Publications

*Corresponding authors; ^⸙NU undergraduate student advised by AI; ^⸎NU graduate (MS or Ph.D.) student advised or co-advised by AI; ^#NU postdoctoral scholar or research scientist supervised or co-supervised by AI.

1. Huang W, Reinhardt JK, Tian A, Zhang X, Li B, ^⸎Gould N, Nallapati S, Ivanov AR, Wang Y, Guo JJ, Budil DE, Weng JK. Cyclochlorotine Hydroxylase CctR Reveals DUF3328 as a Family of Copper-Dependent Metalloenzymes. Angew Chem Int Ed Engl. 2025 Aug 22:e202512449. doi: 10.1002/anie.202512449.
2. ^#Greguš M, ^⸎Gao Y, ^⸎Johnson KR, ^#Ray S, ^#Marie AL, Ivanov AR*. Top-Down Proteomic Analysis of Limited Samples Using Porous Layer Open Tubular Columns and High-Field Asymmetric Ion Mobility Spectrometry Coupled to Mass Spectrometry. Anal Chem. 2025 Jul 15;97(27):14189-14199. doi: 10.1021/acs.analchem.4c06727.
3. ^⸎Figueroa-Navedo AM, Kapre R, Gupta T, Xu Y, ^⸎Phaneuf CG, Jean Beltran PM, Xue L, Ivanov AR, Vitek O. MSstatsTMT Improves Accuracy of Thermal Proteome Profiling. Mol Cell Proteomics. 2025 May 27;24(8):100999. doi: 10.1016/j.mcpro.2025.100999. PMID: 40441441 PMCID: PMC12335990.
4. ^⸎Su X, ^#Júnior GPO, ^#Marie AL, ^#Gregus M, ^⸎Figueroa-Navedo A, Ghiran IC, Ivanov AR*. Enhanced proteomic profiling of human plasma-derived extracellular vesicles through charge-based fractionation to advance biomarker discovery potential. J. Extracell. Vesicles. 2024 Dec;13(12):e70024. doi: 10.1002/jev2.70024. PMID: 39641316 PMCID: PMC11621968.
5. Tran V, ^#de Oliveira-Jr GP, Chidester S, Lu S, Pleet ML, Ivanov AR, Tigges J, Yang M, Jacobson S, Gonçalves MCB, Schmaier AA, Jones J, Ghiran IC. Choice of blood collection methods influences extracellular vesicles counts and miRNA profiling. J. Extracell Biol. 2024 Oct 22;3(10):e70008. doi: 10.1002/jex2.70008. PMID: 39440167 PMCID: PMC11494683.
6. ^⸎Zimmerman AJ, ^#Greguš M, Ivanov AR*. Comprehensive Micro-SPE-Based Bottom-Up Proteomic Workflow for Sensitive Analysis of Limited Samples. Methods Mol Biol. 2024; 2817:19-31. doi: 10.1007/978-1-0716-3934-4_3. PMID: 38907144.
7. ^#Gregus M, ^#Koller A, ^#Ray S, Ivanov AR.* Improved data acquisition settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-based mass spectrometers for proteomic analysis of limited samples. J. Proteome Res., 2024; 23(6):2230-2240. PMID: 38690845, PMCID: PMC11165581.
8. ^#Marie A-L, ^⸎Gao Y, Ivanov AR.* Native N-glycome profiling of single cells and ng-level blood isolates using label-free capillary electrophoresis-mass spectrometry. Nat. Commun. 2024, 15(1):3847. doi: 10.1038/s41467-024-47772-w, PMID: 38719792, PMCID: PMC11079027.
9. ^⸎Shah A, Batabyal D, Qui D, Cui W, Harrahy J, Ivanov AR.* Mapping conformational changes on bispecific antigen-binding biotherapeutic by covalent labeling and mass spectrometry. J. Pharm. Analysis. 2024 Aug;14(8):100966. doi: 10.1016/j.jpha.2024.100966. PMID: 39263356 PMCID: PMC11388688.
10. Webber KGI, Huang S, Truong T, Heninger JL, ^#Gregus M, Ivanov AR, Kelly RT. Open-tubular trap columns: towards simple and robust liquid chromatography separations for single-cell proteomics. Mol Omics. 2024 Mar 25;20(3):184-191. doi: 10.1039/d3mo00249g. PubMed PMID: 38353725; PMCID: PMC10963139.
