Hanno Steen

Publications

1. Dementia with lewy bodies patients with high tau levels display unique proteome profiles. Mol Neurodegener. 2024 Dec 19; 19(1):98. View Abstract
2. Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19. bioRxiv. 2024 Nov 16. View Abstract
3. Predictive gene expression signature diagnoses neonatal sepsis before clinical presentation. EBioMedicine. 2024 Dec; 110:105411. View Abstract
4. The BNT162b2 mRNA vaccine demonstrates reduced age-associated TH1 support in vitro and in vivo. iScience. 2024 Nov 15; 27(11):111055. View Abstract
5. Plasma adenosine deaminase-1 and -2 activities are lower at birth in Papua New Guinea than in The Gambia but converge over the first weeks of life. Front Immunol. 2024; 15:1425349. View Abstract
6. PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks. Bioinformatics. 2024 09 01; 40(Suppl 2):ii70-ii78. View Abstract
7. Longitudinal plasma proteomic analysis of 1117 hospitalized patients with COVID-19 identifies features associated with severity and outcomes. Sci Adv. 2024 May 24; 10(21):eadl5762. View Abstract
8. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. J Clin Invest. 2024 May 01; 134(9). View Abstract
9. Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Sci Transl Med. 2024 Apr 17; 16(743):eadj5154. View Abstract
10. Diagnostic and Prognostic Biomarkers of Chronic Pancreatitis: A Conceptual Framework Based on the PRoBE Design. Gastroenterology. 2024 06; 166(6):957-962.e3. View Abstract
11. Quantitative profiling of posttranslational modifications of pathological tau via sarkosyl fractionation and mass spectrometry. Nat Protoc. 2024 Apr; 19(4):1235-1251. View Abstract
12. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol. 2024 Apr; 153(4):954-968. View Abstract
13. Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nat Commun. 2024 Jan 03; 15(1):216. View Abstract
14. Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants. bioRxiv. 2023 Nov 06. View Abstract
15. Early cellular and molecular signatures correlate with severity of West Nile virus infection. iScience. 2023 Dec 15; 26(12):108387. View Abstract
16. Proteomics-Based Mapping of Bronchopulmonary Dysplasia-Associated Changes in Noninvasively Accessible Oral Secretions. J Pediatr. 2024 Jul; 270:113774. View Abstract
17. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Rep Med. 2023 06 20; 4(6):101079. View Abstract
18. Plasma proteome perturbation for CMV DNAemia in kidney transplantation. PLoS One. 2023; 18(5):e0285870. View Abstract
19. Integrative systems biology characterizes immune-mediated neurodevelopmental changes in murine Zika virus microcephaly. iScience. 2023 Jul 21; 26(7):106909. View Abstract
20. Meta-analysis of published cerebrospinal fluid proteomics data identifies and validates metabolic enzyme panel as Alzheimer's disease biomarkers. Cell Rep Med. 2023 04 18; 4(4):101005. View Abstract
21. A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics. Sci Adv. 2023 03 29; 9(13):eadf9717. View Abstract
22. Choroid plexus-targeted NKCC1 overexpression to treat post-hemorrhagic hydrocephalus. Neuron. 2023 05 17; 111(10):1591-1608.e4. View Abstract
23. Common mouse models of tauopathy reflect early but not late human disease. Mol Neurodegener. 2023 02 02; 18(1):10. View Abstract
24. The mRNA vaccine BNT162b2 demonstrates impaired TH1 immunogenicity in human elders in vitro and aged mice in vivo. Res Sq. 2022 Dec 21. View Abstract
25. Using CSF Proteomics to Investigate Herpesvirus Infections of the Central Nervous System. Viruses. 2022 12 10; 14(12). View Abstract
26. Longitudinal serum proteomics analyses identify unique and overlapping host response pathways in Lyme disease and West Nile virus infection. Front Immunol. 2022; 13:1012824. View Abstract
27. A Parallelization Strategy for the Time Efficient Analysis of Thousands of LC/MS Runs in High-Performance Computing Environment. J Proteome Res. 2022 11 04; 21(11):2810-2814. View Abstract
28. CAF08 adjuvant enables single dose protection against respiratory syncytial virus infection in murine newborns. Nat Commun. 2022 08 02; 13(1):4234. View Abstract
29. Using plasma proteomics to investigate viral infections of the central nervous system including patients with HIV-associated neurocognitive disorders. J Neurovirol. 2022 06; 28(3):341-354. View Abstract
30. Bacille Calmette-Guérin vaccine reprograms human neonatal lipid metabolism in vivo and in vitro. Cell Rep. 2022 05 03; 39(5):110772. View Abstract
