Presentation of PHYLDOG, a piece of software for reconstructing gene and species phylogenies, with a focus on the practical side of things and pointers to a tutorial.
Models of gene duplication, transfer and loss to study genome evolutionboussau
Presentation of the models of gene duplication, transfer, loss, and incomplete lineage sorting developed by my colleagues and myself. Results on gene tree inference, species tree inference are presented. Groups of species studied include mammals, birds, fungi and cyanobacteria.
Overview of the approaches I co-developed to reconstruct species trees and gene trees, in the presence of gene duplications, losses and transfers, or incomplete lineage sorting. Includes Phyldog, ALE, MP-EST*, RevBayes.
Towards inferring the history of life in the presence of lateral gene transfe...boussau
Short presentation given at Evolution 2014 (similar to that given at SMBE 2014). Introduces a new method for estimating a species tree in the presence of gene duplication, loss, and lateral gene transfer, in a statistical framework, based on a large number of gene families. Results on simulations and real data are presented.
BIO 240 Education Specialist / snaptutorial.comMcdonaldRyan131
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Introduction: In recent years, law enforcement has been revolutionized by molecular biology. When human
Bio 240 Exceptional Education / snaptutorial.comDavis142
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Models of gene duplication, transfer and loss to study genome evolutionboussau
Presentation of the models of gene duplication, transfer, loss, and incomplete lineage sorting developed by my colleagues and myself. Results on gene tree inference, species tree inference are presented. Groups of species studied include mammals, birds, fungi and cyanobacteria.
Overview of the approaches I co-developed to reconstruct species trees and gene trees, in the presence of gene duplications, losses and transfers, or incomplete lineage sorting. Includes Phyldog, ALE, MP-EST*, RevBayes.
Towards inferring the history of life in the presence of lateral gene transfe...boussau
Short presentation given at Evolution 2014 (similar to that given at SMBE 2014). Introduces a new method for estimating a species tree in the presence of gene duplication, loss, and lateral gene transfer, in a statistical framework, based on a large number of gene families. Results on simulations and real data are presented.
BIO 240 Education Specialist / snaptutorial.comMcdonaldRyan131
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Introduction: In recent years, law enforcement has been revolutionized by molecular biology. When human
Bio 240 Exceptional Education / snaptutorial.comDavis142
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
BIO 240 Exceptional Education - snaptutorial.comDavisMurphyB28
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Introduction: In recent years, law enforcement has been revolutionized by molecular biology. When human
Bio 240 Education Redefined-snaptutorial.comrobertledwes30
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
BIO 240 Education Organization -- snaptutorial.comDavisMurphyB94
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Bio 240 Enhance teaching / snaptutorial.comHarrisGeorg46
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Introduction: In recent years, law enforcement has been revolutionized by molecular biology. When human tissues are left behind at crime scenes, these tissues can be collected and processed to yield samples of DNA, which can then be treated to isolate specific DNA fragments that are highly variable in the human population.
