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Hanno  Steen, PhD

Hanno Steen PhD
Steen Laboratory
Neurobiology Program
Pathology Research
Hospital Title:
Director of the Proteomics Center
Academic Title:
Associate Professor of Pathology, Harvard Medical School
Research Focus Area:
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Research Overview

Hanno Steen is a pioneer in developing methods for the qualitative and quantitative analysis of protein modifications by mass spectrometry, with special emphasis on tyrosine phosphorylation. In carcinogenesis, the pivotal role of tyrosine phosphorylation is underscored by the notion that almost half of the oncogenes known to date encode tyrosine kinases.

Hanno Steen's interests are focused on proteomics and biological mass spectrometry in general. He is particularly interested in the mass spectrometric analysis of the composition of complex protein mixtures, which includes not only the cataloging but also the comprehensive characterization of the components.

Dr. Steen's lab is working on novel methods for identifying and quantifying various protein modifications that are involved in pediatric diseases in order to provide new insights into the underlying biological processes, a prerequisite for a rational approach to prevent and/or cure these diseases.

Another goal of the lab's research is the development and applications of screening methods to detect and identify diagnostic and prognostic disease markers in body fluids, which offer an easily accessible mirror of the state of the entire body. These biomarkers can guide treatment decisions, predict patient phenotypes, and allow for early diagnosis.

About Hanno Steen

Dr. Steen studied chemistry at the University in Freiburg (Germany), UMIST/Manchester (UK) and Swiss Federal Institute of Technology (ETH) Zurich (Switzerland). He received his PhD in Biochemistry and Molecular Biology from the University of Southern Denmark working in the laboratory of Matthias Mann on the mass spectrometric analysis of protein modifications. He completed postdoctoral fellowships in the laboratories of Steve Gygi and Marc Kirschner at the Departments of Cell Biology and Systems Biology at Harvard Medical School.


Publications powered by Harvard Catalyst Profiles
  1. Hart PA, Topazian M, Raimondo M, Cruz-Monserrate Z, Fisher WE, Lesinski GB, Steen H, Conwell DL. Endoscopic Pancreas Fluid Collection: Methods and Relevance for Clinical Care and Translational Science. Am J Gastroenterol. 2016 Sep; 111(9):1258-66.
  2. Froehlich JW, Kostel SA, Cho PS, Briscoe AC, Steen H, Vaezzadeh AR, Lee RS. Urinary Proteomics Yield Pathological Insights for Ureteropelvic Junction Obstruction. Mol Cell Proteomics. 2016 Aug; 15(8):2607-15.
  3. Chatterjee B, Makarov A, Clemmer DE, Steen H, Steen J, Saffell-Clemmer W, Moghekar AR, Mohan Rao C, Bradshaw RA, Thakur SS. Proteomics in India: A Report on a Brainstorming Meeting at Hyderabad, India. Mol Cell Proteomics. 2016 Jul; 15(7):2229-35.
  4. Tang S, Hemberg M, Cansizoglu E, Belin S, Kosik K, Kreiman G, Steen H, Steen J. f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome. Nucleic Acids Res. 2016 Jun 2; 44(10):e97.
  5. Mair W, Muntel J, Tepper K, Tang S, Biernat J, Seeley WW, Kosik KS, Mandelkow E, Steen H, Steen JA. FLEXITau: Quantifying Post-translational Modifications of Tau Protein in Vitro and in Human Disease. Anal Chem. 2016 Apr 5; 88(7):3704-14.
  6. Oh DY, Dowling DJ, Ahmed S, Choi H, Brightman S, Bergelson I, Berger ST, Sauld JF, Pettengill M, Kho AT, Pollack HJ, Steen H, Levy O. Adjuvant-induced Human Monocyte Secretome Profiles Reveal Adjuvant- and Age-specific Protein Signatures. Mol Cell Proteomics. 2016 Jun; 15(6):1877-94.
  7. Chau KF, Springel MW, Broadbelt KG, Park HY, Topal S, Lun MP, Mullan H, Maynard T, Steen H, LaMantia AS, Lehtinen MK. Progressive Differentiation and Instructive Capacities of Amniotic Fluid and Cerebrospinal Fluid Proteomes following Neural Tube Closure. Dev Cell. 2015 Dec 21; 35(6):789-802.
  8. Muntel J, Xuan Y, Berger ST, Reiter L, Bachur R, Kentsis A, Steen H. Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer. J Proteome Res. 2015 Nov 6; 14(11):4752-62.
  9. Bennike TB, Barnaby O, Steen H, Stensballe A. Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome. Data Brief. 2015 Dec; 5:241-7.
  10. Berger ST, Ahmed S, Muntel J, Cuevas Polo N, Bachur R, Kentsis A, Steen J, Steen H. MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates. Mol Cell Proteomics. 2015 Oct; 14(10):2814-23.
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  12. Dhabaria A, Cifani P, Reed C, Steen H, Kentsis A. A High-Efficiency Cellular Extraction System for Biological Proteomics. J Proteome Res. 2015 Aug 7; 14(8):3403-8.
