Research Chemist
National Institute of Standards and Technology
Current research includes development of new materials for *omic applications and generating standardized proteomic data across non-model species as part of the CoMPARe Program (Comparative Mammalian Proteome Aggregator Resource) and Molecular Innovation in Agriculture Program. Acquiring high-quality *omic data from non-model organisms is especially exciting given the challenges of sequencing and annotating genomes, acquiring samples, and developing computational tools to compare results across species. His other primary focus is emerging proteomic applications, specifically working with stakeholders to optimize and standardize methods for data-independent acquisition and metaproteomic analysis. These projects are generating publicly available standardized methods, data, and data mining tools with the overarching goal of supporting commerce by advancing and harmonizing measurement science as well as developing resources for stakeholders to accelerate research capabilities.
Research Adjunct Faculty
College of Charleston
Currently a Research Adjunct faculty member in the College of Charleston’s Graduate Program in Marine Biology (GPMB). In 2010, also taught a sophmore level biology course, BIOL 211, to science majors.
Staff Scientist
Medical University of South Carolina
Director of Computational Proteomics and Bioinformatics at the MUSC Proteomics Center. Developed new workflows to integrate genomic (NGS) and proteomic data in a meaningful way to create synergy between the approaches, improving their analytical strength and statistical power. These algorithms used open-source platforms with eventual integration of other -omic data such as lipidomic and metabolomic. Additional work to develop novel methods to analyze high dimensional proteomic data and quantitative post-translational modification studies.
Post-Doctoral Scholar
Medical University of South Carolina
Developed a a technique that uses MALDI TOF-MS to identify sea lions with domoic acid toxicosis. Provided support to other projects which has resulted in advancing biomarker identification in numerous diseases, optimized multiple reaction monitoring techniques for protein quantification, and non-parametric tools that are utilized to evaluate experimental results.
Graduate Student
Medical University of South Carolina
Besides developing specialized skills, filled the role of lab manager directing other graduate students, summer students and technicians. Collaborated across many agencies and academic institutions including NIST, NOAA, UKY, USC, UGA and CofC.
Teacher Assistant & Laboratory Technician
The University of Georgia
In addition to teaching the lab for Soils and Hydrology (CRSS 3060) for three semesters, also performed metals (ICP-MS) and organic analyses (GC-MS) on soils from superfund sites.
Research Assistant
The University of Florida
Designed and carried out field and laboratory biogeochemical experiments to investigate nutrient flux (N and P) from sediments in the Lower Saint Johns River across temporal scales.
Boomkweker (Horticulture Exchange Student)
Boomkwekerij Togtema
Helped run operations at a small greenhouse in Buitenpost, Netherlands, from propagation to field planting and transport to auction. Never mastered fierljeppen, but did develop a fondness for Friesland.
Laboratory Technician
Vanderbilt University
Purified and crystalized a CYP450 protein of interest, as well as performed mutagenesis studies of amino acid residues involved with the porphyrin ring. [ref]
Medical University of South Carolina
Ph.D., Biomedical Science (September 2009)
Effect of pH on metal- and nanoparticle-microbe interactions
GPA: 3.688/4.0
The University of Georgia
B.S.E.S., Environmental Soil Science (December 2003)
Graduated Magna Cum Laude, GPA: 3.72/4.0
ACS Editors Choice for Neely et al., 2021
2021 Rising Stars in Proteomics and Metabolomics
1st place student presentation at the 43rd Annual IAAAM Conference, 2012
2nd place poster at the MUSC Student Research Day, 2011
1st place student presentation at the 42nd Annual IAAAM Conference, 2011
1st place poster at Department of Medicines 5th Annual Research Day, 2010
Proteomics Standards Research Group (sPRG; ABRF), Chair (2021-present)
Proteomics Research Group (PRG; ABRF), Member (2018-2024), Co-Chair (2020-2024)
Informatics Proteomics Research Group (ABRF) ad hoc Member (2019-2022)
Steering Committee for Ocean Carbon & Biogeochemistry study (at WHOI, NSF funded; 2019-present)
Viral Emergence Research Initiative (The Verena Consortium; 2020-2023)
US Human Proteome Organization (HUPO) 2022 Conference Organizing Committee
US Human Proteome Organization (HUPO) Virtual Media Outreach Committee, Chair (2022-2023)
US Human Proteome Organization (HUPO) Board of Directors, At-Large Member (2023-present)
Editorial Advisory Board for the Journal of Proteome Research (2020-present)
Editorial Board for the Journal of Biomolecular Techniques (2020-2024)
Editor for Data Independent Acquisition Methods. MassSpectrometryMethods.org (2018-present)
Email
Ben.A.Neely@gmail.com
Other
GitHub
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LinkedIn
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ORCID
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ResearchGate
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Scholar
Blog
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Bluesky
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Mastodon
Is Proteomics the Next Big “Ome”? (GEN Live; 2024)
ABRF 2022 Proteomics and Cloud Computing Workshop
Brewing Up a Storm: Scientists Conduct a Global Beer Proteomics Study (2020)
NIST, bood and proteomics (UC Davis Guest Lecture - 2020)
Blood, Sweat and Genomes: A Quest to Advance Measurement Science in Non-Model Organisms (2019)
Diving Deep into the Dolphin Genome Could Benefit Human Health (2017)
Klein J, Lam H, ... Neely BA, ... Vizcaíno JA, Deutsch EW. "The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF". Anal Chem Article ASAP (2024).
