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Complete Publications

by Stephanie McInnis — last modified Oct 27, 2011 04:40 PM
Updated October 26, 2011.
  1. Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, Goyal P, Keane TM, Jones S, Hirst M, Lorincz MC & Mager DL.  Variation in retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genetics. 2011 Sep;7(9):e1002301. Epub 2011 Sep 29.
  2. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.  Nature 2011 Jul 27;476(7360):298-303
  3. Schrader KA, Heravi-Moussavi A, Waters PJ, Senz J, Whelan J, Ha G, Eydoux P, Nielsen T, Gallagher B, Oloumi A, Boyd N, Fernandez BA, Young TL, Jones SJ, Hirst M, Shah SP, Marra MA, Green J, Huntsman DG. Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities. J Pathol. 2011 Sep;225(1):12-8
  4. Heuser M, Yun H, Berg T, Yung E, Argiropoulos B, Kuchenbauer F, Park G, Hamwi I, Palmqvist L, Lai CK, Leung M, Lin G, Chaturvedi A, Thakur BK, Iwasaki M, Bilenky M, Thiessen N, Robertson G, Hirst M, Kent D, Wilson NK, Göttgens B, Eaves C, Cleary ML, Marra M, Ganser A, Humphries RK. Cell of Origin in AML: Susceptibility to MN1-Induced Transformation Is Regulated by the MEIS1/AbdB-like HOX Protein Complex. Cancer Cell. 2011 Jul 12;20(1):39-52
  5. O'Connor MD, Wederell E, Robertson G, Delaney A, Morozova O, Poon SS, Yap D, Fee J, Zhao Y, McDonald H, Zeng T, Hirst M, Marra MA, Aparicio SA, Eaves CJ. Retinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance. Exp Hematol. 2011 Aug;39(8):866-879.e1.
  6. McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011 May;7(5):e1001138.
  7. Karimi MM., Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL,  Jones S, Hirst M & Lorincz MC. DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs. Cell Stem Cell 8:676-87, 2011.
  8. Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao YJ, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ.  Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011 Feb 15;6(2):e17121.
  9. Diguistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CK, Docking RT, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, Hirst M, Jones SJ, Bohlmann J, Breuil C.  Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen.  Proc Natl Acad Sci U S A. 2011 Jan 24.
  10. Hirst M, Marra MA. Next generation sequencing based approaches to epigenomics. Brief Funct Genomics. 2010 Dec;9(5-6):455-65.
  11. modENCODE Consortium. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787-97
  12. Cerchietti LC, Hatzi K, Caldas-Lopes E, Yang SN, Figueroa ME, Morin RD, Hirst M, Mendez L, Shaknovich R, Cole PA, Bhalla K, Gascoyne RD, Marra M, Chiosis G, Melnick A.  BCL6 repression of EP300 in human diffuse large B cell lymphoma cells provides a basis for rational combinatorial therapy.
  13. J Clin Invest. 2010 Nov 1. pii: 42869
  14. 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. Epub 2010 Oct 20
  15. Gordon Robertson, Jacqueline Schein, Readman Chiu, Richard Corbett, Matthew Field, Shaun D. Jackman, Karen Mungall, Sam Lee, Hisanaga Mark Okada, Jenny Q. Qian, Malachi Griffith, Anthony Raymond, Nina Thiessen, Timothee Cezard, Yaron Butterfield, Richard Newsome, Simon K. Chan, Richard Varhol, Baljit Kamoh, Anna-Liisa Prabhu, Angela Tam, YongJun Zhao, Richard Moore, Martin Hirst, Marco A. Marra, Steven J.M. Jones, Pamela A. Hoodless, Inanc Birol. De novo Assembly and Analysis of Short-read Transcriptome Sequence Data.  Nature Method 2010 7:909-12. Epub 2010 Oct 10.