  13. Prisic S, Hwang H, Dow A, Barnaby O, Pan TS, Lonzanida JA, Chazin WJ, Steen H, Husson RN. Zinc regulates a switch between primary and alternative S18 ribosomal proteins in Mycobacterium tuberculosis. Mol Microbiol. 2015 Jul; 97(2):263-80.
  14. Lun MP, Johnson MB, Broadbelt KG, Watanabe M, Kang YJ, Chau KF, Springel MW, Malesz A, Sousa AM, Pletikos M, Adelita T, Adelita T, Calicchio ML, Zhang Y, Holtzman MJ, Lidov HG, Sestan N, Steen H, Monuki ES, Lehtinen MK. Spatially heterogeneous choroid plexus transcriptomes encode positional identity and contribute to regional CSF production. J Neurosci. 2015 Mar 25; 35(12):4903-16.
  15. Laurent B, Ruitu L, Murn J, Hempel K, Ferrao R, Xiang Y, Liu S, Garcia BA, Wu H, Wu F, Steen H, Shi Y. A specific LSD1/KDM1A isoform regulates neuronal differentiation through H3K9 demethylation. Mol Cell. 2015 Mar 19; 57(6):957-70.
  16. Abu Dayyeh BK, Conwell D, Buttar NS, Kadilaya V, Hart PA, Baumann NA, Bick BL, Chari ST, Chowdhary S, Clain JE, Gleeson FC, Lee LS, Levy MJ, Pearson RK, Petersen BT, Rajan E, Steen H, Suleiman S, Banks PA, Vege SS, Topazian M. Pancreatic juice prostaglandin e2 concentrations are elevated in chronic pancreatitis and improve detection of early disease. Clin Transl Gastroenterol. 2015; 6:e72.
  17. Winter D, Dehghani A, Steen H. Optimization of cell lysis and protein digestion protocols for protein analysis by LC-MS/MS. Methods Mol Biol. 2015; 1295:259-73.
  18. Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M. Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA). Mol Cell Proteomics. 2015 Feb; 14(2):430-40.
  19. Prabakaran S, Hemberg M, Chauhan R, Winter D, Tweedie-Cullen RY, Dittrich C, Hong E, Gunawardena J, Steen H, Kreiman G, Steen JA. Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun. 2014; 5:5429.
  20. Gallardo G, Barowski J, Ravits J, Siddique T, Lingrel JB, Robertson J, Steen H, Bonni A. An a2-Na/K ATPase/a-adducin complex in astrocytes triggers non-cell autonomous neurodegeneration. Nat Neurosci. 2014 Dec; 17(12):1710-9.
  21. Bennike T, Ayturk U, Haslauer CM, Froehlich JW, Proffen BL, Barnaby O, Birkelund S, Murray MM, Warman ML, Stensballe A, Steen H. A normative study of the synovial fluid proteome from healthy porcine knee joints. J Proteome Res. 2014 Oct 3; 13(10):4377-87.
  22. Singh SA, Winter D, Kirchner M, Chauhan R, Ahmed S, Ozlu N, Tzur A, Steen JA, Steen H. Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J. 2014 Feb 18; 33(4):385-99.
  23. Gutierrez A, Pan L, Groen RW, Baleydier F, Kentsis A, Marineau J, Grebliunaite R, Kozakewich E, Reed C, Pflumio F, Poglio S, Uzan B, Clemons P, VerPlank L, An F, Burbank J, Norton S, Tolliday N, Steen H, Weng AP, Yuan H, Bradner JE, Mitsiades C, Look AT, Aster JC. Phenothiazines induce PP2A-mediated apoptosis in T cell acute lymphoblastic leukemia. J Clin Invest. 2014 Feb; 124(2):644-55.
  24. Mosammaparast N, Kim H, Laurent B, Zhao Y, Lim HJ, Majid MC, Dango S, Luo Y, Hempel K, Sowa ME, Gygi SP, Steen H, Harper JW, Yankner B, Shi Y. The histone demethylase LSD1/KDM1A promotes the DNA damage response. J Cell Biol. 2013 Nov 11; 203(3):457-70.
  25. Serang O, Cansizoglu AE, Käll L, Steen H, Steen JA. Nonparametric Bayesian evaluation of differential protein quantification. J Proteome Res. 2013 Oct 4; 12(10):4556-65.
  26. Ikeuchi Y, de la Torre-Ubieta L, Matsuda T, Steen H, Okazawa H, Bonni A. The XLID protein PQBP1 and the GTPase Dynamin 2 define a signaling link that orchestrates ciliary morphogenesis in postmitotic neurons. Cell Rep. 2013 Sep 12; 4(5):879-89.
  27. McDowell GS, Gaun A, Steen H. iFASP: combining isobaric mass tagging with filter-aided sample preparation. J Proteome Res. 2013 Aug 2; 12(8):3809-12.
  28. Paulo JA, Kadiyala V, Brizard S, Banks PA, Steen H, Conwell DL. A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer. JOP. 2013 Jul; 14(4):405-14.
