David Speicher

Summary

Affiliation: The Wistar Institute
Country: USA

Publications

  1. pmc Supervised regularized canonical correlation analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery
    Abhishek Golugula
    Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
    BMC Bioinformatics 12:483. 2011
  2. pmc A fused alpha-beta "mini-spectrin" mimics the intact erythrocyte spectrin head-to-head tetramer
    Sandra L Harper
    Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce St, Philadelphia, PA 19104, USA
    J Biol Chem 285:11003-12. 2010
  3. ncbi request reprint Complex proteome prefractionation using microscale solution isoelectrofocusing
    Hsin Yao Tang
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    Expert Rev Proteomics 2:295-306. 2005
  4. ncbi request reprint Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma
    Lynn A Echan
    The Wistar Institute, Philadelphia, PA 19104, USA
    Proteomics 5:3292-303. 2005
  5. ncbi request reprint A structural model of the erythrocyte spectrin heterodimer initiation site determined using homology modeling and chemical cross-linking
    Donghai Li
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    J Biol Chem 283:1553-62. 2008
  6. pmc Forced unfolding of proteins within cells
    Colin P Johnson
    Biophysical Engineering Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 317:663-6. 2007
  7. ncbi request reprint Microscale solution isoelectrofocusing: a sample prefractionation method for comprehensive proteome analysis
    Xun Zuo
    The Wistar Institute, Philadelphia, PA, USA
    Methods Mol Biol 244:361-75. 2004
  8. doi request reprint Overview of proteome analysis
    Nadeem Ali-Khan
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Curr Protoc Protein Sci . 2003
  9. pmc Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes
    Huan Wang
    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    J Proteome Res 9:1032-40. 2010
  10. doi request reprint Microscale isoelectric focusing in solution: a method for comprehensive and quantitative proteome analysis using 1-D and 2-D DIGE combined with MicroSol IEF prefractionation
    Mee Jung Han
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Methods Mol Biol 424:241-56. 2008

Collaborators

  • Hsin Yao Tang
  • Patrick Gallagher
  • Matthew Raab
  • Kibeom Lee
  • R Marmorstein
  • Mee Jung Han
  • G S Omenn
  • Young Ki Paik
  • R Apweiler
  • Arie Admon
  • H Hermjakob
  • William S Hancock
  • Ruedi H Aebersold
  • Alex J Rai
  • Harald Tammen
  • Ilan Beer
  • Sam Hanash
  • Donghai Li
  • Xun Zuo
  • Sandy Harper
  • Massimiliano Gaetani
  • Colin P Johnson
  • Dennis E Discher
  • Sandra L Harper
  • Nadeem Ali-Khan
  • Richard Law
  • Lynn A Echan
  • Abhishek Golugula
  • Huan Wang
  • Yelena Maksimova
  • Meghan T Mitchell
  • Sarah Dunn Keene
  • Manqing Hong
  • Anwar A Khan
  • Sandra Harper
  • Qin Liu
  • Seth A Hoffman
  • David J States
  • Ian Musselman
  • Jae Min Chong
  • Anant Madabhushi
  • George Lee
  • Stephen R Master
  • John E Tomaszewski
  • Michael D Feldman
  • Tony Chang-Wong
  • F Brad Johnson
  • Emmanuel Skordalakes
  • Jasmine S Smith
  • Mark Mason
  • Rita J Balice-Gordon
  • Todd M Greco
  • Harry Ischiropoulos
  • Ioannis Parastatidis
  • Seon Hwa Lee
  • Ethan G Hughes
  • Toshihiko Hanada
  • Lixiao Zeng
  • Sara Mootien
  • Jong Jin Jeong
  • Cheng Luo
  • Athar H Chishti
  • Mary X Fitzgerald
  • Morvarid Mohseni
  • Brent C Reed
  • Glenn Tan
  • Edward N Pugh
  • Vanessa Ortiz
  • John J Rux
  • Eric A Pierce
  • Won A Joo
  • Christine Carag
  • Tiansen Li
  • Natasha Levenkova
  • Nishant Bhasin
  • Thomas W Blackwell
  • Damian Fermin
  • Jimmy Eng
  • Guoliang Yang
  • George Liao
  • Jeffrey S Rubin
  • Lynn Echan
  • Peter Hembach
  • Aykut Uren