  16. R. Alan Harris, Ting Wang, Cristian Coarfa, Yuanxin Xi, Raman P. Nagarajan, Chibo Hong, Sara Downey, Brett E. Johnson, Shaun D. Fouse, Allen Delaney, Yongjun Zhao, Adam Olshen, Tracy Ballinger, Kevin J. Forsberg, Junchen Gu, Lorigail Echipare, Henriette O’Geen, Ryan Lister, Mattia Pelizzola, Charles B. Epstein, Bradley E. Bernstein, R. David Hawkins, Bing Ren, Wen-Yu Chung, Hongcang Gu, Christoph Bock, Andreas Gnirke, Michael Q. Zhang, David Haussler, Joseph Ecker, Wei Li, Peggy J. Farnham, Robert A. Waterland, Alexander Meissner, Marco A. Marra, Martin Hirst, Aleksandar Milosavljevic, Joseph F. Costello. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct;28(10):1026-8.
  17. Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih IeM, Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct 14:363(16):1532-1543.
  18. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct:28(10): 1045-1048
  19. Griffith M, Griffith O, Mwenifumbo J, Goya R, Morrissy S, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJM, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing.  Nature Methods. 2010;7(10), 843-847.
  20. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7
  21. Morozova O, Vojvodic M, Grinshtein N, Hansford LM, Blakely KM, Maslova A, Hirst M, Cezard T, Morin RD, Moore R, Smith KM, Miller F, Taylor P, Thiessen N, Varhol R, Zhao Y, Jones SJ, Moffat J, Kislinger T, Moran MF, Kaplan D, Marra MA. Systems-level analysis of neuroblastoma tumor-initiating cells implicates AURKB as a novel drug target for neuroblastoma. Clin Cancer Res. 2010 Jul 22. Epub ahead of print
  22. Morin RD, Zhao Y, Prabhu AL, Dhalla N, McDonald H, Pandoh P, Tam A, Zeng T, Hirst M, Marra M. Preparation and Analysis of MicroRNA Libraries Using the Illumina Massively Parallel Sequencing Technology. Methods Mol Biol. 2010;650:173-199.
  23. Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes A, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao YJ, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA.  Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology 2010, 11:R82 9Aug2010. (Nominated for the Biology Prize at Biomed Central’s 5th Annual Research Awards).
  24. Hoffman B, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhai YJ, Hirst M, Verchere B, Helgason CD, Marra MA, Jones SJM, Hoodless PA.  Identifying functional Foxa2, Hnf4a and Pdx1 sites.  Genome Res. 2010 Aug:1037-1051. Epub 2010 Jun 15.
  25. Flibotte S, Edgley ML, Chaudhry I, Taylor J, Neil SE, Rogula A, Zapf R, Hirst M, Butterfied Y, Jones SJ, Marra MM, Barstead RJ, Moerman DG. Whole-Genome Profiling of Mutagenesis in Caenorhabditis elegans. Genetics. 2010 Jun;185(2):431-41. Epub 2010 May 3.
  26. Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez X, Johnson M, McLaren W, Patone G, Petretto E, Plessy C, Rockland K, Rockland K, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravencec M, Hubner N, Jones SJ, Birney E, Aitman T.  The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.  Genome Res. 2010 Jun;20(6):791-803. Epub 2010 Apr 29.
  27. Hudson TJ,Hirst M, etal.  International network of cancer genome projects.  International Cancer genome consortium.  Nature. 2010 Apr 15;464(7291):993-8.
  28. Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.  SNVMix:  predicting single nucleotide variants from next generation sequencing of tumors.  Bioinformatics. 2010 Mar 15;26(6):730-6., Feb 3
  29. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Paul JE, Uyar B, Boyle M, Kuchenbauer F, Petriv OI, Humphries RK, Griffith O, Shah S, Corbett R, Tam A, Varhol R, Zhao YJ, Delaney A, Qian H, Birol I, Aparicio S, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Hirst M, Gascoyne RD, Marra MA. EZH2 (Y641) is Frequently Mutated in Follicular and Diffuse Large B-cell Lymphomas of Germinal Center Origin. Nat Genet. 2010, Feb;42(2):181-5 Epub 2010 Jan 17.