  29. Froehlich JW, Vaezzadeh AR, Kirchner M, Briscoe AC, Hofmann O, Hide W, Steen H, Lee RS. An in-depth comparison of the male pediatric and adult urinary proteomes. Biochim Biophys Acta. 2014 May; 1844(5):1044-50.
  30. Paulo JA, Urrutia R, Kadiyala V, Banks P, Conwell DL, Steen H. Cross-species analysis of nicotine-induced proteomic alterations in pancreatic cells. Proteomics. 2013 May; 13(9):1499-512.
  31. Paulo JA, Kadiyala V, Banks PA, Conwell DL, Steen H. Mass spectrometry-based quantitative proteomic profiling of human pancreatic and hepatic stellate cell lines. Genomics Proteomics Bioinformatics. 2013 Apr; 11(2):105-13.
  32. Paulo JA, Kadiyala V, Brizard S, Banks PA, Steen H, Conwell DL. Post-translational modifications of pancreatic fluid proteins collected via the endoscopic pancreatic function test (ePFT). J Proteomics. 2013 Oct 30; 92:216-27.
  33. Paulo JA, Kadiyala V, Gaun A, Sauld JF, Ghoulidi A, Banks PA, Steen H, Conwell DL. Analysis of endoscopic pancreatic function test (ePFT)-collected pancreatic fluid proteins precipitated via ultracentrifugation. JOP. 2013 Mar; 14(2):176-86.
  34. Berg AH, Drechsler C, Wenger J, Buccafusca R, Hod T, Kalim S, Ramma W, Parikh SM, Steen H, Friedman DJ, Danziger J, Wanner C, Thadhani R, Karumanchi SA. Carbamylation of serum albumin as a risk factor for mortality in patients with kidney failure. Sci Transl Med. 2013 Mar 6; 5(175):175ra29.
  35. Larman HB, Salajegheh M, Nazareno R, Lam T, Sauld J, Steen H, Kong SW, Pinkus JL, Amato AA, Elledge SJ, Greenberg SA. Cytosolic 5'-nucleotidase 1A autoimmunity in sporadic inclusion body myositis. Ann Neurol. 2013 Mar; 73(3):408-18.
  36. Pe'er T, Lahmi R, Sharaby Y, Chorni E, Noach M, Vecsler M, Zlotorynski E, Steen H, Steen JA, Tzur A. Gas2l3, a novel constriction site-associated protein whose regulation is mediated by the APC/C Cdh1 complex. PLoS One. 2013; 8(2):e57532.
  37. Serang O, Froehlich JW, Muntel J, McDowell G, Steen H, Lee RS, Steen JA. SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra. Mol Cell Proteomics. 2013 Jun; 12(6):1735-40.
  38. Paulo JA, Gaun A, Kadiyala V, Ghoulidi A, Banks PA, Conwell DL, Steen H. Subcellular fractionation enhances proteome coverage of pancreatic duct cells. Biochim Biophys Acta. 2013 Apr; 1834(4):791-7.
  39. Serang O, Paulo J, Steen H, Steen JA. A non-parametric cutout index for robust evaluation of identified proteins. Mol Cell Proteomics. 2013 Mar; 12(3):807-12.
  40. Kentsis A, Shulman A, Ahmed S, Brennan E, Monuteaux MC, Lee YH, Lipsett S, Paulo JA, Dedeoglu F, Fuhlbrigge R, Bachur R, Bradwin G, Arditi M, Sundel RP, Newburger JW, Steen H, Kim S. Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease. EMBO Mol Med. 2013 Feb; 5(2):210-20.
  41. Prabakaran S, Lippens G, Steen H, Gunawardena J. Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. Wiley Interdiscip Rev Syst Biol Med. 2012 Nov-Dec; 4(6):565-83.
  42. Huang H, Woo AJ, Waldon Z, Schindler Y, Moran TB, Zhu HH, Feng GS, Steen H, Cantor AB. A Src family kinase-Shp2 axis controls RUNX1 activity in megakaryocyte and T-lymphocyte differentiation. Genes Dev. 2012 Jul 15; 26(14):1587-601.
  43. Yang W, Kim Y, Kim TK, Keay SK, Kim KP, Steen H, Freeman MR, Hwang D, Kim J. Integration analysis of quantitative proteomics and transcriptomics data identifies potential targets of frizzled-8 protein-related antiproliferative factor in vivo. BJU Int. 2012 Dec; 110(11 Pt C):E1138-46.
  44. Zhang X, Abreu JG, Yokota C, MacDonald BT, Singh S, Coburn KL, Cheong SM, Zhang MM, Ye QZ, Hang HC, Steen H, He X. Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivation. Cell. 2012 Jun 22; 149(7):1565-77.
  45. Paulo JA, Kadiyala V, Banks PA, Steen H, Conwell DL. Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal Fluids. Clin Transl Gastroenterol. 2012; 3:e14.
  46. Singh SA, Winter D, Bilimoria PM, Bonni A, Steen H, Steen JA. FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanisms. Nat Methods. 2012 May; 9(5):504-8.