11. ^⸎Figueroa-Navedo AM, Ivanov AR.* Experimental and data analysis advances in thermal proteome profiling. Cell Rep Methods. 2024 Feb 26;4(2):100717. doi: 10.1016/j.crmeth.2024.100717. Review. PubMed PMID: 38412830; PMCID: PMC10921035.
12. Welsh JA, ^⸎Zimmerman A, Ivanov AR, et al. Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles, 2024. doi: 10.1002/jev2.12404. PubMed PMID: 38326288; PMCID: PMC10850029.
13. ^⸎Zimmerman A, ^#de Oliveira GP, ^⸎Su X, ^⸙⸎Wood J, ^⸎Fu Z, Pinckney B, Tigges J, Ghiran IC, Ivanov AR.* Multimode chromatography-based techniques for high purity isolation of extracellular vesicles from human blood plasma. J. Extracell Biology. 2024, Mar;3(3):e147. doi: 10.1002/jex2.147. PMID: 38751711, PMCID: PMC11080799.
14. ^#Marie A-L, Georgescauld F, ^⸎Johnson KR, ^#Ray S, Ivanov AR.* Native capillary electrophoresis-mass spectrometry of the near 1 MDa non-covalent GroEL/GroES/substrate protein complexes. Advanced Science (Weinh). 2024 Mar;11(11):e2306824. doi: 10.1002/advs.202306824. PubMed PMID: 38191978; PMCID: PMC10953559.
15. ^#de Oliveira GP, Welsh JA, Pinckney B, Palu CC, Lu S, ^⸎Zimmerman A, Barbosa RH, Sahu P, Noshin M, Gummuluru S, Tigges J, Jones JC, Ivanov AR, Ghiran IC. Human red blood cells release distinct antigenic and bimodal size microvesicles, which alter neutrophil phagocytosis. J. Extracell Biology 2023, 2(11):e107. doi: 10.1002/jex2.107. PMID: 37942280; PMCID: PMC10629908.
16. ^⸎Shah A, Cui W, Harrahy J, Ivanov AR*. Characterization of charge variants, including post-translational modifications and proteoforms, of bispecific antigen-binding protein by cation-exchange chromatography coupled to native mass spectrometry. Talanta. 2024. 266(Pt 1):125062. doi: 10.1016/j.talanta.2023.125062. Epub 2023 Aug 8. PMID: 37566926; PMCID: PMC10528315.
17. ^#Greguš M, Ivanov AR, Wilson SR. Ultralow flow liquid chromatography and related approaches: A focus on recent bioanalytical applications (Review). J Sep Sci. 2023. 46(18):e2300440. doi: 10.1002/jssc.202300440. PMID: 37528733 PMCID: PMC11087205.
18. Huang T, Staniak M, Veiga Leprevost FD, ^⸎Figueroa-Navedo AM, Ivanov AR, Nesvizhskii AI, Choi M, Vitek O. Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling J Proteome Res. 2023, 22(8):2641-2659. PMID: 37467362. PMID: 37467362 PMCID: PMC11090052.
19. ^⸎Bagwe K, ^⸎Gould N, ^⸎Johnson KR, Ivanov AR.* Single-cell omics profiling using capillary electrophoresis-mass spectrometry. Review. Trends in Anal. Chem. 165:117117. doi: 10.1016/j.trac.2023.117117. PMID: 37388554. PMCID: PMC10306258.
20. ^⸎Phaneuf CG, Aizikov K, Grinfeld D, Kreutzmann A, Mourad D, Lange O, Dai D, Zhang B, Belenky A, Makarov AA, and Ivanov AR.* Experimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays. Nat. Commun. Chem., 2023, 6(1):64. PMID: 37024568. PMCID: PMC10079678.
21. ^#Marie A-L, ^#Ray S, Ivanov AR.* Ultra-sensitive label-free deep profiling of N-glycans released from biomedically-relevant samples. Nat. Commun. 2023, 14(1):1618. PMID: 36959283. PMCID: PMC10036494.
22. Gatto L, Aebersold A, Cox J, Demichev V, Derks J, Emmott E, Franks AM, Ivanov AR, Kelly RT, Khoury L, Leduc A, MacCoss MJ, Nemes P, Perlman DH, Petelski AA, Rose CM, Schoof EM, Van Eyk J, Vanderaa C, Yates III JR, and Slavov N. Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments. Nat. Methods, 2023, 20(3):375-386. PMID: 36864200. PMCID: PMC10130941.
