�ݺ�ߣshows by User: JoeParker6

�ݺ�ߣshows by User: JoeParker6 / http://www.slideshare.net/images/logo.gif �ݺ�ߣshows by User: JoeParker6 / Fri, 14 Sep 2018 21:14:27 GMT �ݺ�ߣShare feed for �ݺ�ߣshows by User: JoeParker6 Challenges and potential of real-time phylogenomics: lessons from a metagenomic Case Study into Acute Oak Decline (AOD) in south-east England. /slideshow/challenges-and-potential-of-realtime-phylogenomics-lessons-from-a-metagenomic-case-study-into-acute-oak-decline-aod-in-southeast-england-114548898/114548898 joeparker-ucl-sept2018-aod-nanopore-180914211427
Talk presented at the UCL Genetics Institute 'Beyond Next-Gen Sequencing' symposium, UCL, London, Weds 12th September 2018.]]>
Talk presented at the UCL Genetics Institute 'Beyond Next-Gen Sequencing' symposium, UCL, London, Weds 12th September 2018.]]> Fri, 14 Sep 2018 21:14:27 GMT /slideshow/challenges-and-potential-of-realtime-phylogenomics-lessons-from-a-metagenomic-case-study-into-acute-oak-decline-aod-in-southeast-england-114548898/114548898 JoeParker6@slideshare.net(JoeParker6) Challenges and potential of real-time phylogenomics: lessons from a metagenomic Case Study into Acute Oak Decline (AOD) in south-east England. JoeParker6 Talk presented at the UCL Genetics Institute 'Beyond Next-Gen Sequencing' symposium, UCL, London, Weds 12th September 2018. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/joeparker-ucl-sept2018-aod-nanopore-180914211427-thumbnail.jpg?width=120&height=120&fit=bounds" /> Talk presented at the UCL Genetics Institute 'Beyond Next-Gen Sequencing' symposium, UCL, London, Weds 12th September 2018.

Challenges and potential of real-time phylogenomics: lessons from a metagenomic Case Study into Acute Oak Decline (AOD) in south-east England. from Joe Parker

]]> 77 2 https://cdn.slidesharecdn.com/ss_thumbnails/joeparker-ucl-sept2018-aod-nanopore-180914211427-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post

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0 Field-based, real-time metagenomics and phylogenomics for responsive pathogen detection: lessons from nanopore analyses of Acute Oak Decline (AOD) sites in the UK. /slideshow/fieldbased-realtime-metagenomics-and-phylogenomics-for-responsive-pathogen-detection-lessons-from-nanopore-analyses-of-acute-oak-decline-aod-sites-in-the-uk/88051198 joe-parker-pirbright-ukindia-180215141918
Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018 Abstract: In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear. This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented. Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort.]]>
Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018 Abstract: In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear. This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented. Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort.]]> Thu, 15 Feb 2018 14:19:18 GMT /slideshow/fieldbased-realtime-metagenomics-and-phylogenomics-for-responsive-pathogen-detection-lessons-from-nanopore-analyses-of-acute-oak-decline-aod-sites-in-the-uk/88051198 JoeParker6@slideshare.net(JoeParker6) Field-based, real-time metagenomics and phylogenomics for responsive pathogen detection: lessons from nanopore analyses of Acute Oak Decline (AOD) sites in the UK. JoeParker6 Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018 Abstract: In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear. This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented. Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/joe-parker-pirbright-ukindia-180215141918-thumbnail.jpg?width=120&height=120&fit=bounds" /> Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018 Abstract: In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear. This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented. Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort.

