Ben Neely

National Institute of Standards and Technology

Address: NIST/HML, 331 Fort Johnson Road, Charleston, SC 29412
Phone: 843.460.9841


Ph.D., 2009, Medical University of South Carolina
B.S., 2003, The Univeristy of Georgia 

Research Interests

  • Development of new materials for *omic applications
  • Generating standardized proteomic data across non-model species as part of the CoMPARe (Comparative Mammalian Proteome Aggregator Resource) Program
  • Emerging proteomic applications, specifically working with stakeholders to optimize and standardize methods for data-independent acquisition and metaproteomic analysis
  • Design and improve quality controls (samples or spike-ins) and/or quality metrics useful for large-scale proteomic workflows
  • Develop new workflows to integrate genomic/transcriptomic and proteomic data in a meaningful way to create synergy between the approaches, improving their analytical strength and statistical power. These algorithms use open-source platforms with eventual integration of other *omic data such as lipidomic and metabolomic
  • Developing and optimizing methods utilizing selected reaction monitoring to quantify multiple prototypic peptides in complex matrices such as serum, cerebral spinal fluid, and/or urine

Current and Planned Research Projects


  • Mulligan JK, Patel K, Williamson T, Reaves N, Carroll W, Stephenson SE, Gao P, Drake RR, Neely BA, Tomlinson S, Schlosser RJ, Atkinson C. 2018. C3a receptor antagonism as a novel therapeutic target for chronic rhinosinusitis." Mucosal Immunol in press.
  • Neely BA, Prager KC, Bland AM, Fontaine C, Gulland FM, Janech MG. 2018. 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.
  • Neely BA, Ellisor DL, Davis WL. 2018. 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. 2017. 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.
  • Zambrano JN, Neely BA, Yeh ES. 2017. Hormonally up-regulated neu-associated kinase: A novel target for breast cancer progression. Pharmacol Res 119:188-194.
  • Shao S, Neely BA, Kao T, Eckhaus J, Bourgeois J, Brooks J, Jones JJ, Drake RR, Zhu K. 2017. 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.
  • Neely BA, Wilkins CE, Marlow LA, Malyarenko D, Kim Y, Ignatchenko A, Sasinowska A, Sasinowski M, Nyalwidhe JO, Kislinger K, Copland JA, Drake RR. 2016. Proteotranscriptomic analysis reveals stage specific changes in the molecular landscape of clear-cell renal cell carcinoma. PLoS ONE 11(4):e0154074.
  • Pehar M, Ball LE, Sharma DR, Harlan BA, Comte-Walters S, Neely BA, Vargas MR. 2015. Changes in protein expression and lysine acetylation induced by decreased glutathione levels in astrocytes. Mol Cell Proteomics 15(2):493-505.
  • Neely BA, Soper JL, Gulland FMD, Bell PD, Kindy M, Arthur JM, Janech MG. 2015. 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.
  • Hobeika L, Hunt KJ, Neely BA, Arthur JM. 2015. Comparison of the rate of renal function decline in non-proteinuric patients with and without diabetes. Am J Med Sci 350(6):447-52.