Hanno Steen

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease
    Alex Kentsis
    Division of Hematology Oncology, Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children s Hospital, Harvard Medical School, Boston, MA, USA
    EMBO Mol Med 5:210-20. 2013
  2. pmc NITPICK: peak identification for mass spectrometry data
    Bernhard Y Renard
    Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany
    BMC Bioinformatics 9:355. 2008
  3. ncbi request reprint Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements
    Hanno Steen
    Department of Pathology, Harvard Medical School and Children s Hospital, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 5:172-81. 2006
  4. pmc Integration analysis of quantitative proteomics and transcriptomics data identifies potential targets of frizzled-8 protein-related antiproliferative factor in vivo
    Wei Yang
    The Urological Diseases Research Center, Children s Hospital Boston, Boston, USA
    BJU Int 110:E1138-46. 2012
  5. pmc An in-depth comparison of the male pediatric and adult urinary proteomes
    John W Froehlich
    Boston Children s Hospital, Urological Diseases Research Center, Department of Urology, Harvard Medical School, Boston, MA, USA Proteomics Center at Boston Children s Hospital, Boston, MA, USA
    Biochim Biophys Acta 1844:1044-50. 2014
  6. ncbi request reprint A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer
    Joao A Paulo
    Department of Pathology, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School Boston, MA 02115, USA
    JOP 14:405-14. 2013
  7. doi request reprint Analysis of endoscopic pancreatic function test (ePFT)-collected pancreatic fluid proteins precipitated via ultracentrifugation
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
    JOP 14:176-86. 2013
  8. pmc Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation
    Sasha A Singh
    Department of Pathology, Boston Children s Hospital and Harvard Medical School, Boston, MA, USA
    EMBO J 33:385-99. 2014
  9. pmc Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, Massachusettes, United States
    J Proteome Res 11:1897-912. 2012
  10. pmc A Src family kinase-Shp2 axis controls RUNX1 activity in megakaryocyte and T-lymphocyte differentiation
    Hui Huang
    Department of Pediatric Hematology Oncology, Children s Hospital Boston, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 26:1587-601. 2012

Detail Information

Publications86

  1. pmc Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease
    Alex Kentsis
    Division of Hematology Oncology, Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children s Hospital, Harvard Medical School, Boston, MA, USA
    EMBO Mol Med 5:210-20. 2013
    ....
  2. pmc NITPICK: peak identification for mass spectrometry data
    Bernhard Y Renard
    Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany
    BMC Bioinformatics 9:355. 2008
    ..The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments...
  3. ncbi request reprint Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements
    Hanno Steen
    Department of Pathology, Harvard Medical School and Children s Hospital, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 5:172-81. 2006
    ....
  4. pmc Integration analysis of quantitative proteomics and transcriptomics data identifies potential targets of frizzled-8 protein-related antiproliferative factor in vivo
    Wei Yang
    The Urological Diseases Research Center, Children s Hospital Boston, Boston, USA
    BJU Int 110:E1138-46. 2012
    ..Our analysis suggests that this pathway might also be relevant in the design of diagnostic tools and medications targeting IC...
  5. pmc An in-depth comparison of the male pediatric and adult urinary proteomes
    John W Froehlich
    Boston Children s Hospital, Urological Diseases Research Center, Department of Urology, Harvard Medical School, Boston, MA, USA Proteomics Center at Boston Children s Hospital, Boston, MA, USA
    Biochim Biophys Acta 1844:1044-50. 2014
    ..These findings highlight the importance of age-matching in urinary proteomics. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. ..
  6. ncbi request reprint A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer
    Joao A Paulo
    Department of Pathology, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School Boston, MA 02115, USA
    JOP 14:405-14. 2013
    ....
  7. doi request reprint Analysis of endoscopic pancreatic function test (ePFT)-collected pancreatic fluid proteins precipitated via ultracentrifugation
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
    JOP 14:176-86. 2013
    ..We have shown previously that trichloroacetic acid precipitation is an effective method of protein extraction from pancreatic fluid for downstream biomarker discovery, compared to other common extraction methods tested...
  8. pmc Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation
    Sasha A Singh
    Department of Pathology, Boston Children s Hospital and Harvard Medical School, Boston, MA, USA
    EMBO J 33:385-99. 2014
    ..The regulation of KIFC1 (de-)phosphorylation and degradation provides insights into the fidelity and proper ordering of substrate degradation by the APC/C during mitosis...