23. ^⸎Shah A, Desai R, Cui W, Harrahy JJ, Ivanov AR.* Characterization of bispecific antigens-binding biotherapeutic fragmentation sites using microfluidic capillary electrophoresis coupled to mass spectrometry (mCZE-MS). Analyst, 2023, 148, 665 – 674. PMID: 36625279. PMCID: PMC9979615.
24. ^⸎Johnson KR, ^⸎Gao Y, ^#Greguš M, Ivanov AR.* On-capillary Cell Lysis Enables Top-down Proteomic Analysis of Single Mammalian Cells by CE-MS/MS. Anal Chem. 2022. 94(41):14358-14367. PMID: 36194750. PMC10118848.
25. ^⸎Johnson KR, ^#Greguš M, Ivanov AR.* Coupling High-Field Asymmetric Ion Mobility Spectrometry with Capillary Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry Improves Protein Identifications in Bottom-Up Proteomic Analysis of Low Nanogram Samples. J Proteome Res. 2022; 21(10):2453-2461. PMID: 36112031. PMCID: PMC10118849.
26. Welsh JA, Killingsworth B, Kepley J, Traynor T, Cook S, Savage J, Marte J, Lee MJ, Maeng HM, Pleet ML, Magana S, Gorgens A, Maire CL, Lamszus K, Ricklefs FL, Merino MJ, Linehan WM, Greten T, Cooks T, Harris CC, Apolo A, Abdel-Mageed A, Ivanov AR, Trepel JB, Roth M, Tkach M, Milosavljevic A, Théry C, LeBlanc A, Berzofsky JA, Ruppin E, Aldape K, Camphausen K, Gulley JL, Ghiran I, Jacobson S, Jones JC. MPA _PASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays. Cell Rep Methods. 2022. 2(1):100136. PMID: 35474866. PMCID: PMC9017130.
27. ^⸎Toole EN, Dufresne C, ^#Ray S, Schwann AB, Sadiki A, Zhou ZS, Cook K, Ivanov AR*. Correction to Rapid Highly-Efficient Digestion and Peptide Mapping of Adeno-Associated Viruses. Anal Chem. 2021, 93(49):16734. PMID: 34850630. PMCID: PMC8764965.
28. ^⸎Geller S, Lieberman H, Belanger A, Yew N, Kloss A, Ivanov AR*. Comparison of microflow and analytical flow liquid chromatography coupled to mass spectrometry global metabolomics methods using a urea cycle disorders mouse model. Journal of Proteome Research, 2022. 21(1):151-163. PMID: 34843255. PMCID: PMC8742624.
29. Chatterjee S, Yabaji SM, Rukhlenko OS, Bhattacharya B, Waligurski E, Vallavoju N, ^#Ray S, Kholodenko BN, Brown LE, Beeler AB, Ivanov AR, Kobzik L, Porco JA Jr, Kramnik I. Channeling macrophage polarization by rocaglates increases macrophage resistance to Mycobacterium tuberculosis. iScience. 2021. PMID: 34381970
30. ^⸎Johnson KR, ^#Greguš M, ^⸙Kostas JC, Ivanov AR*, Capillary electrophoresis coupled to electrospray ionization tandem mass spectrometry (CE-MS/MS) for ultrasensitive proteomic analysis of limited samples. Analytical Chemistry. 2022, 704-713. PMID: 34983182. PMCID: PMC8770592.
31. ^⸎Naggar Toole E, Dufresne C, ^#Ray S, Schwann A, Cook K, Ivanov AR*, Rapid Highly-Efficient Digestion and Peptide Mapping of Adeno-Associated Viruses. 2022. Analytical Chemistry. 93(30):10403-10410. PMID: 34291903. PMCID: PMC8743033.
32. Berger Fridman I, ^⸙Kostas JC, ^#Greguš M, ^#Ray S, Sullivan MR, Ivanov AR, Cohen S, Konry T. High-throughput microfluidic 3D biomimetic model enabling quantitative description of the human breast tumor microenvironment. Acta Biomaterialia. 2021, Jun 18:S1742-7061(21)00399-8. doi: 10.1016/j.actbio.2021.06.025. PMID: 34153511. PMCID: PMC8434998.
33. ^⸙Kostas JC, ^#Greguš M, Schejbal J, ^#Ray S, Ivanov AR*. Simple and efficient micro-SPE tip-based sample preparation workflow to enable sensitive proteomic profiling of limited samples (200 to 10,000 cells). Journal of Proteome Research, 2021, 20(3):1676-1688. PMID: 33625864. PMCID: PMC7954648.