Saito MA, Saunders JK, McIlvin MR, Bertrand EM, ... Neely BA, ... Zhao Z. "Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures". Biogeosciences 21 (21):4889-4908 (2024).
Neely BA, Perez-Riverol Y, Palmblad M. "Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer". J Biomol Tech September 11 (2024).
Ghosh G, Neely BA, Bland AM, Whitmer ER, Field CL, Duignan PJ, Janech MG. "Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (Zalophus californianus). J Prot Res 23(7):2419-2430 (2024).
Jiang Y, Rex DAB, Schuster D, Neely BA,... Moritz RL, Meyer JG. "Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry". ACS Measurement Science Au [link] (2024).
Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim JK, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. "A multipathway phosphopeptide standard for rapid phosphoproteomics assay development". Mol Cell Proteomics 22(10):100639 (2023).
Neely BA, Ellisor DL, Davis WL. "Proteomics as a metrological tool to evaluate genome annotation accuracy following de novo genome assembly: a case study using the Atlantic bottlenose dolphin (Tursiops truncatus). Genes 14(9), 1696 (2023).
Jagtap PD, Hoopmann MR, Neely BA, Harvey A, Käll L, Perez-Riverol Y, Abajorga MK, Thomas JA, Weintraub ST, Palmblad M. "The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)". J Biomol Tech 34(3) (2023).
Kirkpatrick J, Stemmer PM, Searle BC, Herring LE, Martin L, Midha MK, Phinney BS, Shan B, Palmblad M, Wang Y, Jagtap PD, Neely BA. "2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study". J Biomol Tech 34(2) bioRxiv poster (2023).
Neely BA, Dorfer V, Martens L, Bludau I, Bouwmeester R, Degroeve S, Deutsch EW, Gessulat S, Käll L, Palczynski P, Payne SH, Rehfeldt TG, Schmidt T, Schwämmle V, Uszkoreit J, Vizcaíno JA, Wilhelm M, Palmblad M. "Toward an Integrated Machine Learning Model of a Proteomics Experiment." J Prot Res 22(3):681-696 (2023).
Rehfeldt TG, Gabriels R, Bouwmeester R, Gessulat S, Neely BA, Palmblad M, Perez-Riverol Y, Schmidt T, Vizcaíno JA, Deutsch EW. "ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics." J Prot Res 22(2):632-636 (2023).
Neely BA, Palmblad M. "Editorial: Machine Learning in Proteomics and Metabolomics." J Prot Res 21(11):2553-2554 (2022).
Pegg CL, Schulz BL, Neely BA, Albery GF, Carlson CJ. "Glycosylation and the global virome." Mol Ecol 00:1–8 (2022).
Marissen R, Varunjikar M, Laros J, Rasinger J, Neely BA, Palmblad M. "compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets." J Prot Res in press (2022).
Becker DJ, Lei GS, Janech MG, Bland AM, Fenton MB, Simmons NB, Relich RF, Neely BA. "Serum proteomics identifies immune pathways and candidate biomarkers of coronavirus infection in wild vampire bats." Front Virol 2(862961):1-13 (2022).
Albery GF, Becker DJ,... Neely BA,... Carlson CJ. "The science of the host-virus network" Nat Microbiol 6(12):1483-1492 (2021).
Neely BA and Palmblad M. "Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics" J Prot Res 20(10):4640-4645 (2021).
Khudyakov JI, Treat MD, Shanafelt MC, Deyarmin JS, Neely BA, van Breukelen F. "The liver proteome response to torpor in a basoendothermic mammal, Tenrec ecaudatus, provides insights into the evolution of homeothermy" Am J Physiol Regul Integr Comp Physiol 321(4):R614-R624 (2021).
Peart CR,... Neely BA,... JBW Wolf. "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" Mol Ecol Resour21, 2455– 2470 (2021).
Grandal M, Hoggard M, Neely BA, Davis WC, Marí F. "Proteogenomic assessment of intraspecific venom variability: Molecular adaptations in the venom arsenal of Conus purpurascens" Mol Cell Proteomics 20:100100 (2021).
