S. Joshua Swamidass | |
---|---|
Nationality | American |
Occupation(s) | Computational biologist, physician, and academic |
Academic background | |
Education | B.S., Biological Sciences M.S., Information and Computer Sciences Ph.D., Information and Computer Sciences M.D. |
Alma mater | University of California, Irvine Washington University in St. Louis |
Academic work | |
Institutions | Washington University School of Medicine |
S. Joshua Swamidass is an American computational biologist,physician,academic,and author. He is an associate professor of Laboratory and Genomic Medicine,and a Faculty Lead of Translational Bioinformatics in the Institute for Informatics at Washington University in St. Louis. [1]
Swamidass has published over 150 articles. He focuses his research on applications of statistical machine learning and decision theory in the context of chemical biology and medicine. He has also worked on drug discovery,drug metabolism,and translational research. Swamidass is the founder of "Peaceful Science," where he writes regarding the advancement of the civic practice of science. [2] He also serves as an Associate Editor for BMC Medical Informatics and Decision Making. In 2019 he published The Genealogical Adam and Eve.
In 2022,Swamidass became a fellow of the American Academy for Advancement of Science. [3]
Swamidass studied at the University of California,Irvine,and received his bachelor's degree in Biological Sciences in 2000,and master's degree and Doctoral degree in Information and Computer Sciences in 2006 and 2007,respectively. In 2009,he earned his Medical Doctorate degree and subsequently joined Washington University in St. Louis to complete his Clinical Pathology Residency. [1]
Swamidass held appointment as an instructor in the Department of Immunology and Pathology at Washington University School of Medicine in 2010,and was promoted to the position of assistant professor of Laboratory and Genomic Medicine in 2011. He has been serving as a Faculty Lead of Translational Bioinformatics since 2017,and as associate professor of Laboratory and Genomic Medicine since 2018. [1]
Swamidass’research primarily focuses on artificial intelligence applied to scientific problems at the intersection of medicine,biology,and chemistry. [4] His works in the field has been featured in WIRED [5] and The Wall Street Journal . [6]
In his studies of chemical informatics,Swamidass introduced three new kernels:Tanimoto,MinMax,and Hybrid,based on the idea of molecular fingerprints. He studied the properties and tradeoffs of these kernels,and also discussed their applications in terms of predicting mutagenicity,toxicity,and anti-cancer activity on three publicly available data sets. [7] In 2013,he demonstrated that artificial intelligence algorithms can predict metabolic transformations of xenobiotic molecules,and highlighted the role of these processes in the safety,efficacy,and dose of medicines. [8] He also developed and explored algorithms regarding fast exact searches of chemical fingerprints in linear and sub-linear time. [9] He,along with co-authors developed a novel screening method,Influence Relevance Voter (IRV),and provided its advantages over other SVMs and other methods. [10] Moreover,he focused his study to highlight opportunities and obstacles for deep learning in biology and medicine. [11]
Swamidass studied drug metabolism, [12] described its impacts in the context of patient morbidity and mortality,and provided new directions such as joint metabolism and reactivity modeling. [13] While focusing on open source drug discovery with the malaria box,he suggested mechanisms of action for the compounds active in killing multiple life-cycle stages of the malaria parasite,and also defined the processes to catalyze drug discovery for dozens of different indications. [14]
Swamidass published The Genealogical Adam and Eve:The Surprising Science of Universal Ancestry in 2019 based on implications of recent universal genealogical ancestry regarding the theology of the image of God,the fall,and people outside the garden. [15] The appendix includes Swamidass' work The Resurrection,Evidence,and The Scientist,which discusses his reasons for belief in the resurrection of Jesus. [16] In his interview with “BibleProject Podcast”,he discussed the differences between genealogical ancestry and genetic ancestry,and explored the conflict that exists between evolutionary science and creationism. Furthermore,he stated "The genealogical account does not prove [Adam and Eve’s existence],but it’s impossible to disprove the existence of such a couple 6,000 years ago." [17] Anjeanette Roberts praised Swamidass’work and stated that in his book the emphasis on "genealogical ancestry is so clearly biblical that its long-term absence in evangelical conversations about human origins is shocking" and the work also helps to remove "the enmity and barriers that divide scientists,theologians,exegetes,evolutionists,and creationists." [18] Nathan H. Lents thought the book's "bold attempt" to find a place for Adam and Eve within the scientific understanding of human ancestry might help reconcile evangelicals to evolutionary science,and science in general,but thought it unlikely to persuade scientists of a role for the Genesis narrative in human origins. [19]
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: CS1 maint: location missing publisher (link)Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
Cheminformatics refers to the use of physical chemistry theory with computer and information science techniques—so called "in silico" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields. Such in silico techniques are used, for example, by pharmaceutical companies and in academic settings to aid and inform the process of drug discovery, for instance in the design of well-defined combinatorial libraries of synthetic compounds, or to assist in structure-based drug design. The methods can also be used in chemical and allied industries, and such fields as environmental science and pharmacology, where chemical processes are involved or studied.