  47. Renard BY, Xu B, Kirchner M, Zickmann F, Winter D, Korten S, Brattig NW, Tzur A, Hamprecht FA, Steen H. Overcoming species boundaries in peptide identification with Bayesian information criterion-driven error-tolerant peptide search (BICEPS). Mol Cell Proteomics. 2012 Jul; 11(7):M111.014167.
  48. Paulo JA, Kadiyala V, Banks PA, Steen H, Conwell DL. Mass spectrometry-based proteomics for translational research: a technical overview. Yale J Biol Med. 2012 Mar; 85(1):59-73.
  49. Paulo JA, Lee LS, Banks PA, Steen H, Conwell DL. Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. Pancreas. 2012 Mar; 41(2):175-85.
  50. Paulo JA, Kadiyala V, Lee LS, Banks PA, Conwell DL, Steen H. Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis. J Proteome Res. 2012 Mar 2; 11(3):1897-912.
  51. Kentsis A, Ahmed S, Kurek K, Brennan E, Bradwin G, Steen H, Bachur R. Detection and diagnostic value of urine leucine-rich a-2-glycoprotein in children with suspected acute appendicitis. Ann Emerg Med. 2012 Jul; 60(1):78-83.e1.
  52. Singh S, Kirchner M, Steen JA, Steen H. A practical guide to the FLEXIQuant method. Methods Mol Biol. 2012; 893:295-319.
  53. Greenberg SA, Salajegheh M, Judge DP, Feldman MW, Kuncl RW, Waldon Z, Steen H, Wagner KR. Etiology of limb girdle muscular dystrophy 1D/1E determined by laser capture microdissection proteomics. Ann Neurol. 2012 Jan; 71(1):141-5.
  54. Winter D, Steen H. Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MS. Proteomics. 2011 Dec; 11(24):4726-30.
  55. Anderson DS, Kirchner M, Kellogg M, Kalish LA, Jeong JY, Vanasse G, Berliner N, Fleming MD, Steen H. 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. Anal Chem. 2011 Nov 1; 83(21):8357-62.
  56. Broadbelt KG, Rivera KD, Paterson DS, Duncan JR, Trachtenberg FL, Paulo JA, Stapels MD, Borenstein NS, Belliveau RA, Haas EA, Stanley C, Krous HF, Steen H, Kinney HC. Brainstem deficiency of the 14-3-3 regulator of serotonin synthesis: a proteomics analysis in the sudden infant death syndrome. Mol Cell Proteomics. 2012 Jan; 11(1):M111.009530.
  57. Soblik H, Younis AE, Mitreva M, Renard BY, Kirchner M, Geisinger F, Steen H, Brattig NW. Life cycle stage-resolved proteomic analysis of the excretome/secretome from Strongyloides ratti--identification of stage-specific proteases. Mol Cell Proteomics. 2011 Dec; 10(12):M111.010157.
  58. Wilhelm M, Kirchner M, Steen JA, Steen H. mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics. 2012 Jan; 11(1):O111.011379.
  59. Paulo JA, Urrutia R, Banks PA, Conwell DL, Steen H. Proteomic analysis of a rat pancreatic stellate cell line using liquid chromatography tandem mass spectrometry (LC-MS/MS). J Proteomics. 2011 Dec 21; 75(2):708-17.
  60. Vanasse GJ, Jeong JY, Tate J, Bathulapalli H, Anderson D, Steen H, Fleming M, Mattocks K, Telenti A, Fellay J, Justice AC, Berliner N. A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease. Blood. 2011 Nov 17; 118(20):5401-8.
  61. Paulo JA, Urrutia R, Banks PA, Conwell DL, Steen H. Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states. J Proteome Res. 2011 Oct 7; 10(10):4835-44.
  62. Younis AE, Geisinger F, Ajonina-Ekoti I, Soblik H, Steen H, Mitreva M, Erttmann KD, Perbandt M, Liebau E, Brattig NW. Stage-specific excretory-secretory small heat shock proteins from the parasitic nematode Strongyloides ratti--putative links to host's intestinal mucosal defense system. FEBS J. 2011 Sep; 278(18):3319-36.
  63. Lysaght AC, Kao SY, Paulo JA, Merchant SN, Steen H, Stankovic KM. Proteome of human perilymph. J Proteome Res. 2011 Sep 2; 10(9):3845-51.
  64. Dowal L, Yang W, Freeman MR, Steen H, Flaumenhaft R. Proteomic analysis of palmitoylated platelet proteins. Blood. 2011 Sep 29; 118(13):e62-73.
  65. Paulo JA, Lee LS, Banks PA, Steen H, Conwell DL. Difference gel electrophoresis identifies differentially expressed proteins in endoscopically collected pancreatic fluid. Electrophoresis. 2011 Aug; 32(15):1939-51.
  66. Paulo JA, Lee LS, Wu B, Banks PA, Steen H, Conwell DL. Cytokine profiling of pancreatic fluid using the ePFT collection method in tandem with a multiplexed microarray assay. J Immunol Methods. 2011 Jun 30; 369(1-2):98-107.