  9. pmc Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, Massachusettes, United States
    J Proteome Res 11:1897-912. 2012
    ..Our workflow provided a mass spectrometry-based approach for the further study of the pancreatic fluid proteome, which may lead to the discovery potential biomarkers of chronic pancreatitis...
  10. pmc A Src family kinase-Shp2 axis controls RUNX1 activity in megakaryocyte and T-lymphocyte differentiation
    Hui Huang
    Department of Pediatric Hematology Oncology, Children s Hospital Boston, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 26:1587-601. 2012
    ..These findings link SFK and Shp2 signaling pathways to the regulation of RUNX1 activity in hematopoiesis via control of RUNX1 multiprotein complex assembly...
  11. pmc Identification of pancreas-specific proteins in endoscopically (endoscopic pancreatic function test) collected pancreatic fluid with liquid chromatography--tandem mass spectrometry
    Joao A Paulo
    Center for Pancreatic Disease, Division of Gastroenterology, Hepatology, and Endoscopy, Brigham and Women s Hospital, 75 Francis St, Boston, MA 02115, USA
    Pancreas 39:889-96. 2010
    ....
  12. pmc Post-translational modifications of pancreatic fluid proteins collected via the endoscopic pancreatic function test (ePFT)
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, MA, United States Proteomics Center at Children s Hospital Boston, Boston, MA, United States Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, Boston, MA, United States Electronic address
    J Proteomics 92:216-27. 2013
    ..We aimed to identify differences in posttranslational modifications (PTMs) in pancreatic fluid proteins from individuals with chronic pancreatitis (n=9) and non-pancreatitis controls (n=9)...
  13. pmc Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states
    Joao A Paulo
    Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusettes, United States
    J Proteome Res 10:4835-44. 2011
    ..Investigation of the role of PaSC in the pathogenesis of chronic pancreatitis using the mass spectrometry-based proteomics strategy described herein will lead to further insights into the molecular mechanisms associated with the disease...
  14. pmc Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry
    Joao A Paulo
    Department of Pathology, Harvard Medical School, Boston, MA, USA
    Pancreas 41:175-85. 2012
    ..We aim to establish liquid chromatography coupled with tandem mass spectrometry analysis of FFPE pancreatic tissue as a suitable strategy for the study of the pancreas proteome...
  15. pmc Difference gel electrophoresis identifies differentially expressed proteins in endoscopically collected pancreatic fluid
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
    Electrophoresis 32:1939-51. 2011
    ..Endoscopic collection (ePFT) in tandem with DIGE-LC-MS/MS is a suitable approach for pancreatic fluid proteome analysis; however, further optimization of our protocol, as outlined herein, may improve proteome coverage in future analyses...
  16. pmc Mass spectrometry-based proteomics of endoscopically collected pancreatic fluid in chronic pancreatitis research
    Joao A Paulo
    Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
    Proteomics Clin Appl 5:109-20. 2011
    ..We conclude that pancreatic fluid represents a rich reservoir of potential biomarkers and that the study of the molecular mechanisms of chronic pancreatitis may benefit substantially from MS-based proteomics...
  17. pmc Cytokine profiling of pancreatic fluid using the ePFT collection method in tandem with a multiplexed microarray assay
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, MA, United States
    J Immunol Methods 369:98-107. 2011
    ..Further targeted investigation of cytokines in ePFT-collected fluid will broaden our knowledge of pancreatic immune response and pathogenesis in chronic pancreatitis...
  18. pmc FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides
    Sasha Singh
    Department of Pathology, Harvard Medical School and Children s Hospital Boston, Boston, Massachusetts 02115, USA
    J Proteome Res 8:2201-10. 2009
    ..We find evidence of differential regulation at different sites, a phenomenon we believe will be very widespread. FLEXIQuant proved itself to be capable of serving as a general quantitative tool...
  19. pmc Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysis
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
    Electrophoresis 31:2377-87. 2010
    ..We have also determined the addition of protease inhibitors to be assay-dependent. Our optimized sample preparation strategy can be applied to future proteomic analyses of pancreatic fluid...