31. Urine Proteomics Reveals Sex-Specific Response to Total Pancreatectomy With Islet Autotransplantation. Pancreas. 2022 05 01; 51(5):435-444. View Abstract
32. Plasma Proteomic Analysis Distinguishes Severity Outcomes of Human Ebola Virus Disease. mBio. 2022 06 28; 13(3):e0056722. View Abstract
33. Determinants of B-Cell Compartment Hyperactivation in European Adolescents Living With Perinatally Acquired HIV-1 After Over 10 Years of Suppressive Therapy. Front Immunol. 2022; 13:860418. View Abstract
34. multiFLEX-LF: A Computational Approach to Quantify the Modification Stoichiometries in Label-Free Proteomics Data Sets. J Proteome Res. 2022 04 01; 21(4):899-909. View Abstract
35. Urine Proteomics for Noninvasive Monitoring of Biomarkers in Bronchopulmonary Dysplasia. Neonatology. 2022; 119(2):193-203. View Abstract
36. Proteomics based markers of clinical pain severity in juvenile idiopathic arthritis. Pediatr Rheumatol Online J. 2022 Jan 15; 20(1):3. View Abstract
37. Using 'Big Data' to Disentangle Aging and COVID-19. Nat Aging. 2021 06; 1(6):496-497. View Abstract
38. Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. NPJ Syst Biol Appl. 2021 01 29; 7(1):8. View Abstract
39. Biomarkers of Chronic Pancreatitis: A systematic literature review. Pancreatology. 2021 Mar; 21(2):323-333. View Abstract
40. Sample Preparation for High-Throughput Urine Proteomics Using 96-Well Polyvinylidene Fluoride (PVDF) Membranes. Adv Exp Med Biol. 2021; 1306:1-12. View Abstract
41. Delayed Processing of Secretin-Induced Pancreas Fluid Influences the Quality and Integrity of Proteins and Nucleic Acids. Pancreas. 2021 01 01; 50(1):17-28. View Abstract
42. FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data. Elife. 2020 12 07; 9. View Abstract
43. Corrigendum: Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front Pediatr. 2020; 8:610461. View Abstract
44. Tau PTM Profiles Identify Patient Heterogeneity and Stages of Alzheimer's Disease. Cell. 2020 12 10; 183(6):1699-1713.e13. View Abstract
45. Author Correction: PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet. 2020 Nov; 52(11):1265. View Abstract
46. Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life. Front Immunol. 2020; 11:578505. View Abstract
47. Antioxidant functions of DHHC3 suppress anti-cancer drug activities. Cell Mol Life Sci. 2021 Mar; 78(5):2341-2353. View Abstract
48. Phosphorylation of ACTN4 Leads to Podocyte Vulnerability and Proteinuric Glomerulosclerosis. J Am Soc Nephrol. 2020 07; 31(7):1479-1495. View Abstract
49. Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea. Front Pediatr. 2020; 8:197. View Abstract
50. Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility. PLoS Pathog. 2020 04; 16(4):e1008452. View Abstract
51. Influence of Plasmodium falciparum Calcium-Dependent Protein Kinase 5 (PfCDPK5) on the Late Schizont Stage Phosphoproteome. mSphere. 2020 01 08; 5(1). View Abstract
52. Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop. Pancreas. 2019 Nov/Dec; 48(10):1250-1258. View Abstract
53. Prohibitin is a prognostic marker and therapeutic target to block chemotherapy resistance in Wilms' tumor. JCI Insight. 2019 08 08; 4(15). View Abstract
54. Dynamic molecular changes during the first week of human life follow a robust developmental trajectory. Nat Commun. 2019 03 12; 10(1):1092. View Abstract
55. Degradation of the extracellular matrix is part of the pathology of ulcerative colitis. Mol Omics. 2019 02 11; 15(1):67-76. View Abstract
56. Standard Operating Procedures for Biospecimen Collection, Processing, and Storage: From the Consortium for the Study of Chronic Pancreatitis, Diabetes, and Pancreatic Cancer. Pancreas. 2018 Nov/Dec; 47(10):1213-1221. View Abstract
57. A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation. J Proteome Res. 2018 05 04; 17(5):1983-1992. View Abstract
58. Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. mBio. 2018 03 06; 9(2). View Abstract
59. Fetal regional brain protein signature in FASD rat model. Reprod Toxicol. 2018 03; 76:84-92. View Abstract
60. Erratum: PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet. 2017 09 27; 49(10):1558. View Abstract
61. Placental Proteomics Reveal Insights into Fetal Alcohol Spectrum Disorders. Alcohol Clin Exp Res. 2017 Sep; 41(9):1551-1558. View Abstract
62. PIQED: automated identification and quantification of protein modifications from DIA-MS data. Nat Methods. 2017 06 29; 14(7):646-647. View Abstract
63. PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet. 2017 Jul; 49(7):1005-1014. View Abstract
64. High-Throughput Parallel Proteomic Sample Preparation Using 96-Well Polyvinylidene Fluoride (PVDF) Membranes and C18 Purification Plates. Methods Mol Biol. 2017; 1619:395-402. View Abstract
65. Endoscopic Pancreas Fluid Collection: Methods and Relevance for Clinical Care and Translational Science. Am J Gastroenterol. 2016 09; 111(9):1258-66. View Abstract
66. Urinary Proteomics Yield Pathological Insights for Ureteropelvic Junction Obstruction. Mol Cell Proteomics. 2016 08; 15(8):2607-15. View Abstract
67. Proteomics in India: A Report on a Brainstorming Meeting at Hyderabad, India. Mol Cell Proteomics. 2016 07; 15(7):2229-35. View Abstract
68. f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome. Nucleic Acids Res. 2016 06 02; 44(10):e97. View Abstract
69. FLEXITau: Quantifying Post-translational Modifications of Tau Protein in Vitro and in Human Disease. Anal Chem. 2016 Apr 05; 88(7):3704-14. View Abstract
70. Adjuvant-induced Human Monocyte Secretome Profiles Reveal Adjuvant- and Age-specific Protein Signatures. Mol Cell Proteomics. 2016 06; 15(6):1877-94. View Abstract
71. 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. View Abstract
72. Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer. J Proteome Res. 2015 Nov 06; 14(11):4752-62. View Abstract
73. Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome. Data Brief. 2015 Dec; 5:241-7. View Abstract
74. 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. View Abstract
75. A High-Efficiency Cellular Extraction System for Biological Proteomics. J Proteome Res. 2015 Aug 07; 14(8):3403-8. View Abstract
76. Zinc regulates a switch between primary and alternative S18 ribosomal proteins in Mycobacterium tuberculosis. Mol Microbiol. 2015 Jul; 97(2):263-80. View Abstract
77. Spatially heterogeneous choroid plexus transcriptomes encode positional identity and contribute to regional CSF production. J Neurosci. 2015 Mar 25; 35(12):4903-16. View Abstract
78. A specific LSD1/KDM1A isoform regulates neuronal differentiation through H3K9 demethylation. Mol Cell. 2015 Mar 19; 57(6):957-970. View Abstract
79. Pancreatic juice prostaglandin e2 concentrations are elevated in chronic pancreatitis and improve detection of early disease. Clin Transl Gastroenterol. 2015 Jan 29; 6:e72. View Abstract
80. Optimization of cell lysis and protein digestion protocols for protein analysis by LC-MS/MS. Methods Mol Biol. 2015; 1295:259-73. View Abstract
81. Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA). Mol Cell Proteomics. 2015 Feb; 14(2):430-40. View Abstract
82. Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun. 2014 Nov 18; 5:5429. View Abstract
83. An a2-Na/K ATPase/a-adducin complex in astrocytes triggers non-cell autonomous neurodegeneration. Nat Neurosci. 2014 Dec; 17(12):1710-9. View Abstract
84. A normative study of the synovial fluid proteome from healthy porcine knee joints. J Proteome Res. 2014 Oct 03; 13(10):4377-87. View Abstract
85. Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J. 2014 Feb 18; 33(4):385-99. View Abstract
86. Phenothiazines induce PP2A-mediated apoptosis in T cell acute lymphoblastic leukemia. J Clin Invest. 2014 Feb; 124(2):644-55. View Abstract
87. The histone demethylase LSD1/KDM1A promotes the DNA damage response. J Cell Biol. 2013 Nov 11; 203(3):457-70. View Abstract
88. Nonparametric Bayesian evaluation of differential protein quantification. J Proteome Res. 2013 Oct 04; 12(10):4556-65. View Abstract
89. 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. View Abstract
90. iFASP: combining isobaric mass tagging with filter-aided sample preparation. J Proteome Res. 2013 Aug 02; 12(8):3809-12. View Abstract
91. A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer. JOP. 2013 Jul 10; 14(4):405-14. View Abstract
92. An in-depth comparison of the male pediatric and adult urinary proteomes. Biochim Biophys Acta. 2014 May; 1844(5):1044-50. View Abstract
93. Cross-species analysis of nicotine-induced proteomic alterations in pancreatic cells. Proteomics. 2013 May; 13(9):1499-1512. View Abstract
94. Mass spectrometry-based quantitative proteomic profiling of human pancreatic and hepatic stellate cell lines. Genomics Proteomics Bioinformatics. 2013 Apr; 11(2):105-13. View Abstract
