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profileRajagopal Chari, Ph.D.

TitleResearch Fellow in Genetics (EXT)
InstitutionHarvard Medical School
DepartmentGenetics
AddressHarvard Medical School
Genetics NRB 330
77 Avenue Louis Pasteur
Boston MA 02115
Phone617/432-3664
Fax617/432-7663
vCardDownload vCard (login for email)

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Feng J, Jester BW, Tinberg CE, Mandell DJ, Antunes MS, Chari R, Morey KJ, Rios X, Medford JI, Church GM, Fields S, Baker D. A general strategy to construct small molecule biosensors in eukaryotes. Elife. 2015 Dec 29; 4. PMID: 26714111.
    View in: PubMed
  2. Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC. Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integr Biol (Camb). 2015 Dec; 7(12):1587-97. PMID: 26481611.
    View in: PubMed
  3. Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, Church G. Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods. 2015 Nov; 12(11):1051-4. PMID: 26344044; PMCID: PMC4666719.
  4. Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods. 2015 Sep; 12(9):823-6. PMID: 26167643.
    View in: PubMed
  5. Yang L, Grishin D, Wang G, Aach J, Zhang CZ, Chari R, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G. Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun. 2014 Nov 26; 5:5507. PMID: 25425480; PMCID: PMC4352754.
  6. Vucic EA, Chari R, Thu KL, Wilson IM, Cotton AM, Kennett JY, Zhang M, Lonergan KM, Steiling K, Brown CJ, McWilliams A, Ohtani K, Lenburg ME, Sin DD, Spira A, Macaulay CE, Lam S, Lam WL. DNA methylation is globally disrupted and associated with expression changes in chronic obstructive pulmonary disease small airways. Am J Respir Cell Mol Biol. 2014 May; 50(5):912-22. PMID: 24298892; PMCID: PMC4068945.
  7. Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM. High-resolution antibody dynamics of vaccine-induced immune responses. Proc Natl Acad Sci U S A. 2014 Apr 1; 111(13):4928-33. PMID: 24639495; PMCID: PMC3977259.
  8. Pikor LA, Lockwood WW, Thu KL, Vucic EA, Chari R, Gazdar AF, Lam S, Lam WL. YEATS4 is a novel oncogene amplified in non-small cell lung cancer that regulates the p53 pathway. Cancer Res. 2013 Dec 15; 73(24):7301-12. PMID: 24170126; PMCID: PMC3959870.
  9. Ghayee HK, Bhagwandin VJ, Stastny V, Click A, Ding LH, Mizrachi D, Zou YS, Chari R, Lam WL, Bachoo RM, Smith AL, Story MD, Sidhu S, Robinson BG, Nwariaku FE, Gazdar AF, Auchus RJ, Shay JW. Progenitor cell line (hPheo1) derived from a human pheochromocytoma tumor. PLoS One. 2013; 8(6):e65624. PMID: 23785438; PMCID: PMC3681983.
  10. Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res. 2012 Aug; 40(15):e117. PMID: 22740649; PMCID: PMC3424587.
  11. Lockwood WW, Wilson IM, Coe BP, Chari R, Pikor LA, Thu KL, Solis LM, Nunez MI, Behrens C, Yee J, English J, Murray N, Tsao MS, Minna JD, Gazdar AF, Wistuba II, MacAulay CE, Lam S, Lam WL. Divergent genomic and epigenomic landscapes of lung cancer subtypes underscore the selection of different oncogenic pathways during tumor development. PLoS One. 2012; 7(5):e37775. PMID: 22629454; PMCID: PMC3357406.
  12. Thu KL, Vucic EA, Chari R, Zhang W, Lockwood WW, English JC, Fu R, Wang P, Feng Z, MacAulay CE, Gazdar AF, Lam S, Lam WL. Lung adenocarcinoma of never smokers and smokers harbor differential regions of genetic alteration and exhibit different levels of genomic instability. PLoS One. 2012; 7(3):e33003. PMID: 22412972; PMCID: PMC3296775.
  13. Lockwood WW, Thu KL, Lin L, Pikor LA, Chari R, Lam WL, Beer DG. Integrative genomics identified RFC3 as an amplified candidate oncogene in esophageal adenocarcinoma. Clin Cancer Res. 2012 Apr 1; 18(7):1936-46. PMID: 22328562; PMCID: PMC3523177.
  14. Vucic EA, Thu KL, Robison K, Rybaczyk LA, Chari R, Alvarez CE, Lam WL. Translating cancer 'omics' to improved outcomes. Genome Res. 2012 Feb; 22(2):188-95. PMID: 22301133; PMCID: PMC3266027.