  30. Starczynowski D, Kuchenbauer F, Argiropoulos B, Sung S, Morin R, Muranyi A, Hirst M, Hogge D, Marra M, Wells R, Lam W, Humphries K, Karsan A.  Identification of miR-145 and miR-146a as mediators of the 5q-syndrome phenotype.  Nature Methods. 2010 Jan;16(1):49-58. Epub 2009 Nov 8.
  31. Shah SP, Morin R, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R, Severson T, Taylor G, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao YJ, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational evolution and RNA editing in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct 8;461(7265):809-13.
  32. Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies fortranscriptome analysis. Annu Rev Genomics Hum Genet. 2009 Sept;10:135-51.
  33. The MGC Project Teams (incl Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJM, Holt RA, Marra MA). The Completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Oct 28. 19: 2324-2333
  34. Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C,  Jones SJ. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol. 2009 Sep 11;10(9):R94. [Epub ahead of print]
  35. Friedländer MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Jenkin JC, Alvarado AS, Kim JK, Rajewsky N. High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11546-51.
  36. Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones SJ, Zhao Y, Hirst M, Marra MA.  Next-generation tag sequencing for cancer gene expression profiling.  Genome Res.  2009 Oct;19(10):1825-35 [Epub 2009 June 18]
  37. Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ.  De novo Transcriptome Assembly with ABySS.  Bioinformatics.  2009 Nov 1;25(21):2872-7. Epub 2009 Jun 15.
  38. Shah S, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand K, Leung G, Zayed A, Mehl E, Kalloger S, Sun M, Guiliany R, Yorida E, Jones S, Varhol R, Swenerton KD, Miller D, Clement PB, Crane C, Madore J, Provencher D, Leung P, DeFazio A, Khattra J, Turashvili G, Zhao YJ, Zeng T, Glover JNM, Vanderhyden B, Zhao C, Parkinson CA, Jimenez-Linan M, Mes-Masson AM, Brenton JD, Aparicio SA, Boyd N, Hirst M, Gilks CB, Marra MA, Huntsman DG.  Mutation of the FOXL2 Gene in Granulosa Cell tumors of the Ovary.  New England JMedicine. 2009 Jun 25;360(26):2719-29. Epub 2009 Jun 10.
  39. Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the poly-adenylated transcriptome of C. elegans. Genome Res. 2009 Apr 19(4):657-666 Epub 2009 Jan 30.
  40. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, Khattra J, Hirst M, Jones SJ, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, and Kalb JM.  ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult.  Dev Biol. 2009 Mar 15;327(2):551-565.  Epub 2008 Dec 9.
  41. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA and Humphries RK. In depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res. 2008 Nov;18(11):1787-1797. Epub 2008 Oct 10.
  42. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM. (first two are first co-authors) Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 2008 Dec;18(12):1906-17. Epub 2008 Sep 11.
  43. Hirst M and Marra MA. Epigenetics and Human Disease. Int J Biochem Cell Biol. 2009 Jan;41(1):136-46. Epub 2008 Sep 24.
  44. Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones SJM and Hoodless PA. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 2008 Aug;36(14):4549-4564.   Epub 2008 Jul 8.
  45. Morin RD, Bainbridge M,Fejes A, Hirst M, Krzywinski M, Pugh TJ, McDonald H, Varhol R, Jones SJM and Marra MA.   Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008 Jul; 45(1):81-94.
  46. Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, and Jones SJM. Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.  BMC Biol. 2008 Jul 8;6:30.
  47. Shivaswamy S, Bhinge A, Zhao YJ, Jones SJM, Hirst M and Iyer VR.  Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.  PLoS Biology. 2008 Mar 18;6(3):e65.
  48. Morin RD, O’Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T,  Hirst M, Eaves CJ and Marra MA. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008 Apr; 18(4):610-621.  Epub 2008 Feb 19.