Keynote presentation from Plant and Pathogen Bioinformatics workshop at EMBL-EBI, 8-11 July 2014
Slides and teaching material are available at https://github.com/widdowquinn/Teaching-EMBL-Plant-Path-Genomics
PomBase Community Curation: A Fast Track to Capture Expert Knowledge, Antonia Lock, Kim Rutherford, Midori Harris, Mark Mcdowall, Paul Kersey, Stephen Oliver, Jurg Bahler and Valerie Wood.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2Ellinor Michel
Global Digital Infrastructure for Biological Nomenclature and Taxonomy
Ellinor Michel, Dep’t of Life Sciences, The Natural History Museum, London, UK, (e.michel@nhm.ac.uk)
Richard L. Pyle, Natural Sciences Dep’t, Bishop Museum, Honolulu, HI, USA
Robert P. Guralnick, Dep’t of Ecology & Evolutionary Biology, Univ Colorado, Boulder, CO, USA
Jon Todd, Dep’t of Earth Sciences, The Natural History Museum, London, UK,
The future for interoperable scientific information is digital, yet scientific names, the handles for all biodiversity information, remain without an integrated system tied to published descriptions and museum type specimens. Descriptions and type specimens provide standards for the otherwise fluid concepts of biological taxa. We are working to unify the infrastructures for biological nomenclature across nomenclatural codes (including zoological (ICZN - http://iczn.org/), botanical (ICNafp - http://www.iapt-taxon.org/nomen/main.php) and bacterial (ICNB) codes) through the Global Names Architecture (GNA). Our initial focus is on animal names, as these comprise the largest component of metazoan biodiversity and ZooBank (zoobank.org) is the first code-related online nomenclatural registration system. Users are applied scientists in agriculture, medicine, veterinary science and climate change research; biodiversity researchers such as ecologists, physiologists; archives such as museums; the scientific publishing community – in short, all users of scientific names of organisms based on the work of taxonomists.
Sequencing run grief counseling: counting kmers at MG-RASTwltrimbl
Talk by Will Trimble of Argonne National Laboratory on April 29, 2014, at UIC's department of Ecology & Evolution on visualizing and interpreting the redundancy spectrum of long kmers in high-throughput sequence data.
Effective development of a finite-element solver at the UniversityRomain Boman
Keynote lecture presented at ICSAAM 2018 - The 8th International Conference on Structural Analysis of Advanced Materials
August 28-31, 2018 – Tarbes, France
https://icsaam2018.sciencesconf.org/
Software development is usually neglected by academic researchers in the field of computational solid mechanics. This lack of long-term strategy often leads to the loss of valuable numerical models and algorithms. In the first part of this talk, the key ideas behind the management of the source code of METAFOR, a nonlinear finite-element solver developed at the University of Liège, are presented in detail. The primary goal is to continuously integrate all the developments into a single application so that future projects can safely rely on the results from the past. The second part of the talk exhibits several applications of metal forming processes computed with METAFOR and based on the Arbitrary Lagrangian Eulerian formalism.
OpenRepGrid and Friends - Presentation held at the 20th International Conference for Personal Construct Psychology, Sydney, Australia, July 2013
If you have any questions about OpenRepGrid visit the OpenRepGrid Google group under http://groups.google.com/group/openrepgrid
BIO 240 Exceptional Education - snaptutorial.comDavisMurphyB28
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Introduction: In recent years, law enforcement has been revolutionized by molecular biology. When human
Bio 240 Education Redefined-snaptutorial.comrobertledwes30
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
BIO 240 Education Organization -- snaptutorial.comDavisMurphyB94
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Bio 240 Enhance teaching / snaptutorial.comHarrisGeorg46
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Introduction: In recent years, law enforcement has been revolutionized by molecular biology. When human tissues are left behind at crime scenes, these tissues can be collected and processed to yield samples of DNA, which can then be treated to isolate specific DNA fragments that are highly variable in the human population.
Keynote presentation from Plant and Pathogen Bioinformatics workshop at EMBL-EBI, 8-11 July 2014
Slides and teaching material are available at https://github.com/widdowquinn/Teaching-EMBL-Plant-Path-Genomics
PomBase Community Curation: A Fast Track to Capture Expert Knowledge, Antonia Lock, Kim Rutherford, Midori Harris, Mark Mcdowall, Paul Kersey, Stephen Oliver, Jurg Bahler and Valerie Wood.
Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.
Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2Ellinor Michel
Global Digital Infrastructure for Biological Nomenclature and Taxonomy
Ellinor Michel, Dep’t of Life Sciences, The Natural History Museum, London, UK, (e.michel@nhm.ac.uk)
Richard L. Pyle, Natural Sciences Dep’t, Bishop Museum, Honolulu, HI, USA
Robert P. Guralnick, Dep’t of Ecology & Evolutionary Biology, Univ Colorado, Boulder, CO, USA
Jon Todd, Dep’t of Earth Sciences, The Natural History Museum, London, UK,
The future for interoperable scientific information is digital, yet scientific names, the handles for all biodiversity information, remain without an integrated system tied to published descriptions and museum type specimens. Descriptions and type specimens provide standards for the otherwise fluid concepts of biological taxa. We are working to unify the infrastructures for biological nomenclature across nomenclatural codes (including zoological (ICZN - http://iczn.org/), botanical (ICNafp - http://www.iapt-taxon.org/nomen/main.php) and bacterial (ICNB) codes) through the Global Names Architecture (GNA). Our initial focus is on animal names, as these comprise the largest component of metazoan biodiversity and ZooBank (zoobank.org) is the first code-related online nomenclatural registration system. Users are applied scientists in agriculture, medicine, veterinary science and climate change research; biodiversity researchers such as ecologists, physiologists; archives such as museums; the scientific publishing community – in short, all users of scientific names of organisms based on the work of taxonomists.
Sequencing run grief counseling: counting kmers at MG-RASTwltrimbl
Talk by Will Trimble of Argonne National Laboratory on April 29, 2014, at UIC's department of Ecology & Evolution on visualizing and interpreting the redundancy spectrum of long kmers in high-throughput sequence data.
Effective development of a finite-element solver at the UniversityRomain Boman
Keynote lecture presented at ICSAAM 2018 - The 8th International Conference on Structural Analysis of Advanced Materials
August 28-31, 2018 – Tarbes, France
https://icsaam2018.sciencesconf.org/
Software development is usually neglected by academic researchers in the field of computational solid mechanics. This lack of long-term strategy often leads to the loss of valuable numerical models and algorithms. In the first part of this talk, the key ideas behind the management of the source code of METAFOR, a nonlinear finite-element solver developed at the University of Liège, are presented in detail. The primary goal is to continuously integrate all the developments into a single application so that future projects can safely rely on the results from the past. The second part of the talk exhibits several applications of metal forming processes computed with METAFOR and based on the Arbitrary Lagrangian Eulerian formalism.
OpenRepGrid and Friends - Presentation held at the 20th International Conference for Personal Construct Psychology, Sydney, Australia, July 2013
If you have any questions about OpenRepGrid visit the OpenRepGrid Google group under http://groups.google.com/group/openrepgrid
Simple Data Engineering in Python 3.5+ — Pycon.DE 2017 Karlsruhe — Bonobo ETLRomain Dorgueil
Simple Data Engineering in Python 3.5+ using Bonobo ETL, with real world example using Django2 and DBPedia.
https://www.bonobo-project.org/
Presentation from Pycon.DE 2017 in Karlsruhe
Scott Edmunds talk in the "Policies and Standards for Reproducible Research" session on Revolutionizing Data Dissemination: GigaScience, at the Genomic Standards Consortium meeting at Shenzhen. 6th March 2012
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
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Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
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2. Getting the program
• From internet:
• http://pbil.univ-lyon1.fr/software/phyldog/#try
!
• Using the USB keys in the room:
• contain VirtualBox
• contain the application along with the data to analyze
3. • LBBE collaborators (Lyon):
– Gergely Szöllősi (Budapest),
– Eric Tannier,
– Vincent Daubin,
– Manolo Gouy,
– Sophie Abby,
– Laurent Duret,
– Thomas Bigot,
– Magali Semeria
Collaborators
4. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
5. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
6. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
7. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D
8. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
D DL
9. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGTD DL
10. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILSD DL
11. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
PHYLDOG
D DL
12. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
DL
+LGT:
Szollosi
et al.,
PNAS
PHYLDOG
D DL
13. Species: A B C D
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
Species: A B C D
Discrete character:
Continuous character:
a a b a
0.1 0.2 0.2 0.4
T
I
M
E
LGT ILS
DL
+LGT:
Szollosi
et al.,
PNAS
ILS:
Not
yet
PHYLDOG
D DL
14. What is PHYLDOG?
• Program for the coestimation of species and gene trees at the
genome scale
• Probabilistic model of sequence evolution + model of gene
duplication and loss
• Statistical framework
• Branch-wise parameters of duplications and losses
• Gene families evolve independently of each other
• Based on a parallel architecture using MPI
Genome-scale coestimation of species and gene trees. Boussau et al., Genome research. 2013 23:323:330.
