{"entity": "researcher", "timestamp": "2026-08-20T21:05:00.533Z", "family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "affiliations": ["Proteomics Center of Excellence & Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8"}}, "publications": [{"entity": "publication", "iuid": "a03d7d7db4af4dc482c16af3f719109f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a03d7d7db4af4dc482c16af3f719109f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a03d7d7db4af4dc482c16af3f719109f"}}, "title": "Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.", "authors": [{"family": "Quardokus", "given": "Ellen M", "initials": "EM", "orcid": "0000-0001-7655-4833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f0359f5e2f9438aaf591324f1110f64.json"}}, {"family": "Saunders", "given": "Diane C", "initials": "DC", "orcid": "0000-0002-8849-6746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/764f92d32a0d4f2d8c62e84e320ea4ba.json"}}, {"family": "McDonough", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-7524-8260", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa249579f8a94bfcadd1431c1e636832.json"}}, {"family": "Hickey", "given": "John W", "initials": "JW", "orcid": "0000-0001-9961-7673", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/674e42e6f0594fd3960adce6260edf93.json"}}, {"family": "Werlein", "given": "Christopher", "initials": "C", "orcid": "0000-0002-7694-4257", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bc20043daa148b69de69326f6967b10.json"}}, {"family": "Surrette", "given": "Christine", "initials": "C"}, {"family": "Rajbhandari", "given": "Presha", "initials": "P"}, {"family": "Casals", "given": "Anna Martinez", "initials": "AM"}, {"family": "Tian", "given": "Hua", "initials": "H", "orcid": "0000-0002-3598-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cce345ef74b347a7a83076f63c53a23d.json"}}, {"family": "Lowery", "given": "Lisa", "initials": "L"}, {"family": "Neumann", "given": "Elizabeth K", "initials": "EK"}, {"family": "Bj\u00f6rklund", "given": "Frida", "initials": "F"}, {"family": "Neelakantan", "given": "Taruna V", "initials": "TV"}, {"family": "Croteau", "given": "Josh", "initials": "J", "orcid": "0000-0002-8142-0482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5a325b6e1504a8186376dfcfe054a0d.json"}}, {"family": "Wiblin", "given": "Anne E", "initials": "AE", "orcid": "0000-0002-6087-5701", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79355cecf5634e95af8212a4b930782e.json"}}, {"family": "Fisher", "given": "Jeremy", "initials": "J", "orcid": "0000-0002-7296-586X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/165c4a5e54ad4d708f8b2501c71d5e12.json"}}, {"family": "Livengood", "given": "April J", "initials": "AJ"}, {"family": "Dowell", "given": "Karen G", "initials": "KG"}, {"family": "Silverstein", "given": "Jonathan C", "initials": "JC", "orcid": "0000-0002-9252-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a174aa154fd43619faa4d0f09f15e92.json"}}, {"family": "Spraggins", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0001-9198-5498", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20c2567cc66e4915b5536d311961bfbf.json"}}, {"family": "Pryhuber", "given": "Gloria S", "initials": "GS", "orcid": "0000-0002-9185-3994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c259a8236344b128624553ee3c91c58.json"}}, {"family": "Deutsch", "given": "Gail", "initials": "G"}, {"family": "Ginty", "given": "Fiona", "initials": "F"}, {"family": "Nolan", "given": "Garry P", "initials": "GP"}, {"family": "Melov", "given": "Simon", "initials": "S", "orcid": "0000-0001-8554-2834", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cdf3f65ef70d402ea2593dc6a93b52db.json"}}, {"family": "Jonigk", "given": "Danny", "initials": "D", "orcid": "0000-0002-5251-2281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/89891e1c3e104ae88a82c6c147e34c7d.json"}}, {"family": "Caldwell", "given": "Michael A", "initials": "MA"}, {"family": "Vlachos", "given": "Ioannis S", "initials": "IS", "orcid": "0000-0002-8849-808X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/486d1c8f0d984011ac065a50699bfa99.json"}}, {"family": "Muller", "given": "Werner", "initials": "W", "orcid": "0000-0002-1297-9725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d69ed7ac3f0046369857b4ae1c55ad4b.json"}}, {"family": "Gehlenborg", "given": "Nils", "initials": "N", "orcid": "0000-0003-0327-8297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f7f88927584d80b6b5a5447b20dfdb.json"}}, {"family": "Stockwell", "given": "Brent R", "initials": "BR", "orcid": "0000-0002-3532-3868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81510049c217404d9363381818ba6446.