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Applying Logic Programming to Derive Novel Functional Information of Genomes [chapter]

Arvind K. Bansal, Peer Bork
1998 Lecture Notes in Computer Science  
This paper describes an application of the logic programming paradigm to large-scale comparison of complete microbial genomes each containing four-million amino acid characters and approximately two thousand  ...  We present algorithms and a Sicstus Prolog based implementation to model genome comparisons as bipartite graph matching to identify orthologs genes across different genomes with the same function and groups  ...  Warren Gish provided the latest version of BLAST [11] . Paul Hardy provided the portable library of the Smith-Waterman alignment software [12] .  ... 
doi:10.1007/3-540-49201-1_19 fatcat:77bfbxkakrbsjnxbfg76gqiq7q

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.  ...  Recent genome sequencing pipelines allow researchers to retrieve rich genetic and epigenetic information from sampled tissues.  ...  ., [13] ), though not based on logic programming.  ... 
dblp:conf/cilc/PaluDFPP16 fatcat:nf6mppraljfwxmomnfal7wds64

The regulatory genome and the computer

Sorin Istrail, Smadar Ben-Tabou De-Leon, Eric H. Davidson
2007 Developmental Biology  
The functions they execute upon these inputs can be reduced to basic AND, OR and NOT logic functions, which are also the unit logic functions of electronic computers.  ...  The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability.  ...  Acknowledgments Smadar Ben-Tabou de-Leon was supported by the Human Frontier Science Program Organization. Research was supported by NIH grant GM-61005.  ... 
doi:10.1016/j.ydbio.2007.08.009 pmid:17822690 fatcat:z3pxlknqyvchvohhgg5fqn7hg4

Analysis of integrated biomolecular networks using a generic network analysis suite

Matthias Oesterheld, Hans Werner Mewes, Volker Stümpflen
2007 Journal of Integrative Bioinformatics  
well as the derived results of network analysis methods, such as clustering algorithms, in order to provide a service for researchers who are focused towards the functional context of any particular cellular  ...  entity.CABiNet is designed in an easy-to-use and easy-to-extend software framework that allows a straightforward integration of novel components.  ...  in novel genomes.  ... 
doi:10.1515/jib-2007-72 fatcat:hfayyre6iff3ljrxnxfkiqg2gm

Integrative approaches for mining transcriptional regulatory programs in Arabidopsis

A. Krishnan, A. Pereira
2008 Briefings in Functional Genomics & Proteomics  
Integrating information from multiple genomic datasets is seen as a means to this end, capable of providing robust and accurate ways to unravel these functional associations.  ...  Exciting inroads are being made in mining and interpretation of developmental, physiological and environmental-response 'programs' using sequence and functional information.  ...  , as a first step, only by drawing information of many of these experimental and other knowledge-based data and integrating them to derive the underlying structure of the system.  ... 
doi:10.1093/bfgp/eln035 pmid:18632743 fatcat:w4zbyxr2y5hzzl62sr4s2cptoy


2000 Theoretical Computer Science  
This paper should be of interest to researchers in inductive logic programming.  ...  The paper by Vità anyi introduces a novel approach to proving convergence results in genetic programming.  ... 
doi:10.1016/s0304-3975(99)00262-5 fatcat:yev46x3rbncl5dqd7nlwa27l4q

Ontology for Genome Comparison and Genomic Rearrangements

Keith Flanagan, Robert Stevens, Matthew Pocock, Pete Lee, Anil Wipat
2004 Comparative and Functional Genomics  
This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution.  ...  We present an ontology for describing genomes, genome comparisons, their evolution and biological function.  ...  The development of novel computational approaches for comparing genomes and deriving knowledge from those comparisons requires a standard set of terms for comparative genomics.  ... 
doi:10.1002/cfg.436 pmid:18629137 pmcid:PMC2447425 fatcat:mrr7tvbw6zewxh5rpeubidnyda

Modelling Metabolic Pathways Using Stochastic Logic Programs-Based Ensemble Methods [chapter]

Huma Lodhi, Stephen Muggleton
2005 Lecture Notes in Computer Science  
In this paper we present a methodology to estimate rates of enzymatic reactions in metabolic pathways. Our methodology is based on applying stochastic logic learning in ensemble learning.  ...  Stochastic logic programs provide an efficient representation for metabolic pathways and ensemble methods give state-of-the-art performance and are useful for drawing biological inferences.  ...  Acknowledgements The authors would like to acknowledge the support of the DTI Beacon project "Metalog -Integrated Machine Learning of Metabolic Networks Applied to Predictive Toxicology", Grant Reference  ... 
doi:10.1007/978-3-540-25974-9_10 fatcat:hud44bqsxjanlkulndb6t5p24e

