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.
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.
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.
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.
BauhinaGenome.hk slides used for a school visit to talk DNA, genomics and Bauhinia to year 6 (11-12 year old) science class at the CIS school in Hong Kong.
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.
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.
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.
BauhinaGenome.hk slides used for a school visit to talk DNA, genomics and Bauhinia to year 6 (11-12 year old) science class at the CIS school in Hong Kong.
Jonathan Eisen talk for 2019 ADVANCE Scholar Award SymposiumJonathan Eisen
Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium
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.
pro-iBiosphere Towards Open Biodiversity Knowledge COOPEUS 2013millerjeremya
Invited presentation, meeting of COOPEUS - Connecting Research Infrastructures WP6, in conjunction with EGI (European Grid Infrastructure) Technical Forum, Madrid, Spain, September 2013
Jonathan Eisen talk for 2019 ADVANCE Scholar Award SymposiumJonathan Eisen
Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium
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.
pro-iBiosphere Towards Open Biodiversity Knowledge COOPEUS 2013millerjeremya
Invited presentation, meeting of COOPEUS - Connecting Research Infrastructures WP6, in conjunction with EGI (European Grid Infrastructure) Technical Forum, Madrid, Spain, September 2013
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
Phylogenomic Convergence Detection - Evolutionary Biology Meeting in Marseill...Joe Parker
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.
Evolution, Humanity and Religion Where is the evidence for God?William Hall
This hypertextual presentation derives from a nearly completed hypertext book on the co-evolution of and revolutions in tools humans use and human cognition (see below), and was tailored for an atheists and freethinkers group interested in what paleontology, archeology and human genomics have to say about the human origins of religion. Comprehensively detailed scientific evidence for the evolution of modern humans from our primate ancestry leaves no gaps in our long evolution that need any kind of mystical explanation to account for our existence. The presentation begins with a consideration of the biophysical nature of life and the philosopher Karl Popper’s construction of an evolutionary theory of knowledge. These foundation stones explain how natural selection works. The recent development of genomic technology, has enabled detailed genomes to be constructed for many humans, all of the great apes, and two extinct human species, the Neanderthals and Denisovans. The genomes plot the detailed sequences for some 3 billion DNA nucleotides for each species. Humans are 99% identical and chimpanzees / bonobos down to the nucleotide level, 98.4% identical to gorillas, and 97.4% identical to orangutans. Given the vast number of data-points it is easy to unambiguously reconstruct details of the relationships and relative times of speciation in the ancestry. Although scrappy fossils are notoriously difficult to reconstruct they do establish the presence of certain lineages in particular geographic areas. Various forms of radioactive decay allow their ages to be determined with some considerable accuracy. It is clear that we share a “last” common ancestor with chimpanzees and bonobos some 5-7 million years ago. Paleoarcheological evidence traces the initially gradual development of tool use over that period of time. Several videos in the presentation demonstrate that the great apes are also surprisingly accomplished tool users. This evidence is then used to construct in detail the evolution of small-brained tool-using ape men into spear and fire equipped top carnivores into today’s big-brained modern men that are dominating the entire planet. Human speech probably emerged only in the last 100,000 – 200,000 years ago. With the emergence of speech, people could begin to speculate about their origins – positing earth mothers and angry sky gods. Only in the last few decades has the evidence become strong enough to show there is no need for mystical gods and creators to explain human origins. When the writing and editorial work on the book “Application Holy Wars or a New Reformation – A Fugue on the Theory of Knowledge” is finished, it will be published via Kororoit Institute (http://kororoit.org). Crowd funding will be sought to complete the editorial and publishing work. The argument of that book is structured as a fugue, crossing many disciplinary paradigms.
IDENTIFICATION AND IMPORTANCE OF CONSERVED SEQUENCE INDELS (SIGNATURES) FOR UNDERSTANDING MICROBIAL CLASSIFICATION AND PHYLOGENY. Importance of INDELS in humans, with uses as well as limitations both in humans and microbes. There is use of Molecular systematic approach towards identification and classification.
