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Submitted
Loevenich, S., Brunner, E., Deutsch, E. W., King, N. L., Stein, S., Hafen, E., and Aebersold, R., Integrating the Drosophila melanogaster proteome with the genome – PeptideAtlas, a resource for fly genetics and proteomics, 2008, Genome Biology, submitted
Accepted
Orchard S., Albar, J.-P., Deutsch E.W., Binz P.A., Jones A.R., Creasy D.M., and Hermjakob H., Annual Spring Meeting of the Proteomics Standards Initiative, Toledo, Spain 23-25th April 2008, 2008, Proteomics, epub.
2008
Van, P. T., Schmid, A. K., King, N. L., Kaur, A., Pan, M., Whitehead, K., Koide, T., Goo, Y., Deutsch, E. W., Reiss, D. J., Mallick, P., and Baliga, N. S., Halobacterium salinarium NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage, 2008, Journal of Proteome Research, 7, 3755
[ Abstract ]
Lam H., Deutsch, E. W., Eddes J.S., Eng J.K., Stein S.E., Aebersold R., Building Consensus Spectral Libraries for Peptide Identification in Proteomics, 2008, Nature Methods, 5, 873
Deutsch, E. W., mzML: A single, unifying data format for mass spectrometer output, 2008, Proteomics, 8, 14, 2776
[ PDF ]
Lange, V., Malmström,, J. A., Didion, J., King, N. L., Johansson, B. P., Schäfer, J., Rameseder, J., Wong, C., Deutsch, E. W., Brusniak, M., Bühlmann, P., Björk, L., Domon, B., and Aebersold, R., Targeted quantitative mass spectrometric analysis of Streptococcus pyogenes virulence factors by multi-reaction monitoring, 2008, Molecular and Cellular Proteomics, 7, 1489
[ Abstract ]
Taylor, C. F., Field, D., Sansone, S.-A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C., Binz, P.-A., Bogue, M., Booth, T., Brazma, A., Brinkman, R., Clark, A. M., Deutsch, E. W., et al., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project, 2008, Nature Biotechnology, 26, 889
[ On-line PDF ]
Taylor, C. F., Binz, P.-A., Aebersold, R., Affolter, M., Barkovich, R., Deutsch, E. W., Horn, D., M., Hühmer, A., Kussmann, M., Lilley, K., Macht, M., Mann, M., Müller, D., Neubert, T., A., Nickson, J., Patterson, S., D., Raso, R., Resing, K., Seymour, S. L., Tsugita, A., Xenarios, I., Zeng, R., and Julian, R. K., Guidelines for reporting the use of mass spectrometry in proteomics, 2008, Nature Biotechnology, 26, 860
Deutsch, E. W., Lam H., and Aebersold R., PeptideAtlas: A Resource for Target Selection for Emerging Targeted Proteomics Workflows, 2008, EMBO Reports, 9, 429
[ Abstract | PDF ]
Deutsch, E. W., Lam, H., and Aebersold R., Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics, 2008, Physiological Genomics, 33, 18
[ Abstract | Free Full Access ]
Deutsch, E. W., Ball, C. A., Berman, J. J., Bova, G.S., Brazma, A., Bumgarner, R. E., Campbell, D. A., Causton, H. C., Christiansen, J., Davidson, D., et al., Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE), 2008, Nature Biotechnology, 26, 305
[ Abstract | PDF ]
Pascal, L. E., Deutsch, E. W., Campbell, D. S., Korb, M., True, L. D., and Liu, A. Y., The urologic epithelial stem cell database (UESC) – a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder, 2008, BMC Urology, 7, 19
[ Abstract | PDF ]
Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B., M., et al., Human Proteinpedia: A portal for sharing and integrations of human protein data, 2008, Nature Biotechnology, 26, 2, 164
[ Article ]
Pascal, L. E., True, L. D., Campbell, D. S., Deutsch, E. W., Risk, M., Coleman, I. M., Eichner, L. J., Nelson, P. S., and Liu, A. Y., Correlation of mRNA and protein levels : Cell type-specific gene expression of cluster designation antigens in the prostate, 2008, BMC Genomics, 9, 246
[ Abstract | PDF ]
Zhang, Q., Menon, R, Deutsch, E. W., Pitteri, S. J., Faca, V. M., Wang, H., Newcomb, L. F., DePinho, R. A., Bardeesy, N., Dinulescu, D., et al., A Mouse Plasma Peptide Atlas as a Resource for Disease Proteomics, 2008, Genome Biology, 9, 6, R93
[ Abstract | PDF ]
2007
Taylor, C. F., Paton, N.W., Lilley, K.S., Binz, P.-A., Julian, R.K., Jr., Jones, A., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E. W., Dunn, M. J., et al., The minimum information about a proteomics experiment (MIAPE), 2007, Nature Biotechnology, 25, 887
Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E. W., deLichtenberg, U., Rinner, O., Lee, H., et al., A high-quality map of the Drosophila melanogaster proteome, 2007, Nature Biotechnology, 25, 576-583
Lam H., Deutsch, E. W., Eddes J.S., Eng J.K., King N., Stein S.E., Aebersold R., Development and validation of a spectral library searching method for peptide identification from MS/MS, 2007, Proteomics, 7(5), 655-667
Orchard S., Montechi-Palazzi L., Deutsch, E. W., Binz P.A., Jones A.R., Paton N., Pizarro A., Creasy D.M., Wojcik J., Hermjakob H., Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France, 2007, Proteomics, 7(19), 3436-3440
2006
Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I., Mallick, P., Eng, J., Chen, S., Eddes, J., Loevenich, S. N., and Aebersold, R.: The PeptideAtlas Project, Nucleic Acids Research, 2006, 34, D655-D658
Chen, S. S., Deutsch, E. W., Yi, E. C., Li, X-J, Goodlett, D. R., Aebersold, R., Improving mass and liquid chromatography based identification of proteins using Bayesian scoring, 2006, Journal of Proteome Research, 4(6), 2174
Deutsch, E. W., Ball, C. A., Bova, G.S., Brazma, A., Bumgarner, R. E., Campbell, D. A., Causton, H. C., Christiansen, J., Davidson, D., Eichner, L. J., et al., Development of the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE), 2006, OMICS, 10(2), 205
Marzolf, B., Deutsch, E. W., Moss, P., Campbell, D., Johnson M. H., and Galitski, T., SBEAMS Microarray: Database software supporting genomic expression analyses for systems biology, 2006, BMC Bioinformatics, 7:286
King, N. L., Deutsch, E. W., Ranish, J. A., Nesvizhskii, A. I., Eddes, J. S., Mallick, P., Eng, J., Desiere, F., Flory, M., Martin, D., et al., Analysis of the S. cerevisiae proteome with PeptideAtlas, 2006, Genome Biology, 7(11), R106
2005
Desiere, F., Deutsch, E. W., Nesvizhskii, A. I., Mallick, P., King, N. L., Eng, J. K., Aderem, A., Boyle, R., Brunner, E., Donohoe, et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry., Genome Biol. 2005, 6(1):R9
Deutsch, E. W., Eng, J. K., Zhang, H., King, N. K., Nesnizhskii, A. I., Lin, B., Lee, H., Yi, E. C., Ossola, R., Aebersold, R., Human Plasma PeptideAtlas, 2005, Proteomics, 5(13):3497
2004
Yan, W., Lee, H., Deutsch, E. W., Lazaro, C. A., Tang, W., Chen, E., Fausto, N., Katze, M. G., Aebersold, R., A Dataset of Human Liver Proteins Identified by Protein Profiling via Isotope Coded Affinity Tag (ICAT) and Tandem Mass Spectrometry, 2004, Molecular and Cellular Proteomics, Oct;3(10):1039-41
Baliga, N. S., Bonneau, R., Facciotti, M. T., Pan, M., Glusman, G., Deutsch, E. W., Shannon, P., Chiu Y., Weng R. S., Gan R. R., et al., Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea, 2004, Genome Research, Nov;14(11):2221-34
Pedrioli, P. G. A., Eng, J. K., Hubley, R., Vogelzang, M., Deutsch, E. W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R. H., Apweiler, R., et al., A Common Open Representation of Mass Spectrometry Data and its Application to Proteomics Research, 2004, Nature Biotechnology, Nov;22(11):1459-66
Bonneau, R., Baliga, N., Deutsch, E. W., Shannon, P., Hood, L., Comprehensive De Novo Structure Prediction in a Systems-biology Context for the Archaea Halobacterium sp. NRC-1., 2004, Genome Biology, 5(8):R52
2003
Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D., Stead, D. A., Yin, Z., Deutsch, E. W., Selway, L., Walker, J., Riba-Garcia, I., et al., A Systematic Approach to Modeling Capturing and Disseminating Proteomics Experimental Data., 2003, Nature Biotechnology, 21(3), 247
Spellman P. T., Miller M., Stewart J., Troup C., Sarkans U., Chervitz S., Bernhart D., Sherlock G., Ball C., Lepage M., et al., Design and Implementation of Microarray Gene Expression Markup Language (MAGE-ML)., 2002, Genome Biology, 3(9), RESEARCH0046
Previous Astrophysical Research
Deutsch, E. W., Allen, R. J., The Structure of the Inner Eastern Spiral Arm of M83., 1993, Astronomical Journal, 106, 1812
