{"entity": "researcher", "timestamp": "2026-08-20T20:34:39.385Z", "family": "Woodruff", "given": "Tracey J", "initials": "TJ", "orcid": "0000-0003-3622-1297", "affiliations": ["Program on Reproductive Health and the Environment, University of California San Francisco, San Francisco, California 94143, United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ad211bff7564b65ad1a4d6468e0e6b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ad211bff7564b65ad1a4d6468e0e6b7"}}, "publications": [{"entity": "publication", "iuid": "023bdd58c44b4cc6950747cccc3975b3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/023bdd58c44b4cc6950747cccc3975b3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/023bdd58c44b4cc6950747cccc3975b3"}}, "title": "In Silico Structure Predictions for Non-targeted Analysis: From Physicochemical Properties to Molecular Structures.", "authors": [{"family": "Abrahamsson", "given": "Dimitri", "initials": "D", "orcid": "0000-0002-3402-7565", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92f4f8c958e34d8d8a09d629080e6f2a.json"}}, {"family": "Siddharth", "given": "Adi", "initials": "A"}, {"family": "Young", "given": "Thomas M", "initials": "TM", "orcid": "0000-0001-7217-4753", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b7d40a5b1cf4c3497a5f14a176b8352.json"}}, {"family": "Sirota", "given": "Marina", "initials": "M"}, {"family": "Park", "given": "June-Soo", "initials": "JS"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02199c0d99674e2ea5e96e6589c07a00.json"}}, {"family": "Woodruff", "given": "Tracey J", "initials": "TJ", "orcid": "0000-0003-3622-1297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ad211bff7564b65ad1a4d6468e0e6b7.json"}}], "type": "journal article", "published": "2022-07-06", "journal": {"title": "J. Am. Soc. Mass Spectrom.", "issn": "1879-1123", "volume": "33", "issue": "7", "pages": "1134-1147", "issn-l": "1044-0305"}, "abstract": "While important advances have been made in high-resolution mass spectrometry (HRMS) and its applications in non-targeted analysis (NTA), the number of identified compounds in biological and environmental samples often does not exceed 5% of the detected chemical features. Our aim was to develop a computational pipeline that leverages data from HRMS but also incorporates physicochemical properties (equilibrium partition ratios between organic solvents and water; Ksolvent-water) and can propose molecular structures for detected chemical features. As these physicochemical properties are often sufficiently different across isomers, when put together, they can form a unique profile for each isomer, which we describe as the \"physicochemical fingerprint\". In our study, we used a comprehensive database of compounds that have been previously reported in human blood and collected their Ksolvent-water values for 129 partitioning systems. We used RDKit to calculate the number of RDKit fragments and the number of RDKit bits per molecule. We then developed and trained an artificial neural network, which used as an input the physicochemical fingerprint of a chemical feature and predicted the number and types of RDKit fragments and RDKit bits present in that structure. These were then used to search the database and propose chemical structures. The average success rate of predicting the right chemical structure ranged from 60 to 86% for the training set and from 48 to 81% for the testing set. These observations suggest that physicochemical fingerprints can assist in the identification of compounds with NTA and substantially improve the number of identified compounds.", "doi": "10.1021/jasms.1c00386", "pmid": "35649165", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1826615"}, {"db": "pmc", "key": "PMC9365522"}], "notes": [], "created": "2026-08-20T08:43:59.662Z", "modified": "2026-08-20T08:43:59.760Z"}, {"entity": "publication", "iuid": "f1336fd3bdbe4d0fab56982fc188721c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f1336fd3bdbe4d0fab56982fc188721c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f1336fd3bdbe4d0fab56982fc188721c"}}, "title": "Defining the Scope of Exposome Studies and Research Needs from a Multidisciplinary Perspective.", "authors": [{"family": "Zhang", "given": "Pei", "initials": "P", "orcid": "0000-0003-2054-928X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e4af492258b4256992af0279c823400.json"}}, {"family": "Carlsten", "given": "Christopher", "initials": "C"}, {"family": "Chaleckis", "given": "Romanas", "initials": "R", "orcid": "0000-0001-8042-1005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/012934b6c4a64891b76722fbda1e0f28.json"}}, {"family": "Hanhineva", "given": "Kati", "initials": "K", "orcid": "0000-0001-6834-7375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b66883342d1b45938f17d75e73479d50.json"}}, {"family": "Huang", "given": "Mengna", "initials": "M", "orcid": "0000-0002-4626-4816", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baf43d2b06f746078bd69385c9e6cf93.json"}}, {"family": "Isobe", "given": "Tomohiko", "initials": "T", "orcid": "0000-0001-9235-1227", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67986b3e12c1468c9b7cea2709e233a1.json"}}, {"family": "Koistinen", "given": "Ville M", "initials": "VM"}, {"family": "Meister", "given": "Isabel", "initials": "I"}, {"family": "Papazian", "given": "Stefano", "initials": "S"}, {"family": "Sdougkou", "given": "Kalliroi", "initials": "K"}, {"family": "Xie", "given": "Hongyu", "initials": "H"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02199c0d99674e2ea5e96e6589c07a00.json"}}, {"family": "Rappaport", "given": "Stephen M", "initials": "SM", "orcid": "0000-0002-3806-0848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da3132c271b34cc8a758560a68fe241b.json"}}, {"family": "Tsugawa", "given": "Hiroshi", "initials": "H", "orcid": "0000-0002-2015-3958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703a87b2e3444d8ba917253d25d5556.json"}}, {"family": "Walker", "given": "Douglas I", "initials": "DI", "orcid": "0000-0003-2912-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4712c06efd674e4b96f494e33ab9084f.json"}}, {"family": "Woodruff", "given": "Tracey J", "initials": "TJ", "orcid": "0000-0003-3622-1297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ad211bff7564b65ad1a4d6468e0e6b7.json"}}, {"family": "Wright", "given": "Robert O", "initials": "RO"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-8113-0653", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d98abddc2b14a35ade5cb6d6d2f540d.json"}}], "type": "journal article", "published": "2021-10-12", "journal": {"title": "Environ Sci Technol Lett", "issn": "2328-8930", "volume": "8", "issue": "10", "pages": "839-852", "issn-l": null}, "abstract": "The concept of the exposome was introduced over 15 years ago to reflect the important role that the environment exerts on health and disease. While originally viewed as a call-to-arms to develop more comprehensive exposure assessment methods applicable at the individual level and throughout the life course, the scope of the exposome has now expanded to include the associated biological response. In order to explore these concepts, a workshop was hosted by the Gunma University Initiative for Advanced Research (GIAR, Japan) to discuss the scope of exposomics from an international and multidisciplinary perspective. This Global Perspective is a summary of the discussions with emphasis on (1) top-down, bottom-up, and functional approaches to exposomics, (2) the need for integration and standardization of LC- and GC-based high-resolution mass spectrometry methods for untargeted exposome analyses, (3) the design of an exposomics study, (4) the requirement for open science workflows including mass spectral libraries and public databases, (5) the necessity for large investments in mass spectrometry infrastructure in order to sequence the exposome, and (6) the role of the exposome in precision medicine and nutrition to create personalized environmental exposure profiles. Recommendations are made on key issues to encourage continued advancement and cooperation in exposomics.", "doi": "10.1021/acs.estlett.1c00648", "pmid": "34660833", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8515788"}], "notes": [], "created": "2026-08-20T08:10:04.602Z", "modified": "2026-08-20T08:10:05.065Z"}]}