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A unifying framework disentangles genetic, epigenetic, and stochastic sources of drug-response variability in an in vitro model of tumor heterogeneity [article]

Corey E Hayford, Darren R Tyson, C Jack Robbins, Peter L Frick, Vito Quaranta, Leonard Harris
2020 bioRxiv   pre-print
To disentangle genetic, epigenetic, and stochastic components underlying this variability, we adopt a theoretical framework whereby distinct genetic states give rise to multiple epigenetic "basins of attraction  ...  We propose that a theoretical framework deconvolving the complex interplay among genetic, epigenetic, and stochastic sources of intratumoral heterogeneity will lead to novel therapeutic strategies to combat  ...  ACKNOWLEDGEMENTS This work is dedicated to the memory of our friend and colleague Melaine N. Sebastian.  ... 
doi:10.1101/2020.06.05.136119 fatcat:otedawbpvnaz5jybjvxmzgcfsi

Machine Learning Applications for Therapeutic Tasks with Genomics Data [article]

Kexin Huang, Cao Xiao, Lucas M. Glass, Cathy W. Critchlow, Greg Gibson, Jimeng Sun
2021 arXiv   pre-print
Thanks to the increasing availability of genomics and other biomedical data, many machine learning approaches have been proposed for a wide range of therapeutic discovery and development tasks.  ...  In this survey, we review the literature on machine learning applications for genomics through the lens of therapeutic development.  ...  DNN shows improved performance on classification metrics.  ... 
arXiv:2105.01171v1 fatcat:d2nbrjt4tvak7momoxxjlmqk2m

Illuminating the Virosphere Through Global Metagenomics

Lee Call, Stephen Nayfach, Nikos C. Kyrpides
2021 Annual Review of Biomedical Data Science  
In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field.  ...  Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses  ...  , and a flexible set of distance metrics (68) .  ... 
doi:10.1146/annurev-biodatasci-012221-095114 pmid:34465172 fatcat:g3mzsvugu5fbjdhufrypftrm5a

An integrated approach to model cancer cell growth and treatment response with multimodal data sources

Kaitlyn Elizabeth Johnson, 0000-0001-8011-0012, Austin, The University Of Texas At, Amy Brock
2022
Using a large number of single cell resolution growth trajectories acquired at low cell densities, we apply a stochastic parameter estimation framework to systematically evaluate the relevance of an Allee  ...  This dissertation focuses on the development of math modeling frameworks capable of integrating and improving our utilization of these novel data types.  ...  For a more detailed overview of the field of bioinformatics, we refer the reader to comprehensive review papers in bioinformatics (Diniz and Canduri, 2017) , and for a more comprehensive overview of the  ... 
doi:10.26153/tsw/41714 fatcat:eyk3bxvejzdz3epvdkwrb6jmpu