Bohlin, R. C., Deutsch, E. W., McQuade, K. A., Hill, J. K., Landsman, W. B., O'Connell, R. W., Roberts, M. S., Smith, A. M., Stecher, T. P., Ultraviolet Imaging Telescope: Globular Clusters in M31, 1993, Astrophysical Journal, 417, 127
Anderson, S. F., Margon, B., Deutsch, E. W., Downes, R. A., Ultraviolet-excess Selection of the Counterpart to a Globular Cluster X-ray Burster: HST Images of the Core of NGC 6712., 1993, Astronomical Journal, 106, 1049
Deutsch, E. W., Positions and Proper Motions of Dwarf Carbon Stars., 1994, PASP, 106, 1134
Deutsch, E. W., Anderson, S. F.,Margon, B., Downes, R. A., An Ultraviolet-Excess Optical Candidate for the Luminous Globular Cluster X-ray Source in NGC 1851., 1996, Astrophysical Journal, 472, L97
Deutsch, E. W., Margon, B., Wachter, S., Anderson, S. F., HST Imaging of Bright Galactic X-ray Binaries in Crowded Fields., 1996, Astrophysical Journal, 471, 979
Margon, B., Deutsch, E. W., CC Bootis: QSO, Not Variable Halo Giant., 1997, PASP, 109, 673
Anderson, S. F., Margon, B., Deutsch, E. W., Downes, R. A., Allen, R. G., Time-Resolved Ultraviolet Observations of the Globular Cluster X-ray Source in NGC 6624: The Shortest Known Period Binary System., 1997, Astrophysical Journal, 482, L69
Deutsch, E. W., Margon, B., Anderson, S. F., A Search for the Optical Counterpart of the Luminous X-ray Source in NGC 6652., 1998, Astronomical Journal, 116, 1301
Diercks, A., Deutsch, E. W., Castander, F. J., Corson, C, Gilmore, G., Lamb, D. Q., Tanvir, N., Turner, E. L., Wyse, R., The Optical Afterglow of GRB 971214: R and J Photometry., 1998, Astrophysical Journal, 503, L105
Palazzi et al., Optical and Near-infrared Follow-up Observations of GRB 980329., 1998, Astronomy & Astrophysics, 336, L95
Deutsch, E. W., Margon, B., Bland-Hawthorn, J., A Technique for Narrowband Time Series Photometry: the X-ray Star V2116 Oph., 1998, PASP, 110, 912
Margon, B., Deutsch, E. W., Complex Velocity Fields in the Shell of T Pyxidis., 1998, Astrophysical Journal, 498, L61
Deutsch, E. W., Anderson, S. F., Margon, B., Downes, R. A., The Probable Optical Counterpart of the Luminous X-ray Source in NGC 6441., 1998, Astrophysical Journal, 493, 775
Deutsch, E. W., Margon, B., Anderson, S. F., Downes, R. A., Serendipitous Discovery of a Cataclysmic Variable in the Globular Cluster NGC 6624., 1999, Astronomical Journal, 118, 2888
Galama, T. J., et al., Evidence for a Supernova in Reanalyzed Optical and Near-infrared Images of GRB 970228., 1999, Astrophysical Journal, 536, 185
Deutsch, E. W., Empirical Uncertainty Estimators for Astrometry from Digital Databases., 1999, Astronomical Journal, 118, 1882
Deutsch, E. W., Margon, B., Anderson, S. F., Wachter, S., Goss, W. M., Infrared Candidates for the Intense Galactic X-ray Source GX 17+2., 1999, Astrophysical Journal, 524, 406
Deutsch, E. W., Thesis Summary: The Optical Counterparts of the Luminous X-ray Binary Stars in Globular Clusters., 1999, PASP, 111, 916
Margon, B., Deutsch, E. W., The Meinunger `Nicht Rote' Objects., 1999, PASP, 111, 45
Deutsch, E. W., Margon, B., Anderson, S. F., Ultracompact X-ray Binaries in Globular Clusters: Variability of the Optical Counterpart of X1832-330 in NGC 6652., 2000, Astrophysical Journal, 530, L21
Homer, L., Deutsch, E. W., Anderson, S. F., Margon, B., The Rapid Burster in Liller I: the Chandra X-ray Position and a Search for an IR Counterpart., 2001, Astronomical Journal, 122, 2627
Homer, L., Anderson, S. F., Margon, B., Deutsch, E. W., Downes, R. A., Optical Identification of the X-ray Burster in the Globular Cluster NGC 1851., 2001, Astrophysical Journal, 550, L155
Margon, B., et al., Faint High-Latitude Carbon Start Discovered by the Sloan Digital Sky Survey: Methods and Initial Results., 2002, Astronomical Journal, 124, 1651
Homer, L., Anderson, S. F., Margon, B., Downes, R. A., Deutsch, E. W., The Optical Identification of the X-ray Burster X1746-370 in the Globular Cluster NGC6441., 2002, Astronomical Journal, 123, 3255
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