34. Welsh JA, Killingsworth B, Kepley J, Traynor T, McKinnon K, Savage J, Appel D, Aldape K, Camphausen K, Berzofsky JA, Ivanov AR, Ghiran IH, Jones JC. A simple, high-throughput method of protein and label removal from extracellular vesicle samples. Nanoscale, 2021, 13(6):3737-3745. PMID: 33544111. PMCID: PMC7941347.
35. ^⸎Geller S, Lieberman H, Kloss A, Ivanov AR*.  A Systematic Approach to Development of Analytical Scale and Microflow-Based LC-MS Metabolomics Methods to Support Drug Discovery and Development. Journal of Chromatography A, 2021, Epub1642:462047. PMID: 33744605. PMCID: PMC8035295.
36. Tošić I, Heppler LN, Egusquiaguirre SP, Boehnke N, Correa S, Costa DF, Grossman Moore EA, Pal S, Richardson D, Ivanov AR, Haas-Kogan DA, Nomura D, Hammond PT, and Frank DA.  Lipidome-based Targeting of STAT3-driven Breast Cancer Cells Using Poly-L-glutamic acid-coated Layer-by-Layer Nanoparticles. Molecular Cancer Therapeutics, 2021, 20(4):726-738, PMID: 33536189. PMCID: PMC8026705.
37. Bhattacharya B, Xiao S, Chatterjee S, Urbanowski ME, Ordonez AA, Ihms EA, Agrahari G, Lun S, Berland R, Pichugin A, ^⸎Gao Y, Connor JH, Ivanov AR, Yan BS, Kobzik L, Koo BB, Jain SK, Bishai WR, Kramnik I. The integrated stress response mediates necrosis in murine Mycobacterium tuberculosis granulomas. Journal of Clinical Investigation, 2021, Epub Feb 1;131(3):e130319. PMID: 33301427. PMCID: PMC7843230.
38. ^#Marie AL, Ray R, Lu S, Jones J, Ghiran I, and Ivanov AR*.  High-Sensitivity Glycan Profiling of Blood-Derived Immunoglobulin G, Plasma, and Extracellular Vesicle Isolates with Capillary Zone Electrophoresis-Mass Spectrometry. Analytical Chemistry, 2021, 93(4):1991-2002. PMID: 33433994. PMCID: PMC7987205.
39. ^#Greguš M, ^⸙Kostas JC, Ray S, Abbatiello SE, Ivanov AR*.  Improved Sensitivity of Ultralow Flow LC-MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology. Analytical Chemistry, 2020, 92(21):14702-14712. PMID: 33054160. PMCID: PMC7934643.
40. Peng Y, Jain S, Li YF, ^#Greguš M, Ivanov AR, Vitek O, and Radivojac P.  New mixture models for decoy-free false discovery rate estimation in mass-spectrometry proteomics. Bioinformatics, 2020, 36(Supplement_2):i745-i753. PMID: 33381824. PMCID: PMC7773488.
41. Sarkar S, Kang W, Jiang S, Li K, Ray S, Luther E, Ivanov AR, Fu Y, Konry T. Machine learning-aided quantification of antibody-based cancer immunotherapy by natural killer cells in microfluidic droplets. Lab on a Chip. 2020, 20(13):2317-2327. PMID: 32458907. PMCID: PMC7938931.
42. Gandham S, ^⸎Su X, ^⸙⸎Wood J, Nocera AL, Alli SC, Milane L, ^⸎Zimmerman A, Amiji M, and Ivanov AR*.  Technologies and Standardization in Research of Extracellular Vesicles. Trends in Biotechnology, 2020, 38(10):1066-1098. (Review) PMID: 32564882. PMCID: PMC7302792.
43. ^⸎Ali AS, Chen R, Raju R, Kshirsagar R, Gilbert A, Zang L, Karger BL, Ivanov AR*.  Multi-Omics Reveals Impact of Cysteine Feed Concentration and Resulting Redox Imbalance on Cellular Energy Metabolism and Specific Productivity in CHO Cell Bioprocessing.  Biotechnology Journal. 2020, 15(8):e1900565. Epub 2020 Apr 3. PMID: 32170810. PMCID: PMC7880547.
