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Logic Programming Applied to Genome Evolution in Cancer
2016
Italian Conference on Computational Logic
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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
2008
Genomics, Proteomics & Bioinformatics
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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?
2018
Journal of Cancer Research and Therapeutic Oncology
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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
2015
Seminars in Cancer Biology
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2014 pre-print arXiv:1408.2009v1 fatcat:2jubsgpc3bbqnpprtxcghkhomi
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
2000
Artificial Intelligence in Medicine
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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
2017
Italian Conference on Theoretical Computer Science
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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
2015
Seminars in Cell and Developmental Biology
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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
2012
International Journal of Computer Applications
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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
2020
Frontiers in Blockchain
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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
2013
Cancer Letters
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2014 pre-print arXiv:1409.3263v1 fatcat:ac7g5zxpvrh6noaaomr4rscp4i
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
2019
BMC Bioinformatics
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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
2021
Journal of Oleo Science
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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
2021
Journal of Oleo Science
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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
2007
Journal of Biomedical Informatics
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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]
2016
Zenodo
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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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