  20. pmc Detection and diagnostic value of urine leucine-rich α-2-glycoprotein in children with suspected acute appendicitis
    Alex Kentsis
    Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology Oncology, Department of Medicine, Children s Hospital Boston, Harvard Medical School, Boston, MA, USA
    Ann Emerg Med 60:78-83.e1. 2012
    ..Here, we sought to evaluate the diagnostic utility of enzyme-linked immunosorbent assay (ELISA) of urine LRG in a blinded, prospective, cohort study of children being evaluated for acute abdominal pain...
  21. pmc Subcellular fractionation enhances proteome coverage of pancreatic duct cells
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, MA, USA
    Biochim Biophys Acta 1834:791-7. 2013
    ....
  22. doi request reprint A practical guide to the FLEXIQuant method
    Sasha Singh
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA, USA
    Methods Mol Biol 893:295-319. 2012
    ..FLEXIQuantification allows for the unbiased identification of peptides undergoing PTM as a function of a particular biological state. The extent of PTM is also quantified, providing further insight into the regulation of the protein...
  23. pmc Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS
    Hanno Steen
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 102:3948-53. 2005
    ..These approaches were validated and subsequently applied to the phosphorylation of the yeast transcription factor Pho4...
  24. pmc Proteome scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membranes
    Wei Yang
    Urological Diseases Research Center, Department of Urology, Children s Hospital Boston, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 9:54-70. 2010
    ..The PalmPISC approach and the large scale human S-acylated protein data set are expected to provide powerful tools to facilitate our understanding of the functions and mechanisms of protein S-acylation...
  25. pmc Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases
    Sladjana Prisic
    Division of Infectious Diseases, Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 107:7521-6. 2010
    ..tuberculosis and create a resource for understanding how specific phosphorylation events modulate protein activity. The results further provide the potential to predict likely cognate STPKs for newly identified phosphoproteins...
  26. pmc Cross-species analysis of nicotine-induced proteomic alterations in pancreatic cells
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, MA 02115, USA
    Proteomics 13:1499-512. 2013
    ..Further interrogation of such pathways will lead to insights into the potential effect of nicotine on pancreatic cells at the biomolecular level and the extension of this concept to the effect of nicotine on pancreatic disease...
  27. pmc Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis
    Judith A J Steen
    Departments of Neurobiology and Pathology, Harvard Medical School and Children s Hospital Boston, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:6069-74. 2008
    ..We discuss these findings in terms of the variable efficacy of antimitotic drugs in cancer chemotherapy...
  28. doi request reprint Phosphoproteomics
    Nurhan Ozlu
    Proteomics Center at Children s Hospital Boston, Boston, MA, USA
    Wiley Interdiscip Rev Syst Biol Med 2:255-76. 2010
    ..We highlight the tremendous steps the field has made in the last 5 years which allow quantitative global analyses while pointing out caveats in experimentation...
  29. pmc Quantitative proteomics analysis reveals molecular networks regulated by epidermal growth factor receptor level in head and neck cancer
    Wei Yang
    Urological Diseases Research Center, Department of Urology, Children s Hospital Boston, Boston, Massachusetts 02115, USA
    J Proteome Res 9:3073-82. 2010
    ..Further investigation of these molecular networks may not only enhance our understanding of the antitumor mechanisms of EGFR targeting but also improve patient selection and provide novel targets for better therapeutics...
  30. pmc Proteomic analysis of a rat pancreatic stellate cell line using liquid chromatography tandem mass spectrometry (LC-MS/MS)
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, MA 02115, USA
    J Proteomics 75:708-17. 2011
    ....
  31. pmc Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding
    Sudhakaran Prabakaran
    Department of Systems Biology, Harvard Medical School, Boston, MA, USA
    Wiley Interdiscip Rev Syst Biol Med 4:565-83. 2012
    ..We focus particularly on examples other than the well-known 'histone code', to emphasize the pervasive use of information encoding in molecular biology. Finally, we touch briefly on new methods for measuring mod-form distributions...
  32. pmc Mass spectrometry-based proteomics for translational research: a technical overview
    Joao A Paulo
    Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
    Yale J Biol Med 85:59-73. 2012
    ..Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease...
  33. pmc Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition
    Nurhan Ozlu
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 9:336-50. 2010
    ..Concretely, we report a central role for Aurora-B in regulating the C phase cytoskeleton...
  34. doi request reprint Computational protein profile similarity screening for quantitative mass spectrometry experiments
    Marc Kirchner
    Department of Pathology, Proteomics Center, Children s Hospital Boston, Boston, MA, USA
    Bioinformatics 26:77-83. 2010
    ..This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account...
