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Tensor-structured decomposition improves systems serology analysis.
Tan, Zhixin Cyrillus; Murphy, Madeleine C; Alpay, Hakan S; Taylor, Scott D; Meyer, Aaron S.
  • Tan ZC; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA.
  • Murphy MC; Computational and Systems Biology, University of California, Los Angeles, Los Angeles, CA, USA.
  • Alpay HS; Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
  • Taylor SD; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.
  • Meyer AS; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA.
Mol Syst Biol ; 17(9): e10243, 2021 09.
Article in English | MEDLINE | ID: covidwho-1395372
ABSTRACT
Systems serology provides a broad view of humoral immunity by profiling both the antigen-binding and Fc properties of antibodies. These studies contain structured biophysical profiling across disease-relevant antigen targets, alongside additional measurements made for single antigens or in an antigen-generic manner. Identifying patterns in these measurements helps guide vaccine and therapeutic antibody development, improve our understanding of diseases, and discover conserved regulatory mechanisms. Here, we report that coupled matrix-tensor factorization (CMTF) can reduce these data into consistent patterns by recognizing the intrinsic structure of these data. We use measurements from two previous studies of HIV- and SARS-CoV-2-infected subjects as examples. CMTF outperforms standard methods like principal components analysis in the extent of data reduction while maintaining equivalent prediction of immune functional responses and disease status. Under CMTF, model interpretation improves through effective data reduction, separation of the Fc and antigen-binding effects, and recognition of consistent patterns across individual measurements. Data reduction also helps make prediction models more replicable. Therefore, we propose that CMTF is an effective general strategy for data exploration in systems serology.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: AIDS Serodiagnosis / HIV Infections / Data Interpretation, Statistical / COVID-19 Serological Testing / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Vaccines Limits: Humans Language: English Journal: Mol Syst Biol Journal subject: Molecular Biology / Biotechnology Year: 2021 Document Type: Article Affiliation country: Msb.202110243

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Full text: Available Collection: International databases Database: MEDLINE Main subject: AIDS Serodiagnosis / HIV Infections / Data Interpretation, Statistical / COVID-19 Serological Testing / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Vaccines Limits: Humans Language: English Journal: Mol Syst Biol Journal subject: Molecular Biology / Biotechnology Year: 2021 Document Type: Article Affiliation country: Msb.202110243