  67. Prabakaran S, Everley RA, Landrieu I, Wieruszeski JM, Lippens G, Steen H, Gunawardena J. Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions. Mol Syst Biol. 2011 Apr 12; 7:482.
  68. Yang W, Chung YG, Kim Y, Kim TK, Keay SK, Zhang CO, Ji M, Hwang D, Kim KP, Steen H, Freeman MR, Kim J. Quantitative proteomics identifies a beta-catenin network as an element of the signaling response to Frizzled-8 protein-related antiproliferative factor. Mol Cell Proteomics. 2011 Jun; 10(6):M110.007492.
  69. Paulo JA, Lee LS, Wu B, Banks PA, Steen H, Conwell DL. Mass spectrometry-based proteomics of endoscopically collected pancreatic fluid in chronic pancreatitis research. Proteomics Clin Appl. 2011 Apr; 5(3-4):109-20.
  70. Kirchner M, Xu B, Steen H, Steen JA. libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data. Bioinformatics. 2011 Apr 15; 27(8):1166-7.
  71. Vaezzadeh AR, Briscoe AC, Steen H, Lee RS. One-step sample concentration, purification, and albumin depletion method for urinary proteomics. J Proteome Res. 2010 Nov 5; 9(11):6082-9.
  72. Armand P, Kim HT, Rhodes J, Sainvil MM, Cutler C, Ho VT, Koreth J, Alyea EP, Hearsey D, Neufeld EJ, Fleming MD, Steen H, Anderson D, Kwong RY, Soiffer RJ, Antin JH. Iron overload in patients with acute leukemia or MDS undergoing myeloablative stem cell transplantation. Biol Blood Marrow Transplant. 2011 Jun; 17(6):852-60.
  73. Paulo JA, Lee LS, Wu B, Repas K, Banks PA, Conwell DL, Steen H. Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MS. Proteomics Clin Appl. 2010 Sep; 4(8-9):715-25.
  74. Paulo JA, Lee LS, Wu B, Repas K, Mortele KJ, Banks PA, Steen H, Conwell DL. Identification of pancreas-specific proteins in endoscopically (endoscopic pancreatic function test) collected pancreatic fluid with liquid chromatography--tandem mass spectrometry. Pancreas. 2010 Aug; 39(6):889-96.
  75. Paulo JA, Lee LS, Wu B, Repas K, Banks PA, Conwell DL, Steen H. Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysis. Electrophoresis. 2010 Jul; 31(14):2377-87.
  76. Yang W, Cai Q, Lui VW, Everley PA, Kim J, Bhola N, Quesnelle KM, Zetter BR, Steen H, Freeman MR, Grandis JR. Quantitative proteomics analysis reveals molecular networks regulated by epidermal growth factor receptor level in head and neck cancer. J Proteome Res. 2010 Jun 4; 9(6):3073-82.
  77. Renard BY, Timm W, Kirchner M, Steen JA, Hamprecht FA, Steen H. Estimating the confidence of peptide identifications without decoy databases. Anal Chem. 2010 Jun 1; 82(11):4314-8.
  78. Timm W, Ozlu N, Steen JJ, Steen H. Effect of high-accuracy precursor masses on phosphopeptide identification from MS3 spectra. Anal Chem. 2010 May 15; 82(10):3977-80.
  79. Kirchner M, Steen JA, Hamprecht FA, Steen H. MGFp: an open Mascot Generic Format parser library implementation. J Proteome Res. 2010 May 7; 9(5):2762-3.
  80. Lou X, Kirchner M, Renard BY, Köthe U, Boppel S, Graf C, Lee CT, Steen JA, Steen H, Mayer MP, Hamprecht FA. Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. Bioinformatics. 2010 Jun 15; 26(12):1535-41.
  81. Ozlu N, Akten B, Timm W, Haseley N, Steen H, Steen JA. Phosphoproteomics. Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun; 2(3):255-76.
  82. Prisic S, Dankwa S, Schwartz D, Chou MF, Locasale JW, Kang CM, Bemis G, Church GM, Steen H, Husson RN. Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc Natl Acad Sci U S A. 2010 Apr 20; 107(16):7521-6.
  83. Anderson DS, Heeney MM, Roth U, Menzel C, Fleming MD, Steen H. High-throughput matrix-assisted laser desorption ionization-time-of-flight mass spectrometry method for quantification of hepcidin in human urine. Anal Chem. 2010 Feb 15; 82(4):1551-5.
  84. Kirchner M, Timm W, Fong P, Wangemann P, Steen H. Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments. Bioinformatics. 2010 Mar 15; 26(6):791-7.
  85. Renard BY, Kirchner M, Monigatti F, Ivanov AR, Rappsilber J, Winter D, Steen JA, Hamprecht FA, Steen H. When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification. Proteomics. 2009 Nov; 9(21):4978-84.
  86. Kirchner M, Renard BY, Köthe U, Pappin DJ, Hamprecht FA, Steen H, Steen JA. Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinformatics. 2010 Jan 1; 26(1):77-83.