  49. Griffith M, Tang MJ, Griffith OL, Morin RD,Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones SJM, Morin GB, Tai IT and Marra MA. ALEXA: a microarray design platform for alternative expression analysis. Nat Methods. 2008 Feb;5(2):118.
  50. Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O’Connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu A-L, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt RA, Jones SJM, Gerhard DS, Thomson JA, Eaves CJ and Marra MA.  LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol. 2007 ;8(6):R113.
  51. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra MA, Snyder M, and Jones SJM. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-657. Epub 2007 Jun 11.
  52. Joshi PB, Hirst M, Malcolm T, Parent J, Mitchell D, Lund K and Sadowski I.   Identification of protein interaction antagonists using the repressed transactivator two-hybrid system. Biotechniques. 2007 May;42(5):635-644.
  53. Quayle SN, Hare H, Delaney AD, Hirst M, Hwang D, Schein JE, Jones SJM, Marra MA and Sadar MD.  Novel expressed sequences identified in a model of androgen independent prostate cancer.   BMC Genomics. 2007 Jan 26;8:32.
  54. Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt RA, Hirst M, Hoodless PA and Marra MA. Large scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res. 2007 Jan;17(1):108-116. Epub 2006 Nov 29.
  55. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD Siddiqui AS, Marra MA and Jones SJM.  Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.  BMC Genomics. 2006 Sep 29;7:246.
  56. Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BY-L, Lee LL, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Pradhu A, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie Y-Y, Yang G, Zhang I, Hirst M, Jones SJM, Helgason CD, Simpson EM, Hoodless PA and Marra MA. A mouse altas of gene expression: Large-scale digital gene expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci USA. 2005 Dec 20;102(51):18485-18490.  Epub 2005 Dec 13.
  57. Hirst M, Astell C, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed A, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Li Y, Kobasa D, Booth T and Paetzel M. Novel avian influenza H7N3 strain outbreak, British Columbia. Emerg Infect Dis. 2004 Dec;10(12):2192-2195.
  58. Tweed SA, Skowronski DM, David ST, Larder A, Petric M, Lees W, Li Y, Katz J, Krajden M, Tellier R, Halpert C, Hirst M, Astell C, Lawrence D and Mak A. Human illness from avian influenza H7N3, British Columbia. Emerg. Infect. Dis. 2004 Dec;10(12):2196-2199.
  59. Wafa LA, Cheng H, Rao MA, Nelson CC, Cox M, Hirst M, Sadowski I and Rennie PS. Isolation and identification of L-dopa decarboxylase as a protein that binds to and enhances transcriptional activity of the androgen receptor using the repressed transactivator yeast two-hybrid system. Biochem J. 2003 Oct 15;375(Pt2):373-383.
  60. Hirst M, Ho C, Sabourin L, Rudniki M, Penn L and Sadowski I.  A two-hybrid system for transactivator bait proteins. Proc Natl Acad Sci USA. 2001 Jul 17;98(15):8726-8731.  Epub 2001 Jul 10.
  61. Estable MC, Hirst M, Bell B, O'Shaughnessy MV and Sadowski I.  Purification of RBF-2, a transcription factor with specificity for the most conserved cis-element of naturally occurring HIV-1 LTRs.  J Biomed Sci. 1999 Sep-Oct;6(5):320-332.
  62. Hirst M, Kobor MS, Kuriakose N, Greenblatt J and Sadowski I.  GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8.  Mol Cell. 1999 May;3(5):673-678.
  63. Yokota H, Nickerson DA, Trask BJ, van den Engh G, Hirst M, Sadowski I and Aebersold R. Mapping a protein-binding site on straightened DNA by atomic force microscopy. Anal Biochem. 1998 Nov 15;264(2):158-164.
  64. Estable MC, Bell B, Hirst M and Sadowski I. Naturally occurring human immunodeficiency virus type 1 long terminal repeats have a frequently observed duplication that binds RBF-2 and represses transcription. J Virol. 1998 Aug;72(8):6465-6474.
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