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Complex Systems Biology Informed Data Analysis and Machine Learning

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Dmitry Grapov
Dmitry Grapov

Summary of biochemical data analysis methods enabling complex systems biology based inference.

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Complex Systems Biology informed Data Analysis Dmitry Grapov, PhD CDS- Creative Data Solutions www.createdatasol.com
About Me Born: Minsk, Belarus in 1981 Minsk, Belarus University of Utah (2000-2007) •B.S. Biology •B.S. Chemistry Salt Lake City, UT University of California, Davis (2007-2012) •Ph.D. Analytical Chemistry with Emphasis in Biotechnology •Post doc, Oliver Fiehn Lab Davis, CA data visualization network analysis machine learning predictive modeling biochemistry software WCMC - West Coast Metabolomics Center •Principal Statistician at the NIH West Coast Metabolomics Center (WCMC) Bioinformatics and Data Science •CDS - Creative Data Solutions St. Louis, MO
Structural similarity Complex Metabolic Systems Biology Biochemistry
http://www.archaeology.org/issues/207- 1603/features/4157-arles-roman-wall-paintings Sample Variable experimental design - organism, sex, age etc. analyte description and metadata - biochemical class, mass spectra, etc. VariableSample Biological Data
http://www.archaeology.org/issues/207- 1603/features/4157-arles-roman-wall-paintings Materials of Connected Biological Data Analysis and Visualization Quality Assessment • use replicated measurements and/or internal standards to estimate analytical variance Statistical and Multivariate • use the experimental design to test hypotheses and/or identify trends in analytes Functional • use statistical and multivariate results to identify impacted biochemical domains Network and Predictive • integrate statistical and multivariate results with the experimental design and analyte metadata
Predictive Modeling Within a Biochemical Context Grapov et. al., Circ. Cardiovasc. Genet. 2014 Personalized Medicine Complex Data Integration Grapov et. al.,PLoS ONE (2014) doi:10.1371/journal.pone.0084260 J. Proteome Res., 2015, 14 (1), pp 557–566 DOI: 10.1021/pr500782g Biomarker Discovery
Abundance Time Drift in >400 replicated measurements across >100 analytical batches for a single analyte Quality Controls (QCs) embedded among >5,500 samples (1:10) collected over 1.5 years Analytical Batch Principal Component Analysis (PCA) of all analytes, showing QC sample scores biological effect vs. analytical variance Time Biochemical Signal Over Time
Data Quality and Normalization Analyte specific data quality overview normalizations can be used to remove analytical variance Raw Data Normalized Data log mean low precision %RSD high precision
Example of data normalization using a LOESS model fit QCs Raw Data Normalized Data Samples QCs LOESS Data Normalization Strategies
Maximizing Metabolomic Coverage American Journal of Physiology - Endocrinology and Metabolism 2015 Vol. no. , DOI: 10.1152/ajpendo.00019.2015
trans-Omic Biochemical Signal http://dx.doi.org/10.1016/j.tibtech.2015.12.013
Signal State trans-Omic Signal
~10% variance explained Many diseases, including aging, have dominant metabolic components (e.g. metabolic syndrome) PMID:24204828 Genotype + metabolome >40% variance explained Type 2 Diabetes Is More Data the Answer?
Biochemically Orthogonal Evidence http://dx.doi.org/10.1016/j.tibtech.2015.12.013
Systems Biology Informed Personalized Medicine http://dx.doi.org/10.1016/j.tibtech.2015.12.013 Grapov et. al., Circ. Cardiovasc. Genet. 2014
Can You Spot the Signal? metabolites proteins increase
Omic’ data integration strategies Biomarker Insights 2015:Suppl. 4 1-6 DOI: 10.4137/BMI.S29511 Empirical correlation Network based Biochemical pathway
MetaMapR: Metabolomic network calculation www.createdatasol.com
MappingsNetwork Mapped Network Grapov D.,American Society of Mass Spectrometry Conference (2013, 2014) Network Mapping + =
Biochemically Defined Wellness
DeviumWeb: Data analysis and visualization www.createdatasol.com
DeviumWeb: Cluster Analysis www.createdatasol.com
DeviumWeb: Predictive Modeling www.createdatasol.com
DeviumWeb: Pathway analysis www.createdatasol.com
http://karpathy.github.io/2014/09/02/what-i-learned-from-competing-against-a-convnet-on-imagenet/ Machine Learning Biology
https://commons.wikimedia.org/w/index.php?curid=2776582 Biochemical PageRank
https://arxiv.org/ftp/arxiv/papers/1603/1603.06430.pdf Biochemical Deep Learning
data visualization network analysis machine learning predictive modeling biochemistry software www.createdatasol.com

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