17. Option files
family_X.option: options specific to gene family X (alignment
file, substitution model options, gene tree search options)
GeneralOptions.txt: options concerning the species tree search,
and options common to all gene families (species tree search
options, duplication/loss model options, list of gene families)
18. Option files
family_X.option: options specific to gene family X (alignment
file, substitution model options, gene tree search options)
GeneralOptions.txt: options concerning the species tree search,
and options common to all gene families (species tree search
options, duplication/loss model options, list of gene families)
Easy generation of basic option files using the
prepareData.py script
19. PHYLDOG tutorial
http://www.prabi.fr/redmine/projects/phyldogtoolt/wiki/Tutorial
• Installing PHYLDOG
• Downloading files
• Basic input files
• Generating all the option files using the prepareData.py script
• Running PHYLDOG
• Diminishing the number of species considered
• Diminishing the number of gene families considered
• Running PHYLDOG, at last
• Interpreting PHYLDOG's output
• Going further
23. •Gene alignments:
•Error prone
•Short
•Point estimates
•Gene trees:
•based on alignments
•Point estimates
•Species trees:
•based on gene trees
Why our current pipeline can be improved
24. •Gene alignments:
•Error prone
•Short
•Point estimates
•Gene trees:
•based on alignments
•Point estimates
•Species trees:
•based on gene trees
Why our current pipeline can be improved
35. Study of mammalian genomes
• Challenging but well-studied phylogeny
• 36 mammalian genomes available in Ensembl v. 57
• About 7000 gene families
• Correction for incomplete genomes
42. • Two approaches:
1. Looking at ancestral genome sizes
2. Assessing how well one can recover ancestral syntenies using
reconstructed gene trees (Bérard et al., Bioinformatics)
Assessing the quality of gene trees
43. • Two approaches:
1. Looking at ancestral genome sizes
2. Assessing how well one can recover ancestral syntenies using
reconstructed gene trees (Bérard et al., Bioinformatics)
• Comparison between:
– PhyML (PhylomeDB and Homolens databases )
– TreeBeST (Ensembl-Compara database)
– PHYLDOG
Assessing the quality of gene trees
44. 1) Junk trees generate obesity
• Errors in gene tree reconstruction result in larger
ancestral genomes
– Better algorithms should yield smaller ancestral genomes
47. 2) Junk trees break synteny groups
• We use Deco (Bérard et al. Bioinformatics 2013) to
reconstruct ancestral synteny groups using gene trees
• Errors in gene tree reconstruction break synteny
groups
– Better algorithms should yield more genes in ancestral
synteny groups
50. Perspectives
!
• Improvement of the algorithms to reconstruct gene
trees (e.g. Magali Semeria)
• Improvement of the algorithms to reconstruct the
species tree
• Dealing with ILS
• Joint reconstruction of gene trees and gene
alignments
51. Perspectives
!
• Improvement of the algorithms to reconstruct gene
trees (e.g. Magali Semeria)
• Improvement of the algorithms to reconstruct the
species tree
• Dealing with ILS
• Joint reconstruction of gene trees and gene
alignments
52. The Ancestrome project
• Reconstructing a species tree and gene trees for a large
number of species
• Reconstructing ancestral gene contents
• Inferring ancient metabolisms and lifestyles
• Inferring ancient communities
New insights into the evolution of life on Earth,
and into genomic evolution