Field-based, real-time metagenomics and phylogenomics for responsive pathogen detection: lessons from nanopore analyses of Acute Oak Decline (AOD) sites in the UK. from Joe Parker

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0 Real-time Phylogenomics: Joe Parker /slideshow/realtime-phylogenomics-joe-parker-87391225/87391225 joe-parker-reak-time-phylogenomics-180207132740
Talk given at a technology/informatics company, London, Feb 2018.]]>
Talk given at a technology/informatics company, London, Feb 2018.]]> Wed, 07 Feb 2018 13:27:40 GMT /slideshow/realtime-phylogenomics-joe-parker-87391225/87391225 JoeParker6@slideshare.net(JoeParker6) Real-time Phylogenomics: Joe Parker JoeParker6 Talk given at a technology/informatics company, London, Feb 2018. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/joe-parker-reak-time-phylogenomics-180207132740-thumbnail.jpg?width=120&height=120&fit=bounds" /> Talk given at a technology/informatics company, London, Feb 2018.

Real-time Phylogenomics: Joe Parker from Joe Parker

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0 Inference and informatics in a 'sequenced' world /slideshow/inference-and-informatics-in-a-sequenced-world/78587606 2017readingbioinfforgenomics-joeparker-final3-170805084405
Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs. University of Reading, 2nd August 2017]]>
Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs. University of Reading, 2nd August 2017]]> Sat, 05 Aug 2017 08:44:05 GMT /slideshow/inference-and-informatics-in-a-sequenced-world/78587606 JoeParker6@slideshare.net(JoeParker6) Inference and informatics in a 'sequenced' world JoeParker6 Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs. University of Reading, 2nd August 2017 <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/2017readingbioinfforgenomics-joeparker-final3-170805084405-thumbnail.jpg?width=120&height=120&fit=bounds" /> Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs. University of Reading, 2nd August 2017

Inference and informatics in a 'sequenced' world from Joe Parker

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0 Reframing Phylogenomics /slideshow/reframing-phylogenomics/72833818 joeparker-reframingphylogeneticsunbiased-final-170305195117
Unbiased comparative methods for environmental metagenomics sampling. (NERC IRF Panel presentation, April 2014) ]]>
Unbiased comparative methods for environmental metagenomics sampling. (NERC IRF Panel presentation, April 2014) ]]> Sun, 05 Mar 2017 19:51:17 GMT /slideshow/reframing-phylogenomics/72833818 JoeParker6@slideshare.net(JoeParker6) Reframing Phylogenomics JoeParker6 Unbiased comparative methods for environmental metagenomics sampling. (NERC IRF Panel presentation, April 2014) <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/joeparker-reframingphylogeneticsunbiased-final-170305195117-thumbnail.jpg?width=120&height=120&fit=bounds" /> Unbiased comparative methods for environmental metagenomics sampling. (NERC IRF Panel presentation, April 2014)

Reframing Phylogenomics from Joe Parker

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0 Using field-based DNA sequencing to accelerate phylogenomics /slideshow/using-fieldbased-dna-sequencing-to-accelerate-phylogenomics/69767351 2016oxfordzoojoeparker-161202163931
Invited seminar at the Department of Zoology, Oxford University, 30th November 2016. Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology. ]]>
Invited seminar at the Department of Zoology, Oxford University, 30th November 2016. Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology. ]]> Fri, 02 Dec 2016 16:39:31 GMT /slideshow/using-fieldbased-dna-sequencing-to-accelerate-phylogenomics/69767351 JoeParker6@slideshare.net(JoeParker6) Using field-based DNA sequencing to accelerate phylogenomics JoeParker6 Invited seminar at the Department of Zoology, Oxford University, 30th November 2016. Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/2016oxfordzoojoeparker-161202163931-thumbnail.jpg?width=120&height=120&fit=bounds" /> Invited seminar at the Department of Zoology, Oxford University, 30th November 2016. Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology.