  35. pmc One-step sample concentration, purification, and albumin depletion method for urinary proteomics
    Ali R Vaezzadeh
    Department of Urology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Proteome Res 9:6082-9. 2010
    ....
  36. doi request reprint Proteomics and opportunities for clinical translation in urological disease
    Ali R Vaezzadeh
    Department of Urology, Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
    J Urol 182:835-43. 2009
    ..We present an overview of current proteomics technologies, a review of proteomics applications in urology and a perspective on the future of proteomics in clinical medicine...
  37. pmc SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra
    Oliver Serang
    Departments of Neurobiology, Harvard Medical School, Boston, Massachusetts 02119, USA
    Mol Cell Proteomics 12:1735-40. 2013
    ..This study presents a novel tool for annotating spectra and producing glycan graphs from LC-MS/MS spectra. The tool is evaluated and shown to perform similarly to an expert on manually curated data...
  38. ncbi request reprint Mass spectrometry-based quantitative proteomic profiling of human pancreatic and hepatic stellate cell lines
    Joao A Paulo
    Department of Pathology, Boston Children s Hospital, Boston, MA 02115, USA
    Genomics Proteomics Bioinformatics 11:105-13. 2013
    ....
  39. pmc A non-parametric cutout index for robust evaluation of identified proteins
    Oliver Serang
    Department of Neurobiology, Harvard Medical School, Boston, MA, USA
    Mol Cell Proteomics 12:807-12. 2013
    ..The general statistical approach can be applied to other types of data (e.g. RNA sequencing) and generalizes to multivariate problems...
  40. doi request reprint Design and validation of a high-throughput matrix-assisted laser desorption ionization time-of-flight mass spectrometry method for quantification of hepcidin in human plasma
    Damon S Anderson
    Departments of Pathology, Children s Hospital Boston, Boston, Massachusetts 02115, United States
    Anal Chem 83:8357-62. 2011
    ..0096). We discuss these preliminary reference ranges and correlations with additional parameters in light of the utility and limitations of hepcidin measurements as a stand-alone diagnostic and as a tool for therapeutic intervention...
  41. doi request reprint Optimizing sample handling for urinary proteomics
    Richard S Lee
    Department of Urology, Urological Diseases Research Center, Harvard Medical School and Children s Hospital Boston, Boston, Massachusetts 02115, USA
    J Proteome Res 7:4022-30. 2008
    ....
  42. doi request reprint MGFp: an open Mascot Generic Format parser library implementation
    Marc Kirchner
    Proteomics Center, Children s Hospital Boston, Boston, Massachusettes 02115, USA
    J Proteome Res 9:2762-3. 2010
    ..We provide a formal grammar and a portable, efficient C++ implementation for a Mascot Generic Format (MGF) parser. Software and technical documentation are available from http://software.steenlab.org/mgfp/...
  43. doi request reprint Discovery and validation of urine markers of acute pediatric appendicitis using high-accuracy mass spectrometry
    Alex Kentsis
    Division of Emergency Medicine, Department of Medicine, Children s Hospital Boston, Harvard Medical School, Boston, MA, USA
    Ann Emerg Med 55:62-70.e4. 2010
    ..Here, we sought to profile the urine of patients with appendicitis, with the goal of identifying new diagnostic markers...
  44. ncbi request reprint iFASP: combining isobaric mass tagging with filter-aided sample preparation
    Gary S McDowell
    Proteomics Center and Department of Pathology, Boston Children s Hospital, Boston, Massachusetts 02115, USA
    J Proteome Res 12:3809-12. 2013
    ....
  45. doi request reprint Cytosolic 5'-nucleotidase 1A autoimmunity in sporadic inclusion body myositis
    H Benjamin Larman
    Department of Genetics, Harvard University Medical School, Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Ann Neurol 73:408-18. 2013
    ..Here, we sought to identify the molecular target of this IBM autoantibody, understand the relationship between IBM autoimmunity and muscle degeneration, and develop an IBM blood test with high diagnostic accuracy...
  46. pmc Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal Fluids
    Joao A Paulo
    1 Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts, USA 2 Proteomics Center at Children s Hospital Boston, Boston, Massachusetts, USA 3 Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
    Clin Transl Gastroenterol 3:e14. 2012
    ..We test the hypothesis that these endoscopically collected fluids have different proteomes. As such, we aim to show that the ePFT method can be used to collect fluid enriched in pancreatic proteins to test for pancreatic function...
