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Logic Programming Applied to Genome Evolution in Cancer

Alessandro Dal Palù, Agostino Dovier, Andrea Formisano, Alberto Policriti, Enrico Pontelli
2016 Italian Conference on Computational Logic  
This paper presents a project for a logic programming based analysis that processes time-related genomic information.  ...  in the understanding of the general rules that drive cancer genesis and evolution.  ...  However there are no applications nor combinations of these techniques in the study of genome evolution in cancer.  ... 
dblp:conf/cilc/PaluDFPP16 fatcat:nf6mppraljfwxmomnfal7wds64

Identification of Tumor Evolution Patterns by Means of Inductive Logic Programming

Vitoantonio Bevilacqua, Patrizia Chiarappa, Giuseppe Mastronardi, Filippo Menolascina, Angelo Paradiso, Stefania Tommasi
2008 Genomics, Proteomics & Bioinformatics  
In this work, we propose an inductive logic programming approach to the problem of modeling evolution patterns for breast cancer.  ...  In considering key events of genomic disorders in the development and progression of cancer, the correlation between genomic instability and carcinogenesis is currently under investigation.  ...  In particular, we show how a particular approach to association rule mining can be used in the development of a coherent model of cancer evolution through the use of Tertius, an inductive logic programming  ... 
doi:10.1016/s1672-0229(08)60024-8 pmid:18973865 pmcid:PMC5054107 fatcat:kgtzprgo7fhavcl4m3fjzd5pjy

Cancer as an Emergent Phenomenon?

Anderson KM
2018 Journal of Cancer Research and Therapeutic Oncology  
A forward or a retrogressive evolution of individual cancer cells could be viewed as subsets of emergent phenomena in which random genetic / epigenetic events can also meld with other ongoing, underlying  ...  The relationship between the emergent phenomena of evolution, including the development of cancer cells expressing apparently "random" genetic / epigenetic events and the influence of "scale" are also  ...  To the extent that deviant development of cancer progeny is subject to random genomic or epi-genomic variation, evolution of sub-species of cancers believed to originate from a given malignantly transformed  ... 
doi:10.17303/jcrto.2018.103 fatcat:irmwhcdqt5huvm3cnskjld72oe

Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data

Edwin Wang, Naif Zaman, Shauna Mcgee, Jean-Sébastien Milanese, Ali Masoudi-Nejad, Maureen O'Connor-McCourt
2015 Seminars in Cancer Biology  
We discuss a cancer hallmark network framework for modelling genome-sequencing data to predict cancer clonal evolution and associated clinical phenotypes.  ...  Strategies of using this framework in conjunction with genome sequencing data in an attempt to predict personalized drug targets, drug resistance, and metastasis for a cancer patient, as well as cancer  ...  For example, a drug can be applied to different cancer cell lines, followed by genome sequencing to identify mutational patterns derived from that specific drug treatment.  ... 
doi:10.1016/j.semcancer.2014.04.002 pmid:24747696 fatcat:u35vrng5pvdzhkmyqyd6swmrvy

Evolutionary computation in medicine: an overview

Carlos Andrés Peña-Reyes, Moshe Sipper
2000 Artificial Intelligence in Medicine  
This paper provides an overview of evolutionary computation as applied to problems in the medical domains.  ...  We begin by outlining the basic workings of six types of evolutionary algorithms: genetic algorithms, genetic programming, evolution strategies, evolutionary programming, classifier systems, and hybrid  ...  The first decision to take when applying such an algorithm is how to encode candidate solutions within the genome.  ... 
doi:10.1016/s0933-3657(99)00047-0 pmid:10767613 fatcat:zz5hgh56zvfzrluxkj2a7krm3a

Towards a Logic Programming Tool for Cancer Analysis

Alice Tarzariol, Agostino Dovier, Alberto Policriti
2017 Italian Conference on Theoretical Computer Science  
The system is modular: the reasoning tool can be replaced by any logic programming tool (e.g., Prolog, ILP) for different kinds of data analysis.  ...  The reasoning core is based on Answer Set Programming that, allowing to deal with NP or Σ P 2 properties, is capable of deducing complex info from data.  ...  In [1] the authors propose an inductive logic programming approach to the problem of modeling evolution patterns for breast cancer.  ... 
dblp:conf/ictcs/TarzariolDP17 fatcat:v2ifqkdlqreblaagg3g2x3ymze

Cell death in genome evolution

Xinchen Teng, J. Marie Hardwick
2015 Seminars in Cell and Developmental Biology  
Analysis of gene-dependent death in yeast revealed the surprising influence of single gene mutations on subsequent eukaryotic genome evolution.  ...  The possibility that an early random mutation might drive the selection for a cancer driver mutation is conceivable but difficult to demonstrate.  ...  Hypothesized cancer genome evolution model.  ... 
doi:10.1016/j.semcdb.2015.02.014 pmid:25725369 pmcid:PMC4410082 fatcat:sf5xd5xb6nelfc26pl4fmb4ww4

Role of the Computational Intelligence in Drugs Discovery and Design: Introduction, Techniques and Software

