Eric W. Deutsch

发表

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Juan Antonio Vizcaíno, Fawaz Ghali, Gerben Menschaert, 2017 .

Data standards for Omics data: the basis of data sharing and reuse.

Chris F. Taylor, John Quackenbush, Eric W. Deutsch, 2011, Methods in molecular biology.

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

Stephen E. Stein, Eric W. Deutsch, Ruedi Aebersold, 2009, BMC Bioinformatics.

Big biomedical data as the key resource for discovery science

Arthur W. Toga, Ian T. Foster, Carl Kesselman, 2015, J. Am. Medical Informatics Assoc..

Author response: An open-source computational and data resource to analyze digital maps of immunopeptidomes

Sangtae Kim, Eric W. Deutsch, Miguel Marcilla, 2015 .

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

Robert E. Kearney, Eric W. Deutsch, Tommy Nilsson, 2009, Nature Methods.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics*

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2017, Molecular & Cellular Proteomics.

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

Chris F. Taylor, Norman W. Paton, Douglas B. Kell, 2003, Nature Biotechnology.

Annual Spring Meeting of the Proteomics Standards Initiative 23–25 April 2008, Toledo, Spain

Henning Hermjakob, Andrew R. Jones, Eric W. Deutsch, 2008, Proteomics.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

Jingchun Chen, Eric W. Deutsch, Ruedi Aebersold, 2011, BMC Bioinformatics.

Development of data representation standards by the human proteome organization proteomics standards initiative

Martin Eisenacher, Juan Antonio Vizcaíno, Juan P. Albar, 2015, J. Am. Medical Informatics Assoc..

Standards for Functional Genomics

Chris F. Taylor, Eric W. Deutsch, Helen Parkinson, 2009 .

Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto, Canada

Martin Eisenacher, Henning Hermjakob, Eric W. Deutsch, 2010, Proteomics.

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology

Eric W. Deutsch, Michael H. Johnson, Bruz Marzolf, 2006, BMC Bioinformatics.

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

Martin Eisenacher, Johannes Griss, Juan Antonio Vizcaíno, 2012, Molecular & Cellular Proteomics.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

Martin Eisenacher, Juan Antonio Vizcaíno, Henning Hermjakob, 2013, Database J. Biol. Databases Curation.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

Eric W. Deutsch, Nuno Bandeira, Lydie Lane, 2019, bioRxiv.

The SysteMHC Atlas project

Roman A. Zubarev, Emanuel Schmid, Witold Wolski, 2017, Nucleic Acids Res..

44 Assessing the impact of key preprocessing concepts on the pseudo CT generation

Eric W. Deutsch, N. Paragios, Lucas Fidon, 2019 .

CHAPTER 13:Trans-Proteomic Pipeline for the Identification, Validation, and Quantification of Proteins

Eric W. Deutsch, Luis Mendoza, Robert L. Moritz, 2020 .

A repository of assays to quantify 10,000 human proteins by SWATH-MS

Eric W. Deutsch, Ruedi Aebersold, Yansheng Liu, 2014, Scientific Data.

I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets

Arthur W. Toga, Carole A. Goble, Ian T. Foster, 2016, 2016 IEEE International Conference on Big Data (Big Data).

The HUPO-PSI standardized spectral library format

Wout Bittremieux, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2020 .

Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Wout Bittremieux, Yasset Perez-Riverol, Eric W. Deutsch, 2020, EuPA Open Proteomics.

File Formats Commonly Used in Mass Spectrometry Proteomics*

Eric W. Deutsch, E. Deutsch, 2012, Molecular & Cellular Proteomics.

Improved support for targeted proteomics workflows in PeptideAtlas

Henry H N Lam, Eric W. Deutsch, Ruedi Aebersold, 2009 .

mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements

Andrew R. Jones, Eric W. Deutsch, Andrew W. Dowsey, 2020, bioRxiv.

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Akira R. Kinjo, Núria Queralt-Rosinach, Michel Dumontier, 2020, F1000Research.

The PeptideAtlas project

Eric W. Deutsch, Alexey I. Nesvizhskii, Jimmy K. Eng, 2005, Nucleic Acids Res..

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

Eric W. Deutsch, Luis Mendoza, Mukul Kumar Midha, 2019, bioRxiv.

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice

Martin Eisenacher, Christian Stephan, Juan Antonio Vizcaíno, 2014, Biochimica et biophysica acta.

Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

Yasset Perez-Riverol, Eric W. Deutsch, Christian Panse, 2020, bioRxiv.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

Juan Antonio Vizcaíno, Henning Hermjakob, Eric W. Deutsch, 2016, Nucleic Acids Res..

Combining Results of Multiple Search Engines in Proteomics*

Eric W. Deutsch, Alexey I. Nesvizhskii, Robert L. Moritz, 2013, Molecular & Cellular Proteomics.

Predictive Big Data Analytics: A Study of Parkinson’s Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations

Ming Tang, Ian Foster, Arthur W. Toga, 2016, PloS one.

Universal Spectrum Identifier for mass spectra

Wout Bittremieux, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2020, Nature Methods.

Mass Spectrometer Output File Format mzML

Eric W. Deutsch, E. Deutsch, 2010, Proteome Bioinformatics.

The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics

Martin Eisenacher, Jun Fan, Juan Antonio Vizcaíno, 2013, Molecular & Cellular Proteomics.

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

Henning Hermjakob, Eric W. Deutsch, John Boyle, 2012, BMC Bioinformatics.

Interfaces to PeptideAtlas: a case study of standard data access systems

Eric W. Deutsch, John Boyle, Sarah A. Killcoyne, 2012, Briefings Bioinform..

Development of a spectral library building tool and re-analysis of Human Plasma PeptideAtlas datasets using spectral searching

Stephen E. Stein, Henry H N Lam, Eric W. Deutsch, 2007 .

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2019, bioRxiv.

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists*

Lennart Martens, Fredrik Levander, Matthew Chambers, 2011, Molecular & Cellular Proteomics.

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

Eric W. Deutsch, Ruedi Aebersold, Bernd Wollscheid, 2013, Nature.

CC BOOTIS: QSO, NOT VARIABLE HALO GIANT

Eric W. Deutsch, Bruce Margon, 1997 .

Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, according to the HUPO Human Proteome Project.

Eric W. Deutsch, Nuno Bandeira, Ruedi Aebersold, 2020, Journal of proteome research.

Optical Identification of the X-Ray Burster X1746−370 in the Globular Cluster NGC 6441

Eric W. Deutsch, L. Homer, Bruce Margon, 2002, astro-ph/0201550.

PASSEL: The PeptideAtlas SRMexperiment library

Eric W. Deutsch, Luis Mendoza, Nathalie Selevsek, 2012, Proteomics.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Chris Sander, Eric W. Deutsch, Emek Demir, 2016, Cell.