  15. Starczynowski DT, Lockwood WW, Deléhouzée S, Chari R, Wegrzyn J, Fuller M, Tsao MS, Lam S, Gazdar AF, Lam WL, Karsan A. TRAF6 is an amplified oncogene bridging the RAS and NF-?B pathways in human lung cancer. J Clin Invest. 2011 Oct; 121(10):4095-105. PMID: 21911935; PMCID: PMC3195480.
  16. Thu KL, Chari R, Lockwood WW, Lam S, Lam WL. miR-101 DNA copy loss is a prominent subtype specific event in lung cancer. J Thorac Oncol. 2011 Sep; 6(9):1594-8. PMID: 21849855.
    View in: PubMed
  17. Gibb EA, Enfield KS, Stewart GL, Lonergan KM, Chari R, Ng RT, Zhang L, MacAulay CE, Rosin MP, Lam WL. Long non-coding RNAs are expressed in oral mucosa and altered in oral premalignant lesions. Oral Oncol. 2011 Nov; 47(11):1055-61. PMID: 21835683.
    View in: PubMed
  18. Enfield KS, Stewart GL, Pikor LA, Alvarez CE, Lam S, Lam WL, Chari R. MicroRNA gene dosage alterations and drug response in lung cancer. J Biomed Biotechnol. 2011; 2011:474632. PMID: 21541180; PMCID: PMC3085440.
  19. Gibb EA, Enfield KS, Tsui IF, Chari R, Lam S, Alvarez CE, Lam WL. Deciphering squamous cell carcinoma using multidimensional genomic approaches. J Skin Cancer. 2011; 2011:541405. PMID: 21234096; PMCID: PMC3017908.
  20. 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. Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations. Blood. 2011 Jan 13; 117(2):595-607. PMID: 20962326.
    View in: PubMed
  21. Chari R, Lonergan KM, Pikor LA, Coe BP, Zhu CQ, Chan TH, MacAulay CE, Tsao MS, Lam S, Ng RT, Lam WL. A sequence-based approach to identify reference genes for gene expression analysis. BMC Med Genomics. 2010 Aug 03; 3:32. PMID: 20682026; PMCID: PMC2928167.
  22. Lockwood WW, Chari R, Coe BP, Thu KL, Garnis C, Malloff CA, Campbell J, Williams AC, Hwang D, Zhu CQ, Buys TP, Yee J, English JC, Macaulay C, Tsao MS, Gazdar AF, Minna JD, Lam S, Lam WL. Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma. PLoS Med. 2010 Jul 27; 7(7):e1000315. PMID: 20668658; PMCID: PMC2910599.
  23. Coe BP, Chari R, MacAulay C, Lam WL. FACADE: a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data. Nucleic Acids Res. 2010 Aug; 38(15):e157. PMID: 20551132; PMCID: PMC2926625.
  24. Chari R, Coe BP, Vucic EA, Lockwood WW, Lam WL. An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. BMC Syst Biol. 2010 May 17; 4:67. PMID: 20478067; PMCID: PMC2880289.
  25. Lonergan KM, Chari R, Coe BP, Wilson IM, Tsao MS, Ng RT, Macaulay C, Lam S, Lam WL. Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE. PLoS One. 2010 Feb 11; 5(2):e9162. PMID: 20161782; PMCID: PMC2820080.
  26. Soh J, Okumura N, Lockwood WW, Yamamoto H, Shigematsu H, Zhang W, Chari R, Shames DS, Tang X, MacAulay C, Varella-Garcia M, Vooder T, Wistuba II, Lam S, Brekken R, Toyooka S, Minna JD, Lam WL, Gazdar AF. Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells. PLoS One. 2009 Oct 14; 4(10):e7464. PMID: 19826477; PMCID: PMC2757721.
  27. Garnis C, Chari R, Buys TP, Zhang L, Ng RT, Rosin MP, Lam WL. Genomic imbalances in precancerous tissues signal oral cancer risk. Mol Cancer. 2009 Jul 23; 8:50. PMID: 19627613; PMCID: PMC2726119.
  28. Coe BP, Lockwood WW, Chari R, Lam WL. Comparative genomic hybridization on BAC arrays. Methods Mol Biol. 2009; 556:7-19. PMID: 19488868.
    View in: PubMed
  29. Campbell JM, Lockwood WW, Buys TP, Chari R, Coe BP, Lam S, Lam WL. Integrative genomic and gene expression analysis of chromosome 7 identified novel oncogene loci in non-small cell lung cancer. Genome. 2008 Dec; 51(12):1032-9. PMID: 19088816.