95. Post-translational modifications of pancreatic fluid proteins collected via the endoscopic pancreatic function test (ePFT). J Proteomics. 2013 Oct 30; 92:216-27. View Abstract
96. Analysis of endoscopic pancreatic function test (ePFT)-collected pancreatic fluid proteins precipitated via ultracentrifugation. JOP. 2013 Mar 10; 14(2):176-86. View Abstract
97. Carbamylation of serum albumin as a risk factor for mortality in patients with kidney failure. Sci Transl Med. 2013 Mar 06; 5(175):175ra29. View Abstract
98. Cytosolic 5'-nucleotidase 1A autoimmunity in sporadic inclusion body myositis. Ann Neurol. 2013 Mar; 73(3):408-18. View Abstract
99. Gas2l3, a novel constriction site-associated protein whose regulation is mediated by the APC/C Cdh1 complex. PLoS One. 2013; 8(2):e57532. View Abstract
100. SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra. Mol Cell Proteomics. 2013 Jun; 12(6):1735-40. View Abstract
101. Subcellular fractionation enhances proteome coverage of pancreatic duct cells. Biochim Biophys Acta. 2013 Apr; 1834(4):791-7. View Abstract
102. A non-parametric cutout index for robust evaluation of identified proteins. Mol Cell Proteomics. 2013 Mar; 12(3):807-12. View Abstract
103. Short Gel, Long Gradient Liquid Chromatography Tandem Mass Spectrometry to Discover Urinary Biomarkers of Chronic Pancreatitis. Open Proteomics J. 2013; 6:1-13. View Abstract
104. Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease. EMBO Mol Med. 2013 Feb; 5(2):210-20. View Abstract
105. 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. View Abstract
106. A Src family kinase-Shp2 axis controls RUNX1 activity in megakaryocyte and T-lymphocyte differentiation. Genes Dev. 2012 Jul 15; 26(14):1587-601. View Abstract
107. 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. View Abstract
108. Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivation. Cell. 2012 Jun 22; 149(7):1565-77. View Abstract
109. Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal Fluids. Clin Transl Gastroenterol. 2012 May 03; 3:e14. View Abstract
110. FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanisms. Nat Methods. 2012 Apr 08; 9(5):504-8. View Abstract
111. 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. View Abstract
112. Mass spectrometry-based proteomics for translational research: a technical overview. Yale J Biol Med. 2012 Mar; 85(1):59-73. View Abstract
113. Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. Pancreas. 2012 Mar; 41(2):175-85. View Abstract
114. Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis. J Proteome Res. 2012 Mar 02; 11(3):1897-912. View Abstract
115. 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. View Abstract
116. Etiology of limb girdle muscular dystrophy 1D/1E determined by laser capture microdissection proteomics. Ann Neurol. 2012 Jan; 71(1):141-5. View Abstract
117. A practical guide to the FLEXIQuant method. Methods Mol Biol. 2012; 893:295-319. View Abstract
118. 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. View Abstract
119. 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 01; 83(21):8357-62. View Abstract
120. 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. View Abstract
121. 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. View Abstract
122. mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics. 2012 Jan; 11(1):O111.011379. View Abstract
123. 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. View Abstract
124. A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease. Blood. 2011 Nov 17; 118(20):5401-8. View Abstract
125. 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 07; 10(10):4835-44. View Abstract
126. 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. View Abstract
127. Proteome of human perilymph. J Proteome Res. 2011 Sep 02; 10(9):3845-51. View Abstract
128. Proteomic analysis of palmitoylated platelet proteins. Blood. 2011 Sep 29; 118(13):e62-73. View Abstract
129. Difference gel electrophoresis identifies differentially expressed proteins in endoscopically collected pancreatic fluid. Electrophoresis. 2011 Aug; 32(15):1939-51. View Abstract
130. 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. View Abstract
131. Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions. Mol Syst Biol. 2011 Apr 12; 7:482. View Abstract
132. 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. View Abstract
133. Mass spectrometry-based proteomics of endoscopically collected pancreatic fluid in chronic pancreatitis research. Proteomics Clin Appl. 2011 Apr; 5(3-4):109-20. View Abstract
134. libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data. Bioinformatics. 2011 Apr 15; 27(8):1166-7. View Abstract
135. One-step sample concentration, purification, and albumin depletion method for urinary proteomics. J Proteome Res. 2010 Nov 05; 9(11):6082-9. View Abstract
136. Iron overload in patients with acute leukemia or MDS undergoing myeloablative stem cell transplantation. Biol Blood Marrow Transplant. 2011 Jun; 17(6):852-60. View Abstract
137. 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. View Abstract
138. 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. View Abstract
139. Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysis. Electrophoresis. 2010 Jul; 31(14):2377-87. View Abstract
140. Quantitative proteomics analysis reveals molecular networks regulated by epidermal growth factor receptor level in head and neck cancer. J Proteome Res. 2010 Jun 04; 9(6):3073-82. View Abstract
141. Estimating the confidence of peptide identifications without decoy databases. Anal Chem. 2010 Jun 01; 82(11):4314-8. View Abstract
142. Effect of high-accuracy precursor masses on phosphopeptide identification from MS3 spectra. Anal Chem. 2010 May 15; 82(10):3977-80. View Abstract
143. MGFp: an open Mascot Generic Format parser library implementation. J Proteome Res. 2010 May 07; 9(5):2762-3. View Abstract
144. Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. Bioinformatics. 2010 Jun 15; 26(12):1535-41. View Abstract
145. Phosphoproteomics. Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun; 2(3):255-276. View Abstract
146. 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. View Abstract
147. 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. View Abstract
148. 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. View Abstract
149. When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification. Proteomics. 2009 Nov; 9(21):4978-84. View Abstract
150. Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinformatics. 2010 Jan 01; 26(1):77-83. View Abstract
151. 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. View Abstract
152. Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition. Mol Cell Proteomics. 2010 Feb; 9(2):336-50. View Abstract
153. Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clin Appl. 2009 Sep 01; 3(9):1052-1061. View Abstract
154. Molecular and functional characterisation of the heat shock protein 10 of Strongyloides ratti. Mol Biochem Parasitol. 2009 Dec; 168(2):149-57. View Abstract
155. Proteomics and opportunities for clinical translation in urological disease. J Urol. 2009 Sep; 182(3):835-43. View Abstract
156. 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. View Abstract
157. Differentiation-dependent interactions between RUNX-1 and FLI-1 during megakaryocyte development. Mol Cell Biol. 2009 Aug; 29(15):4103-15. View Abstract
158. 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. View Abstract
159. The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in Xenopus. Development. 2009 May; 136(9):1539-48. View Abstract
160. A simple and effective method for detecting phosphopeptides for phosphoproteomic analysis. J Proteomics. 2009 Jul 21; 72(5):831-5. View Abstract
161. Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clin Appl. 2009; 3:1052-61. View Abstract
162. NITPICK: peak identification for mass spectrometry data. BMC Bioinformatics. 2008 Aug 28; 9:355. View Abstract
163. Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics. J Proteome Res. 2008 Sep; 7(9):3708-17. View Abstract
164. Optimizing sample handling for urinary proteomics. J Proteome Res. 2008 Sep; 7(9):4022-30. View Abstract
165. Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis. BMC Cell Biol. 2008 Jun 05; 9:30. View Abstract
166. Alkaline Phosphatase Treatment of Phosphopeptides: In-Solution Dephosphorylation prior to MALDI-MS Analysis. CSH Protoc. 2008 May 01; 2008:pdb.prot4610. View Abstract
167. Alkaline Phosphatase Treatment of Phosphopeptides: In-Solution Dephosphorylation after MALDI-MS Analysis. CSH Protoc. 2008 May 01; 2008:pdb.prot4611. View Abstract
168. Alkaline Phosphatase Treatment of Phosphopeptides: On-Probe Dephosphorylation after MALDI-MS Analysis. CSH Protoc. 2008 May 01; 2008:pdb.prot4612. View Abstract
169. 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. View Abstract