Using field-based DNA sequencing to accelerate phylogenomics from Joe Parker

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0 Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications /slideshow/singlemolecule-realtime-smrt-nanopore-sequencing-for-plant-pathology-applications/66051562 smrt-nanopore-gcpp-joeparker-160915100855
A short presentation to the British Society for Plant Pathology's 'Grand Challenges in Plant Pathology' workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications. Doctoral Training Centre, University of Oxford, 14th September 2016.]]>
A short presentation to the British Society for Plant Pathology's 'Grand Challenges in Plant Pathology' workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications. Doctoral Training Centre, University of Oxford, 14th September 2016.]]> Thu, 15 Sep 2016 10:08:55 GMT /slideshow/singlemolecule-realtime-smrt-nanopore-sequencing-for-plant-pathology-applications/66051562 JoeParker6@slideshare.net(JoeParker6) Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications JoeParker6 A short presentation to the British Society for Plant Pathology's 'Grand Challenges in Plant Pathology' workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications. Doctoral Training Centre, University of Oxford, 14th September 2016. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/smrt-nanopore-gcpp-joeparker-160915100855-thumbnail.jpg?width=120&height=120&fit=bounds" /> A short presentation to the British Society for Plant Pathology's 'Grand Challenges in Plant Pathology' workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications. Doctoral Training Centre, University of Oxford, 14th September 2016.

Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications from Joe Parker

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0 Joe parker-benchmarking-bioinformatics /slideshow/joe-parkerbenchmarkingbioinformatics/61147571 joe-parker-benchmarking-bioinformatics-160420140811
Talk presented at Benchmarking 2016 symposium, KCL, London, 20th April 2016. Covers performance measurement strategies (or lack of) in common genomics workflows.]]>
Talk presented at Benchmarking 2016 symposium, KCL, London, 20th April 2016. Covers performance measurement strategies (or lack of) in common genomics workflows.]]> Wed, 20 Apr 2016 14:08:11 GMT /slideshow/joe-parkerbenchmarkingbioinformatics/61147571 JoeParker6@slideshare.net(JoeParker6) Joe parker-benchmarking-bioinformatics JoeParker6 Talk presented at Benchmarking 2016 symposium, KCL, London, 20th April 2016. Covers performance measurement strategies (or lack of) in common genomics workflows. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/joe-parker-benchmarking-bioinformatics-160420140811-thumbnail.jpg?width=120&height=120&fit=bounds" /> Talk presented at Benchmarking 2016 symposium, KCL, London, 20th April 2016. Covers performance measurement strategies (or lack of) in common genomics workflows.

Joe parker-benchmarking-bioinformatics from Joe Parker

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0 Real-time Phylogenomics: Joe Parker /slideshow/realtime-phylogenomics-joe-parker/54651010 real-time-phylogenomics-joeparker-151102162613-lva1-app6892
General science talk about the potential of real-time phylogenomics, delivered at the Jodrell Lecture Theatre, Kew Gardens, November 2nd 2015]]>
General science talk about the potential of real-time phylogenomics, delivered at the Jodrell Lecture Theatre, Kew Gardens, November 2nd 2015]]> Mon, 02 Nov 2015 16:26:12 GMT /slideshow/realtime-phylogenomics-joe-parker/54651010 JoeParker6@slideshare.net(JoeParker6) Real-time Phylogenomics: Joe Parker JoeParker6 General science talk about the potential of real-time phylogenomics, delivered at the Jodrell Lecture Theatre, Kew Gardens, November 2nd 2015 <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/real-time-phylogenomics-joeparker-151102162613-lva1-app6892-thumbnail.jpg?width=120&height=120&fit=bounds" /> General science talk about the potential of real-time phylogenomics, delivered at the Jodrell Lecture Theatre, Kew Gardens, November 2nd 2015