Detail Information

Publications34

  1. pmc Supervised regularized canonical correlation analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery
    Abhishek Golugula
    Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
    BMC Bioinformatics 12:483. 2011
    ..We leverage this SRCCA framework towards the fusion of proteomic and histologic image signatures for identifying prostate cancer patients at the risk of 5 year biochemical recurrence following radical prostatectomy...
  2. pmc A fused alpha-beta "mini-spectrin" mimics the intact erythrocyte spectrin head-to-head tetramer
    Sandra L Harper
    Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce St, Philadelphia, PA 19104, USA
    J Biol Chem 285:11003-12. 2010
    ..Caffrey, M. S., Johnson, M. E., and Fung, L. W. (2003) J. Biol. Chem. 278, 21837-21844). This fusion protein should serve as a useful template for structural and functional studies of the divalent tetramer site...
  3. ncbi request reprint Complex proteome prefractionation using microscale solution isoelectrofocusing
    Hsin Yao Tang
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    Expert Rev Proteomics 2:295-306. 2005
    ..This review focuses on the application of microscale solution isoelectrofocusing prefractionation and subsequent downstream strategies in expanding protein profiling capacities and mining low-abundance proteins of complex proteomes...
  4. ncbi request reprint Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma
    Lynn A Echan
    The Wistar Institute, Philadelphia, PA 19104, USA
    Proteomics 5:3292-303. 2005
    ..Hence, non2-D methods such as protein array pixelation are more promising strategies for detecting lower abundance proteins after depleting the six abundant proteins...
  5. ncbi request reprint A structural model of the erythrocyte spectrin heterodimer initiation site determined using homology modeling and chemical cross-linking
    Donghai Li
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    J Biol Chem 283:1553-62. 2008
    ..This model supports the hypothesis that initial docking of the correct alpha and beta repeats from among many very similar repeats in both subunits is driven primarily by long range electrostatic interactions...
  6. pmc Forced unfolding of proteins within cells
    Colin P Johnson
    Biophysical Engineering Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 317:663-6. 2007
    ....
  7. ncbi request reprint Microscale solution isoelectrofocusing: a sample prefractionation method for comprehensive proteome analysis
    Xun Zuo
    The Wistar Institute, Philadelphia, PA, USA
    Methods Mol Biol 244:361-75. 2004
  8. doi request reprint Overview of proteome analysis
    Nadeem Ali-Khan
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Curr Protoc Protein Sci . 2003
    ..The complexity of different types of proteomes, the merits of targeted versus global proteome studies, and the advantages of alternative separation and analysis technologies are discussed...
  9. pmc Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes
    Huan Wang
    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    J Proteome Res 9:1032-40. 2010
    ..Hence, high reproducibility of complex proteomes, such as human cancer cell lysates, readily can be achieved when using multidimensional separation methods with good depth of analysis...
  10. doi request reprint Microscale isoelectric focusing in solution: a method for comprehensive and quantitative proteome analysis using 1-D and 2-D DIGE combined with MicroSol IEF prefractionation
    Mee Jung Han
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Methods Mol Biol 424:241-56. 2008
    ..The combination of DIGE and MicroSol IEF produces a powerful method for more comprehensive and quantitative comparison of protein profiles of complex proteomes...
  11. pmc Structural and functional effects of hereditary hemolytic anemia-associated point mutations in the alpha spectrin tetramer site
    Massimiliano Gaetani
    The Wistar Institute, Philadelphia, PA 19104, USA
    Blood 111:5712-20. 2008
    ..All alpha0 HE/HPP mutations studied here appear to exert their destabilizing effects through molecular recognition rather than structural mechanisms...
  12. doi request reprint Protein profiling by microscale solution isoelectrofocusing (MicroSol-IEF)
    Xun Zuo
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Curr Protoc Protein Sci . 2005
    ..In addition, methods are provided for evaluating the effectiveness of the prefractionation, using 1-D and 2-D gel electrophoresis. Approaches for quantitative protein profiling that incorporate MicroSol-IEF are also discussed...
  13. ncbi request reprint Initiation and propagation of spectrin heterodimer assembly involves distinct energetic processes
    Donghai Li
    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    Biochemistry 46:10585-94. 2007
    ..On the basis of this analysis of heterodimer thermodynamics, a detailed model of spectrin dimer assembly is proposed...
  14. doi request reprint Human serum and plasma proteomics
    Ian Musselman
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Curr Protoc Protein Sci . 2005
    ..Additional protein profiling methods and strategies are also discussed...
  15. ncbi request reprint Influence of lateral association on forced unfolding of antiparallel spectrin heterodimers
    Richard Law
    Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6315, USA
    J Biol Chem 279:16410-6. 2004
    ..Weak lateral interactions do not inhibit unfolding, but strong lateral interactions facilitate simultaneous unfolding analogous to serial repeat coupling within spectrin family proteins...
  16. ncbi request reprint In vivo phosphorylation of human erythrocyte spectrin occurs in a sequential manner
    Hsin Yao Tang
    The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
    Biochemistry 43:4251-62. 2004
    ....
  17. pmc Pathway shifts and thermal softening in temperature-coupled forced unfolding of spectrin domains
    Richard Law
