My Bibliography

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Podust LM, Kim Y, Arase M, Neely BA, Beck BJ, Bach H, Sherman DH, Lamb DC, Kelly SL, Waterman MR. The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems. J Biol Chem. 2003 Apr 4;278(14):12214-21. doi: 10.1074/jbc.M212210200. Epub 2003 Jan 7. PubMed PMID: 12519772.

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Van Nostrand JD, Khijniak TJ, Neely B, Sattar MA, Sowder AG, Mills G, Bertsch PM, Morris PJ. Reduction of nickel and uranium toxicity and enhanced trichloroethylene degradation to Burkholderia vietnamiensis PR1301 with hydroxyapatite amendment. Environ Sci Technol. 2007 Mar 15;41(6):1877-82. doi: 10.1021/es0616581. PubMed PMID: 17410778.

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Van Nostrand JD, Arthur JM, Kilpatrick LE, Neely BA, Bertsch PM, Morris PJ. Changes in protein expression in Burkholderia vietnamiensis PR1 301 at pH 5 and 7 with and without nickel. Microbiology (Reading). 2008 Dec;154(Pt 12):3813-3824. doi: 10.1099/mic.0.2008/017178-0. PubMed PMID: 19047749.

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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. 2012 Mar 19;10(1):18. doi: 10.1186/1477-5956-10-18. PubMed PMID: 22429742; PubMed Central PMCID: PMC3338078.

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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. 2012 Oct;343(1):34-43. doi: 10.1124/jpet.112.196964. Epub 2012 Jun 26. PubMed PMID: 22736507; PubMed Central PMCID: PMC3464039.

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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. 2013 Feb;8(2):184-93. doi: 10.2215/CJN.06280612. Epub 2012 Nov 8. PubMed PMID: 23143504; PubMed Central PMCID: PMC3562861.

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Alge JL, Karakala N, Neely BA, Janech MG, Velez JC, Arthur JM. Urinary angiotensinogen predicts adverse outcomes among acute kidney injury patients in the intensive care unit. Crit Care. 2013 Apr 15;17(2):R69. doi: 10.1186/cc12612. PubMed PMID: 23587112; PubMed Central PMCID: PMC3672721.

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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. 2013 Jun;7(5-6):367-71. doi: 10.1002/prca.201300006. PubMed PMID: 23687070; PubMed Central PMCID: PMC4331031.

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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. 2013 Jun;83(6):1136-43. doi: 10.1038/ki.2013.57. Epub 2013 Mar 27. PubMed PMID: 23536133; PubMed Central PMCID: PMC3672380.

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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 (Lausanne). 2013;4:132. doi: 10.3389/fendo.2013.00132. eCollection 2013. PubMed PMID: 24065958; PubMed Central PMCID: PMC3778387.

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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 (Lausanne). 2013;4:136. doi: 10.3389/fendo.2013.00136. eCollection 2013. PubMed PMID: 24130551; PubMed Central PMCID: PMC3793200.

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Alge JL, Karakala N, Neely BA, Janech MG, Tumlin JA, Chawla LS, Shaw AD, Arthur JM. Association of elevated urinary concentration of renin-angiotensin system components and severe AKI. Clin J Am Soc Nephrol. 2013 Dec;8(12):2043-52. doi: 10.2215/CJN.03510413. Epub 2013 Sep 5. PubMed PMID: 24009222; PubMed Central PMCID: PMC3848399.

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Arthur JM, Hill EG, Alge JL, Lewis EC, Neely BA, Janech MG, Tumlin JA, Chawla LS, Shaw AD. Evaluation of 32 urine biomarkers to predict the progression of acute kidney injury after cardiac surgery. Kidney Int. 2014 Feb;85(2):431-8. doi: 10.1038/ki.2013.333. Epub 2013 Sep 4. PubMed PMID: 24005224; PubMed Central PMCID: PMC3880389.

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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. 2014 Apr;14(7-8):924-35. doi: 10.1002/pmic.201300434. Epub 2014 Mar 3. PubMed PMID: 24497498; PubMed Central PMCID: PMC4331029.

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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. 2014;9(9):e106255. doi: 10.1371/journal.pone.0106255. eCollection 2014. PubMed PMID: 25184632; PubMed Central PMCID: PMC4153616.

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Neely BA, Ferrante JA, Chaves JM, Soper JL, Almeida JS, Arthur JM, Gulland FM, 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. 2014;10(4):e0123295. doi: 10.1371/journal.pone.0123295. eCollection 2014. PubMed PMID: 25919366; PubMed Central PMCID: PMC4412824.

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Neely BA, Soper JL, Gulland FM, 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. 2015 Dec;15(23-24):4051-63. doi: 10.1002/pmic.201500167. Epub 2015 Oct 13. PubMed PMID: 26364553.

