Publications by authors named "Benjamin A Neely"

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Proteomics Approaches to Ecoimmunology: New Insights into Wildlife Immunity and Disease.
Amanda Vicente-Santos, Natalia Sandoval-Herrera, Gábor Á Czirják, Benjamin A Neely, Daniel J Becker

Integr Comp Biol· December 2025

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VerteBrain reveals novel neural and non-neural protein assemblies conserved across vertebrate evolution.
Vy Dang, Brittney Voigt, David Yang, Gabriel Hoogerbrugge, Muyoung Lee, Benjamin A Neely

bioRxiv· July 2025

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Controlled environment agriculture: An opportunity to strengthen interagency research collaboration in the US government.
Abigail P Boyd, Paul Zankowski, Raymond Wheeler, Jennifer R Stokes-Draut, Yaroslav Chudnovsky, Benjamin A Neely

PNAS Nexus· June 2025

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Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions.
Amie M Solosky, Iliana M Claudio, Jessie R Chappel, Kaylie I Kirkwood-Donelson, Michael G Janech, Benjamin A Neely

J Proteome Res· December 2024

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The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.
Joshua Klein, Henry Lam, Tytus D Mak, Wout Bittremieux, Yasset Perez-Riverol, Benjamin A Neely

Anal Chem· November 2024

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Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions.
Amie M Solosky, Iliana M Claudio, Jessie R Chappel, Kaylie I Kirkwood-Donelson, Michael G Janech, Benjamin A Neely

bioRxiv· September 2024

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Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.
Benjamin A Neely, Yasset Perez-Riverol, Magnus Palmblad

J Biomol Tech· September 2024

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Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.
Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A Neely, Germán L Rosano

ACS Meas Sci Au· August 2024

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Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions ().
Gautam Ghosh, Benjamin A Neely, Alison M Bland, Emily R Whitmer, Cara L Field

J Proteome Res· July 2024

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Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry.
Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A Neely, Germán L Rosano

ArXiv· November 2023

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A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development.
Brian C Searle, Allis Chien, Antonius Koller, David Hawke, Anthony W Herren, Benjamin A Neely

Mol Cell Proteomics· October 2023

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The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).
Pratik D Jagtap, Michael R Hoopmann, Benjamin A Neely, Antony Harvey, Lukas Käll

J Biomol Tech· September 2023

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Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin ().
Benjamin A Neely, Debra L Ellisor, W Clay Davis

Genes (Basel)· August 2023

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2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.
Joanna Kirkpatrick, Paul M Stemmer, Brian C Searle, Laura E Herring, LeRoy Martin, Benjamin A Neely

J Biomol Tech· July 2023

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Toward an Integrated Machine Learning Model of a Proteomics Experiment.
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester

J Proteome Res· March 2023

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compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets.
Rob Marissen, Madhushri S Varunjikar, Jeroen F J Laros, Josef D Rasinger, Benjamin A Neely

J Proteome Res· February 2023

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ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics.
Tobias G Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely

J Proteome Res· February 2023

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Glycosylation and the global virome.
Cassandra L Pegg, Benjamin L Schulz, Benjamin A Neely, Gregory F Albery, Colin J Carlson

Mol Ecol· January 2023

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Machine Learning in Proteomics and Metabolomics.
Benjamin A Neely, Magnus Palmblad

J Proteome Res· November 2022

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The science of the host-virus network.
Gregory F Albery, Daniel J Becker, Liam Brierley, Cara E Brook, Rebecca C Christofferson, Benjamin A Neely

Nat Microbiol· December 2021

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Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution.
Claire R Peart, Christina Williams, Saurabh D Pophaly, Benjamin A Neely, Frances M D Gulland

Mol Ecol Resour· October 2021

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Liver proteome response to torpor in a basoendothermic mammal, , provides insights into the evolution of homeothermy.
Jane I Khudyakov, Michael D Treat, Mikayla C Shanafelt, Jared S Deyarmin, Benjamin A Neely

Am J Physiol Regul Integr Comp Physiol· October 2021

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Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics.
Benjamin A Neely, Magnus Palmblad

J Proteome Res· October 2021

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Surveying the Vampire Bat () Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens.
Benjamin A Neely, Michael G Janech, M Brock Fenton, Nancy B Simmons, Alison M Bland

J Proteome Res· May 2021

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Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments.
Benjamin A Neely

J Proteome Res· April 2021

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