Real-time Phylogenomics: Joe Parker from Joe Parker

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0 'Omics in extreme Environments (Lightweight bioinformatics) /slideshow/joe-parker-lightweightbioinformatics/50251856 joeparkerlightweightbioinformatics-150707112254-lva1-app6892
Presentation on lightweight bioinformatics (Raspi / cloud computing) for real-time field-based analyses. Presented at iEOS2015, St. Andrews, 3-6th July 2015.]]>
Presentation on lightweight bioinformatics (Raspi / cloud computing) for real-time field-based analyses. Presented at iEOS2015, St. Andrews, 3-6th July 2015.]]> Tue, 07 Jul 2015 11:22:53 GMT /slideshow/joe-parker-lightweightbioinformatics/50251856 JoeParker6@slideshare.net(JoeParker6) 'Omics in extreme Environments (Lightweight bioinformatics) JoeParker6 Presentation on lightweight bioinformatics (Raspi / cloud computing) for real-time field-based analyses. Presented at iEOS2015, St. Andrews, 3-6th July 2015. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/joeparkerlightweightbioinformatics-150707112254-lva1-app6892-thumbnail.jpg?width=120&height=120&fit=bounds" /> Presentation on lightweight bioinformatics (Raspi / cloud computing) for real-time field-based analyses. Presented at iEOS2015, St. Andrews, 3-6th July 2015.

'Omics in extreme Environments (Lightweight bioinformatics) from Joe Parker

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0 Interpreting ‘tree space’ in the context of very large empirical datasets /slideshow/joe-parker-multiplephylogenies/41858965 joeparker-multiplephylogenies-141121092909-conversion-gate02
Seminar presented at the Maths Department, University of Portsmouth, 19th November 2014 Evolutionary biologists represent actual or hypothesised evolutionary relations between living organisms using phylogenies, directed bifurcating graphs (trees) that describe evolutionary processes in terms of speciation or splitting events (nodes) and elapsed evolutionary time or distance (edges). Molecular evolution itself is largely dominated by mutations in DNA sequences, a stochastic process. Traditionally, probabilistic models of molecular evolution and phylogenies are fitted to DNA sequence data by maximum likelihood on the assumption that a single simple phylogeny will serve to approximate the evolution of a majority of DNA positions in the dataset. However modern studies now routinely sample several orders of magnitude more DNA positions, and this assumption no longer holds. Unfortunately, our conception of ‘tree space’ - a notional multidimensional surface containing all possible phylogenies - is extremely imprecise, and similarly techniques to model phylogeny model fitting in very large datasets are limited. I will show the background to this field and present some of the challenges arising from the present limited analytical framework.]]>
Seminar presented at the Maths Department, University of Portsmouth, 19th November 2014 Evolutionary biologists represent actual or hypothesised evolutionary relations between living organisms using phylogenies, directed bifurcating graphs (trees) that describe evolutionary processes in terms of speciation or splitting events (nodes) and elapsed evolutionary time or distance (edges). Molecular evolution itself is largely dominated by mutations in DNA sequences, a stochastic process. Traditionally, probabilistic models of molecular evolution and phylogenies are fitted to DNA sequence data by maximum likelihood on the assumption that a single simple phylogeny will serve to approximate the evolution of a majority of DNA positions in the dataset. However modern studies now routinely sample several orders of magnitude more DNA positions, and this assumption no longer holds. Unfortunately, our conception of ‘tree space’ - a notional multidimensional surface containing all possible phylogenies - is extremely imprecise, and similarly techniques to model phylogeny model fitting in very large datasets are limited. I will show the background to this field and present some of the challenges arising from the present limited analytical framework.]]> Fri, 21 Nov 2014 09:29:09 GMT /slideshow/joe-parker-multiplephylogenies/41858965 JoeParker6@slideshare.net(JoeParker6) Interpreting ‘tree space’ in the context of very large empirical datasets JoeParker6 Seminar presented at the Maths Department, University of Portsmouth, 19th November 2014 Evolutionary biologists represent actual or hypothesised evolutionary relations between living organisms using phylogenies, directed bifurcating graphs (trees) that describe evolutionary processes in terms of speciation or splitting events (nodes) and elapsed evolutionary time or distance (edges). Molecular evolution itself is largely dominated by mutations in DNA sequences, a stochastic process. Traditionally, probabilistic models of molecular evolution and phylogenies are fitted to DNA sequence data by maximum likelihood on the assumption that a single simple phylogeny will serve to approximate the evolution of a majority of DNA positions in the dataset. However modern studies now routinely sample several orders of magnitude more DNA positions, and this assumption no longer holds. Unfortunately, our conception of ‘tree space’ - a notional multidimensional surface containing all possible phylogenies - is extremely imprecise, and similarly techniques to model phylogeny model fitting in very large datasets are limited. I will show the background to this field and present some of the challenges arising from the present limited analytical framework. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/joeparker-multiplephylogenies-141121092909-conversion-gate02-thumbnail.jpg?width=120&height=120&fit=bounds" /> Seminar presented at the Maths Department, University of Portsmouth, 19th November 2014 Evolutionary biologists represent actual or hypothesised evolutionary relations between living organisms using phylogenies, directed bifurcating graphs (trees) that describe evolutionary processes in terms of speciation or splitting events (nodes) and elapsed evolutionary time or distance (edges). Molecular evolution itself is largely dominated by mutations in DNA sequences, a stochastic process. Traditionally, probabilistic models of molecular evolution and phylogenies are fitted to DNA sequence data by maximum likelihood on the assumption that a single simple phylogeny will serve to approximate the evolution of a majority of DNA positions in the dataset. However modern studies now routinely sample several orders of magnitude more DNA positions, and this assumption no longer holds. Unfortunately, our conception of ‘tree space’ - a notional multidimensional surface containing all possible phylogenies - is extremely imprecise, and similarly techniques to model phylogeny model fitting in very large datasets are limited. I will show the background to this field and present some of the challenges arising from the present limited analytical framework.