    View in: PubMed
  30. Coe BP, Chari R, Lockwood WW, Lam WL. Evolving strategies for global gene expression analysis of cancer. J Cell Physiol. 2008 Dec; 217(3):590-7. PMID: 18680120.
    View in: PubMed
  31. Chari R, Coe BP, Wedseltoft C, Benetti M, Wilson IM, Vucic EA, MacAulay C, Ng RT, Lam WL. SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. BMC Bioinformatics. 2008 Oct 07; 9:422. PMID: 18840289; PMCID: PMC2571113.
  32. 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. Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia. BMC Genomics. 2008 Feb 04; 9:64. PMID: 18248679; PMCID: PMC2277413.
  33. Buys TP, Chari R, Lee EH, Zhang M, MacAulay C, Lam S, Lam WL, Ling V. Genetic changes in the evolution of multidrug resistance for cultured human ovarian cancer cells. Genes Chromosomes Cancer. 2007 Dec; 46(12):1069-79. PMID: 17726699.
    View in: PubMed
  34. Chari R, Lonergan KM, Ng RT, MacAulay C, Lam WL, Lam S. Effect of active smoking on the human bronchial epithelium transcriptome. BMC Genomics. 2007 Aug 29; 8:297. PMID: 17727719; PMCID: PMC2001199.
  35. 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. Comprehensive serial analysis of gene expression of the cervical transcriptome. BMC Genomics. 2007 Jun 01; 8:142. PMID: 17543121; PMCID: PMC1899502.
  36. Deleeuw RJ, Zettl A, Klinker E, Haralambieva E, Trottier M, Chari R, Ge Y, Gascoyne RD, Chott A, Müller-Hermelink HK, Lam WL. Whole-genome analysis and HLA genotyping of enteropathy-type T-cell lymphoma reveals 2 distinct lymphoma subtypes. Gastroenterology. 2007 May; 132(5):1902-11. PMID: 17484883.
    View in: PubMed
  37. Chari R, Lockwood WW, Coe BP, Chu A, Macey D, Thomson A, Davies JJ, MacAulay C, Lam WL. SIGMA: a system for integrative genomic microarray analysis of cancer genomes. BMC Genomics. 2006 Dec 27; 7:324. PMID: 17192189; PMCID: PMC1764892.
  38. Lonergan KM, Chari R, Deleeuw RJ, Shadeo A, Chi B, Tsao MS, Jones S, Marra M, Ling V, Ng R, Macaulay C, Lam S, Lam WL. Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression. Am J Respir Cell Mol Biol. 2006 Dec; 35(6):651-61. PMID: 16809635.
    View in: PubMed
  39. Lockwood WW, Chari R, Chi B, Lam WL. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet. 2006 Feb; 14(2):139-48. PMID: 16288307.
    View in: PubMed
  40. Tsui IF, Chari R, Buys TP, Lam WL. Public databases and software for the pathway analysis of cancer genomes. Cancer Inform. 2007 Dec 12; 3:379-97. PMID: 19455256; PMCID: PMC2410087.
  41. 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. Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. Cancer Metastasis Rev. 2010 Mar; 29(1):73-93. PMID: 20108112; PMCID: PMC3415277.
  42. Thu KL, Pikor LA, Chari R, Wilson IM, Macaulay CE, English JC, Tsao MS, Gazdar AF, Lam S, Lam WL, Lockwood WW. Genetic disruption of KEAP1/CUL3 E3 ubiquitin ligase complex components is a key mechanism of NF-kappaB pathway activation in lung cancer. J Thorac Oncol. 2011 Sep; 6(9):1521-9. PMID: 21795997; PMCID: PMC3164321.
  43. Chari R, Lockwood WW, Lam WL. Computational methods for the analysis of array comparative genomic hybridization. Cancer Inform. 2007 Feb 10; 2:48-58. PMID: 17992253.
    View in: PubMed
  44. Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJ, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G. Comparison of Cas9 activators in multiple species. Nat Methods. 2016 Jul; 13(7):563-7. PMID: 27214048.
    View in: PubMed
  45. Lee EH, Chari R, Lam A, Ng RT, Yee J, English J, Evans KG, Macaulay C, Lam S, Lam WL. Disruption of the non-canonical WNT pathway in lung squamous cell carcinoma. Clin Med Oncol. 2008 Apr 1; 2008(2):169-179. PMID: 20401333.
    View in: PubMed
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