44. MacDonald JA, Bothun AM, Annis SN, Sheehan H, Ray S, ^⸎Gao Y, Ivanov AR, Khrapko K, Tilly JL, Woods DC.  A nanoscale, multi-parametric flow cytometry-based platform to study mitochondrial heterogeneity and mitochondrial DNA dynamics. Communications Biology. 2019, 2(1):258. PMID: 31925087.
45. Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri JL, Sarin R, Chen B, Lantz C, Jung W, ^⸎Johnson KR, ^#Koller A, Wolff JJ, Campuzano I.D.G., Auclair JR, Ivanov AR, Whitelegge JP, Paša-Tolić L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, Agar JN. Best Practices and Benchmarks for Intact Protein Analysis for Top-down Mass Spectrometry. Nature Methods. 2019;16(7):587-594. PMID: 31249407.
46. Schmitt ND, Rawlins CM, Randall EC, Wang X, ^#Koller A, Auclair JR, Kowalski JM, Kowalski PJ, Luther E, Ivanov AR, Agar NYR, Agar JN.  Genetically Encoded Fluorescent Proteins Enable High-Throughput Assignment of Cell Cohorts Directly from MALDI-MS Images. Analytical Chemistry, 2019; 91(6):3810-3817. PMID: 30839199.
47. ^⸎Ali AS, Raju R, Kshirsagar R, Ivanov AR, Gilbert A, Zang L, Karger BL. Multi-Omics Study on the Impact of Cysteine Feed Level on Cell Viability and mAb Production in a CHO Bioprocess.  Biotechnology Journal, 2019, 14(4):e1800352. PMID: 30485675
48. ^⸎Belov AM, Zang L, Sebastiano R, Santos MR, ^#Bush DR, Karger BL, Ivanov AR*. Complementary middle-down and intact monoclonal antibody proteoform characterization by capillary zone electrophoresis – mass spectrometry. Electrophoresis, 2018, 39(16) 2069-2082. PMID: 29749064 (Cover Story)
49. Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. How many human proteoforms are there?  Nature Chemical Biology, 2018, 14(3):206-214. PMID: 29443976.
50. ^⸎Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR*.  Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis – Native Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 2017, 28(12):2614-2634. PMID: 28875426
51. ^⸎Kreimer S, Ivanov AR*.  Rapid Isolation of Extracellular Vesicles from Blood Plasma with Size-Exclusion Chromatography Followed by Mass Spectrometry-Based Proteomic Profiling. Methods in Molecular Biology, 2017; 1660: 295-302. PMID: 28828666
52. ^⸎Kreimer S, ^⸎Gao Y, Ray S, Jin M, Tan Z, Mussa NA, Tao L, Li Z, Ivanov AR, Karger BL.  Host Cell Protein Profiling by Targeted and Untargeted Analysis of Data Independent Acquisition Mass Spectrometry Data with Parallel Reaction Monitoring Verification. Analytical Chemistry, 2017; 89(10):5294-5302. PMID: 28402653
53. Mallipeddi S, ^⸎Kreimer S, Zvonok N, Vemuri K, Karger BL, Ivanov AR, Makriyannis A.  Binding Site Characterization of AM1336, a Novel Covalent Inverse Agonist at Human Cannabinoid 2 Receptor, Using Mass Spectrometric Analysis. Journal of Proteome Research, 2017; 16(7):2419-2428. PMID: 28374590
54. ^⸎Kreimer S, Belov ME, Danielson WF, Levitsky LI, Gorshkov MV, Karger BL, and Ivanov AR*.  Advanced Precursor Ion Selection Algorithms for Increased Depth of Bottom-Up Proteomic Profiling. Journal of Proteome Research, 2016, Oct 7;15(10):3563-3573. PMID: 27569903.
55. ^⸎Gao Y, Ray S, Dai S, Ivanov AR, Abu-Absi NR, Lewis AM, Huang Z, Xing Z, Borys MC, Li ZJ, Karger BL.  Combined metabolomics and proteomics reveals hypoxia as a cause of lower productivity on scale-up to a 5000-liter CHO bioprocess. Biotechnology Journal, 2016, 11(9):1190-200. PMID: 27213298.
56. Moskovets EV and Ivanov AR*, Comparative studies on peak intensities and chromatographic separation of proteolytic digests, PTMs, and intact proteins obtained in the nanoLC-ESI MS analysis at room and elevated temperatures. Analytical and Bioanalytical Chemistry, 2016, 408(15):3953-68. PMID: 26898204.