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Snyder", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9e294ff3b64f7caa770c883d12514c.json"}}, {"family": "Germain", "given": "Ronald N", "initials": "RN", "orcid": "0000-0003-1495-9143", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bc6225f3eef4506a319016701a261d8.json"}}, {"family": "Camarillo", "given": "Jeannie M", "initials": "JM"}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "B\u00f6rner", "given": "Katy", "initials": "K", "orcid": "0000-0002-3321-6137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b8e7ebf67ae49e3b436a7c1252f7126.json"}}, {"family": "Radtke", "given": "Andrea J", "initials": "AJ", "orcid": "0000-0003-4379-8967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c54f64fc7c54f7d9279266878839455.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "20", "issue": "8", "pages": "1174-1178", "issn-l": "1548-7091"}, "abstract": "Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.", "doi": "10.1038/s41592-023-01846-7", "pmid": "37468619", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10406602"}, {"db": "pii", "key": "10.1038/s41592-023-01846-7"}], "notes": [], "created": "2026-08-20T09:02:53.512Z", "modified": "2026-08-20T09:02:54.263Z"}, {"entity": "publication", "iuid": "0f57550e021d409b9b359cb41520fee2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0f57550e021d409b9b359cb41520fee2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0f57550e021d409b9b359cb41520fee2"}}, "title": "Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?", "authors": [{"family": "Plubell", "given": "Deanna L", "initials": "DL", "orcid": "0000-0002-6580-8073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c353f24426604d199be325edcde06be7.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Webb-Robertson", "given": "Bobbie-Jo", "initials": "BJ"}, {"family": "Bramer", "given": "Lisa M", "initials": "LM", "orcid": "0000-0002-8384-1926", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e214d736fc5d44d3be3baff22c478df2.json"}}, {"family": "Ives", "given": "Ashley", "initials": "A", "orcid": "0000-0002-1318-5732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f27079ba95934664ab1fc288fa121cbf.json"}}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "Smith", "given": "Lloyd M", "initials": "LM"}, {"family": "Montine", "given": "Thomas J", "initials": "TJ", "orcid": "0000-0002-1346-2728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a2c2ba8b0d49ccb31bceea9e11206b.json"}}, {"family": "Wu", "given": "Christine C", "initials": "CC"}, {"family": "MacCoss", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1853-0256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603.json"}}], "type": "journal article", "published": "2022-04-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "21", "issue": "4", "pages": "891-898", "issn-l": "1535-3893"}, "abstract": "Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. Commonly, a single quantitative value is reported for each protein-coding gene by aggregating peptide quantities into protein groups following protein inference or parsimony. However, given the complexity of both RNA splicing and post-translational protein modification, it is overly simplistic to assume that all peptides that map to a singular protein-coding gene will demonstrate the same quantitative response. By assuming that all peptides from a protein-coding sequence are representative of the same protein, we may miss the discovery of important biological differences. To capture the contributions of existing proteoforms, we need to reconsider the practice of aggregating protein values to a single quantity per protein-coding gene.", "doi": "10.1021/acs.jproteome.1c00894", "pmid": "35220718", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1789966"}, {"db": "pmc", "key": "PMC8976764"}], "notes": [], "created": "2026-08-20T08:11:26.625Z", "modified": "2026-08-20T08:11:26.897Z"}, {"entity": "publication", "iuid": "e2d4fb84644f47e5a2a95070b950ad34", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e2d4fb84644f47e5a2a95070b950ad34.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e2d4fb84644f47e5a2a95070b950ad34"}}, "title": "The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.", "authors": [{"family": "Melani", "given": "Rafael D", "initials": "RD", "orcid": "0000-0002-0349-235X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1a600cae8fc94b58b9cdea65860575d6.json"}}, {"family": "Gerbasi", "given": "Vincent R", "initials": "VR", "orcid": "0000-0001-5573-0578", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d1f20c4ecca5498989be77da3d7ebe13.json"}}, {"family": "Anderson", "given": "Lissa C", "initials": "LC", "orcid": "0000-0001-8633-0251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48fec347905f4530bbb8a3fa00f43707.json"}}, {"family": "Sikora", "given": "Jacek W", "initials": "JW", "orcid": "0000-0003-0240-567X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a83a3f7d4ce34f2baa775364ab9727d4.json"}}, {"family": "Toby", "given": "Timothy K", "initials": "TK", "orcid": "0000-0001-9599-7410", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f02525713c9424ea4eb49093957a599.json"}}, {"family": "Hutton", "given": "Josiah E", "initials": "JE", "orcid": "0000-0002-5518-9651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4f0319c95ef43f2b64e48d562111ef0.json"}}, {"family": "Butcher", "given": "David