  87. Yang W, Di Vizio D, Kirchner M, Steen H, Freeman MR. Proteome scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membranes. Mol Cell Proteomics. 2010 Jan; 9(1):54-70.
  88. Ozlü N, Monigatti F, Renard BY, Field CM, Steen H, Mitchison TJ, Steen JJ. Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition. Mol Cell Proteomics. 2010 Feb; 9(2):336-50.
  89. Tazir Y, Steisslinger V, Soblik H, Younis AE, Beckmann S, Grevelding CG, Steen H, Brattig NW, Erttmann KD. Molecular and functional characterisation of the heat shock protein 10 of Strongyloides ratti. Mol Biochem Parasitol. 2009 Dec; 168(2):149-57.
  90. Vaezzadeh AR, Steen H, Freeman MR, Lee RS. Proteomics and opportunities for clinical translation in urological disease. J Urol. 2009 Sep; 182(3):835-43.
  91. Kentsis A, Lin YY, Kurek K, Calicchio M, Wang YY, Monigatti F, Campagne F, Lee R, Horwitz B, Steen H, Bachur R. Discovery and validation of urine markers of acute pediatric appendicitis using high-accuracy mass spectrometry. Ann Emerg Med. 2010 Jan; 55(1):62-70.e4.
  92. Huang H, Yu M, Akie TE, Moran TB, Woo AJ, Tu N, Waldon Z, Lin YY, Steen H, Cantor AB. Differentiation-dependent interactions between RUNX-1 and FLI-1 during megakaryocyte development. Mol Cell Biol. 2009 Aug; 29(15):4103-15.
  93. Singh S, Springer M, Steen J, Kirschner MW, Steen H. FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J Proteome Res. 2009 May; 8(5):2201-10.
  94. Jorgensen P, Steen JA, Steen H, Kirschner MW. The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in Xenopus. Development. 2009 May; 136(9):1539-48.
  95. Wang Z, Dong G, Singh S, Steen H, Li J. A simple and effective method for detecting phosphopeptides for phosphoproteomic analysis. J Proteomics. 2009 Jul 21; 72(5):831-5.
  96. Kentsis A, Monigatti F, Dorff K, Campagne F, Bachur R, Steen H. Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clin Appl. 2009; 3:1052-61.
  97. Renard BY, Kirchner M, Steen H, Steen JA, Hamprecht FA. NITPICK: peak identification for mass spectrometry data. BMC Bioinformatics. 2008; 9:355.
  98. Koenig T, Menze BH, Kirchner M, Monigatti F, Parker KC, Patterson T, Steen JJ, Hamprecht FA, Steen H. Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics. J Proteome Res. 2008 Sep; 7(9):3708-17.
  99. Lee RS, Monigatti F, Briscoe AC, Waldon Z, Freeman MR, Steen H. Optimizing sample handling for urinary proteomics. J Proteome Res. 2008 Sep; 7(9):4022-30.
  100. Adam RM, Yang W, Di Vizio D, Mukhopadhyay NK, Steen H. Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis. BMC Cell Biol. 2008; 9:30.
  101. Steen H, Stensballe A, Jensen ON. Alkaline Phosphatase Treatment of Phosphopeptides: On-Probe Dephosphorylation after MALDI-MS Analysis. CSH Protoc. 2008; 2008:pdb.prot4612.
  102. Steen H, Stensballe A, Jensen ON. Alkaline Phosphatase Treatment of Phosphopeptides: In-Solution Dephosphorylation prior to MALDI-MS Analysis. CSH Protoc. 2008; 2008:pdb.prot4610.
  103. Steen H, Stensballe A, Jensen ON. Alkaline Phosphatase Treatment of Phosphopeptides: In-Solution Dephosphorylation after MALDI-MS Analysis. CSH Protoc. 2008; 2008:pdb.prot4611.
  104. Steen JA, Steen H, Georgi A, Parker K, Springer M, Kirchner M, Hamprecht F, Kirschner MW. Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis. Proc Natl Acad Sci U S A. 2008 Apr 22; 105(16):6069-74.
  105. Monigatti F, Steen H. SALAMI (Spectrum ALignments using high Accuracy Mass and hIgh sensitivity data): how to make the best out of hybrid MS/MS data. J Proteome Res. 2008 May; 7(5):1984-93.
  106. Lee RS, Monigatti F, Lutchman M, Patterson T, Budnik B, Steen JA, Freeman MR, Steen H. Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation. Proteomics. 2008 Mar; 8(5):1097-112.
  107. Yang W, Steen H, Freeman MR. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics. 2008 Feb; 8(4):832-51.
  108. Steen H, Stensballe A, Jensen ON. Phosphopeptide Purification by IMAC with Fe(III) and Ga(III). CSH Protoc. 2007; 2007:pdb.prot4607.
  109. Steen H, Stensballe A, Jensen ON. Preparation and Use of Microcolumns for Sample Desalting or Nanoscale IMAC. CSH Protoc. 2007; 2007:pdb.prot4608.
