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Robert Holt Publications

by Kirsten San Juan — last modified Nov 04, 2011 02:30 PM
Robert Holt Complete Bibliography
  1. Warren RL, Holt RA. Targeted assembly of short sequence reads. PLoS ONE. 2011 Jan 1;6(5):e19816.
  2. Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res. 2011 Feb 24.
  3. 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, Wolcock 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 SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Aug 18;476(7360):298-303.
  4. Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chénard C, Friedman JM, Suttle CA, Zhao Y, Holt RA. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS ONE. 2011 Jan 1;6(5):e19838.
  5. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, BIrol I, Lem M, Sharma MK, ELwood K, Jones SJM, Brinkman FSL, Brunham RC, Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011 Feb 24;364(8):730-9.

  6. D'Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BFF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA. Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts. MBio. 2011 Jan 1;2(1).

  7. DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hess-Orce U, Alamouti SM, Tsui CKM, Docking RT, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, Hirst M, Jones SJM, 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 USA. 2011 Feb 8;108(6):2504-9.

  8. Bhat RK, Ellestad KK, Wheatley BM, Warren R, Holt RA, Power C. Age- and Disease-Dependent HERV-W Envelope Allelic Variation in Brain: Association with Neuroimmune Gene Expression. PLoS ONE. 2011 Jan 1;6(4):e19176.

  9. Zhou W, Cai F, Li Y, Yang GS, O'Connor KD, Holt RA, Song W. BACE1 Gene Promoter Single-Nucleotide Polymorphisms in Alzheimer's Disease. Journal of molecular neuroscience : MN. 2010 May 9.

  10. Warren RL, Holt RA. A census of predicted mutational epitopes suitable for immunologic cancer control. Hum Immunol. 2010 Mar 1;71(3):245-54.

  11. Portales-Casamar E, Swanson DJ, Liu L, de Leeuw CN, Banks KG, Ho Sui SJ, Fulton DL, Ali J, Amirabbasi M, Arenillas DJ, Babyak N, Black SF, Bonaguro RJ, Brauer E, Candido TR, Castellarin M, Chen J, Chen Y, Cheng JCY, Chopra V, Docking TR, Dreolini L, D’Souza CA, Flynn EK, Glenn R, Hatakka K, Hearty TG, Imanian B, Jiang S, Khorasan-zadeh S, Komljenovic I, Laprise S, Liao NY, Lim JS, Lithwick S, Liu F, Liu J, Lu Meifen McConechy M, McLeod AJ, Milisavljevic M, Mis J, O’connor K, Palma B, Palmquist DL, Schmouth J, Swanson MI, Tam B, TIcoll A, Turner JL, Varhol R, Vermeulen J, Watkins RF, Wilson G, Wong BKY, Wong SH, Wong TYT, Yang GS, Ypsilanti AR, Jones SJM, Holt RA, Goldowitz D, Wasserman WW, Simpson EM. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc Natl Acad Sci USA. 2010 Sep 21;107(38):16589-94.

  12. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, KuchenBauer F, Yap D, Humphries RK, Griffith OL, Shah Sohrab, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet. 2010 Feb 1;42(2):181-5.

  13. Mead C-LR, Kuzyk MA, Moradian A, Wilson GM, Holt RA, Morin GB. Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin. J Neurochem. 2010 Mar 17.

  14. Leong JS, Jantzen SG, von Schalburg KR, Cooper GA, Messmer AM, Liao NY, Munro S, Moore R, Holt RA, Jones SJM, Davidson WS, Koop BF. Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. BMC Genomics. 2010 Jan 1;11:279.

  15. Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes AP, 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 Y, 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 Biol. 2010 Jan 1;11(8):R82.

  16. Horspool DR, Coope RJ, Holt RA. Efficient assembly of very short oligonucleotides using T4 DNA Ligase. BMC Res Notes. 2010 Jan 1;3:291.

