David SpeicherSummaryAffiliation: The Wistar Institute Country: USA Publications
Research Grants
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Detail Information
Publications
Supervised regularized canonical correlation analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgeryAbhishek 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...- A fused alpha-beta "mini-spectrin" mimics the intact erythrocyte spectrin head-to-head tetramerSandra 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... 
Complex proteome prefractionation using microscale solution isoelectrofocusingHsin 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...- Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasmaLynn 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... - A structural model of the erythrocyte spectrin heterodimer initiation site determined using homology modeling and chemical cross-linkingDonghai 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... - Forced unfolding of proteins within cellsColin P Johnson
Biophysical Engineering Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
Science 317:663-6. 2007.... - Microscale solution isoelectrofocusing: a sample prefractionation method for comprehensive proteome analysisXun Zuo
The Wistar Institute, Philadelphia, PA, USA
Methods Mol Biol 244:361-75. 2004 - Overview of proteome analysisNadeem 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... - Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomesHuan 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... 
Microscale isoelectric focusing in solution: a method for comprehensive and quantitative proteome analysis using 1-D and 2-D DIGE combined with MicroSol IEF prefractionationMee 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...- Structural and functional effects of hereditary hemolytic anemia-associated point mutations in the alpha spectrin tetramer siteMassimiliano 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... - 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... - Initiation and propagation of spectrin heterodimer assembly involves distinct energetic processesDonghai 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... - Human serum and plasma proteomicsIan Musselman
The Wistar Institute, Philadelphia, Pennsylvania, USA
Curr Protoc Protein Sci . 2005..Additional protein profiling methods and strategies are also discussed... - Influence of lateral association on forced unfolding of antiparallel spectrin heterodimersRichard 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... - In vivo phosphorylation of human erythrocyte spectrin occurs in a sequential mannerHsin Yao Tang
The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
Biochemistry 43:4251-62. 2004.... - Pathway shifts and thermal softening in temperature-coupled forced unfolding of spectrin domainsRichard 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... - Comprehensive analysis of complex proteomes using microscale solution isoelectrofocusing prior to narrow pH range two-dimensional electrophoresisXun Zuo
The Wistar Institute, Philadelphia, PA 19104, USA
Proteomics 2:58-68. 2002.... - Enhanced analysis of human breast cancer proteomes using micro-scale solution isoelectrofocusing combined with high resolution 1-D and 2-D gelsXun Zuo
The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
J Chromatogr B Analyt Technol Biomed Life Sci 782:253-65. 2002.... - A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomesHsin-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... - Structural basis for dimerization in DNA recognition by Gal4Manqing 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... - Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretomeSarah Dunn Keene
Stokes Research Institute and Department of Pediatrics, Children s Hospital of Philadelphia, Philadelphia, PA 19104 4318, USA
Proteomics 9:768-82. 2009.... - A comprehensive model of the spectrin divalent tetramer binding region deduced using homology modeling and chemical cross-linking of a mini-spectrinDonghai Li
Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
J Biol Chem 285:29535-45. 2010.... - Cdc13 N-terminal dimerization, DNA binding, and telomere length regulationMeghan 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... - Pathogenic proline mutation in the linker between spectrin repeats: disease caused by spectrin unfoldingColin 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... - Determination of disulfide-bond linkages in proteinsHsin-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... - Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasmaSeth 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... - The proteome of the mouse photoreceptor sensory cilium complexQin 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.... - Disulfide bond assignments of secreted Frizzled-related protein-1 provide insights about Frizzled homology and netrin modulesJae 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... - Microscale solution IEF combined with 2-D DIGE substantially enhances analysis depth of complex proteomes such as mammalian cell and tissue extractsMee 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... - HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samplesAlex 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... - Dematin and adducin provide a novel link between the spectrin cytoskeleton and human erythrocyte membrane by directly interacting with glucose transporter-1Anwar 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... - 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 databaseGilbert S Omenn
Internal Medicine, University of Michigan, Ann Arbor, MI 48109 0656, USA
Proteomics 5:3226-45. 2005.... - Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative studyDavid J States
University of Michigan, 100 Washtenaw Rd, Palmer Commons 2035B, Ann Arbor, Michigan 48109, USA
Nat Biotechnol 24:333-8. 2006....
Research Grants
- Development of Methods for Cancer Biomarker DetectionDavid Speicher; Fiscal Year: 2004..abstract_text> ..
- Novel Comprehensive Proteome Analyses of MetastasisDavid Speicher; Fiscal Year: 2004..abstract_text> ..
- TECHNOLOGIES FOR IDENTIFYING PROTEINS SECRETED BY TUMORSDavid 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 ..
- Membrane Proteins of Normal & Abnormal Red CellsDavid 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. ..
- Purchase of an ion trap mass spectrometerDavid 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. ..
- Discovery and validation of novel serological biomarkers of colon cancerDavid Speicher; Fiscal Year: 2007..It is most likely that groups of biomarkers (biomarker signatures) will have greater power to monitor cancer than individual biomarkers. ..
- Membrane Proteins of Normal and Abnormal Red CellsDavid Speicher; Fiscal Year: 2009....
- Discovery and validation of novel serological biomarkers of colon cancerDavid Speicher; Fiscal Year: 2009..It is most likely that groups of biomarkers (biomarker signatures) will have greater power to monitor cancer than individual biomarkers. ..
- Identification of ovarian cancer plasma biomarkersDavid Speicher; Fiscal Year: 2009....
- Membrane Proteins of Normal and Abnormal Red CellsDavid W Speicher; Fiscal Year: 2010....
- Identification of ovarian cancer plasma biomarkersDavid W Speicher; Fiscal Year: 2010....
- MEMBRANE PROTEINS OF NORMAL AND ABNORMAL HUMAN RED CELLSDavid 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?..
- MEMBRANE PROTEINS OF NORMAL AND ABNORMAL HUMAN RED CELLSDavid Speicher; Fiscal Year: 1991....
- TECHNOLOGIES FOR IDENTIFYING PROTEINS SECRETED BY TUMORSDavid Speicher; Fiscal Year: 2000....
- MEMBRANE PROTEINS OF NORMAL/ABNORMAL RED CELLSDavid Speicher; Fiscal Year: 2001....
- Discovery and validation of novel serological biomarkers of colon cancerDavid 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. ..