Geeta Yadav, Yugal Kumar, G. Sahoo
2012 International Journal of Computer Applications  
Earlier, computational techniques are use in the field of computer science, electrical engineering and electronics & communication engineering to solve the problems.  ...  Programming, Evolutionary Programming, Evolutionary Strategy and also provide a tabular comparison of these techniques as well as a list of computational tools/ software.  ...  Several new technologies such as genomic data, chemical genomics, high throughput screening in the drug discovery process and computational tool/software have been developed and applied in drug discovery  ... 
doi:10.5120/8076-1476 fatcat:osddvf4ygnevdktvyhqwb3did4

Blockchain Biology

Alfred C. Chin
2020 Frontiers in Blockchain  
Clonal evolution in cancer exhibits strikingly similar features as blockchain ( Figure 1A) .  ...  DECENTRALIZED LEDGERS AND MODELING CANCER EVOLUTION The rigorous recordkeeping capabilities of blockchain can be harnessed to probe cancer evolution and lineage tracing.  ... 
doi:10.3389/fbloc.2020.606413 fatcat:bjobtongjbds3lt2jxnhnzfhmu

Understanding genomic alterations in cancer genomes using an integrative network approach

Edwin Wang
2013 Cancer Letters  
Genomic alterations spur cancer genome evolution. Thus, the relationship between cancer clonal evolution and cancer stems cells is commented.  ...  To develop a comprehensive understanding of the function of these genomic alterations in cancer, an integrative network framework is proposed and discussed.  ...  Acknowledgements This work is supported by Canadian Institute of Health Research and NRC's Genome and Health Initiative.  ... 
doi:10.1016/j.canlet.2012.11.050 pmid:23266571 fatcat:b3iczmqitnfrxoiaqkpeciuhtm

BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics

Francesca Cordero, Raffaele A. Calogero, Michele Caselle
2019 BMC Bioinformatics  
The Conference was held in Torino, Italy, from June 27th to 29th, 2018.  ...  This preface introduces the content of the BioMed Central Bioinformatics journal Supplement related to the 15th annual meeting of the Bioinformatics Italian Society, BITS2018.  ...  Acknowledgments We are extremely grateful to the referees for their dedication and effort in peer reviewing the manuscripts.  ... 
doi:10.1186/s12859-019-3175-9 pmid:31757202 pmcid:PMC6873652 fatcat:jl5mpr2hlnfynca4n2vecxkxfa

Anti-oral Cancer Biological Activity Evaluation and Chloroplast Genome Analyses of Populus euphratica

Hong-Ying Wang, Xiao-Qing Yang
2021 Journal of Oleo Science  
Next, the high-throughput Illumina pair-end sequencing was performed to detect the chloroplast (cp) genome of Populus euphratica for genome evolution assessment.  ...  In this research, the anti-cancer activity of the Populus euphratica extract was evaluated with Cell Counting Kit-8 (CCK-8) assay.  ...  Data Availability Statement The data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih. gov, reference number MT593375.  ... 
doi:10.5650/jos.ess21099 pmid:34349089 fatcat:fscawuedufd2pbzrxga4ln7gx4

Excellent Anti-lung Cancer Activity of Populus nigra and Phylogenetic Analysis

Jun Ma, Yang Gao, Tao Jiang, Feng Tian
2021 Journal of Oleo Science  
In this present research, we aimed to evaluate the anti-cancer activity of the Populus nigra extract against the lung cancer and study the genome evolution of the Populus nigra.  ...  In addition to this, the chloroplast (cp) genome of Populus nigra was sequenced with high-throughput Illumina pair-end sequencing, which was a classical useful model for genome evolution assessment.  ...  According to the intraspecific genetic diversity, genome evolution assessment was carried out to reveal the evolutionary relationship of the Populus nigra with other species 8, 9) .  ... 
doi:10.5650/jos.ess21220 pmid:34866109 fatcat:4yonokv3r5gjbfh3fklb3rrr2a

Bio*Medical informatics and genomic medicine: Research and training

Peter Tarczy-Hornoch, Mia K. Markey, John A. Smith, Tadaaki Hiruki
2007 Journal of Biomedical Informatics  
Bioinformatics (computational biology in particular) has been fundamental in applying developments in the computing and information sciences to helping manage and make sense of vast quantities of genomic  ...  In genetics we have gone from the elucidation of DNA as the mechanism of inheritance in 1953 [2] to the sequencing of the human genome completed in 2003 [3] .  ...  Acknowledgment We are grateful to Ms. Donna Knight for her excellent communication between the editors and the authors. et al.  ... 
doi:10.1016/j.jbi.2006.10.002 pmid:18239725 pmcid:PMC1920185 fatcat:chp4j3i4pzhqxa56elsugmopbe

Aging Is Programmed! (A Response To Kowald-Kirkwood " Can Aging Be Programmed? A Critical Literature Review " ) [article]

Theodore C. Goldsmith
2016 Zenodo  
More recently advances in genetics have exposed major complexities in the evolution process some of which specifically enable adaptive programmed aging.  ...  However, for more than a century programmed aging was widely considered to be theoretically impossible because of the nature of the evolution process.  ...  Evolvability benefits the evolution process, applies to any size group, and does not suffer from the present/future problem.  ... 
doi:10.5281/zenodo.883623 fatcat:hxafeclzfbgwzn6ekhmh2ut6e4
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