Interpreting ‘tree space’ in the context of very large empirical datasets from Joe Parker

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0 Phylogenomic methods for comparative evolutionary biology - University College Dublin MSc - Joe Parker - 24th October 2014 /slideshow/phylogenomic/41517492 ucdmscphylogenomicsjoeparkeredit-141113103421-conversion-gate02
Invited research seminar given to MSc students at University College Dublin on 24th October 2013. I introduce the discipline of phylogenomics - comparative phylogenetic analyses of DNA sequences across genomes - and some of the applications and recent breakthroughs in the field. As an in-depth case study I explain the methods and significance of our 2013 Nature paper on adaptive genotypic molecular convergence in echolocating mammals. I then highlight some of the avenues of study on the frontiers of current research.]]>
Invited research seminar given to MSc students at University College Dublin on 24th October 2013. I introduce the discipline of phylogenomics - comparative phylogenetic analyses of DNA sequences across genomes - and some of the applications and recent breakthroughs in the field. As an in-depth case study I explain the methods and significance of our 2013 Nature paper on adaptive genotypic molecular convergence in echolocating mammals. I then highlight some of the avenues of study on the frontiers of current research.]]> Thu, 13 Nov 2014 10:34:21 GMT /slideshow/phylogenomic/41517492 JoeParker6@slideshare.net(JoeParker6) Phylogenomic methods for comparative evolutionary biology - University College Dublin MSc - Joe Parker - 24th October 2014 JoeParker6 Invited research seminar given to MSc students at University College Dublin on 24th October 2013. I introduce the discipline of phylogenomics - comparative phylogenetic analyses of DNA sequences across genomes - and some of the applications and recent breakthroughs in the field. As an in-depth case study I explain the methods and significance of our 2013 Nature paper on adaptive genotypic molecular convergence in echolocating mammals. I then highlight some of the avenues of study on the frontiers of current research. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/ucdmscphylogenomicsjoeparkeredit-141113103421-conversion-gate02-thumbnail.jpg?width=120&height=120&fit=bounds" /> Invited research seminar given to MSc students at University College Dublin on 24th October 2013. I introduce the discipline of phylogenomics - comparative phylogenetic analyses of DNA sequences across genomes - and some of the applications and recent breakthroughs in the field. As an in-depth case study I explain the methods and significance of our 2013 Nature paper on adaptive genotypic molecular convergence in echolocating mammals. I then highlight some of the avenues of study on the frontiers of current research.

