Publications

• 2009 |
• 2008 |
• 2007 |
• 2006 |
• 2005-1998

2009

• CGDSNPdb: A curated mouse SNP database.
  Hutchins LN, Ding Y, Szatkiewicz JP, Von Smith R, Yang H, de Villena FP, Churchill GA, Graber JH. 2009.(In revision).
• Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes.
  Singh P, Alley TL, Wright SM, Kamdar S, Schott W, Wilpan RY, Mills KD, Graber JH. 2009. Cancer Res. (in press).
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation.
Salisbury J, Hutchison KW, Wigglesworth K, Eppig JJ, Graber JH. 2009. PLoSOne,Research Article, published 16 Oct 2009 | doi:10.1371/journal.pone.0007479
• 
  A customized and versatile high-density genotyping array for the mouse
  Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, Graber JH, de Villena FP, Churchill GA. Nat Methods. 2009 Sep;6(9):663-6. PMCID: PMC2735580 [Available on 2010/03/01].

2008

• Position-dependent motif characterization using non-negative matrix factorization. Hutchins LN, Murphy SM, Singh P, Graber JH. 2008 . Bioinformatics. 24(23):2384-2690.
• Reprogramming and differentiation in mammals: motifs and mechanisms De Vries WN, Evsikov AV, Brogan LJ, Anderson CP, Graber JH, Knowles BB, Solter D. 2008. Cold Spring Harb Symp Quant Biol. PMID:19022741
• The recombinational anatomy of a mouse chromosome Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng SH, Graber JH, Broman KW, Petkov PM. 2008. PLoS Genet. 4:e1000119.
• An imputed genotype resource for the laboratory mouse Jin P. Szatkiewicz, Glen L. Beane, Yueming Ding, Lucie Hutchins, Fernando Pardo-Manuel de Villena, Gary A. Churchill . Mamm Genome. 2008 Mar;19(3):199-208. PMCID: PMC2725522.

2007

• C. elegans sequences that control trans-splicing and operon pre-mRNA processing
  Graber JH, Hutchins LN, Salisbury J, Blumenthal T.RNA.Jul 13,2007;
• 
  Evidence of a large-scale functional organization of Mammalian chromosomes Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K. PLoS Biol. May 16 2007 ;5(5):e127; PMID: 17503963
• Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis
  Liu D, Brockman JM, Dass B, Hutchins LN, Singh P, McCarrey JR, MacDonald CC, Graber JH. Nucleic Acids Res. 2007;35(1):234-46. Epub 2006 Dec 8. PMID: 17158511

2006

• Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo.
  Evsikov AV, Graber JH, Brockman JM, Hampl A, Holbrook AE, Singh P, Eppig JJ, Solter D, Knowles BB. Genes Dev. 2006 Oct 1;20(19):2713-27. PMID: 17015433
• Patterns and mechanisms of genome organization in the mouse
  Graber JH, Churchill GA, Dipetrillo KJ, King BL, Petkov PM, Paigen K. J Exp Zoolog A Comp Exp Biol. 2006 Sep 1;305(9):683-8. PMID: 16902958
• A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif
  Salisbury J, Hutchison KW, Graber JH. BMC Genomics. 2006 Mar 16; 7:55. PMID: 16542450
• Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation
  Liu D, Graber JH.BMC Bioinformatics. 2006 Feb 17; 7(1):77. PMID: 16503995.

2005-1998

• Evidence of a Large-Scale Functional Organization of Mammalian Chromosomes
  Petkov PM, Graber JH, Churchill GA, Dipetrillo K, King BL, Paigen K.PLoS Genet. 2005 Sep 9;1(3):e33. PMID: 16163395
• PACdb: PolyA Cleavage Site and 3'-UTR Database.
  Brockman JM, Singh P, Liu D, Quinlan S, Salisbury J, Graber JH.Bioinformatics. 2005 Sep 15;21(18):3691-3. Epub 2005 Jul 19. PMID: 16030070
• Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos.
  Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB.Dev Cell. 2004 Oct;7(4):597-606. PMID: 15469847
• Variations in yeast 3'-processing cis-elements correlate with transcript stability.
  Graber JH.Trends Genet. 2003 Sep;19(9):473-6. PMID: 12957538
• On the normalization of RNA equilibrium free energy to the length of the sequence.
  Pervouchine DD, Graber JH, Kasif S.Nucleic Acids Res. 2003 May 1;31(9):e49. PMID: 12711694
• A ubiquitous and conserved signal for RNA localization in chordates.
  Betley JN, Frith MC, Graber JH, Choo S, Deshler JO.Curr Biol. 2002 Oct 15;12(20):1756-61. PMID: 12401170
• Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.
  Graber JH, McAllister GD, Smith TF.Nucleic Acids Res. 2002 Apr 15;30(8):1851-8. PMID: 11937640
• In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species.
  Graber JH, Cantor CR, Mohr SC, Smith TF.Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):14055-60. PMID: 10570197
• Differential sequencing with mass spectrometry.
  Graber JH, Smith CL, Cantor CR.Genet Anal. 1999 Feb;14(5-6):215-9. Review. PMID: 10084117
• Genomic detection of new yeast pre-mRNA 3'-end-processing signals.
  Graber JH, Cantor CR, Mohr SC, Smith TF.Nucleic Acids Res. 1999 Feb 1;27(3):888-94. PMID: 9889288
• Advances in DNA diagnostics.
  Graber JH, O'Donnell MJ, Smith CL, Cantor CR. Curr Opin Biotechnol. 1998 Feb;9(1):14-8. Review. PMID: 9537747