S", "initials": "DS", "orcid": "0000-0002-1268-4150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c44374c245dd47e8b453929795746875.json"}}, {"family": "Negr\u00e3o", "given": "Fernanda", "initials": "F"}, {"family": "Seckler", "given": "Henrique S", "initials": "HS"}, {"family": "Srzenti\u0107", "given": "Kristina", "initials": "K"}, {"family": "Fornelli", "given": "Luca", "initials": "L", "orcid": "0000-0001-6334-1046", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7082cd63d2d84cc4a01c7c75ad8d391c.json"}}, {"family": "Camarillo", "given": "Jeannie M", "initials": "JM", "orcid": "0000-0001-9699-0931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9748d9540a241a6a67f5895cb10943e.json"}}, {"family": "LeDuc", "given": "Richard D", "initials": "RD", "orcid": "0000-0002-6951-2923", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfae785b55854c1ea8e853e5453057af.json"}}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Greer", "given": "Joseph B", "initials": "JB", "orcid": "0000-0002-3865-9279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1292d4e7b7f466dab8f244c570bec64.json"}}, {"family": "Fellers", "given": "Ryan T", "initials": "RT", "orcid": "0000-0002-0710-3462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/434ef23c16594c9d9e3214489e687230.json"}}, {"family": "Robey", "given": "Matthew T", "initials": "MT", "orcid": "0000-0002-3596-9597", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eef54cb504854df988d144f324d56000.json"}}, {"family": "DeHart", "given": "Caroline J", "initials": "CJ", "orcid": "0000-0002-5652-700X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22e443e2bf7f4bb0a24ab8a3c3edcb37.json"}}, {"family": "Forte", "given": "Eleonora", "initials": "E"}, {"family": "Hendrickson", "given": "Christopher L", "initials": "CL", "orcid": "0000-0002-4272-2939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b244246e07f64ad1be05e3683d9cf232.json"}}, {"family": "Abbatiello", "given": "Susan E", "initials": "SE", "orcid": "0000-0001-7477-2749", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4645aa8d27bc4087aeecc2b669b26171.json"}}, {"family": "Thomas", "given": "Paul M", "initials": "PM", "orcid": "0000-0003-2887-4765", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/102e9862b7f24f60a72167590647c4db.json"}}, {"family": "Kokaji", "given": "Andy I", "initials": "AI"}, {"family": "Levitsky", "given": "Josh", "initials": "J", "orcid": "0000-0001-7527-6093", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a055a69de9f64282884ea5153df9a772.json"}}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}], "type": "journal article", "published": "2022-01-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "375", "issue": "6579", "pages": "411-418", "issn-l": "0036-8075"}, "abstract": "Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of ~30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma from human blood and bone marrow. The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. We demonstrate the potential for clinical application, by interrogating the BPA in the context of liver transplantation and identifying cell and proteoform signatures that distinguish normal graft function from acute rejection and other causes of graft dysfunction.", "doi": "10.1126/science.aaz5284", "pmid": "35084980", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1792185"}, {"db": "pmc", "key": "PMC9097315"}], "notes": [], "created": "2026-08-20T11:59:16.945Z", "modified": "2026-08-20T11:59:17.758Z"}, {"entity": "publication", "iuid": "9b67e9b516cb40128033ab972207b9fa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9b67e9b516cb40128033ab972207b9fa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9b67e9b516cb40128033ab972207b9fa"}}, "title": "Can we put Humpty Dumpty back together again? What does protein quantification mean in bottom-up proteomics?", "authors": [{"family": "Plubell", "given": "Deanna L", "initials": "DL", "orcid": "0000-0002-6580-8073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c353f24426604d199be325edcde06be7.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Webb-Robertson", "given": "Bobbie Jo", "initials": "BJ", "orcid": "0000-0002-4744-2397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6a368f002a24dd996fecb43b53a6a2c.json"}}, {"family": "Bramer", "given": "Lisa", "initials": "L"}, {"family": "Ives", "given": "Ashley", "initials": "A"}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "Smith", "given": "Lloyd M", "initials": "LM"}, {"family": "Montine", "given": "Thomas J", "initials": "TJ"}, {"family": "Wu", "given": "Christine C", "initials": "CC"}, {"family": "MacCoss", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1853-0256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603.json"}}], "type": "posted-content", "published": "2021-01-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.01.25.428175", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:01:15.591Z", "modified": "2026-08-20T10:01:15.707Z"}]}