  17. Hesse-Orce U, Diguistini S, Keeling CI, Wang Y, Li M, Henderson H, Docking R, Liao NY, Robertson G, Holt RA, Jones SJ, Bohlmann J, Breuil C. Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera. BMC Genomics. 2010 Oct 4;11(1):536.

  18. Portales-Casamar E, Swanson DJ, Liu L, de Leeuw CN, Banks KG, Ho Sui SJ, Fulton DL, Ali J, Amirabbasi M, Arenillas DJ, Babyak N, Black SF, Bonaguro RJ, Brauer E, Candido TR, Castellarin M, Chen J, Chen Y, Cheng JC, Chopra V, Docking TR, Dreolini L, D'Souza CA, Flynn EK, Glenn R, Hatakka K, Hearty TG, Imanian B, Jiang S, Khorasan-zadeh S, Komljenovic I, Laprise S, Liao NY, Lim JS, Lithwick S, Liu F, Liu J, Lu M, McConechy M, McLeod AJ, Milisavljevic M, Mis J, O'Connor K, Palma B, Palmquist DL, Schmouth JF, Swanson MI, Tam B, Ticoll A, Turner JL, Varhol R, Vermeulen J, Watkins RF, Wilson G, Wong BK, Wong SH, Wong TY, Yang GS, Ypsilanti AR, Jones SJ, Holt RA, Goldowitz D, Wasserman WW, Simpson EM. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proceedings of National Academy of Sciences USA. 2010 Sep 21;107(38):16589-94.

  19. Zhou W, Cai F, Li Y, Yang GS, O'Connor KD, Holt RA, Song W. BACE1 Gene Promoter Single-Nucleotide Polymorphisms in Alzheimer's Disease.  Journal of Molecular Neuroscience. 2010 Sep;42(1):127-133. 

  20. Jones SJ, 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 Y, 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 Aug 9;11(8):R82.