  110. Bensadek D, Monigatti F, Steen JAJ, Steen H. Why b, y’s? Sodiation-induced tryptic peptide-like fragmentation of non-tryptic peptides. Int J Mass Spectrom. 2007; 268:181-189.
  111. Kirchner M, Saussen B, Steen H, Steen JAJ, Hamprecht FA. amsrpm: Robust Point Matching for Retention Time Alignment of LC/MS Data with R. J Stat Software. 2007; 18:4.
  112. Monigatti F, Hekking B, Steen H. Protein sulfation analysis--A primer. Biochim Biophys Acta. 2006 Dec; 1764(12):1904-13.
  113. MacLellan DL, Steen H, Adam RM, Garlick M, Zurakowski D, Gygi SP, Freeman MR, Solomon KR. A quantitative proteomic analysis of growth factor-induced compositional changes in lipid rafts of human smooth muscle cells. Proteomics. 2005 Dec; 5(18):4733-42.
  114. Steen H, Jebanathirajah JA, Rush J, Morrice N, Kirschner MW. Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements. Mol Cell Proteomics. 2006 Jan; 5(1):172-81.
  115. Steen H, Jebanathirajah JA, Springer M, Kirschner MW. Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci U S A. 2005 Mar 15; 102(11):3948-53.
  116. Auty R, Steen H, Myers LC, Persinger J, Bartholomew B, Gygi SP, Buratowski S. Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator function. J Biol Chem. 2004 Nov 26; 279(48):49973-81.
  117. Steen H, Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol. 2004 Sep; 5(9):699-711.
  118. Argetsinger LS, Kouadio JL, Steen H, Stensballe A, Jensen ON, Carter-Su C. Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity. Mol Cell Biol. 2004 Jun; 24(11):4955-67.
  119. Gautreau A, Ho HY, Li J, Steen H, Gygi SP, Kirschner MW. Purification and architecture of the ubiquitous Wave complex. Proc Natl Acad Sci U S A. 2004 Mar 30; 101(13):4379-83.
  120. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct; 13(10):2363-71.
  121. Li J, Steen H, Gygi SP. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol Cell Proteomics. 2003 Nov; 2(11):1198-204.
  122. Jebanathirajah J, Steen H, Roepstorff P. Using optimized collision energies and high resolution, high accuracy fragment ion selection to improve glycopeptide detection by precursor ion scanning. J Am Soc Mass Spectrom. 2003 Jul; 14(7):777-84.
  123. Steen H, Fernandez M, Ghaffari S, Pandey A, Mann M. Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Mol Cell Proteomics. 2003 Mar; 2(3):138-45.
  124. Steen H, Mann M. Analysis of bromotryptophan and hydroxyproline modifications by high-resolution, high-accuracy precursor ion scanning utilizing fragment ions with mass-deficient mass tags. Anal Chem. 2002 Dec 15; 74(24):6230-6.
  125. Steen H, Pandey A, Andersen JS, Mann M. Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method. Sci STKE. 2002 Oct 15; 2002(154):pl16.
  126. Steen H, Pandey A. Proteomics goes quantitative: measuring protein abundance. Trends Biotechnol. 2002 Sep; 20(9):361-4.
  127. Steen H, Mann M. A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode. J Am Soc Mass Spectrom. 2002 Aug; 13(8):996-1003.
  128. Mann M, Ong SE, Grønborg M, Steen H, Jensen ON, Pandey A. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 2002 Jun; 20(6):261-8.
  129. Steen H, Jensen ON. Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry. Mass Spectrom Rev. 2002 May-Jun; 21(3):163-82.
  130. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002 May; 1(5):376-86.
  131. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI. Directed proteomic analysis of the human nucleolus. Curr Biol. 2002 Jan 8; 12(1):1-11.
  132. Peri S, Steen H, Pandey A. GPMAW--a software tool for analyzing proteins and peptides. Trends Biochem Sci. 2001 Nov; 26(11):687-9.
  133. Steen H, Kuster B, Fernandez M, Pandey A, Mann M. Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J Biol Chem. 2002 Jan 11; 277(2):1031-9.
  134. Steen H, Petersen J, Mann M, Jensen ON. Mass spectrometric analysis of a UV-cross-linked protein-DNA complex: tryptophans 54 and 88 of E. coli SSB cross-link to DNA. Protein Sci. 2001 Oct; 10(10):1989-2001.
  135. Steen H, Küster B, Mann M. Quadrupole time-of-flight versus triple-quadrupole mass spectrometry for the determination of phosphopeptides by precursor ion scanning. J Mass Spectrom. 2001 Jul; 36(7):782-90.
  136. Rappsilber J, Steen H, Mann M. Labile sulfogroup allows differentiation of sulfotyrosine and phosphotyrosine in peptides. J Mass Spectrom. 2001 Jul; 36(7):832-3.
  137. Petersson AS, Steen H, Kalume DE, Caidahl K, Roepstorff P. Investigation of tyrosine nitration in proteins by mass spectrometry. J Mass Spectrom. 2001 Jun; 36(6):616-25.
