NCGR Publications - 2008

Management of High-Throughput DNA Sequencing Projects: Alpheus
Neil A. Miller,Andrew D. Farmer, Stephen F. Kingsmore, Raymond J. Langley, Faye D. Schilkey, Joann Mudge, John A. Crow, Alvaro J. Gonzalez, Ryan J. Kim, Jennifer C. van Velkinburgh, Gregory D. May, C. Forrest Black, M. Kathy Myers, John P. Utsey, Nicholas S. Frost, and Ernest F. Retzel.

J Comp Sci Syst Biol 2008 [Full Text]

Cord immunoproteins as predictors of respiratory outcome in preterm infants. 
Kaukola T, Tuimala J, Herva R, Kingsmore S, Hallman M. 
Am. J. Obstet. Gynecol. Nov 20. PMID: 19026401

Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum.
Joann Mudge, Neil A. Miller, Irina Khrebtukova, Ingrid E. Lindquist, Gregory D. May, Jim J. Huntley, Shujun Luo, Lu Zhang, Jennifer C. van Velkinburgh, Andrew D. Farmer, Sharon Lewis, William D. Beavis, Faye D. Schilkey, Selene M. Virk, C. Forrest Black, M. Kathy Myers, Lar C. Madar, Ray J. Langley, John P. Utsey, Ryan W. Kim, Rosalinda C. Roberts, Sat Kirpal Khalsa, Meredith Garcia, Victoria Ambriz-Griffith, Richard Harlan, Wendy Czika, Stanton Martin, Russel D. Wolfinger, Nora I. Perrone-Bizzozero, Gary P. Schroth, Stephen F. Kingsmore (2008)
PLos One 2008
PMID: 18985160 [Abstract

Alternative isoform regulation in human tissue transcriptomes.
Wang ET, Sandbery R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 
Nature 2008 PMID: 18978772

Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in presence and absence of a tight-binding inhibitor.
Salsbury Jr FR, Crowder MW, Kingsmore SF, Huntley JJA. (2008)
J Mol Model 2008 PMID: 19039608

Identification of diagnostic biomarkers for infection in premature neonates.
Kingsmore SF, Kennedy N, Halliday HL, Van Velkinburgh JC, Zhong S, Gabriel V, Grant J, Beavis WD, Tchernev VT, Perlee L, Lejnine S, Grimwade B, Sorette M, Edgar JDM. (2008)
Mol Cell Proteomics. Jul 13, 2008 PMID: 18622029 [Abstract]

Sepsis and the Genomic Revolution: Risk, Diagnosis, Prognosis, and Therapeutics.
Woods CW, Feezor RJ, Kingsmore SF. (2008)
Genomic and Personalized Medicine,eds.Willard H and Ginsburg G. Elsevier. 2008

Genome-wide association studies: progress and potential for drug discovery and development.
Kingsmore SF, Lindquist IE, Mudge J, Gessler DD, Beavis WD. (2008)
Nat Rev Drug Discov. 2008 Mar;7(3):221-30. Review. PMID: 18274536 [Abstract]

Transcriptome sequencing of malignant pleural mesothelioma tumors.
Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, Maulik G, Glickman JN, Chirieac LR, Hartman ML, Taillon BE, Du L, Bouffard P, Kingsmore SF, Miller NA, Farmer AD, Jensen RV, Gullans SR, Bueno R. (2008)
Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3521-6. Epub 2008 Feb 26. PMID: 18303113 [Abstract ]

Origin of the Flax Cultivar 'Appar' and Its Position within the Linum perenne Complex.
Pendleton, R., Kitchen, S., Mudge, J., and McArthur, E.D. (2008)
International Journal of Plant Sciences 169, 445-453. [Full Text]

The Long and the Short of it: Uniqueness of short DNA sequences in plants.
Mudge, J., Farmer, A.D., and May, G.D.
Plant & Animal Genomes XVI Conference, January 12-16, 2008, San Diego, CA [Abstract]

Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages.
Mian MA, Zhang Y, Wang ZY, Zhang JY, Cheng X, Chen L, Chekhovskiy K, Dai X, Mao C, Cheung F, Zhao X, He J, Scott AD, Town CD, May, GD (2008)
BMC Plant Biol. 2008 Mar 4;8:27. PMID: 18318913 [Abstract] [Full Text]

Alpheus: A Web Software Tool for Variant Detection using Next-Generation Sequencing Technologies.
Schilkey, F.D., Miller, N.A., Mudge, J., Mader, L.C., Weems, D.,Virk, S.M., Black, C.F., Myers, M.K., Rice, M., Gomez, T., et al.
Plant & Animal Genomes XVI Conference, January 12-16, 2008, San Diego, CA [Abstract]


The ‘Appar’Flax Release: origin, distinguishing characteristics, and use; and a native alternative
R. L. Pendleton, S. G. Kitchen, E. D. McArthur and J. E. Mudge

Native Plants Journal. 2008; 9(1):18-24.