Neely BA, Janech MG, Fenton MG, Simmons NB, Bland AM, Becker DJ. "Surveying the vampire bat (Desmodus rotundus) serum proteome: a resource for identifying immunological proteins and detecting pathogens" J Prot Res 20(5): 2547–2559 (2021).
Neely BA. "Cloudy with a chance of peptides: accessibility, scalability and reproducibility with cloud-hosted environments" J Prot Res 20(4): 2076–2082; OSF Preprints:doi:10.31219/osf.io/bgwve (2021).
Heck M and Neely BA. "Proteomics in non-model organisms: A new analytical frontier" J Prot Res 19(9):3595–3606 (2020).
Orsburn BC, Jenkins C, Miller SM, Neely BA, Bumpus NN. In silico approach toward the identification of unique peptides from viral protein infection: Application to COVID-19. bioRxiv doi:10.1101/2020.03.08.980383 (2020).
Davis WC, Kilpatrick LE, Ellisor DL, Neely BA. "Characterization of a human liver reference material fit for proteomics applications" Sci Data 6:324 (2019).
Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ, Hettich RL, Jagtap P, Janech MG, Kinkade DB, Leary D, McIlvin M, Moore E, Morris R, Neely BA, Nunn B, Saunders JK, Shepherd A, Symmonds N, Walsh D. "Progress and challenges in ocean metaproteomics and proposed best practices for data sharing" J Prot Res 18(4):1461-1476 (2019).
Mulligan JK, Patel K, Williamson T, Reaves N, Carroll W, Stephenson SE, Gao P, Drake RR, Neely BA, Tomlinson S, Schlosser RJ, Atkinson C. "C3a receptor antagonism as a novel therapeutic target for chronic rhinosinusitis." Mucosal Immunol 11(5):1375-1385 (2018).
Neely BA, Prager KC, Bland AM, Fontaine C, Gulland FM, Janech MG. "Proteomic analysis of urine from California sea lions (Zalophus californianus): a resource for urinary biomarker discovery." J Prot Res 17(9):3281-3291; bioRxiv doi:10.1101/336867 (2018).
Neely BA, Ellisor DL, Davis WL. "Proteomics as a metrological tool to evaluate genome annotation accuracy following de novo genome assembly: a case study using the Atlantic bottlenose dolphin (Tursiops truncatus)". bioRxiv doi:10.1101/254250 (2018).
Neely BA, Anderson PE. "Complementary domain prioritization: A method to improve biologically relevant detection in multi-omic data sets." Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS 3:68-80 (2017). [link]
Zambrano JN, Neely BA, Yeh ES. "Hormonally up-regulated neu-associated kinase: A novel target for breast cancer progression." Pharmacol Res 119:188-194 (2017).
Shao S, Neely BA, Kao T, Eckhaus J, Bourgeois J, Brooks J, Jones JJ, Drake RR, Zhu K. "Proteomic profiling of serial pre-diagnostic serum samples for early detection of colon cancer in the U.S. military". Cancer Epidemiol Biomarkers Prev 26(5):711-718 (2017).
Neely BA, Wilkins CE, Marlow LA, Malyarenko D, Kim Y, Ignatchenko A, Sasinowska H, Sasinowski M, Nyalwidhe JO, Kislinger T, Copland JA, Drake RR. "Proteotranscriptomic analysis reveals stage specific changes in the molecular landscape of clear-cell renal cell carcinoma". PLoS ONE 11(4):e0154074 (2016). [link]
Pehar M, Ball LE, Sharma DR, Harlan BA, Comte-Walters S, Neely BA, Vargas MR. "Changes in protein expression and lysine acetylation induced by decreased glutathione levels in astrocytes." Mol Cell Proteomics 15(2):493-505 (2015).
Neely BA, Soper JL, Gulland FMD, Bell PD, Kindy M, Arthur JM, Janech MG. "Proteomic analysis of cerebrospinal fluid in California sea lions (Zalophus californianus) with domoic acid toxicosis identifies proteins associated with neurodegeneration." Proteomics 15(23-24):4051-63 (2015).[link]
Hobeika L, Hunt KJ, Neely BA, Arthur JM. "Comparison of the rate of renal function decline in non-proteinuric patients with and without diabetes." Am J Med Sci 350(6):447-52 (2015).
Neely BA, Ferrante JA, Chaves JM, Soper JL, Almeida JS, Arthur JM, Gulland FMD, Janech MG. "Proteomic analysis of plasma from California sea lions (Zalophus californianus) reveals apolipoprotein E as a candidate biomarker of chronic domoic acid toxicosis." PLoS One 10(4):e0123295 (2015). [link]
Powers TW, Neely BA, Shao Y, Tang H, Troyer DA, Mehta AS, Haab BB, Drake RR. "MALDI imaging mass spectrometry profiling of N-glycans in formalin-fixed paraffin embedded clinical tissue blocks and tissue microarrays." PLoS One 9(9):e106255 (2014).
