-
Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping.
Billings T, Sargent EE, Szatkiewicz JP, Leahy N, Kwak IY, Bektassova N, Walker M, Hassold T, Graber JH, Broman KW, Petkov PM.
PLoS One. 2010 Dec 8;5(12):e15340.PMID: 21170346
-
Gene-specific RNA polymerase II phosphorylation and the CTD code.
Kim H, Erickson B, Luo W, Seward D, Graber JH, Pollock DD, Megee PC, Bentley DL.
Nat Struct Mol Biol. 2010 Oct;17(10):1279-86. PMID: 20835241
-
Interrogating the transcriptome of oocytes and preimplantation embryos
HPeaston AE, Graber JH, Knowles BB, de Vries WN.
Methods Enzymol. 2010;477:481-510.PMID: 20699156.
-
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs
Hutchins LN, Ding Y, Szatkiewicz JP, Von Smith R, Yang H, de Villena FP, Churchill GA, Graber JH.
Database 2010. PMID: 20624716
http://cgd.jax.org/cgdsnpdb/
-
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.
Cancer Res. 2009 Dec 15;69(24):9422-30. PMID: 19934316
APA in tumors
-
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation.
Salisbury J, Hutchison KW, Wigglesworth K, Eppig JJ, Graber JH.
PLoSOne, Research Article, 2009 Oct 16;4(10) PMID: 19834616
Arabidopsis 3'-studies
-
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. PMID: 19668205
-
Position-dependent motif characterization using non-negative matrix factorization.
Hutchins LN, Murphy SM, Singh P, Graber JH.
Bioinformatics. 2008 Dec 1;24(23):2684-90. PMID: 18852176
Nonnegative matrix factorization
-
Reprogramming and differentiation in mammals: motifs and mechanisms
De Vries WN, Evsikov AV, Brogan LJ, Anderson CP, Graber JH, Knowles BB, Solter D.
Cold Spring Harb Symp Quant Biol. 2008;73:33-8. 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.
PLoS Genet. 2008 Jul 11;4(7):e1000119. PMID: 18617997
-
An imputed genotype resource for the laboratory mouse
Szatkiewicz JP, Beane GL, Ding Y, Hutchins LN, de Villena FP, Churchill GA.
Mamm Genome. 2008 Mar;19(3):199-208. PMID: 18301946.
-
C. elegans sequences that control trans-splicing and operon pre-mRNA processing
Graber JH, Hutchins LN, Salisbury J, Blumenthal T.
RNA. 2007 Sep;13(9):1409-26. PMID: 17630324
Nematode analysis
-
Evidence of a large-scale functional organization of Mammalian chromosomes
Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K.
PLoS Biol. 2007 May;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. PMID: 17158511
Spermatogenesis analysis
-
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
EST library analysis
-
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation
Liu D, Graber JH.
BMC Bioinformatics. 2006 Feb 17; 7:77. PMID: 16503995.
EST Library Search Tool
-
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. PMID: 16030070
Arabidopsis 3'-studies
-
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
Yeast turnover studies
-
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
Yeast 3'-studies
-
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
|
|