Using natural products for drug discovery: the impact of the genomics era

Mingzi M Zhang, Yuan Qiao, Ee Lui Ang, Huimin Zhao
2017 Expert Opinion on Drug Discovery  
In the 1990s, pharmaceutical companies scaled down their natural product discovery programs in favor of synthetic chemical libraries due to major challenges such as high rediscovery rates, challenging  ...  cluster expression in native and heterologous host systems for the production of pharmaceutically relevant metabolites and their derivatives.  ...  Acknowledgments Funding: The authors gratefully acknowledge financial support from the National Institutes of Health (GM077596) (to H Zhao), the A*STAR Visiting Investigator Program (to H Zhao), and  ... 
doi:10.1080/17460441.2017.1303478 pmid:28277838 pmcid:PMC5563975 fatcat:y3svjklwezbp5cdo73kmyyswcy

LONETSSOM Platform: Enabling Distributed Processing, Managing and Mining of Biological Data through Fusion of Logical Network and Web Technologies in NETWORK Infrastructure

N. KannaiyaRaja, K. Arulandam, A. Senthamaraiselvan, K. Babu
2012 International Journal of Computer Applications  
The LONETSSOM aims to setup a generic paradigm of efficient knowledge mining that promotes throughput in translation of biomedicine field through the fusion of logical network and creation of semantic  ...  The advanced framework of logical network system is LONETSSOM which perform efficient versatile annotation system and integrative analysis through multi-application programming interface delivered in the  ...  We wish to thank the ICJA Publisher and the entire team of ICJA Publication for their suggestion and support.  ... 
doi:10.5120/4793-7042 fatcat:rtablnccp5fq7o2hxzkebf3vsi

The Use of Functional Genomics in Synthetic Promoter Design [chapter]

Michael L.
2011 Computational Biology and Applied Bioinformatics  
the function and behavior of a living being.  ...  , and correlate huge data sets of complex information.  ...  Biology and Applied Bioinformatics www.intechopen.comThe Use of Functional Genomics in Synthetic Promoter Design  ... 
doi:10.5772/20653 fatcat:cuvqdjmlojbntaepfwmnyq4sci

SEALS: a system for easy analysis of lots of sequences

D R Walker, E V Koonin
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
at the scale of whole genomes.  ...  We present a system of programs designed to facilitate sequence analysis projects involving large amounts of data.  ...  Acknowledgements: DRW thanks Colombe Chappey for her generous assistance, and gratefully acknowledges the support of the Foundation for Advanced Education in the Sciences.  ... 
pmid:9322058 fatcat:zkiht3bqhfgb3a5asshi7xjasu

Current trends in antimicrobial agent research: chemo- and bioinformatics approaches

Riadh Hammami, Ismail Fliss
2010 Drug Discovery Today  
Databases and chemo-and bioinformatics tools that contain genomic, proteomic and functional information have become indispensable for antimicrobial drug research.  ...  The computational approach to antimicrobial agent discovery and design encompasses genomics, molecular simulation and dynamics, molecular docking, structural and/or functional class prediction, and quantitative  ...  Acknowledgements The authors thank Stephen Davids for crucial reading of the manuscript. Thanks are also due to Caillard Romain for his helpful discussions.  ... 
doi:10.1016/j.drudis.2010.05.002 pmid:20546918 fatcat:2ujsjcp6inerjfdu226dcwa44e


Genome annotation helps in understanding the biological functions of the sequences of those genomes.  ...  The falling value of genome sequencing manifests a good impact on the research community with relevancy to the annotation of genomes.  ...  The fundamental advantage of this method is the use of metagenome input to learn the classifier models and apply them to predict on new genomes.  ... 
doi:10.6084/m9.figshare.14938374.v1 fatcat:gpblejfmj5a63c4pvzdbgkieu4

Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology [article]

Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook (+2 others)
2020 arXiv   pre-print
The possibility to describe and build in silico whole-cells offers an opportunity to develop increasingly automatized, precise and accessible computer-aided design tools and strategies throughout novel  ...  Ultimately, the increased precision in the design phase will have a dramatic impact on the production of designer cells and organisms with bespoke functions and increased modularity.  ...  funded by the Engineering and Physical Sciences Research Council (EPSRC) within the remits of the Big Ideas initiative.  ... 
arXiv:2006.02720v1 fatcat:zyv26a5mhvfxnfm2wsmcyjn5km
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