Phylogenomic methods for comparative evolutionary biology - University College Dublin MSc - Joe Parker - 24th October 2014 from Joe Parker

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0 Phylogenomic Convergence Detection - Evolutionary Biology Meeting in Marseille 2014 /slideshow/phylogenomic-convergence-detection-evolutionary-biology-meeting-in-marseille-2014/41517262 ebmjoeparkerconvergencefinal-recover-nosampling-141113102943-conversion-gate01
Invited talk presented at the 18th EBM in Marseille, 16th September 2014. I outline the state-of-the-art in methods of genomic convergence detection, including adaptive molecular convergence, and highlight some of the next challenges in developing these techniques, including recent results.]]>
Invited talk presented at the 18th EBM in Marseille, 16th September 2014. I outline the state-of-the-art in methods of genomic convergence detection, including adaptive molecular convergence, and highlight some of the next challenges in developing these techniques, including recent results.]]> Thu, 13 Nov 2014 10:29:43 GMT /slideshow/phylogenomic-convergence-detection-evolutionary-biology-meeting-in-marseille-2014/41517262 JoeParker6@slideshare.net(JoeParker6) Phylogenomic Convergence Detection - Evolutionary Biology Meeting in Marseille 2014 JoeParker6 Invited talk presented at the 18th EBM in Marseille, 16th September 2014. I outline the state-of-the-art in methods of genomic convergence detection, including adaptive molecular convergence, and highlight some of the next challenges in developing these techniques, including recent results. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/ebmjoeparkerconvergencefinal-recover-nosampling-141113102943-conversion-gate01-thumbnail.jpg?width=120&height=120&fit=bounds" /> Invited talk presented at the 18th EBM in Marseille, 16th September 2014. I outline the state-of-the-art in methods of genomic convergence detection, including adaptive molecular convergence, and highlight some of the next challenges in developing these techniques, including recent results.

Phylogenomic Convergence Detection - Evolutionary Biology Meeting in Marseille 2014 from Joe Parker

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0 https://cdn.slidesharecdn.com/profile-photo-JoeParker6-48x48.jpg?cb=1560422871 Scientist: Carried out cutting-edge applied and theoretical research into the evolutionary biology of RNA viruses, including development and implementation of novel algorithms, data pipelines and analysis frameworks. Research publications including presentations, conference posters and peer-reviewed journals. 'Shannon' software won an international bioinformatics competition. Leader: Managed two medium-sized voluntary media organizations on a limited budget: achieved professional-quality work with national recognition and organized internal structures to improve productivity and long-term prospects for growth. Songwriter: Published songwriter / lyricist (Sotones/PRS) with proven track r... http://soundcloud.com/lonely-joe-parker https://cdn.slidesharecdn.com/ss_thumbnails/joeparker-ucl-sept2018-aod-nanopore-180914211427-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/challenges-and-potential-of-realtime-phylogenomics-lessons-from-a-metagenomic-case-study-into-acute-oak-decline-aod-in-southeast-england-114548898/114548898 Challenges and potenti... https://cdn.slidesharecdn.com/ss_thumbnails/joe-parker-pirbright-ukindia-180215141918-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/fieldbased-realtime-metagenomics-and-phylogenomics-for-responsive-pathogen-detection-lessons-from-nanopore-analyses-of-acute-oak-decline-aod-sites-in-the-uk/88051198 Field-based, real-time... https://cdn.slidesharecdn.com/ss_thumbnails/joe-parker-reak-time-phylogenomics-180207132740-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/realtime-phylogenomics-joe-parker-87391225/87391225 Real-time Phylogenomic...