Effects of density on spacing patterns and habitat associations of a Neotropi...Nicole Angeli
Presentation at Ecological Society of America, August 2013. Minneapolis, USA. –Oral Paper
Angeli, N. F., K. Lips, G. V. DiRenzo, and A. Cunha. “Effects of density on spacing patterns
and habitat associations in the Neotropical Glassfrog Espadarana prosoblepon.”
Bradley Voytek - Berkeley Cognitive Neuroscience 2018UC San Diego
Through careful measurement and consideration of the brain signals we record, we can build massive databases of brain activity.
We can link these with other open neuroscience data sources to mine for links between brain activity, connectivity, gene expression, cell type, and function in new ways.
We can leverage data mining to generate new hypotheses *for us*.
Our relevant papers:
oscillation parameterization:
https://www.biorxiv.org/content/early/2018/04/11/299859
waveform shape analysis:
https://www.biorxiv.org/content/early/2018/04/16/302000
hypothesis generation:
http://voyteklab.com/wp-content/uploads/Voytek-JNeurosciMethods2012.pdf
open data ecosystems:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005037
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
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/
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
3. Gene trees provide confusing signals about
species relationships
Boussau, Gueguen, Gouy, BMC Evol. Biol. 2008HOGENOM database
4. Gene transfers and the quixotic pursuit of the TOL
Doolittle WF,
Science 1999
5. Gene transfers and the quixotic pursuit of the TOL
Doolittle WF,
Science 1999
6. Gene transfers and the quixotic pursuit of the TOL
Doolittle WF,
Science 1999
“The monistic concept of a single universal tree appears […]
increasingly obsolete. […][It is] no longer the most
scientifically productive position to hold[…][It] accounts for
only a minority of observations from genomes.”
Bapteste, O’Malley, Beiko, Ereshefsky, Gogarten, Franklin-Hall,
Lapointe, Dupré, Dagan, Boucher, Martin, Biology Direct 2009.
7. Gene transfers and the quixotic pursuit of the TOL
Doolittle WF,
Science 1999
“The monistic concept of a single universal tree appears […]
increasingly obsolete. […][It is] no longer the most
scientifically productive position to hold[…][It] accounts for
only a minority of observations from genomes.”
Bapteste, O’Malley, Beiko, Ereshefsky, Gogarten, Franklin-Hall,
Lapointe, Dupré, Dagan, Boucher, Martin, Biology Direct 2009.
“Bien parece, respondió Don Quijote, que no estás
cursado en esto de las aventuras”
!
"Obviously," replied Don Quijote,
"you don't know much about adventures”
Don Quijote, VIII
8. Can we extract some signal from the noise?
Huge amounts of gene tree incongruence in genomic
data
1. What proportion of it is biological (=signal) and
what proportion of it comes from our failure to
correctly infer gene trees (=noise)?
2. Amid the signal, is there trace of a tree of life?
9. 1-Removing the noise in gene trees
Usual
approach
ALE
+DTL
RFdistancetorealtree
Szöllősi et al., Syst. Biol. 2013
10. 1-Removing the noise in gene trees
Usual
approach
ALE
+DTL
Transfereventsperfamily
Usual
approach
ALE
+DTL
RFdistancetorealtree
Szöllősi et al., Syst. Biol. 2013
11. 2-Amid the signal, is there trace of a tree of life?
• STRALE:
• A Bayesian probabilistic method that can interpret thousands of
gene trees in terms of:
• speciation events
• duplication events (D)
• transfer events (T)
• loss events (L)
• A method able to estimate the DTL rates
• A method able to reconstruct the species tree
• A method able to order the nodes of the species tree
20. Conclusion, perspectives
• STRALE:
• A Bayesian probabilistic method that can interpret thousands of
gene trees with DTL events and reconstruct a time-ordered
species tree
• Currently undergoing tests
• Can run on thousands of gene families (parallel architecture)
• Will be open access
• Can run on dozens of species
