Gazdar AF, Lam WL (2006) Differential regulation of cell cycle pathways in small cell and non-small cell lung cancer. British Journal of Cancer (12):1927-35.
  28. Chari R*, Lockwood WW*, Lam WL (2006) Computational methods for the analysis of array comparative genomic hybridization. Cancer Informatics (2):48-58. *these authors contributed equally
  29. Lockwood WW*, Chari R*, Chi B, Lam WL (2006) Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. European Journal of Human Genetics 14(2):139-48. *these authors contributed equally
  30. Buys TPH, Wilson IM, Coe BP, Lee EHL, Kennett JY, Lockwood WW, Tsui IFL, Shadeo A, Chari R, Garnis C, Lam WL (2006) Detailed Comparisons of Cancer Genomes. In Comparative Genomics: Fundamental and Applied Perspectives (Brown JR, ed.), CRC Press / Taylor and Francis, LLC. Boca Raton, FLA, pp. 245-259.
  31. Buys TPH, Wilson IM, Coe BP, Lockwood WW, Davies JJ, Chari R, DeLeeuw RJ, Shadeo A, MacAulay C, Lam WL (2005) Key Features of BAC Array Production and Usage. In DNA Microarrays (Methods Express Series) (Schena M, ed), Scion Publishing, Ltd., Bloxham. pp. 115-145.

Selected Oral Presentations

  1. Chari R, Lockwood WW, Coe BP, Buys TPH, MacAulay C, Lam S, Lam WL. (2009) Multi-dimensional and integrative genetic, epigenetic, and gene expression analysis of lung adenocarcinoma.  ComBio2009, Christchurch, New Zealand, December 6-10, 2009, Stream: "Genetics and Genomics", Symposium: "Systems Biology".
  2. Chari R. (2006) SIGMA Viewer: A platform to visualize and analyze DNA copy number microarray data. 11th Annual Conference Advancing Practice, Instruction and Innovation through Informatics, Vancouver, BC, August 16th, 2006. Best Scientific Presentation – Bioinformatics

Selected Abstracts 

  1. Gazdar AF, Chari R, Lockwood WW, Coe BP, Soh J, MacAulay C, Minna JD, Lam S, Lam WL. (2010) Oncogenes and uniparental disomy: Changing the landscape of the lung cancer genome. AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer: Prospects for Personalized Prevention and Therapy, Coronado, CA, U.S.A., January 11-14, 2010.
  2. Lam WL, Wilson IM, Chari R, Thu KL, Lockwood WW, Coe BP, Laird-Offringa I, Yee J, Lam S, MacAulay C, Zhang Y, Gazdar AF. (2009) The EDRN-Canary Project on Lung Cancer in Never Smokers: gene discovery through integrating multiple platforms.  6th NCI Early Detection Research Network Scientific Workshop, Bethesda, MD, U.S.A., Abstract #38.
  3. Chari R, Lockwood WW, Malloff C, Coe BP, Buys TPH, MacAulay C, Lam S, Lam WL. (2009) Integrative genetic, epigenetic, and gene expression analysis of lung adenocarcinoma.  13th World Conference on Lung Cancer, San Francisco, CA, U.S.A., July 31 - August 4, 2009, Abstract #PD10.2.6.
  4. Lockwood WW, Chari R, Coe BP, Garnis C, Campbell J, Williams AC, Hwang D, Zhu CQ, Buys TPH, Yee J, English J, MacAulay C, Tsao M-S, Gazdar AF, Minna JD, Lam S, Lam WL. (2009)  BRF2 is a lineage specific oncogene amplified early in squamous cell lung cancer development.  13th World Conference on Lung Cancer, San Francisco, CA, U.S.A., July 31 - August 4, 2009, Abstract #C3.4.
  5. Chari R, Coe BP, Wedseltoft C, Benetti M, Wilson IM, Vucic EA, MacAulay C, Ng RT, Lam WL. (2008)  SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. MC-GARD Workshop 2: Genome bioinformatic techniques, Braga, Portugal, September 8 - 13, 2008, Poster #2.
  6. Chari R, Shadeo A, Vucic E, Kennett JY, Lam WL. (2008)  Multi-dimensional genetic, epigenetic and gene expression analysis of breast cancer genomes.  Canadian Breast Cancer Research Alliance, Reasons for Hope, Vancouver, BC, Canada, April 25 - 27, 2008, Poster# 58.
  7. Chari R, Coe BP, Ng RT, MacAulay C, Yee J, English J, Lam S, Lam WL. (2007) Expression networks regulated by gene dosage in lung adenocarcinoma.  12th World Conference on Lung Cancer, Seoul, Korea, September 2-6, 2007, Abstract# P2-005.
  8. Lockwood WW, Chari R, Coe BP, Buys TPH, English J, Yee J, Tsao M-S, MacAulay C, Lam S, Lam WL. (2007) Integrative genomic and gene expression analysis of NSCLC identifies subtype-specific signatures of pathway disruption.  12th World Conference on Lung Cancer, Seoul, Korea, September 2-6, 2007, Abstract# A6-06.
  9. Chari R, Coe BP, MacAulay C, Lam WL. (2007) A system for integrative multi-dimensional analysis of genomes. HUGO's 12th Human Genome Meeting, Montreal, Quebec, Canada, May 21-24, 2007, Poster #133.
  10. Chari R, Lonergan KM, Ng RT, MacAulay C, Lam WL, Lam S. (2007)  Effect of active smoking on the bronchial epithelium transcriptome.  American Association for Cancer Research Annual Conference, Los Angeles, CA, U.S.A., April 14-18, 2007, Abstract #4994.
  11. Chari R, Lockwood WW, Coe BP, MacAulay C, Lam WL. (2006)  A comprehensive and interactive array comparative genomic hybridization database of cancer genomes.  11th Annual Conference Advancing Practice, Instruction and Innovation through Informatics, August 15th-18th, 2006, Archives of Pathology and Laboratory Medicine, May 2007, 131:813-814.
  12. Chari R, Lonergan KM, deLeeuw RJ, Shadeo A, Chi B, Tsao M-S, Jones S, Marra M, Ling V, Ng R, MacAulay C, Lam S, Lam WL. (2006)  Identification of novel lung-specific genes in bronchial epithelium using Serial Analysis of Gene Expression (SAGE).  American Association for Cancer Research Annual Conference, Washington, DC, U.S.A., April 1-5, 2006. Abstract #201.
  13. Chari R, Lockwood WW, Coe BP, MacAulay C, Lam WL. (2006)  A comprehensive and interactive array comparative genomic hybridization (CGH) database.  American Association for Cancer Research Annual Conference, Washington, DC, U.S.A., April 1-5, 2006.  Abstract #616.
  14. Lam S, Chari R, Lockwood WW, Lam WL, MacAulay C, Sin D, Gazdar AF, Khoury J, Yao R, You M. (2006) Progress in lung cancer chemoprevention.  American Association for Cancer Research Annual Conference, Washington, DC, U.S.A., April 1-5, 2006.  Abstract #ED07-03.
  15. Chari R, Lonergan KM, Girard L, Minna JD, Gazdar AF, Ng R, Lam WL, MacAulay C, Lam S.  (2005)  Effect of inhaled budesonide in smokers with bronchial dysplasia.  11th World Congress of Lung Cancer.  Lung Cancer, Suppl. 2, 49:S120, Abstract P-017, 2005.  

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| BCCA | BCCRC | Integrative Oncology | Cancer Genetics | Wan Lam Lab | Raj Chari |