Author

Ryan Peckner

Broad Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Systems Biology· 2

Signature Assays, Organisms & Methods

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Assay:proteomics· 4 Approach:statistical model· 4 Research Focus:benchmarking· 2 Organism:human· 2 Research Focus:cell-cell communication· 1 Research Focus:database / resource· 1 Research Focus:deconvolution· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Jacob D. JaffeiD· 4 shared Alvaro Sebastian Vaca JácomeiD· 3 shared Michael J. MacCossiD· 3 shared Steven A. CarriD· 3 shared Adam Officer· 2 shared Brendan MacLeaniD· 2 shared Jarrett D. EgertsoniD· 2 shared Jennifer G. AbeliniD· 2 shared

Activity by Year

2018-2021 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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4 shared papersSystems Biology

Jacob D. JaffeORCID

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Author profile →

4 papers

Recent·Most cited

Causal interactions from proteomic profiles: molecular data meets pathway knowledge

Özgün Babur, Augustin Luna, Anil Korkut, Funda Durupınar, Metin Can Siper, Uğur Doğrusöz, Alvaro Sebastian Vaca Jácome, Ryan Peckner, Karen E. Christianson, Jacob D. Jaffe, Paul T. Spellman, Joseph E. Aslan, Chris Sander, Emek Demir

The paper introduces a computational method to generate causal explanations for proteomic profiles by integrating molecular data with prior biological pathway knowledge, demonstrating its application in various biological contexts.

Patterns · May 12, 2021Peer-reviewedSystems Biology

Avant-garde: An automated data-driven DIA data curation tool.

Alvaro Sebastian Vaca Jácome, Ryan Peckner, Nicholas Shulman, Karsten Krug, Katherine C. DeRuff, Adam Officer, Karen E. Christianson, Brendan MacLean, Michael J. MacCoss, Steven A. Carr, Jacob D. Jaffe

Avant-garde improves DIA data analysis by refining signals, reducing interference, and controlling false discovery rates through a data-driven approach.

Nature Methods · Nov 16, 2020Peer-reviewedBioinformatics

Specter: linear deconvolution as a new paradigm for targeted analysis of data-independent acquisition mass spectrometry proteomics

Ryan Peckner, Samuel A. Myers, Alvaro Sebastian Vaca Jácome, Jarrett D. Egertson, Jennifer G. Abelin, Michael J. MacCoss, Steven A. Carr, Jacob D. Jaffe

Specter improves DIA proteomics by directly deconvoluting spectra using linear algebra, enhancing sensitivity for similar peptides and challenging cases.

Nature Methods · Apr 2, 2018Peer-reviewedBioinformatics

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

Lev Litichevskiy, Ryan Peckner, Jennifer G. Abelin, Jacob K. Asiedu, Amanda L. Creech, John F. Davis, Desiree Davison, Caitlin M. Dunning, Jarrett D. Egertson, Shawn B. Egri, Joshua Gould, Tak Ko, Sarah Johnson, David L. Lahr, Daniel Lam, , Jacob D. Jaffe

The paper creates a proteomic resource profiling 90 drugs in six cell lines, revealing cell-specific responses and enabling integration with transcriptional data to identify therapeutic opportunities.

Cell Systems · Apr 1, 2018Peer-reviewedSystems Biology