Institute for Systems Biology
  ISB: Senior Research Scientists: Eric Deutsch: Publications

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

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.

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 ]

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

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

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

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

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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