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Hobeika L, Hunt KJ, Neely BA, Arthur JM. Comparison of the Rate of Renal Function Decline in NonProteinuric Patients With and Without Diabetes. Am J Med Sci. 2015 Dec;350(6):447-52. doi: 10.1097/MAJ.0000000000000583. PubMed PMID: 26624901; PubMed Central PMCID: PMC4667356.

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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. 2016 Feb;15(2):493-505. doi: 10.1074/mcp.M115.049288. Epub 2015 Oct 20. PubMed PMID: 26486419; PubMed Central PMCID: PMC4739669.

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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. 2016;11(4):e0154074. doi: 10.1371/journal.pone.0154074. eCollection 2016. PubMed PMID: 27128972; PubMed Central PMCID: PMC4851420.

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Zambrano JN, Neely BA, Yeh ES. Hormonally up-regulated neu-associated kinase: A novel target for breast cancer progression. Pharmacol Res. 2017 May;119:188-194. doi: 10.1016/j.phrs.2017.02.007. Epub 2017 Feb 9. Review. PubMed PMID: 28189783; PubMed Central PMCID: PMC5392418.

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Shao S, Neely BA, Kao TC, Eckhaus J, Bourgeois J, Brooks J, Jones EE, Drake RR, Zhu K. Proteomic Profiling of Serial Prediagnostic Serum Samples for Early Detection of Colon Cancer in the U.S. Military. Cancer Epidemiol Biomarkers Prev. 2017 May;26(5):711-718. doi: 10.1158/1055-9965.EPI-16-0732. Epub 2016 Dec 21. PubMed PMID: 28003179; PubMed Central PMCID: PMC5413427.

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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. 2018 Sep;11(5):1375-1385. doi: 10.1038/s41385-018-0048-x. Epub 2018 Jun 15. PubMed PMID: 29907871; PubMed Central PMCID: PMC6162114.

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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 Proteome Res. 2018 Sep 7;17(9):3281-3291. doi: 10.1021/acs.jproteome.8b00416. Epub 2018 Aug 28. PubMed PMID: 30113852; PubMed Central PMCID: PMC7607554.

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Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ 4th, Hettich RL, Jagtap PD, Janech MG, Kinkade DB, Leary DH, McIlvin MR, Moore EK, Morris RM, Neely BA, Nunn BL, Saunders JK, Shepherd AI, Symmonds NI, Walsh DA. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. J Proteome Res. 2019 Apr 5;18(4):1461-1476. doi: 10.1021/acs.jproteome.8b00761. Epub 2019 Mar 12. Review. PubMed PMID: 30702898; PubMed Central PMCID: PMC7575043.

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Davis WC, Kilpatrick LE, Ellisor DL, Neely BA. Characterization of a human liver reference material fit for proteomics applications. Sci Data. 2019 Dec 18;6(1):324. doi: 10.1038/s41597-019-0336-7. PubMed PMID: 31852895; PubMed Central PMCID: PMC6920408.

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Heck M, Neely BA. Proteomics in Non-model Organisms: A New Analytical Frontier. J Proteome Res. 2020 Sep 4;19(9):3595-3606. doi: 10.1021/acs.jproteome.0c00448. Epub 2020 Aug 20. PubMed PMID: 32786681; PubMed Central PMCID: PMC7874939.

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Neely BA. Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments. J Proteome Res. 2021 Apr 2;20(4):2076-2082. doi: 10.1021/acs.jproteome.0c00920. Epub 2021 Jan 29. PubMed PMID: 33513299; PubMed Central PMCID: PMC8637422.

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Neely BA, Janech MG, Fenton MB, Simmons NB, Bland AM, Becker DJ. Surveying the Vampire Bat (Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens. J Proteome Res. 2021 May 7;20(5):2547-2559. doi: 10.1021/acs.jproteome.0c00995. Epub 2021 Apr 10. PubMed PMID: 33840197; PubMed Central PMCID: PMC9812275.

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Grandal M, Hoggard M, Neely B, Davis WC, Marí F. Proteogenomic Assessment of Intraspecific Venom Variability: Molecular Adaptations in the Venom Arsenal of Conus purpurascens. Mol Cell Proteomics. 2021;20:100100. doi: 10.1016/j.mcpro.2021.100100. Epub 2021 May 23. PubMed PMID: 34029722; PubMed Central PMCID: PMC8260871.

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Khudyakov JI, Treat MD, Shanafelt MC, Deyarmin JS, Neely BA, van Breukelen F. 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. 2021 Oct 1;321(4):R614-R624. doi: 10.1152/ajpregu.00150.2021. Epub 2021 Aug 25. PubMed PMID: 34431404.

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Neely BA, Palmblad M. Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics. J Proteome Res. 2021 Oct 1;20(10):4640-4645. doi: 10.1021/acs.jproteome.1c00528. Epub 2021 Sep 15. PubMed PMID: 34523928; PubMed Central PMCID: PMC8491155.