57. Khoory J, Estanislau J, Elkhal A, Lazaar A, Melhorn MI, Brodsky A, Illigens B, Hamachi I, Kurishita Y, Ivanov AR, Shevkoplyas S, Shapiro NI, Ghiran IC.  Ligation of Glycophorin A Generates Reactive Oxygen Species Leading to Decreased Red Blood Cell Function. PLOS One, 2016, 11(1). PMID: 26784696.
58. Danielson KM, Estanislau J, Tigges J, Toxavidis V, Camacho V, Felton EJ, Khoory J, Kreimer S, Ivanov AR, Mantel PY, Jones J, Akuthota P, Das S, Ghiran I. Diurnal Variations of Circulating Extracellular Vesicles Measured by Nano Flow Cytometry. PLOS One, 2016, 11(1). PMID: 26745887
59. ^#Bush DR, Zang L, ^⸎Belov AM, Ivanov AR, Karger BL. High Resolution CZE-MS Quantitative Characterization of Intact Biopharmaceutical Proteins: Proteoforms of Interferon-β1. Analytical Chemistry, 2016; 88(2):1138-46. PMID: 26641950
60. Tarasova IA, Goloborodko AA, Perlova TY, Pridatchenko ML, Gorshkov AV, Evreinov VV, Ivanov AR*, Gorshkov MV*. Application of Statistical Thermodynamics to Predict the Adsorption Properties of Polypeptides in Reversed-Phase HPLC. Analytical Chemistry,  2015; 87(13):6562-9. PMID: 26023813.
61. Yeh JE, ^⸎Kreimer S, Walker SR, Emori MM, Krystal H, Richardson A, Ivanov AR, Frank DA. Granulin, a novel STAT3-interacting protein, enhances STAT3 transcriptional function and correlates with poorer prognosis in breast cancer. Genes Cancer., 2015, 6(3-4):153-68. PMID: 26000098.
62. ^⸎Kreimer S, ^⸎Belov AM, Ghiran I, Murthy SK, Frank DA, Ivanov AR.*  Mass-spectrometry-based molecular characterization of extracellular vesicles: lipidomics and proteomics. Journal of Proteome Research, 2015; 14(6):2367-84. PMID: 25927954. (Review)
63.  ^⸎Li S, Plouffe BD, ^⸎Belov AM, Ray S, Wang X, Murthy SK, Karger BL, Ivanov AR.*  An Integrated Platform for Isolation, Processing and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood. Molecular & Cellular Proteomics, 2015, 14(6):1672-83. PMID: 25755294. (Cover Story)
64.  Keskin DB, Reinhold BB, Zhang GL, Ivanov AR, Karger BL, Reinherz EL.  Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity.  Proceedings of the National Academy of Sciences of the USA,  2015, 112(7):2151-6.  PMID: 25646416.
65. Sun J, Zhang G, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V.  Pathway Analysis and Transcriptomics Improve Protein Identification by Shotgun Proteomics from Samples Comprising Small Numbers of Cells: A Benchmarking Study.  BMC Genomics, 2014, 15, S1  PMID: 25521637.
66. Mantel PY, Hoang AN, Goldowitz I, Potashnikova D, Hamza B, Vorobjev I, Ghiran I, Toner M, Irimia D, Ivanov AR, Barteneva N, Marti M. Malaria-infected erythrocyte-derived microvesicles mediate cellular communication within the parasite population and with the host immune system. Cell Host & Microbe, 2013, 13(5):521-34, PMID: 23684304
67. Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST.  Interlaboratory studies and initiatives developing standards for proteomics. Proteomics, 2013, 13(6):904-9. PMID: 23319436.
68. Momen-Heravi F, Balaj L, Alian S, Tigges J, Toxavidis V, Ericsson M, Distel RJ, Ivanov AR, Skog J, Kuo WP. Alternative methods for characterization of extracellular vesicles. Frontiers in Physiology, 2012, 3:354. PMID: 22973237.
69. Jafari M, Primo V, Smejkal GB, Moskovets EV, Kuo WP, Ivanov AR.* Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling. Electrophoresis, 2012, 33(16):2516-26. PMID: 22899259.
70. Powell BS, Lazarev AV, Carlson G, Ivanov AR, Rozak DA. Pressure cycling technology in systems biology. Methods Mol Biol. 2012; 881:27-62. PMID: 22639209.
71. Fu S, Li P, Yang L, Hofmann O, Dicker L, Hide W, Lin X, Watkins SM, Ivanov AR, and Hotamisligil GS, Aberrant lipid metabolism disrupts calcium homeostasis causing liver endoplasmic reticulum stress in obesity. Nature, 2011, 473(7348):528-31. PMID: 21532591.
