Alexey I Nesvizhskii

Alexey I Nesvizhskii

UNVERIFIED PROFILE

Are you Alexey I Nesvizhskii?   Register this Author

Register author
Alexey I Nesvizhskii

Alexey I Nesvizhskii

Publications by authors named "Alexey I Nesvizhskii"

Are you Alexey I Nesvizhskii?   Register this Author

100Publications

2603Reads

28Profile Views

Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry.

Anal Chem 2020 Mar 26;92(6):4217-4225. Epub 2020 Feb 26.

Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.9b04418DOI Listing
March 2020

Proteogenomic Characterization of Endometrial Carcinoma.

Cell 2020 Feb 13;180(4):729-748.e26. Epub 2020 Feb 13.

Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2020.01.026DOI Listing
February 2020

Mapping low-affinity/high-specificity peptide-protein interactions using ligand-footprinting mass spectrometry.

Proc Natl Acad Sci U S A 2019 10 2;116(42):21001-21011. Epub 2019 Oct 2.

Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1819533116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800362PMC
October 2019

Oxygen and Conformation Dependent Protein Oxidation and Aggregation by Porphyrins in Hepatocytes and Light-Exposed Cells.

Cell Mol Gastroenterol Hepatol 2019 4;8(4):659-682.e1. Epub 2019 Jun 4.

Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan; Cell Biology, Faculty of Science and Technology, Åbo Akademi University, Turku, Finland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jcmgh.2019.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889786PMC
June 2019

Constitutive release of CPS1 in bile and its role as a protective cytokine during acute liver injury.

Proc Natl Acad Sci U S A 2019 04 12;116(18):9125-9134. Epub 2019 Apr 12.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1822173116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500125PMC
April 2019

DeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results.

J Proteome Res 2019 02 17;18(2):715-720. Epub 2018 Dec 17.

Department of Pathology , University of Michigan , Ann Arbor , Michigan 48109 , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.8b00728DOI Listing
February 2019

The Landscape of Circular RNA in Cancer.

Cell 2019 02;176(4):869-881.e13

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2018.12.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6601354PMC
February 2019

Nuclear lamina genetic variants, including a truncated LAP2, in twins and siblings with nonalcoholic fatty liver disease.

Hepatology 2018 05 24;67(5):1710-1725. Epub 2018 Mar 24.

Department of Molecular and Integrative Physiology and Department of Internal Medicine, University of Michigan, Ann Arbor, MI.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/hep.29522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849478PMC
May 2018

IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry.

Anal Chem 2018 02 16;90(3):2369-2375. Epub 2018 Jan 16.

Department of Pathology, ‡Department of Chemistry, and §Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.7b04999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826643PMC
February 2018

ProHits-viz: a suite of web tools for visualizing interaction proteomics data.

Nat Methods 2017 06;14(7):645-646

Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.4330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831326PMC
June 2017

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.

Nat Methods 2017 May 10;14(5):513-520. Epub 2017 Apr 10.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/doifinder/10.1038/nmeth.4256
Publisher Site
http://dx.doi.org/10.1038/nmeth.4256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409104PMC
May 2017

Data Independent Acquisition analysis in ProHits 4.0.

J Proteomics 2016 10 29;149:64-68. Epub 2016 Apr 29.

Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079801PMC
http://dx.doi.org/10.1016/j.jprot.2016.04.042DOI Listing
October 2016

Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.

Proteomics 2016 08 22;16(15-16):2257-71. Epub 2016 Jul 22.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/pmic.201500526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5476226PMC
August 2016

BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.

J Proteome Res 2016 08 28;15(8):2500-9. Epub 2016 Jun 28.

Department of Pathology, ‡BRCF Metabolomics Core, and §Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.6b00021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583644PMC
August 2016

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Anal Chem 2016 06 24;88(11):5733-41. Epub 2016 May 24.

Department of Biomedical Informatics, Vanderbilt University , Nashville, Tennessee 37203, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.analchem.6b00021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996967PMC
June 2016

MLL1 Inhibition Reprograms Epiblast Stem Cells to Naive Pluripotency.

Cell Stem Cell 2016 Apr 17;18(4):481-94. Epub 2016 Mar 17.

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2016.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4826731PMC
April 2016

Two-pass alignment improves novel splice junction quantification.

Bioinformatics 2016 Jan 30;32(1):43-9. Epub 2015 Oct 30.

Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, Department of Pathology.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006238PMC
January 2016

Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics.

