R
Richard D. LeDuc
Researcher at Northwestern University
Publications - 68
Citations - 10120
Richard D. LeDuc is an academic researcher from Northwestern University. The author has contributed to research in topics: Top-down proteomics & Proteomics. The author has an hindex of 28, co-authored 63 publications receiving 8202 citations. Previous affiliations of Richard D. LeDuc include Washington University in St. Louis & Great Lakes Bioenergy Research Center.
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Journal ArticleDOI
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +24 more
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
Journal ArticleDOI
Mapping intact protein isoforms in discovery mode using top-down proteomics
John C. Tran,Leonid Zamdborg,Dorothy R. Ahlf,Dorothy R. Ahlf,Ji Eun Lee,Ji Eun Lee,Adam D. Catherman,Adam D. Catherman,Kenneth R. Durbin,Kenneth R. Durbin,Jeremiah D. Tipton,Adaikkalam Vellaichamy,Adaikkalam Vellaichamy,John F. Kellie,John F. Kellie,Mingxi Li,Mingxi Li,Cong Wu,Steve M. M. Sweet,Steve M. M. Sweet,Bryan P. Early,Bryan P. Early,Nertila Siuti,Nertila Siuti,Richard D. LeDuc,Philip D. Compton,Paul M. Thomas,Paul M. Thomas,Neil L. Kelleher,Neil L. Kelleher +29 more
TL;DR: Identification of 1,043 gene products from human cells that are dispersed into more than 3,000 protein species created by post-translational modification, RNA splicing and proteolysis is shown, using a new four-dimensional separation system.
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +22 more
TL;DR: This protocol describes the use of the Trinity platform for de novo transcriptome assembly from RNA-Seq data in non-model organisms and presents Trinity’s supported companion utilities for downstream applications, including RSEM for transcript abundance estimation and R/Bioconductor packages for identifying differentially expressed transcripts across samples.
Journal ArticleDOI
ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry.
Leonid Zamdborg,Richard D. LeDuc,Kevin J. Glowacz,Yong Bin Kim,Vinayak Viswanathan,Ian T. Spaulding,Bryan P. Early,Eric J. Bluhm,Shannee Babai,Neil L. Kelleher +9 more
TL;DR: ProSight PTM 2.0 introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing).
Journal ArticleDOI
ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry.
Richard D. LeDuc,Gregory K. Taylor,Yong Bin Kim,Thomas E. Januszyk,Lee H. Bynum,Joseph V. Sola,John S. Garavelli,Neil L. Kelleher +7 more
TL;DR: Sequence databases from across the phylogenetic tree are supported, with a new database strategy of 'shotgun annotation' used to assist characterization of wild-type proteins.