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    USHUPO 2013 Talk

    March 13th, 2013, 11:01 am

    Accepted talk at the 2013 USHUPO conference in Baltimore, in the Tuesday morning “Systems Proteomics” session.

    Application of Generalized Protein Parsimony and Spectral Counting to Functional Enrichment Analysis and Protein Isoform Detection

    Nathan Edwards
    Georgetown University Medical Center, Washington, DC

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    ASMS Sanibel Conference on Top-down Mass-Spectrometry 2013 Talk

    March 13th, 2013, 10:54 am

    Invited talk at the 2013  ASMS Sanibel Conference on Top-Down Mass Spectrometry.

    Top-down Characterization of Proteins in Bacteria with Unsequenced Genomes

    Nathan Edwards
    Georgetown University Medical Center, Washington, DC

     

     


    NIH Proteomics Interest Group (ProtIG) 2012 Talk

    November 13th, 2012, 11:33 am

    Talk in the NIH Proteomics Interest Group seminar series on November 9th, 2012.

    Generalized Protein Parsimony and Spectral Counting for Functional Enrichment Analysis

    Nathan Edwards
    Georgetown University Medical Center, Washington, DC

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    Warren Workshop 2012 Invited Talk

    September 13th, 2012, 11:16 pm

    Invited talk at the 2012 Warren Workshop in Athens, GA. Slides are here.

    Exploring Glycoprotein Microheterogeneity via N-Glycopeptide Identification from CID Tandem Mass Spectra using Glycan Databases and False Discovery Rate Estimation

    Kevin Brown Chandler, Petr Pompach, Radoslav Goldman, and Nathan Edwards
    Georgetown University, Washington, D.C.

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    International HUPO 2012 Talk

    September 13th, 2012, 11:03 pm

    Talk at the 2012 HUPO World Congress in Boston, MA. Slides are here.

    False-Discovery-Rate Aware Protein Inference by Generalized Protein Parsimony

    Nathan Edwards
    Georgetown University Medical Center, Washington, DC

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    RECOMB Computational Proteomics 2012 Poster-Flash Presentation

    May 4th, 2012, 3:16 pm

    Poster-Flash presentation at the 2012 RECOMB-CP Satellite Workshop in San Diego, CA. Poster is here.

    Generalized Protein Parsimony

    Nathan Edwards
    Georgetown University Medical Center, Washington, DC

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    US HUPO Annual Conference 2012 Poster

    April 10th, 2012, 12:09 pm

    Poster at 2012 USHUPO Annual Conference in San Francisco, CA.

    Protein Inference by Generalized Protein Parsimony reduces False Positive Proteins in Bottom-Up Workflows

    Nathan Edwards
    Georgetown University Medical Center, Washington, DC

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    RECOMB Computational Proteomics 2012 Poster

    April 10th, 2012, 12:02 pm

    Poster at the 2012 RECOMB-CP Satellite Workshop in San Diego, CA. Poster-Flash presentation is here.

    Protein Inference by Generalized Protein Parsimony reduces False Positive Proteins in Bottom-Up Workflows

    Nathan Edwards
    Georgetown University Medical Center, Washington, DC

    Read the rest of this entry »


    USHUPO 2011 Talk

    March 22nd, 2011, 10:32 am

    I gave a talk in the Monday morning “Bioinformatics/Statistics” session at the 7th Annual Conference of US HUPO, presenting the culmination of work by David Retz for his Masters practicum project in the Biostatistics department.

    Novel empirical FDR estimation techniques in the PepArML meta-search peptide identification platform

    David Retz and Nathan Edwards

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    CPTI eProtein Newsletter Researcher Spotlight feature

    November 9th, 2010, 11:30 am

    My work, and links to my tools, have been featured in the clinical proteomics technology initiative (CPTI) eProtein newsletter, “Researcher Spotlight: Enabling the Search for Novel Cancer Protein Variants.” Check it out, and give the Peptide Sequence Database (PepSeqDB), Peptide Arbiter by Machine Learning (PepArML) Meta-Search Engine, and PeptideMapper tools a try.

    The PepSeqDB fasta sequence databases provide a comprehensive enumeration of (putative) peptide sequences from ESTs, mRNAs, and protein sequence databases for human, mouse, rat, and zebra-fish.

    The PepArML meta-search engine searches tandem mass-spectra against protein sequence databases (including PepSeqDB) using seven search engines (Mascot, Tandem, Tandem with K-Score and S-Score scoring plugins, OMSSA, Myrimatch, and InsPecT) and combines the search results using unsupervised machine-learning. This infrastructure typically identifies two-to-three times more spectra than individual search engines at 10% FDR.

    The PeptideMapper web-service provides real-time, one-click mapping of peptide sequences for human, mouse, or rat, to a genome annotation track of the UCSC genome browser, and onto their protein, mRNA, and genomic evidence. Peptides containing (coding) single nucleotide polymorphisms (SNPs) at also mapped, making it possible to evaluate cSNPs by their mass-delta, amino-acid substitution, and genomic context.