J Proteome Res 2015 Dec 24;14(12):5169-78. Epub 2015 Nov 24.

Department of Computational Medicine and Bioinformatics and ‡Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.5b00504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748730PMC
December 2015

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

J Proteomics 2015 Nov 4;129:121-126. Epub 2015 Aug 4.

Departments of Pathology and Computational Medicine and Bioinformatics, University of Michigan Medical School.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jprot.2015.07.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4630079PMC
November 2015

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

J Proteomics 2015 Nov 15;129:108-120. Epub 2015 Sep 15.

Saw Swee Hock School of Public Health, National University of Singapore, Singapore. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jprot.2015.09.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4630088PMC
November 2015

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

J Proteome Res 2015 Sep 30;14(9):3452-60. Epub 2015 Jul 30.

Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.5b00499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755311PMC
September 2015

Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks.

Mol Endocrinol 2015 Aug 16;29(8):1195-218. Epub 2015 Jul 16.

Department of Molecular Physiology and Biophysics (J.J.H., B.H.N., M.M.S., H.D.M., M.E.W.), Carver College of Medicine, The University of Iowa, Iowa City, Iowa 52242; Department of Pharmacology (H.D.M., R.J.J., I.V.H., M.E.W.), School of Medicine and Genome Center, University of California, Davis, California 95616; Departments of Pathology and Computational Medicine and Bioinformatics (D.F., A.I.N.), University of Michigan, Ann Arbor, Michigan 48109; and Department of Genome Sciences (J.K.E.), University of Washington, Seattle, Washington 98195.

View Article

Download full-text PDF

Source
https://academic.oup.com/mend/article-lookup/doi/10.1210/me.
Publisher Site
http://dx.doi.org/10.1210/me.2015-1021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517998PMC
August 2015

The landscape of antisense gene expression in human cancers.

Genome Res 2015 Jul 10;25(7):1068-79. Epub 2015 Jun 10.

Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA; Department of Urology, University of Michigan, Ann Arbor, Michigan 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.180596.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484389PMC
July 2015

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

Bioinformatics 2015 Apr 25;31(7):1141-3. Epub 2014 Nov 25.

Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382907PMC
April 2015

Targeting the MLL complex in castration-resistant prostate cancer.

Nat Med 2015 Apr 30;21(4):344-52. Epub 2015 Mar 30.

1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA. [3] Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA. [4] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA. [5] Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA. [6] Department of Urology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://www.pcf.org/atf/cf/%7B7c77d6a2-5859-4d60-af47-132fd0f
Web Search
http://www.nature.com/doifinder/10.1038/nm.3830
Publisher Site
http://dx.doi.org/10.1038/nm.3830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390530PMC
April 2015

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

Nat Methods 2015 Mar 19;12(3):258-64, 7 p following 264. Epub 2015 Jan 19.

1] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399776PMC
March 2015

Proteogenomics: concepts, applications and computational strategies.

Nat Methods 2014 Nov;11(11):1114-25

1] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392723PMC
November 2014

Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS.

J Proteome Res 2014 Sep 28;13(9):4113-9. Epub 2014 Jul 28.

Department of Computational Medicine and Bioinformatics and ‡Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr500496pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156250PMC
September 2014

Reconstructing targetable pathways in lung cancer by integrating diverse omics data.

Nat Commun 2013 ;4:2617

1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 8109, USA [2] Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA [3] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms3617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107456PMC
May 2014

Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas.

Am J Pathol 2014 May 22;184(5):1331-42. Epub 2014 Mar 22.

Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan; Center for Protein Folding Disease, University of Michigan Medical School, Ann Arbor, Michigan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajpath.2014.01.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005972PMC
May 2014

SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software.

J Proteomics 2014 Apr 26;100:37-43. Epub 2013 Oct 26.

Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S18743919130053
Publisher Site
http://dx.doi.org/10.1016/j.jprot.2013.10.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102138PMC
April 2014

The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response.

PLoS Genet 2014 Mar 6;10(3):e1004183. Epub 2014 Mar 6.

Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1004183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945295PMC
March 2014

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics.

J Proteome Res 2013 Dec 14;12(12):5666-80. Epub 2013 Nov 14.

Department of Pathology, University of Michigan , 4237 Medical Science I, 1301 Catherine Road, Ann Arbor, Michigan 48109, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr400611hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076643PMC
December 2013

LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.

