Výsledky vyhledávání - "Benjamin A Neely"

Akademický článek

Serum Proteomics Identifies Immune Pathways and Candidate Biomarkers of Coronavirus Infection in Wild Vampire Bats

Autor: Daniel J. Becker, Guang-Sheng Lei, Michael G. Janech, Alison M. Bland, M. Brock Fenton, Nancy B. Simmons, Ryan F. Relich, Benjamin A. Neely

Publikováno v: Frontiers in Virology, Vol 2 (2022)

The apparent ability of bats to harbor many virulent viruses without showing disease is likely driven by distinct immune responses that coevolved with mammalian flight and the exceptional longevity of this order. Yet our understanding of the immune m

Externí odkaz: https://doaj.org/article/4459478b42d84b299e7c886a414d6dd3

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CompareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets

Autor: Rob Marissen, Madhushri S. Varunjikar, Jeroen F. J. Laros, Josef D. Rasinger, Benjamin A. Neely, Magnus Palmblad

Publikováno v: Journal of Proteome Research, 22(2), 514-519. AMER CHEMICAL SOC
Journal of Proteome Research

It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely colle

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::88ac8819bc3357a8d9cd16cc69a9c611
https://doi.org/10.1021/acs.jproteome.2c00457

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Toward an integrated machine Learning model of a proteomics experiment

Autor: Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaíno, Mathias Wilhelm, Magnus Palmblad

Publikováno v: JOURNAL OF PROTEOME RESEARCH
Journal of Proteome Research, 22(3), 681-696. AMER CHEMICAL SOC

In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals to evaluat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dfc4ca9a0380127a89a8b4a6f3f41108
https://hdl.handle.net/1887/3590801

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ProteomicsML

Autor: Tobias G. Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno, Eric W. Deutsch

Publikováno v: Journal of Proteome Research, 22(2), 632-636. AMER CHEMICAL SOC
JOURNAL OF PROTEOME RESEARCH

Data set acquisition and curation are often the most difficult and time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based liquid chromatography (LC) coupled to mass spectrometry (MS) data sets, due to the hi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::836e703fc3403d47ed95c4b6be9f9465
https://hdl.handle.net/1887/3593850

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Glycosylation and the global virome

Autor: Cassandra L. Pegg, Benjamin L. Schulz, Benjamin A. Neely, Gregory F. Albery, Colin J. Carlson

Publikováno v: Molecular ecologyREFERENCES.

The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harnessing it for

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::65bfbea5aee65da0fc274fea64801008
https://pubmed.ncbi.nlm.nih.gov/36217579

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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

Publikováno v: Molecular Ecology Resources. 21:2455-2470

With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale ge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f04f617e4be1f4d187476ff19f9d0a9
https://doi.org/10.1111/1755-0998.13443

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Akademický článek

Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma.

Autor: Benjamin A Neely, Christopher E Wilkins, Laura A Marlow, Dariya Malyarenko, Yunee Kim, Alexandr Ignatchenko, Heather Sasinowska, Maciek Sasinowski, Julius O Nyalwidhe, Thomas Kislinger, John A Copland, Richard R Drake

Publikováno v: PLoS ONE, Vol 11, Iss 4, p e0154074 (2016)

Renal cell carcinoma comprises 2 to 3% of malignancies in adults with the most prevalent subtype being clear-cell RCC (ccRCC). This type of cancer is well characterized at the genomic and transcriptomic level and is associated with a loss of VHL that

Externí odkaz: https://doaj.org/article/10369ea30c0d4d4086e6400209b1e76a

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Proteomics in Non-model Organisms: A New Analytical Frontier

Autor: Michelle Heck, Benjamin A. Neely

Publikováno v: J Proteome Res

For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly, and annotation, non-model organisms may be studied with the same advanced bioanalytical

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cff014b605d2330171649554927bbcab
https://doi.org/10.1021/acs.jproteome.0c00448

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