  47. doi request reprint Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MS
    Dominic Winter
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
    Proteomics 11:4726-30. 2011
    ..The result is a proposal for an optimized protocol to prepare the whole cell lysate samples from HeLa S3 cells...
  48. pmc mz5: space- and time-efficient storage of mass spectrometry data sets
    Mathias Wilhelm
    Proteomics Center, Children s Hospital Boston, Boston, Massachusetts, USA
    Mol Cell Proteomics 11:O111.011379. 2012
    ..The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5...
  49. pmc Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis
    Rosalyn M Adam
    Urological Diseases Research Center, Children s Hospital Boston and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
    BMC Cell Biol 9:30. 2008
    ..To address these issues, we have modified a published differential detergent extraction method to enable rapid DRM isolation that minimizes nuclear contamination and yields fractions compatible with mass spectrometry...
  50. doi request reprint Proteomic approaches to the analysis of multiprotein signaling complexes
    Wei Yang
    The Urological Diseases Research Center, Department of Urology, Children s Hospital Boston, Boston, MA 02115, USA
    Proteomics 8:832-51. 2008
    ..Challenges associated with proteomic analysis of signaling complexes are also discussed...
  51. pmc The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in Xenopus
    Paul Jorgensen
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Development 136:1539-48. 2009
    ..But yolk consumption does not appear to be triggered by embryonic cells declining to a critically small size. Frog embryos offer a promising platform for the in vivo analysis of metabolism...
  52. pmc Proteomic analysis of palmitoylated platelet proteins
    Louisa Dowal
    Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Boston, MA, USA
    Blood 118:e62-73. 2011
    ..The discovery of new platelet palmitoyl protein candidates will provide a resource for subsequent investigations to validate the palmitoylation of these proteins and to determine the role palmitoylation plays in their function...
  53. pmc Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments
    Marc Kirchner
    Proteomics Center, Children s Hospital Boston, Boston, MA, USA
    Bioinformatics 26:791-7. 2010
    ..DDA/IDA methods do not exploit valuable information that is contained in the fractional mass of high-accuracy precursor mass measurements delivered by current instrumentation...
  54. doi request reprint libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data
    Marc Kirchner
    Proteomics Center, Department of Pathology, Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 27:1166-7. 2011
    ....
  55. ncbi request reprint Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method
    Hanno Steen
    Harvard Medical School, Department of Cell Biology, 240 Longwood Avenue, Boston, MA 02115, USA
    Sci STKE 2002:pl16. 2002
    ..Because of its simplicity and specificity, PSI scanning is likely to become an important tool in proteomic studies of pathways involving tyrosine phosphorylation...
  56. pmc The XLID protein PQBP1 and the GTPase Dynamin 2 define a signaling link that orchestrates ciliary morphogenesis in postmitotic neurons
    Yoshiho Ikeuchi
    Department of Anatomy and Neurobiology, Washington University School of Medicine, St Louis, MO 63110, USA Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
    Cell Rep 4:879-89. 2013
    ..These findings define PQBP1 and Dynamin 2 as components of a signaling pathway that orchestrates neuronal ciliary morphogenesis in the brain. ..
  57. pmc FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanisms
    Sasha A Singh
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts, USA
    Nat Methods 9:504-8. 2012
    ....
  58. pmc Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivation
    Xinjun Zhang
    The F M Kirby Neurobiology Center, Boston Children s Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
    Cell 149:1565-77. 2012
    ..TIKI proteins may represent potential therapeutic targets...
  59. doi request reprint Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation
    Richard S Lee
    Department of Urology, Harvard Medical School, Urological Diseases Research Center, Children s Hospital Boston, Boston, MA 02115, USA
    Proteomics 8:1097-112. 2008
    ..Further characterization of the normal urinary proteome may provide the basis for identification of urinary biomarkers of diseases of the urinary tract...
  60. pmc Quantitative proteomics identifies a beta-catenin network as an element of the signaling response to Frizzled-8 protein-related antiproliferative factor
    Wei Yang
    Urological Diseases Research Center, Children s Hospital Boston, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell Proteomics 10:M110.007492. 2011
    ....