  21. Mead C-LR, Kuzyk MA, Moradian A, Wilson GM, Holt RA and Morin GB. Cytosolic Protein Interactions of the Schizophrenia Susceptibility Gene Dysbindin.  Journal of Neurochemistry. 2010 Jun;113(6):1491-503.
  22. Warren RL and Holt RA. A census of predicted tumour mutational epitopes.  Human Immunology. 2010, 713(3):245-54. 
  23. Romanuik TL, Wang G, Holt RA, Jones SJM, Marra MA, Sadar M. Identification of novel androgen-responsive genes by sequencing of LongSAGE Libraries.  BMC Genomics. 2009, 10:476
  24. 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 Y, 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, 461:809-813
  25. The MGC Project Team. The Completion of the Mammalian Gene Collection (MGC).  Genome Research. 2009 Dec;19(12):2324-33. [Epub 2009 Sep 18.]
  26. Pel J, Broemeling D, Mai L, Poon H-L, Tropini G, Warren RL, Holt RA, Marziali A. Non-linear Electrophoretic Response Yields a New Parameter for Separation of Biomolecules.  Proceedings of the National Academy of Sciences. 2009,106:14796-14801.
  27. Freeman JD, Warren RL, Webb JR, Nelson BH and Holt RA. Profiling the T-cell Receptor Beta-chain Repertoire by Massively Parallel Sequencing. Genome Research 2009, 19:1817-1824.
  28. Wang X, Zhao Y, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D.  Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE.  BMC Genomics 2009, 10:213
  29. The Bovine Sequencing and Analysis Consortium. The Genome sequence of taurine cattle: A window to ruminant biology and evolution.  Science. 2009 April 24 324(5926): 425-556.
  30. Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaughry I, Fox RM, Miller III DM, Baillie DL, Holt RA, Jones SJM, Marra MA, Moerman DG. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans.  PLoS Genetic. 2009. 5(6): e1000537.
  31. Warren RL, Nelson BH, Holt RA. Profiling model T cell metagenomes with short reads.  Bioinformatics. 2009 Feb 15;25(4):458-464.
  32. Yang GS, Banks KG, Bonaguro RJ, Wilson G, Dreolini L, de Leeuw CN, Liu L, Swanson DJ, Goldowitz D, Holt RA, Simpson EM. Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the Hprt1 locus.  Genomics. 2008.
  33. D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ. Identification of a set of genes showing regionally enriched expression in the mouse brain.  BMC Neurosci. 2008. 14:9:66.
  34. Warren RL, Freeman JD, Levesque RC, Smailus DE, Flibotte S, Holt RA. Transcription of foreign DNA in Escherichia coli.  Genome Research. 2008. 18:1798-805.
  35. Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, Robb A, Beetz-Sargent M, Holt RA, Moore R, Brahmbhatt S, Rosner J, Rexroad III CE, McGowan CR and Davidson WS. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.  BMC Genomics 2008, 9:545
  36. Holt RA and Jones SJM. The new paradigm of flow cell sequencing. Genome Research. Invited review article.  Genome Research, 18:839-846. 2008.
  37. Smailus DE, Warren R L and Holt RA. Constructing large DNA segments by iterative clone recombination.  Systems and Synthetic Biology. 2008. 1;139-144.
  38. Cai F, Chen B, Zhou W, Zis O, Liu S, Holt RA, Honer GW, Song W. SP1 Regulates the Human SNAP-25 Gene Expression.  Journal of Neurochemistry. 105;512-523. 2008.
  39. Ralph S, Chun H, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan G, Douglas C, Holt R, Jones S, Marra M, Bohlmann J. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding.  BMC Genomics. 9:57. 2008.
  40. Von Schalburg KR, Leong J, Cooper GA, Robb A, Beetz-Sargent MR, Lieph R, Holt RA, Moore R, Ewart KV, Driedzic WR, Ten Hallers BF, Zhu B, de Jong PJ, Davidson WS, Koop BF. Rainbow Smelt (Osmerus mordax) Genomic Library and EST Resources.  Marine Biotechnology. 10(5): 487-491. 2008.
  41. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt RA, Jann O, Jones SJ, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mattewson CA, Matukumalli LK, Moore SS, Murdroch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TP, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S; International Bovine BAC Mapping Consortium. A physical map of the bovine genome.  Genome Biology. 14;R165. 2007
  42. Holt RA, Warren R, Flibotte S, Missirlis PI and Smailus DE. Rebuilding microbial genomes.  Bioessays. 29: 580-590. 2007.
  43. Butland SL, Devon RS, Huang Y, Mead CL, Meynert AM, Neal SJ, Lee SS, Wilkinson A, Yang GS, Yuen MMS, Hayden MR, Holt RA, Leavitt BR and Ouellette BFF. CAG-encoded polyglutamine length polymorphism in the human genome.  BMC Genomics. 8:126. 2007.
  44. Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE.  Bioinformatics. 23: 500-501.2007. Citations: 61