  138. Steen H, Küster B, Fernandez M, Pandey A, Mann M. Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode. Anal Chem. 2001 Apr 1; 73(7):1440-8.
  139. Spada F, Steen H, Troedsson C, Kallesoe T, Spriet E, Mann M, Thompson EM. Molecular patterning of the oikoplastic epithelium of the larvacean tunicate Oikopleura dioica. J Biol Chem. 2001 Jun 8; 276(23):20624-32.
  140. Steen H, Mann M. Similarity between condensed phase and gas phase chemistry: fragmentation of peptides containing oxidized cysteine residues and its implications for proteomics. J Am Soc Mass Spectrom. 2001 Feb; 12(2):228-32.
  141. Steen, H. Mass Spectrometry for the Analysis of Protein Modifications (Ph.D. Thesis). 2001.
  142. Pandey A, Fernandez MM, Steen H, Blagoev B, Nielsen MM, Roche S, Mann M, Lodish HF. Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. J Biol Chem. 2000 Dec 8; 275(49):38633-9.
  143. Dahle J, Mikalsen SO, Rivedal E, Steen HB. Gap junctional intercellular communication is not a major mediator in the bystander effect in photodynamic treatment of MDCK II cells. Radiat Res. 2000 Sep; 154(3):331-41.
  144. Dahle J, Bagdonas S, Kaalhus O, Olsen G, Steen HB, Moan J. The bystander effect in photodynamic inactivation of cells. Biochim Biophys Acta. 2000 Jul 26; 1475(3):273-80.
  145. Gobom J, Kraeuter KO, Persson R, Steen H, Roepstorff P, Ekman R. Detection and quantification of neurotensin in human brain tissue by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem. 2000 Jul 15; 72(14):3320-6.
  146. Summerfield SG, Steen H, O’Malley M, Gaskell SJ. Phenyl thiocarbamoyl and related derivatives of peptides: Edman chemistry in the gas phase. Int J Mass Spectrom. 1999; 188:95-103.
  147. Studer A, Steen H. The SHi Reaction at Silicon – A New Entry into Cyclic Alkoxy-silanes. Chem Eur J. 1999; 5:759-73.
  148. Steen, H. Intramolecular Homolytic Substitution on Silicon – Influence of the Degree of Substitution on the Rate of Cyclisation (Dipl. Chem. Thesis). 1998.
  149. Studer A, Bossart M, Steen H. Stereoselective Phenyl Migration from Silicon to Carbon. Tetrahedron Lett. 1998; 39:8829-32.
  150. Steen, H. Techniques for the Mass Spectrometric Localisation of Double Bonds (B.Sc. Thesis). 1995.
  151. Wold S, Skarstad K, Steen HB, Stokke T, Boye E. The initiation mass for DNA replication in Escherichia coli K-12 is dependent on growth rate. EMBO J. 1994 May 1; 13(9):2097-102.
  152. Kvam E, Berg K, Steen HB. Characterization of singlet oxygen-induced guanine residue damage after photochemical treatment of free nucleosides and DNA. Biochim Biophys Acta. 1994 Jan 18; 1217(1):9-15.
  153. Kvam E, Stokke T, Moan J, Steen HB. Plateau distributions of DNA fragment lengths produced by extended light exposure of extranuclear photosensitizers in human cells. Nucleic Acids Res. 1992 Dec 25; 20(24):6687-93.
  154. Stokke T, Holte H, Smeland EB, Lie SO, Steen HB. Differential chromatin structure-dependent binding of 7-aminoactinomycin D in normal and malignant bone marrow hematopoietic cells. Cancer Res. 1992 Sep 15; 52(18):5007-12.
  155. Berg K, Steen HB, Winkelman JW, Moan J. Synergistic effects of photoactivated tetra(4-sulfonatophenyl)porphine and nocodazole on microtubule assembly, accumulation of cells in mitosis and cell survival. J Photochem Photobiol B. 1992 Apr 15; 13(1):59-70.
  156. Stokke T, Erikstein B, Holte H, Funderud S, Steen HB. Cell cycle-specific expression and nuclear binding of DNA polymerase alpha. Mol Cell Biol. 1991 Jun; 11(6):3384-9.
  157. Stokke T, Steen HB. Fluorescence spectra of Hoechst 33258 bound to chromatin. Biochim Biophys Acta. 1986 Oct 16; 868(1):17-23.
  158. Skarstad K, Boye E, Steen HB. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J. 1986 Jul; 5(7):1711-7.
  159. Stokke T, Steen HB. Neither adriamycin nor actinomycin D displaces Tb3+ from DNA. Biochim Biophys Acta. 1985 Aug 21; 825(4):416-8.
  160. Steen HB. Further developments of a microscope-based flow cytometer: light scatter detection and excitation intensity compensation. Cytometry. 1980 Jul; 1(1):26-31.
  161. Steen HB. Molecular excitations in radiation damage as studies by the radiation-induced luminescence of proteins. Scand J Clin Lab Invest Suppl. 1968; 106:21-30.
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