  61. ncbi request reprint Effect of High-Accuracy Precursor Masses on Phosphopeptide Identification from MS(3) Spectra
    Wiebke Timm
    Proteomics Center at Children s Hospital Boston, Boston, Massachusetts 02115, Department of Pathology, Harvard Medical School and Children s Hospital Boston, Boston, Massachusetts 02115, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, F M Kirby Neurobiology Center, Children s Hospital Boston, Boston, Massachusetts 02115, and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115
    Anal Chem 82:3977-80. 2010
    ....
  62. pmc Differentiation-dependent interactions between RUNX-1 and FLI-1 during megakaryocyte development
    Hui Huang
    Children s Hospital Boston, 300 Longwood Ave, Boston, MA 02115, USA
    Mol Cell Biol 29:4103-15. 2009
    ..We propose that dephosphorylation of FLI-1 is a key event in the transcriptional regulation of megakaryocyte maturation. These findings have implications for other cell types where interactions between runx and ets family proteins occur...
  63. pmc A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease
    Gary J Vanasse
    Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
    Blood 118:5401-8. 2011
    ..This association was replicated in an independent cohort of HIV(+) women. Our study provides novel insight into the association between genetic variability in the leptin gene and anemia in HIV(+) individuals...
  64. doi request reprint Etiology of limb girdle muscular dystrophy 1D/1E determined by laser capture microdissection proteomics
    Steven A Greenberg
    Department of Neurology, Division of Neuromuscular Disease, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Ann Neurol 71:141-5. 2012
    ..Sequencing in this patient and family members identified the genetic basis of the previously reported 6q23 linked LGMD1D/1E to be due to an intron splice donor site mutation (IVS3+3A>G) of the desmin gene located on chromosome 2q35...
  65. ncbi request reprint Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator function
    Roy Auty
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    J Biol Chem 279:49973-81. 2004
    ..TFIID supports basal transcription and activated transcription, both of which are enhanced by TFIIA...
  66. pmc Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions
    Sudhakaran Prabakaran
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 7:482. 2011
    ..This combined MS strategy provides an optimal mixture of accuracy and coverage for quantifying distributions, but positional isomers remain a challenging problem...
  67. pmc Brainstem deficiency of the 14-3-3 regulator of serotonin synthesis: a proteomics analysis in the sudden infant death syndrome
    Kevin G Broadbelt
    Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 11:M111.009530. 2012
    ..These data suggest a potential molecular defect in SIDS related to TPH2 regulation, as 14-3-3 is critical in this process...
  68. doi request reprint SALAMI (Spectrum ALignments using high Accuracy Mass and hIgh sensitivity data): how to make the best out of hybrid MS/MS data
    Flavio Monigatti
    Department of Pathology, Harvard Medical School and Children s Hospital Boston, Boston, MA 02115, USA
    J Proteome Res 7:1984-93. 2008
    ..This approach utilizes the parallel spectrum measurement capabilities of the LTQ-Orbitrap. We present our approach to handling this type of hybrid data, explain our alignment program, and discuss the advantages of the chosen methodology...
  69. ncbi request reprint Protein sulfation analysis--A primer
    Flavio Monigatti
    Department of Pathology Enders 1130, Harvard Medical School and Children s Hospital Boston, 320 Longwood Ave, Boston, MA 02115, USA
    Biochim Biophys Acta 1764:1904-13. 2006
    ..2). We will highlight strengths and limitations of different strategies and approaches (including references), providing a primer for newcomers to protein sulfation analysis...
  70. pmc Purification and architecture of the ubiquitous Wave complex
    Alexis Gautreau
    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:4379-83. 2004
    ..The complex is organized around a core of Nap and Abi. Sra is a peripheral subunit recruited on the Nap side, whereas the Wave and Hspc subunits are recruited on the Abi side of the core...
  71. ncbi request reprint A quantitative proteomic analysis of growth factor-induced compositional changes in lipid rafts of human smooth muscle cells
    Dawn L MacLellan
    Department of Urology, The Urological Diseases Research Center, Boston, MA, USA
    Proteomics 5:4733-42. 2005
    ..In addition, eight Rho family members were localized to rafts by ICAT analysis. Collectively, these observations suggest a role for lipid rafts in regulation of PDGF-stimulated changes in the cytoskeleton...