  45. 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 S, Gerhard DS, Thomson JA, Eaves CJ and Marra MA. LongSAGE transcriptome analysis of nine human embryonic stem cell lines reveals novel transcripts and an over-representation of RNA binding proteins.  Genome Biology. 8:R113. 2007.
  46. Kelleher CT, Chiu R. Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin TM, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O’Connor K, Pradhu A-L, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ and Schein JE. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation.  The Plant Journal. 50:1063-78. 2007.
  47. Khattra J, Delaney AD, Zhao Y, Siddiqui A, Hirst M, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu A, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Jones S, Holt RA, Hoodless P and Marra MA. Large scale production of SAGE libraries from microdissected tissues.  Genome Research. 17:108-116. 2007.
  48. Peng FY, Reid KE, Liao N, Schlosser J, Holt RA, Martínez Zapater JM, Jones S, Marra M, Bohlmann J, Lund ST. Generation and Analysis of Expressed Sequence Tags in Vitis vinifera Wine Grape (Cabernet Sauvignon) and Table Grape (Muscat Hamburg) Cultivars. Enhancing the Functional Genomics Platform for Grapevine. Gene. 402:40-50. 2007
  49. Etchberger JF, Lorch A, Sleumer M, Zapf R, Jones SJ, Marra MA, Holt RA, Moerman DG, Hobert O. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron.  Genes & Development. 21:1653-1674.2007.
  50. DiGustini S, Ralph S, Lim Y, Holt RA, Jones S, Bohlmann J and Breuil C. Generation and annotation of lodgepole pine and oleoresin induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle associated pathogen.  FEMS Microbiol Lett. 267; 151-158. 2007.
  51. McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG and Robertson AG. The ELT-2 GATA-Factor and the Global Regulation of Transcription in the C. elegans Intestine.  Developmental Biology. 302: 627-645. 2006.
  52. Missirlis PI, Smailus DE and Holt RA. A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination.  BMC Genomics. 7:73. 2006.
  53. Wilson GM, Flibotte S, Chopra V, Melnyk BL, Honer WG and Holt RA. DNA copy number analysis in bipolar disorder and schizophrenia reveals aberrations in genes involved in glutamate signing.  Human Molecular Genetics. 15: 743-749. 2006.
  54. Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG and Holt RA. Identification by full coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.  Genome Research. 16:173-181. 2006.
  55. Scheinman JE, Holt RA, Auerbach MR, Stewart CB. Duplication and Divergence of Two Distinct Pancreatic Ribonuclease Genes in Leaf-Eating African and Asian Colobine Monkeys.  Molecular Biology and Evolution. 23:1465-1479. 2006.
  56. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley III CP, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SK, Blakesley RW, Prange C, Myers RM, Green ED, Wagner K, Gerhard DS, Marra MA, Jones SJM and Holt RA. Sequencing and analysis of 10967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis.  Genome Research. 16:796-803. 2006.
  57. McLeod MP, Warren RL, Araki N, Hsiao WWL, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJM, Holt RA, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. The complete genome of Rhodoccocus sp. RHA1: insights into a catabolic powerhouse.  Proceedings of the National Academy of Sciences USA. 103:15582-15587. 2006. Citations: 59
  58. Tuskan G, DiFazio S, Bohlmann J, Griogoriev I, Hellsten U, Jansson S, Putnam N, Ralph S, Rombauts S, Salanov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho P, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Dupleissis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henirssat B, Holligan D, Holt RA et al. The Genome of Black Cottonwood Populus trichocarpa. Science. 313:1596-1604. 2006. Citations: 539
  59. Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJM, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Eydoux P, Marra MA. Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation.  American Journal of Human Genetics. 79:500-513. 2006. Citations: 87
  60. Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, Benoit F, Rigby T, Nantel A, Butterfield YSN, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA et al. Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar. Molecular Ecology. 15:1275-1297. 2006.
  61. 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, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA et al. A Mouse Atlas of Gene Expression: Large-Scale Digital Gene Expression Profiles from Precisely Defined Developing C57BL/6J mouse tissues and cells.  Proceedings of the National Academy of Sciences. USA. 102: 18485-18490. 2005.
  62. Smailus DE, Marziali A, Dextras P, Marra MA and Holt RA. Simple, robust methods for high-throughput nanoliter-scale DNA sequencing.  Genome Research. 15: 1447-1450. 2005.