72. Smejkal G, Rivas-Morello C, Chang RG, Freeman E, Trachtenberg A, Lazarev A, Ivanov AR, Kuo WP, Stabilization of Tissues and the Preservation of Protein Phosphorylation States for Two-Dimensional Gel Electrophoresis. Electrophoresis, 2011, 32(16):2206-15. PMID: 21792998.
73. Freeman E, Ivanov AR*, Proteomics under pressure: searching for effective alternatives for sample preparation in proteomics. Journal of Proteome Research, 2011, 10(12):5536-46. PMID: 22029901.
74. Dicker L, Lin X, Ivanov AR*, Increased Power for the Analysis of Label-Free LC-MS/MS Proteomic Data by Combining Spectral Counts and Peptide Peak Attributes. Molecular Cellular Proteomics, 2010, 9(12):2704-18. PMID: 20823122
75.  T.Y. Perlova; A.A. Goloborodko; Y. Margolin; M.L. Pridatchenko, I.A. Tarasova; A.V. Gorshkov; E. Moskovets; A.R. Ivanov*; M.V. Gorshkov*. Retention time prediction using the model of liquid chromatography of biomacromolecules at critical conditions in LC-MS phosphopeptide analysis. Proteomics, 2010, 10(19):3458-68. PMID: 20815086.
76.  Ivanov AR*, The state of proteome research at the Harvard School of Public Health Proteomics Resource. Expert Review of Proteomics, 2010, 7(4S): 31.
77. Freeman E, Ivanov AR*, Development of essential sample preparation techniques in proteomics using ultra-high pressure. Expert Review of Proteomics, 2010, 7(4S): 18.
78. Renard BY, Kirchner M, Monigatti F, Ivanov AR, Rappsilber J, Winter D, Steen JA, Hamprecht FA, Steen H. When Less Can Yield More – Computational Preprocessing of MS/MS Spectra for Peptide Identification. Proteomics, 2009, 9(21):4978-84.
79. Jones MR, Quinton LJ, Blahna MT, Fu S, Ivanov AR, Wolf DA, Mizgerd JP, Zcchc11 Directs cytokine expression by microRNA uridylation. Nature Cell Biology, 2009, 11(9):1157-63.
80. Albè E, Chang JH, Azar NF, Ivanov AR, Azar DT. Proteomic Analysis of the Hyaloid Vascular System Regression during Ocular Development. Journal of Proteome Research, 2008, 7(11):4904-4913.
81. Clements RT, Smejkal G, Sodha NR, Ivanov AR, Asara JM, Feng J, Lazarev A, Gautam S, Senthilnathan V, Khabbaz KR, Bianchi C, Sellke FW. Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass. Circulation, 2008, 118 (14 Suppl):S24-31.
82. Gross V, Carlson G, Kwan AT, Smejkal G, Freeman E, Ivanov AR, Lazarev A, Tissue Fractionation by Hydrostatic Pressure Cycling Technology: The Unified Sample Preparation Technique for Systems Biology Studies. Journal of Biomolecular Techniques, 2008, 19(3): 189–199
83.  Schmidt MW, Houseman A, Ivanov AR, Wolf DA, Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe, Molecular Systems Biology, 2007, 3:79.
84. Heilig EA, Thompson KJ, Molina RM, Ivanov AR, Brain JD, Wessling-Resnick M. Manganese and Iron Transport Across Pulmonary Epithelium. American Journal of Physiology – Lung Cellular and Molecular Physiology, 2006, 290(6):L1247-59
85. Zhou C, Arslan F, Wee S, Krishnan S, Ivanov AR, Oliva A, Leatherwood J, Wolf DA, PCI Proteins eIF3e and eIF3m Define Distinct Translation Initiation Factor 3 Complexes, BMC Biology, 2005, 3:14.
86. Baczek T, Bucinski A, Ivanov AR, Kaliszan R. Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics. Analytical Chemistry, 2004, 76, 1726-1732.
87. Andreev VP, Rejtar T, Chen H-S, Moscovets, EV, Ivanov AR, Karger BL. A universal denoising and peak picking algorithm for LC-MS based on matched filtration in the chromatographic time domain. Analytical Chemistry, 2003, 75, 6314-6326.