    Biophysical Engineering Lab, Institute for Medicine and Engineering, and School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6315, USA
    Biophys J 85:3286-93. 2003
    ..In sum, structural changes with temperature correlate with both single-molecule unfolding forces and shifts in unfolding pathways...
  18. ncbi request reprint Comprehensive analysis of complex proteomes using microscale solution isoelectrofocusing prior to narrow pH range two-dimensional electrophoresis
    Xun Zuo
    The Wistar Institute, Philadelphia, PA 19104, USA
    Proteomics 2:58-68. 2002
    ....
  19. ncbi request reprint Enhanced analysis of human breast cancer proteomes using micro-scale solution isoelectrofocusing combined with high resolution 1-D and 2-D gels
    Xun Zuo
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 782:253-65. 2002
    ....
  20. ncbi request reprint A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes
    Hsin Yao Tang
    The Wistar Institute, Philadelphia, PA 19104, USA
    Proteomics 5:3329-42. 2005
    ..With further refinement, this method has the potential for even higher capacity and higher throughput...
  21. pmc Structural basis for dimerization in DNA recognition by Gal4
    Manqing Hong
    The Wistar Institute, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
    Structure 16:1019-26. 2008
    ..Associated biochemical studies show that the dimerization domain of Gal4 is important for DNA binding and protein thermostability. We also map the interaction surface of the Gal4 dimerization domain with Gal11P...
  22. pmc Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome
    Sarah Dunn Keene
    Stokes Research Institute and Department of Pediatrics, Children s Hospital of Philadelphia, Philadelphia, PA 19104 4318, USA
    Proteomics 9:768-82. 2009
    ....
  23. pmc A comprehensive model of the spectrin divalent tetramer binding region deduced using homology modeling and chemical cross-linking of a mini-spectrin
    Donghai Li
    Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    J Biol Chem 285:29535-45. 2010
    ....
  24. pmc Cdc13 N-terminal dimerization, DNA binding, and telomere length regulation
    Meghan T Mitchell
    The Wistar Institute, 3601 Spruce St, Philadelphia, PA 19104, USA
    Mol Cell Biol 30:5325-34. 2010
    ..The multiple DNA binding domains and dimeric nature of Cdc13 offer unique insights into how it coordinates the recruitment and regulation of telomerase access to the telomeres...
  25. pmc Pathogenic proline mutation in the linker between spectrin repeats: disease caused by spectrin unfolding
    Colin P Johnson
    Molecular and Cell Biophysics Laboratory, University of Pennsylvania, 3699 Market Street, Philadelphia, PA 19104, USA
    Blood 109:3538-43. 2007
    ..The results suggest a molecular mechanism for the high frequency of disease caused by proline mutations in spectrin linkers...
  26. doi request reprint Determination of disulfide-bond linkages in proteins
    Hsin Yao Tang
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Curr Protoc Protein Sci . 2004
    ..A partial reduction and alkylation strategy for mapping disulfide linkages in peptides with multiple disulfide bonds is also presented...
  27. ncbi request reprint Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma
    Seth A Hoffman
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 849:43-52. 2007
    ..In contrast, new higher dimensional (Hi-D) separation strategies, utilizing more than two dimensions of fractionation, can profile the low abundance proteome...
  28. pmc The proteome of the mouse photoreceptor sensory cilium complex
    Qin Liu
    F M Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Mol Cell Proteomics 6:1299-317. 2007
    ....
  29. ncbi request reprint Disulfide bond assignments of secreted Frizzled-related protein-1 provide insights about Frizzled homology and netrin modules
    Jae Min Chong
    Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    J Biol Chem 277:5134-44. 2002
    ..The major C-terminal processing event was removal of the terminal amino acid (Lys(313)) with only a trace amount of unprocessed protein detected...
  30. doi request reprint Microscale solution IEF combined with 2-D DIGE substantially enhances analysis depth of complex proteomes such as mammalian cell and tissue extracts
    Mee Jung Han
    Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology, Yuseong Gu, Daejeon, Republic of Korea
    Electrophoresis 29:695-705. 2008
    ..Thus the 3-D DIGE strategy produces a powerful method for more comprehensive and more reliable quantitative comparisons of protein profiles of very complex proteomes...
  31. ncbi request reprint HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples
    Alex J Rai
    The Johns Hopkins University School of Medicine, Department of Pathology, Division of Clinical Chemistry, Baltimore, MD 21287 7065, USA
    Proteomics 5:3262-77. 2005
    ..These findings help provide guidance on sample handling issues, with the overall suggestion being to be conscious of all possible pre-analytical variables as a prerequisite of any proteomic study...
  32. pmc Dematin and adducin provide a novel link between the spectrin cytoskeleton and human erythrocyte membrane by directly interacting with glucose transporter-1
    Anwar A Khan
    Department of Pharmacology, University of Illinois Cancer Center, University of Illinois College of Medicine, Chicago, IL 60612, USA
    J Biol Chem 283:14600-9. 2008
    ..Because homologues of dematin, adducin, and glucose transporter-1 exist in many non-erythroid cells, we propose that a conserved mechanism may exist that couples sugar and other related transporters to the actin cytoskeleton...
  33. ncbi request reprint Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    Gilbert S Omenn
    Internal Medicine, University of Michigan, Ann Arbor, MI 48109 0656, USA
    Proteomics 5:3226-45. 2005
    ....
  34. ncbi request reprint Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
    David J States
    University of Michigan, 100 Washtenaw Rd, Palmer Commons 2035B, Ann Arbor, Michigan 48109, USA
    Nat Biotechnol 24:333-8. 2006
    ....