Jones EE, Powers TW, Neely BA, Cazares LH, Troyer DA, Parker AS, Drake RR. "MALDI Imaging mass spectrometry profiling of proteins and lipids in clear cell renal cell carcinoma." Proteomics 14(7-8):924-35 (2014).
Neely BA, Carlin KP, Arthur JM, McFee WE, Janech MG. "Ratiometric measurements of adiponectin by mass spectrometry in bottlenose dolphins (Tursiops truncatus) with iron overload reveal an association with insulin resistance and glucagon." Front Endocrinol 4:132 (2013). [link]
Venn-Watson S, Smith CR, Stevenson S, Parry C, Daniels R, Jensen E, Cendejas V, Balmer B, Janech M, Neely BA, Wells R. "Blood-based indicators of insulin resistance and metabolic syndrome in bottlenose dolphins (Tursiops truncatus)". Front Endocrinol 4:136 (2013).
Alge JL, Karakala N, Neely BA, Janech MG, Tumlin JA, Chawla LS, Shaw AD, Arthur JM and for the SAKInet Investigators. "Association of elevated urinary concentration of renin-angiotensin system components and severe AKI." Clin J Am Soc Nephrol 8(12):2043-52 (2013).
Arthur JM, Hill EG, Alge JL, Lewis EC, Neely BA, Janech MG, Tumlin JA, Chawla LS, Shaw AD and for the SAKInet Investigators. "Evaluation of 32 urine biomarkers to predict progression of AKI after cardiac surgery." Kidney Int 85(2):431-8 (2013).
Roper SM, Zemskova M, Neely BA, Martin A, Gao P, Jones EE, Kraft AS, Drake RR. "Targeted glycoprotein enrichment and identification in stromal cell secretomes using azido sugar metabolic labeling." Proteomics Clin Appl 7(5-6):367-71 (2013).
Alge JL, Karakala N, Neely BA, Janech MG, Valez JC, Arthur JM, SAKInet Investigators. "Urinary angiotensinogen predicts adverse outcomes among acute kidney injury patients in the intensive care unit." Crit Care 17(2):R69 (2013).
Bhensdadia NM, Hunt KJ, Lopes-Virella MF, Michael Tucker J, Mataria MR, Alge JL, Neely BA, Janech MG, Arthur JM. "Urine haptoglobin levels predict early renal functional decline in patients with type 2 diabetes." Kidney Int 83:1136-1143 (2013).
Alge JL, Karakala N, Neely BA, Janech MG, Tumlin JA, Chawla LS, Shaw AD, Arthur JM. "Urinary angiotensinogen and risk of severe AKI." Clin J Am Soc Nephrol 8(2):184-93 (2013).
Korrapati MC, Shaner BE, Neely BA, Alge JL, Arthur JM, Schnellmann RG. "Diabetes-induced renal injury in rats is attenuated by suramin." J Pharmacol Exp Ther 343(1):34-43 (2012).
Neely BA, Soper JL, Greig DJ, Carlin KP, Favre EG, Gulland FM, Almeida JS, Janech MG. "Serum profiling by MALDI-TOF mass spectrometry as a diagnostic tool for domoic acid toxicosis in California sea lions." Proteome Sci 10(1):18 (2012). [link]
Van Nostrand JD, Arthur JM, Kilpatrick LE, Neely BA, Bertsch PM, Morris PJ. "Changes in protein expression in Burkholderia vietnamiensis PR1301 at pH 5 and 7 with and without nickel." Microbiol 154:3813-3824 (2008).
Van Nostrand JD, Khijniak TJ, Neely BA, Sowder AG, Satter A, Bertsch PM, Morris PJ. "Reduction of nickel and uranium toxicity and enhanced trichloroethylene degradation to Burkholderia vietnamiensis PR1301 with hydroxyapatite amendment." Environ Sci Technol 41:1877-1882 (2007).
Podust LM, Kim Y, Arase M, Neely BA, Beck BJ, Bach H, Sherman DH, Lamb DC, Kelly SL, Waterman M.R. "The 1.92-angstrom structure of Streptomyces coelicolor A3(2) CYP154C1 - A new monooxygenase that functionalizes macrolide ring systems" J Biol Chem 278(14):12214-12221 (2003).
Assay for Measurement of Adiponectin and High Molecular Weight Adiponectin, 6/2013 (provisional, not converted)
Glycan panels as specific tumor tissue biomarkers, 9/2014 (provisional, not converted)