Mol Cell Proteomics 2013 Nov 5;12(11):3409-19. Epub 2013 Aug 5.

Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.M113.028928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820951PMC
November 2013

Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer.

Mol Cell Proteomics 2013 Oct 8;12(10):2714-23. Epub 2013 Jul 8.

Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.M113.029926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790285PMC
October 2013

Combining results of multiple search engines in proteomics.

Mol Cell Proteomics 2013 Sep 29;12(9):2383-93. Epub 2013 May 29.

Institute for Systems Biology, Seattle, Washington 98109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.R113.027797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769318PMC
September 2013

The functional interactome landscape of the human histone deacetylase family.

Mol Syst Biol 2013 ;9:672

Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/msb.2013.26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964310PMC
September 2013

A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet.

BMC Bioinformatics 2012 5;13 Suppl 16:S1. Epub 2012 Nov 5.

Department of Statistics, Purdue University, 250 N. University Street, West Lafayette, Indiana, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-13-S16-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489532PMC
May 2013

Sparsely correlated hidden Markov models with application to genome-wide location studies.

Bioinformatics 2013 Mar 16;29(5):533-41. Epub 2013 Jan 16.

National University of Singapore and National University Health System, Singapore 117597, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582268PMC
March 2013

Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.

Curr Protoc Bioinformatics 2012 Sep;Chapter 8:Unit8.15

Saw Swee Hock School of Public Health, National University of Singapore, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi0815s39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446209PMC
September 2012

Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data.

Curr Protoc Bioinformatics 2012 Sep;Chapter 8:Unit8.16

Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi0816s39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669397PMC
September 2012

Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.

J Proteome Res 2012 Apr 29;11(4):2261-71. Epub 2012 Feb 29.

Department of Pathology and §Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/pr201052x
Publisher Site
http://dx.doi.org/10.1021/pr201052xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744887PMC
April 2012

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments.

J Proteome Res 2012 Apr 2;11(4):2619-24. Epub 2012 Mar 2.

Saw Swee Hock School of Public Health, National University of Singapore, Singapore.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/pr201185r
Publisher Site
http://dx.doi.org/10.1021/pr201185rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744231PMC
April 2012

Proteomic study of the mucin granulae in an intestinal goblet cell model.

J Proteome Res 2012 Mar 2;11(3):1879-90. Epub 2012 Feb 2.

Department of Medical Biochemistry and Cell Biology, University of Gothenburg , Box 440, 40530 Gothenburg, Sweden.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr2010988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3292267PMC
March 2012

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

J Proteome Res 2011 Jul 29;10(7):2949-58. Epub 2011 Apr 29.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/pr2002116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3128686PMC
July 2011

Global analysis of protein palmitoylation in African trypanosomes.

Eukaryot Cell 2011 Mar 30;10(3):455-63. Epub 2010 Dec 30.

Dept. of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/EC.00248-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067466PMC
March 2011

The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment.

BMC Bioinformatics 2010 Dec 14;11 Suppl 11:S14. Epub 2010 Dec 14.

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-11-S11-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024872PMC
December 2010

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.

J Proteomics 2010 Oct 8;73(11):2092-123. Epub 2010 Sep 8.

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jprot.2010.08.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956504PMC
October 2010

Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets.

Proteomics 2010 Jul;10(14):2712-8

Department of Pathology, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/pmic.200900473
Publisher Site
http://dx.doi.org/10.1002/pmic.200900473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517130PMC
July 2010

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.

Bioinformatics 2009 Jul 14;25(14):1715-21. Epub 2009 May 14.

Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp312DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732365PMC
July 2009

Significance analysis of spectral count data in label-free shotgun proteomics.

Mol Cell Proteomics 2008 Dec 20;7(12):2373-85. Epub 2008 Jul 20.

Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.M800203-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596341PMC
December 2008

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

J Proteome Res 2008 Nov 13;7(11):4878-89. Epub 2008 Sep 13.

Department of Pathology, Department of Biostatistics, and Center for Computational Biology and Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/abs/10.1021/pr800484x
Publisher Site
http://dx.doi.org/10.1021/pr800484xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744223PMC
November 2008

Improved sequence tag generation method for peptide identification in tandem mass spectrometry.

J Proteome Res 2008 Oct 12;7(10):4422-34. Epub 2008 Sep 12.

Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/abs/10.1021/pr800400q
Publisher Site
http://dx.doi.org/10.1021/pr800400qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744226PMC
October 2008