88. Ivanov AR, Horvath C, Karger BL. High-efficiency peptide analysis on monolithic multi-mode capillary columns: pressure assisted CEC/CE coupled to UV and ESI-MS. Electrophoresis. 2003, 24 No. 21, 3663-3673.
89.  Ivanov AR, Zang L, Karger BL. Low Attomole ESI-MS/MS Analysis of tryptic peptides using 20-μm I.D. monolithic capillary columns. Analytical Chemistry, 2003, 75, 5306-5316.
90. Ivanov AR, Nazimov IV, Baratova LA. Determination of biologically active low-molecular-mass thiols in human blood. II. High-performance capillary electrophoresis with photometric detection. Journal of Chromatography A, 2000; 20: 895(1-2):167-171.
91.  Ivanov AR, Nazimov IV, Baratova LA. Determination of biologically active low-molecular-mass thiols in human blood. I. Fast qualitative and quantitative, gradient and isocratic reversed-phase high-performance liquid chromatography with photometric and fluorescence detection.  Journal of Chromatography A, 2000; 20:895(1-2):157-166.
92. Ivanov AR, Nazimov IV. Identification of unusual (modified and non-encoded) amino acid residues in peptides by combinations of high-performance liquid chromatography and high-performance capillary electrophoresis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Journal of Chromatography A, 2000; 18:870(1-2):255-269.
93. Ivanov AR, Nazimov IV, Baratova LA. Qualitative and quantitative determination of biologically active low-molecular-mass thiols in human blood by reversed-phase high-performance liquid chromatography with photometry and fluorescence detection. Journal of Chromatography A, 2000;18:870(1-2):433-442.
94. Ivanov AR, Nazimov IV, Lobazov AP, Popkovich GB. Direct determination of amino acids and carbohydrates by high-performance capillary electrophoresis with refractometric detection. Journal of Chromatography A, 2000;13:894(1-2):253-257.

Books:

Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer. 2011, ISBN: 978-94-007-0758-0. (As of January 2015: over 60,000 downloads, which placed the book sales in the top 5% of all Springer’s book portfolio on Biomedicine, Life Sciences and Clinical Medicine).

Book Chapters:

6.  A.J. Zimmerman, M. Gregus, and A.R. Ivanov, Comprehensive Micro-SPE-Based Bottom-Up Proteomic Workflow for Sensitive Analysis of Limited Samples. In Mass Spectrometry Based Single Cell Proteomics: Methods and Protocols. Springer, 2024. DOI: 10.1007/978-1-0716-3934-4_3. Ed.: Akos Vegvari, Jaakko Teppo, and Roman A. Zubarev

5.  P.S. Powell, A.V. Lazarev, G. Carlson, A.R. Ivanov, D.A. Rozak, Pressure Cycling Technology in Systems Biology. In Microbial Systems Biology: Methods and Protocols. In Methods in Molecular Biology, Humana. Press, Springer, New York. Ed.: Ali Navid, Chapter 17, 2013.

4.  E. Freeman, V. Gross, I. Romanovsky, A. Lazarev, A.R. Ivanov, Adipose Tissue Lysis and Protein Extraction Followed by MS-based Proteomic Profiling Reveals Constituents of Oxidative Stress in Obesity. In Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer, Chapter 30, 2011, ISBN: 978-94-007-0758-0.

3.  E. Freeman, Y. Margolin, A.R. Ivanov, Pressure-Assisted Lysis of Mammalian Cell Cultures Prior to Proteomic Analysis. In Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer, Chapter 5, 2011, ISBN: 978-94-007-0758-0.

2.  A.V.Lazarev, A.R. Ivanov, Materialistic Dualism of Sample Preparation: Boring but Important! In Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer, Chapter 1, 2011, ISBN: 978-94-007-0758-0.

1.  Ivanov AR, Polymeric Monolithic Capillary Columns in Proteomics. In Separation Methods in Proteomics. Eds.: Smejkal GB, Lazarev A, Apex Publishing, LLC, Chapter 22, 419-435, 2005.

Patents Granted:

Ivanov AR, Zang L, Karger BL.  Narrow I.D. (50-µm I.D. or less) Monolithic capillary columns coupled to electrospray ionization mass spectrometry for high-efficiency separation and high-sensitive analysis of biomolecules. US patent # US 8,691,088.

Moskovets E, Ivanov AR, Doroshenko V. A thermo-stabilized nano- and micro-flow LC/ESI-MS interface and a method thereof. US Patent # US 8,410,434 B1.