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KEGG is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
This page describes mining for molecules. Since molecules may be represented by molecular graphs this is strongly related to graph mining and structured data mining. The main problem is how to represent molecules while discriminating the data instances. One way to do this is chemical similarity metrics, which has a long tradition in the field of cheminformatics.
Chlorcyclizine is a first-generation antihistamine of the diphenylmethylpiperazine group marketed in the United States and certain other countries. It is used primarily to treat allergy symptoms such as rhinitis, urticaria, and pruritus, and may also be used as an antiemetic. In addition to its antihistamine effects, chlorcyclizine also has some anticholinergic, antiserotonergic, and local anesthetic properties. It also has been studied as a potential treatment for various flaviviruses like Hepatitis C and Zika Virus.
Søren Brunak is a Danish biological and physical scientist working in bioinformatics, systems biology, and medical informatics. He is a professor of Disease Systems Biology at the University of Copenhagen and professor of bioinformatics at the Technical University of Denmark. As Research Director at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen Medical School, he leads a research effort where molecular-level systems biology data are combined with phenotypic data from the healthcare sector, such as electronic patient records, registry information, and biobank questionnaires. A major aim is to understand the network biology basis for time-ordered comorbidities and discriminate between treatment-related disease correlations and other comorbidities in disease trajectories. Søren Brunak also holds a position as a Medical Informatics Officer at Rigshospitalet, the Capital Region of Denmark.
Chemical similarity refers to the similarity of chemical elements, molecules or chemical compounds with respect to either structural or functional qualities, i.e. the effect that the chemical compound has on reaction partners in inorganic or biological settings. Biological effects and thus also similarity of effects are usually quantified using the biological activity of a compound. In general terms, function can be related to the chemical activity of compounds.
ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug inducing properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK.
Ming-Ming Zhou is an American scientist who focuses on structural and chemical biology, NMR spectroscopy, and drug design. He is the Dr. Harold, Golden Lamport Professor, and Chairman of the Department of Pharmacological Sciences. He is also the Co-Director of the Drug Discovery Institute at the Icahn School of Medicine at Mount Sinai and Mount Sinai Health System in New York City, as well as Professor of Sciences.
Translational bioinformatics (TBI) is a field that emerged in the 2010s to study health informatics, focused on the convergence of molecular bioinformatics, biostatistics, statistical genetics and clinical informatics. Its focus is on applying informatics methodology to the increasing amount of biomedical and genomic data to formulate knowledge and medical tools, which can be utilized by scientists, clinicians, and patients. Furthermore, it involves applying biomedical research to improve human health through the use of computer-based information system. TBI employs data mining and analyzing biomedical informatics in order to generate clinical knowledge for application. Clinical knowledge includes finding similarities in patient populations, interpreting biological information to suggest therapy treatments and predict health outcomes.
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eTOX is a temporary consortium established in 2010 to share and use toxicology data. It is a pre-competitive collaboration which main goal is to create and distribute tools to predict drug side-effects based on pre-clinical experiments. Aims are a better in silico predictability of potential adverse events and a decrease of the use of animals in toxicological research. eTOX is funded by the Innovative Medicines Initiative (IMI).
Marta Filizola is a computational biophysicist who studies membrane proteins. Filizola's research concerns drug discovery the application of methods of computational chemistry and theoretical chemistry to biochemical and biomedical problems.
Gary Bryce Fogel is an American biologist and computer scientist. He is the Chief Executive Officer of Natural Selection, Inc. He is most known for his applications of computational intelligence and machine learning to bioinformatics, computational biology, and industrial optimization.
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Jason W. Locasale is an American scientist and university professor. His focus is on metabolism.
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