  63. Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt RA, Marra M, Séguin A, Retzel E, Bousquet J and MacKay J. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.  BMC Genomics. 6:144. 2005.
  64. Missirlis PI, Mead CL, Butland SL, Ouellette BFF, Devon RS, Leavitt BR and Holt RA. Satellog: A Database for the Identification and Prioritization of Satellite Repeats in Disease Association Studies.  BMC Bioinformatics. 6:145. 2005.
  65. Blacque OE, Perens EA, Boroevich KA, Inglis PN, LiC, Warner A, Khattra J, Holt RA, Ou G, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJ, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR. Functional Genomics of the Cilium, A Sensory Organelle.  Current Biology. 15:935-941. 2005. Citations: 68
  66. Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJM, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of Long-lived C. elegans daf-2 Mutants using Serial Analysis of Gene Expression.  Genome Research. 15:603-615. 2005.
  67. Yang GS, Stott JM, Smailus D, Barber SA, Balasundaram M, Marra MA, Holt RA. High Throughput Sequencing: A failure mode analysis.  BMC Genomics. 6:2. 2005.
  68. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, DUnn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mattewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF Guigo R, Smit A, Dubchak I Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium. The Rat Genome Sequencing Project Consortium. Genome Sequence of the Brown Norway Rat Yields Insights Into Mammalian Evolution.  Nature. 428:475-476. 2004. Citations: 714
  69. Hirst M, Astell CR, 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 SH, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Li Y, Konasa D, Booth T, Paetzel M (2004). A novel avian influenza H7N3 strain associated with an Avian Influenza Outbreak in British Columiba.  Emerging Infectious Diseases. 10:2192-2195. 2004.
  70. The MGC Project Team. The Status, Quality and Expansion of the NIH Full-length cDNA project: the Mammalian Gene Collection (MGC).  Genome Research. 14: 2093-2101. 2004.
  71. Baross A, Butterfield YSN, Coughlin SM, Zeng T, Griffith M, Griffith OL, Anca AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, Marra MA. Systematic recovery and analysis of full-ORF human cDNA clones.  Genome Research. 14: 2083-2092. 2004.
  72. Warren R, Hsiao WWL, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt RA, Marra MA, Jones S, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. Functional Characterization of Catabolic Plasmid from Polychlorinated-Biphenyl-Degrading Rhodococcus sp. RHA1.  Journal of Bacteriology. 186;7783-7795. 2004.
  73. Mongin E, Louis C, Holt RA, Birney E and Collins FH. The Anopheles gambiae genome: an update on sequence, data, annotation and access.  Trends in Parasitology. 20: 49-52. 2003.
  74. Marra MA, Jones SJ, Astell CR, Holt RA et al. The genome sequence of the SARS-associated coronavirus.  Science. 300:1399-1404. 2003. Citations: 903
  75. Holt RA et al. The genome sequence of the malaria mosquito Anopheles gambiae.  Science. 298:129-149. 2002. Citations: 788
  76. Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC and Bork P. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.  Science. 298: 149-159. 2002. Citations: 247
  77. Mural RJ, Adams MD, Myers EW, Smith HO, Gabor Miklos GL, Wides R, Halpern A, Li PW, Sutton G, Nadeau J, Salzberg SL, Holt RA et al. A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome.  Science. 296: 1661-1671. 2002. Citations: 181
  78. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al. The sequence of the human genome.  Science. 291:1304-51. 2001. Citations: 4956
  79. Adams MD, Celniker SE, Holt RA et al.  The genome sequence of Drosophila melanogaster.  Science. 287:2185-95. 2000. Citations: 2750
    *Breakthrough of the Year (Science 290, 2255).
  80. Holt RA, Bateson AN and Martin IL. Decreased GABA enhancement of benzodiazepine binding after a single dose of diazepam.  Journal of Neurochemistry. 1999. 72:2219-2222.
  81. Holt RA, Bateson AN and Martin IL. Chronic zolpidem treatment alters GABAA receptor mRNA levels in the rat cortex.  European Journal of Pharmacol. 1997. 329:129-132.
  82. Holt RA, Martin IL and Bateson AN. Chronic diazepam exposure decreases transcription of the rat GABAA receptor gamma2-subunit gene.  Molecular Brain Research. 1997. 48:164-166.
  83. Holt RA, Bateson AN and Martin IL. Chronic treatment with diazepam or abecarnil differently affects the expression of GABAA receptor subunit mRNAs in the rat cortex.  Neuropharmacology. 1996. 35(9-10):1457-1463. Citations: 72
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