Research Grants38

  1. Development of Methods for Cancer Biomarker Detection
    David Speicher; Fiscal Year: 2004
    ..abstract_text> ..
  2. Novel Comprehensive Proteome Analyses of Metastasis
    David Speicher; Fiscal Year: 2004
    ..abstract_text> ..
  3. TECHNOLOGIES FOR IDENTIFYING PROTEINS SECRETED BY TUMORS
    David Speicher; Fiscal Year: 2005
    ..nanoscale in-gel digestion method; 3) Compare the 1-D gel pixelation approach with MudPIT analyses using prefractionated serum; and 4) Produce and systematically evaluate serum samples from SCID mice with ovarian tumors ..
  4. Membrane Proteins of Normal & Abnormal Red Cells
    David Speicher; Fiscal Year: 2006
    ..Structural properties will be analyzed using protein microchemistry methods that will include high-resolution 2D gels, in-gel protease digestion, mass spectrometry (MS), hydrogen-deuterium exchange/MS analyses, and related methods. ..
  5. Purchase of an ion trap mass spectrometer
    David Speicher; Fiscal Year: 2007
    ..The Wistar Institute is committed to housing, maintaining and staffing the requested mass spectrometer for its useful lifetime as verified by an accompanying letter from the Institute President and CEO. ..
  6. Discovery and validation of novel serological biomarkers of colon cancer
    David Speicher; Fiscal Year: 2007
    ..It is most likely that groups of biomarkers (biomarker signatures) will have greater power to monitor cancer than individual biomarkers. ..
  7. Membrane Proteins of Normal and Abnormal Red Cells
    David Speicher; Fiscal Year: 2009
    ....
  8. Discovery and validation of novel serological biomarkers of colon cancer
    David Speicher; Fiscal Year: 2009
    ..It is most likely that groups of biomarkers (biomarker signatures) will have greater power to monitor cancer than individual biomarkers. ..
  9. Identification of ovarian cancer plasma biomarkers
    David Speicher; Fiscal Year: 2009
    ....
  10. Membrane Proteins of Normal and Abnormal Red Cells
    David W Speicher; Fiscal Year: 2010
    ....
  11. Identification of ovarian cancer plasma biomarkers
    David W Speicher; Fiscal Year: 2010
    ....
  12. MEMBRANE PROTEINS OF NORMAL AND ABNORMAL HUMAN RED CELLS
    David Speicher; Fiscal Year: 1993
    ..interaction and how are they regulated; 4) what is the actual molecular shape of spectrin in the intact cell, - is it an elastic, compact 60 nm or an extended 200 nm tetrameric actin crossbridge; 5) what is the conformation of spectrin?..
  13. MEMBRANE PROTEINS OF NORMAL AND ABNORMAL HUMAN RED CELLS
    David Speicher; Fiscal Year: 1991
    ....
  14. TECHNOLOGIES FOR IDENTIFYING PROTEINS SECRETED BY TUMORS
    David Speicher; Fiscal Year: 2000
    ....
  15. MEMBRANE PROTEINS OF NORMAL/ABNORMAL RED CELLS
    David Speicher; Fiscal Year: 2001
    ....
  16. Discovery and validation of novel serological biomarkers of colon cancer
    David W Speicher; Fiscal Year: 2010
    ..It is most likely that groups of biomarkers (biomarker signatures) will have greater power to monitor cancer than individual biomarkers. ..