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Peart CR, Williams C, Pophaly SD, Neely BA, Gulland FMD, Adams DJ, Ng BL, Cheng W, Goebel ME, Fedrigo O, Haase B, Mountcastle J, Fungtammasan A, Formenti G, Collins J, Wood J, Sims Y, Torrance J, Tracey A, Howe K, Rhie A, Hoffman JI, Johnson J, Jarvis ED, Breen M, Wolf JBW. 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 Resour. 2021 Oct;21(7):2455-2470. doi: 10.1111/1755-0998.13443. Epub 2021 Jun 27. PubMed PMID: 34097816; PubMed Central PMCID: PMC9732816.

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Albery GF, Becker DJ, Brierley L, Brook CE, Christofferson RC, Cohen LE, Dallas TA, Eskew EA, Fagre A, Farrell MJ, Glennon E, Guth S, Joseph MB, Mollentze N, Neely BA, Poisot T, Rasmussen AL, Ryan SJ, Seifert S, Sjodin AR, Sorrell EM, Carlson CJ. The science of the host-virus network. Nat Microbiol. 2021 Dec;6(12):1483-1492. doi: 10.1038/s41564-021-00999-5. Epub 2021 Nov 24. Review. PubMed PMID: 34819645.

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Neely BA, Palmblad M. Machine Learning in Proteomics and Metabolomics. J Proteome Res. 2022 Nov 4;21(11):2553-2554. doi: 10.1021/acs.jproteome.2c00566. Epub 2022 Oct 4. PubMed PMID: 36193949.

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Pegg CL, Schulz BL, Neely BA, Albery GF, Carlson CJ. Glycosylation and the global virome. Mol Ecol. 2023 Jan;32(1):37-44. doi: 10.1111/mec.16731. Epub 2022 Oct 21. PubMed PMID: 36217579; PubMed Central PMCID: PMC10947461.

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Marissen R, Varunjikar MS, Laros JFJ, Rasinger JD, Neely BA, Palmblad M. compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets. J Proteome Res. 2023 Feb 3;22(2):514-519. doi: 10.1021/acs.jproteome.2c00457. Epub 2022 Sep 29. PubMed PMID: 36173614; PubMed Central PMCID: PMC9903320.

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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 Proteome Res. 2023 Feb 3;22(2):632-636. doi: 10.1021/acs.jproteome.2c00629. Epub 2023 Jan 24. PubMed PMID: 36693629; PubMed Central PMCID: PMC9903315.

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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 Proteome Res. 2023 Mar 3;22(3):681-696. doi: 10.1021/acs.jproteome.2c00711. Epub 2023 Feb 6. Review. PubMed PMID: 36744821; PubMed Central PMCID: PMC9990124.

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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 Proteomics Study. J Biomol Tech. 2023 Jul 1;34(2). doi: 10.7171/3fc1f5fe.9b78d780. eCollection 2023 Jul 1. PubMed PMID: 37435391; PubMed Central PMCID: PMC10332336.

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Neely BA, Ellisor DL, Davis WC. 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 (Basel). 2023 Aug 25;14(9). doi: 10.3390/genes14091696. PubMed PMID: 37761836; PubMed Central PMCID: PMC10531373.

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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. 2023 Sep 30;34(3). doi: 10.7171/3fc1f5fe.a058bad4. eCollection 2023 Sep 30. PubMed PMID: 37969874; PubMed Central PMCID: PMC10644979.

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Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, 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. 2023 Oct;22(10):100639. doi: 10.1016/j.mcpro.2023.100639. Epub 2023 Aug 30. PubMed PMID: 37657519; PubMed Central PMCID: PMC10561125.

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Jiang Y, Rex DAB, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Mayta ML, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry. ArXiv. 2023 Nov 13;. PubMed PMID: 38013887; PubMed Central PMCID: PMC10680866.

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Vicente-Santos A, Lock LR, Allira M, Dyer KE, Dunsmore A, Tu W, Volokhov DV, Herrera C, Lei GS, Relich RF, Janech MG, Bland AM, Simmons NB, Becker DJ. Serum proteomics reveals a tolerant immune phenotype across multiple pathogen taxa in wild vampire bats. Front Immunol. 2023;14:1281732. doi: 10.3389/fimmu.2023.1281732. eCollection 2023. PubMed PMID: 38193073; PubMed Central PMCID: PMC10773587.

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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 Proteome Res. 2024 Jul 5;23(7):2419-2430. doi: 10.1021/acs.jproteome.4c00103. Epub 2024 May 28. PubMed PMID: 38807289; PubMed Central PMCID: PMC11232103.

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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. Forthcoming; 3:68-80. doi: 10.5220/0006151500680080.