Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks

Evolutionary Bioinformatics Online
Daniele RamazzottiMarco Antoniotti

Abstract

Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wild-type conditions. Cancer and HIV are 2 common examples of such diseases, where the mutational load in the cancerous/viral population increases over time. In these cases, selective pressures are often observed along with competition, co-operation, and parasitism among distinct cellular clones. Recently, we presented a mathematical framework to model these phenomena, based on a combination of Bayesian inference and Suppes' theory of probabilistic causation, depicted in graphical structures dubbed Suppes-Bayes Causal Networks (SBCNs). The SBCNs are generative probabilistic graphical models that recapitulate the potential ordering of accumulation of such DNA changes during the progression of the disease. Such models can be inferred from data by exploiting likelihood-based model selection strategies with regularization. In this article, we discuss the theoretical foundations of our approach and we investigate in depth the influence on the model selection task of (1) the poset based on Suppes' theory and (2) different regularization strategies. Furthermore, we provide an example of application of our framew...Continue Reading

References

Oct 1, 1976·Science·P C Nowell
May 1, 1999·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R DesperA A Schäffer
Jan 27, 2000·Cell·D Hanahan, R A Weinberg
Jan 10, 2003·Nucleic Acids Research·Soo-Yon RheeRobert W Shafer
Aug 13, 2005·Proceedings. Biological Sciences·Alison P Galvani
Apr 8, 2006·Science·Daniel M WeinreichDaniel L Hartl
Nov 17, 2006·Nature Reviews. Cancer·Lauren M F MerloCarlo C Maley
Jan 26, 2007·Nature·Frank J PoelwijkSander J Tans
Feb 7, 1975·Science·P J BickelJ W O'connell
Jul 10, 2009·Proceedings of the National Academy of Sciences of the United States of America·Elena R LozovskyDaniel L Hartl
Aug 21, 2009·Bioinformatics·Moritz GerstungNiko Beerenwinkel
Mar 8, 2011·Cell·Douglas Hanahan, Robert A Weinberg
Mar 9, 2012·The New England Journal of Medicine·Marco GerlingerCharles Swanton
Mar 30, 2013·Science·Bert VogelsteinKenneth W Kinzler
Jun 27, 2013·PloS One·Hossein Shahrabi Farahani, Jens Lagergren
Sep 21, 2013·Nature·Rebecca A BurrellCharles Swanton
Sep 16, 2014·Genome Biology·Nicholas E Navin
Oct 9, 2014·Systematic Biology·Niko BeerenwinkelFlorian Markowetz
Oct 10, 2014·PloS One·Loes Olde LoohuisBud Mishra
May 15, 2015·Bioinformatics·Daniele RamazzottiBud Mishra
Jul 1, 2016·Proceedings of the National Academy of Sciences of the United States of America·Giulio CaravagnaBud Mishra

❮ Previous
Next ❯

Citations

Sep 8, 2021·PLoS Computational Biology·Susana Posada-CéspedesNiko Beerenwinkel
Oct 15, 2021·Bioinformatics·Fabrizio AngaroniDaniele Ramazotti

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.