  72. pmc Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MS
    Joao A Paulo
    Department of Pathology, Children s Hospital Boston, Boston, MA, USA
    Proteomics Clin Appl 4:715-25. 2010
    ..We use in-gel tryptic digestion followed by LC-MS/MS (GeLC-MS/MS) to profile the proteome of gastroduodenal fluid collected during the endoscopic pancreatic function test (ePFT)...
  73. pmc Iron overload in patients with acute leukemia or MDS undergoing myeloablative stem cell transplantation
    Philippe Armand
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Biol Blood Marrow Transplant 17:852-60. 2011
    ..These results contribute to our understanding of the prevalence, mechanism, and consequences of iron overload in HSCT...
  74. pmc High-throughput matrix-assisted laser desorption ionization-time-of-flight mass spectrometry method for quantification of hepcidin in human urine
    Damon S Anderson
    Department of Pathology, Children s Hospital Boston, Boston, Massachusetts 02115, USA
    Anal Chem 82:1551-5. 2010
    ..The assay is simple, accurate, and efficient, and the high-throughput performance features of the assay make large-scale clinical research studies feasible...
  75. ncbi request reprint The ABC's (and XYZ's) of peptide sequencing
    Hanno Steen
    Department of Systems Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nat Rev Mol Cell Biol 5:699-711. 2004
    ..The key - but little understood - technology in mass-spectrometry-based proteomics is peptide sequencing, which we describe and review here in an easily accessible format...
  76. ncbi request reprint Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response
    Jiaxu Li
    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115 5730, USA
    Mol Cell Proteomics 2:1198-204. 2003
    ..These results indicate that salt stress and amino acid starvation cause overlapping cellular responses and are likely to be physiologically linked...
  77. ncbi request reprint Proteomics goes quantitative: measuring protein abundance
    Hanno Steen
    Department Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Trends Biotechnol 20:361-4. 2002
    ..Furthermore, methods for the quantitation of relative protein abundance at the protein level are getting more advanced, which should complement gene expression monitoring at the mRNA level...
  78. ncbi request reprint Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning
    Hanno Steen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
    Mol Cell Proteomics 2:138-45. 2003
    ..This study shows the power of phosphotyrosine-specific immonium ion scanning for sensitive phosphotyrosine mapping when limited amounts of samples are available...
  79. ncbi request reprint Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway
    Hanno Steen
    Protein Interaction Laboratory, Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    J Biol Chem 277:1031-9. 2002
    ..Because of its sensitivity and selectivity, this approach will be useful in proteomic approaches to study tyrosine phosphorylation in a number of signal transduction pathways...
  80. ncbi request reprint Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    Shao En Ong
    Protein Interaction Laboratory, University of Southern Denmark, Odense, Denmark
    Mol Cell Proteomics 1:376-86. 2002
    ..SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system...
  81. ncbi request reprint Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome
    Matthias Mann
    Center for Experimental Bioinformatics, University of Southern Denmark, M, DK 5230, Odense, Denmark
    Trends Biotechnol 20:261-8. 2002
    ..In this article, we outline several methods for enrichment of phosphorylated proteins and peptides and discuss various options for their identification and quantitation with special emphasis on mass spectrometry-based techniques...
  82. ncbi request reprint A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode
    Hanno Steen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense
    J Am Soc Mass Spectrom 13:996-1003. 2002
    ....
  83. ncbi request reprint Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry
    Hanno Steen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    Mass Spectrom Rev 21:163-82. 2002
    ....
  84. ncbi request reprint Directed proteomic analysis of the human nucleolus
    Jens S Andersen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230, Odense M, Denmark
    Curr Biol 12:1-11. 2002
    ..Recent studies suggest it may also have roles in RNA transport, RNA modification, and cell cycle regulation. Despite over 150 years of research into nucleoli, many aspects of their structure and function remain uncharacterized...
  85. pmc Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity
    Lawrence S Argetsinger
    Department of Molecular and Integrative Physiology, The University of Michigan Medical School, Ann Arbor, MI 48109 0622, USA
    Mol Cell Biol 24:4955-67. 2004
    ....
  86. doi request reprint Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics
    Thomas Koenig
    Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
    J Proteome Res 7:3708-17. 2008
    ....

Research Grants1

  1. Defining the true nature of the minimal cell cycle with quantitative proteomics
    Hanno Steen; Fiscal Year: 2010
    ..Apart from furthering our fundamental understanding of the cell cycle, the development of preventatives, treatments and therapies for/of these diseases and malignancies will benefit greatly from this study. ..