170. 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. View Abstract
171. Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation. Proteomics. 2008 Mar; 8(5):1097-112. View Abstract
172. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics. 2008 Feb; 8(4):832-51. View Abstract
173. Phosphopeptide Purification by IMAC with Fe(III) and Ga(III). CSH Protoc. 2007 Nov 01; 2007:pdb.prot4607. View Abstract
174. Preparation and Use of Microcolumns for Sample Desalting or Nanoscale IMAC. CSH Protoc. 2007 Nov 01; 2007:pdb.prot4608. View Abstract
175. amsrpm: Robust Point Matching for Retention Time Alignment of LC/MS Data with R. J Stat Software. 2007; 18:4. View Abstract
176. Why b, y’s? Sodiation-induced tryptic peptide-like fragmentation of non-tryptic peptides. Int J Mass Spectrom. 2007; 268:181-189. View Abstract
177. Protein sulfation analysis--A primer. Biochim Biophys Acta. 2006 Dec; 1764(12):1904-13. View Abstract
178. 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. View Abstract
179. Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements. Mol Cell Proteomics. 2006 Jan; 5(1):172-81. View Abstract
180. 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. View Abstract
181. Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator function. J Biol Chem. 2004 Nov 26; 279(48):49973-81. View Abstract
182. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol. 2004 Sep; 5(9):699-711. View Abstract
183. Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity. Mol Cell Biol. 2004 Jun; 24(11):4955-67. View Abstract
184. Purification and architecture of the ubiquitous Wave complex. Proc Natl Acad Sci U S A. 2004 Mar 30; 101(13):4379-83. View Abstract
185. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct; 13(10):2363-71. View Abstract
186. Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol Cell Proteomics. 2003 Nov; 2(11):1198-204. View Abstract
187. 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. View Abstract
188. Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanning. Mol Cell Proteomics. 2003 Mar; 2(3):138-45. View Abstract
189. 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. View Abstract
190. Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method. Sci STKE. 2002 Oct 15; 2002(154):pl16. View Abstract
191. Proteomics goes quantitative: measuring protein abundance. Trends Biotechnol. 2002 Sep; 20(9):361-4. View Abstract
192. 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. View Abstract
193. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 2002 Jun; 20(6):261-8. View Abstract
194. 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. View Abstract
195. Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry. Mass Spectrom Rev. 2002 May-Jun; 21(3):163-82. View Abstract
196. Multi-Protein Complexes Studied by Mass Spectrometry. ScientificWorldJournal. 2002; 2:91-92. View Abstract
197. Directed proteomic analysis of the human nucleolus. Curr Biol. 2002 Jan 08; 12(1):1-11. View Abstract
198. Loss of chromosome 11q21-23.1 and 17p and gain of chromosome 6p are independent prognostic indicators in B-cell non-Hodgkin's lymphoma. Br J Cancer. 2001 Dec 14; 85(12):1900-13. View Abstract
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200. Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J Biol Chem. 2002 Jan 11; 277(2):1031-9. View Abstract
201. 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. View Abstract
202. 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. View Abstract
203. Labile sulfogroup allows differentiation of sulfotyrosine and phosphotyrosine in peptides. J Mass Spectrom. 2001 Jul; 36(7):832-3. View Abstract
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206. Molecular patterning of the oikoplastic epithelium of the larvacean tunicate Oikopleura dioica. J Biol Chem. 2001 Jun 08; 276(23):20624-32. View Abstract
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209. 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 08; 275(49):38633-9. View Abstract
210. 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. View Abstract
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212. Oncogenic aberrations in the p53 pathway are associated with a high S phase fraction and poor patient survival in B-cell Non-Hodgkin's lymphoma. Int J Cancer. 2000 Jul 20; 89(4):313-24. View Abstract
213. 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. View Abstract
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