Systems biology and proteomics

David J. States Research Group

David States publications on PubMed

Selected Publications

Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. Cancer Res. 2009 Jan 1;69(1):300-9.

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Damian Fermin, Baxter B Allen, Thomas W Blackwell, Rajasree Menon, Marcin Adamski, Yin Xu, Peter Ulintz, Gilbert S Omenn and David J States (2006) Genome Biology 7:R35.

Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States and H. V. Jagadish (2007) Nucleic Acids Research D566–D571.

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
Marcin Adamski, Thomas Blackwell, Rajasree Menon, Lennart Martens, Henning Hermjakob, Chris Taylor, Gilbert S. Omenn and David J. States (2005) Proteomics 5:3246–3261

Both src-dependent and -independent mechanisms mediate phosphatidylinositol 3-kinase regulation of colony-stimulating factor 1-activated mitogen-activated protein kinases in myeloid progenitors. Lee, AW, D.J. States. (2000) Mol Cell Biol. 20(18):6779-98.

UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences. Kan, Z. Y., W. Gish, E. Rouchka, J. Glasscock, and D. J. States. (2000) ISMB, 8:218-227.

Identity by Descent Genome Segmentation Based on Single Nucleotide Polymorphism Distributions. Blackwell, T.W., Rouchka, E. C., States, D.J. (1999) ISMB, 7:54-59.

Filter matrix estimation in automated DNA sequencing. Huang W., D. R. Fuhrmann. D. G. Politte, L. J. Thomas, and D. J. States. (1998) IEEE Trans Biomed Eng. 45(4):422-8.

Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis. Rouchka, E.C., States, D.J. (1998) ISMB, 6:140-147.

Comparative accuracy of methods for protein sequence similarity search. Agrawal, P. and D. J. States. (1998) Bioinformatics. 14(1):40-7.

Lane tracking software for four-color fluorescence-based electrophoretic gel images. Cooper, M. L., D. R. Maffitt., J.D. Parsons, L. Hillier, and D. J. States. (1996) Genome Res. 6(11):1110-7.

Compact encoding strategies for DNA sequence similarity search. States, D. J. and P. Agrawal. (1996)
ISMB. 4:211-7.

A Bayesian Evolutionary Distance for Parametrically Aligned Sequences. Agarwal, P., and States, D.J. (1996) J. Comput. Biol. 3:1-17.

Combined use of sequence similarity and codon bias for coding region identification. States, D. J. and W. Gish. (1994) J Comput Biol. 1(1):39-50.

Ancient conserved regions in new gene sequences and the protein databases. Green, P., D. Lipman, L. Hillier, R. Waterston, D. States. and J. M. Claverie. (1993) Science. 19;259(5102):1711-6.

The Repeat Pattern Toolkit (RPT): Analyzing the structure and evolution of the C. elegans genome. Agarwal, P., and States, D.J. (1994) ISMB 2:1-9.

Identification of protein coding regions by database similarity search. Gish, W. and D. J. States. (1993)
Nat Genet. 3(3):266-72.

Computationally efficient representation of classes in protein sequence megaclassification. States, D.J., Harris, N.L. and Hunter, L. (1993) Proc. Intel. Syst. for Mol. Biol.(ISMB) 1:387-394.

Molecular sequence accuracy: analysing imperfect data. States, D.J. (1992) Trends Genet. Feb;8(2):52-5. Review.

Molecular sequence accuracy and the analysis of protein coding regions. States, D.J. and Botstein D. (1991) Proc Natl Acad Sci U S A. 88:5518-22.