GRC Workshop at Churchill College on Sep 21, 2014. This is Michael Schatz's talk on the theory and practice of representing population data in graph structures.
GRC Workshop at Churchill College on Sep 21, 2014. This is Michael Schatz's talk on the theory and practice of representing population data in graph structures.
Presentation by Benedict Paten at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on updates to the human reference assembly, GRCh38.
Presentation at IMGC 2019 workshop describing the latest improvements to the mouse reference genome assembly and analyses performed in preparation for the next release of the mouse genome assembly (GRCm39).
GRC Workshop at Churchill College on Sep 21, 2014. This is Paul Kitt's talk describing the NCBI approach to annotation the full human reference assembly.
GRC Workshop at Churchill College on Sep 21, 2014. This is Aaron Quinlan's talk on issues with representing variants in the full assembly, with suggestions for VCF modifications for handling variant calls on the alts.
Presentation by Valerie Schneider discussing Genome Reference Consortium (GRC) plans for the mouse and zebrafish reference genome assemblies, presented at the 2016 meeting of the The Allied Genetic Conference (TAGC). Includes description of resources at the National Center for Biotechnology Information (NCBI) for working with reference genome assemblies.
Presentation by Karen Miga at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on centromere assemblies.
Presentation at 2019 ASHG GRC/GIAB workshop describing goals and progress of the telomere-to-telomere consortium to generate a genome assembly that provides representation of all sequences, including repetitive regions.
Presentation by Benedict Paten at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on updates to the human reference assembly, GRCh38.
Presentation at IMGC 2019 workshop describing the latest improvements to the mouse reference genome assembly and analyses performed in preparation for the next release of the mouse genome assembly (GRCm39).
GRC Workshop at Churchill College on Sep 21, 2014. This is Paul Kitt's talk describing the NCBI approach to annotation the full human reference assembly.
GRC Workshop at Churchill College on Sep 21, 2014. This is Aaron Quinlan's talk on issues with representing variants in the full assembly, with suggestions for VCF modifications for handling variant calls on the alts.
Presentation by Valerie Schneider discussing Genome Reference Consortium (GRC) plans for the mouse and zebrafish reference genome assemblies, presented at the 2016 meeting of the The Allied Genetic Conference (TAGC). Includes description of resources at the National Center for Biotechnology Information (NCBI) for working with reference genome assemblies.
Presentation by Karen Miga at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on centromere assemblies.
Presentation at 2019 ASHG GRC/GIAB workshop describing goals and progress of the telomere-to-telomere consortium to generate a genome assembly that provides representation of all sequences, including repetitive regions.
Exploring DNA/RNA-Seq Analysis Results with Golden Helix GenomeBrowse and SVSGolden Helix Inc
GenomeBrowse, a free visualization tool for all types of sequence data, was introduced in 2012 to broad acclaim. Researchers using GenomeBrowse discovered a product far beyond the status quo with seamless navigation of sequence alignments and other genomic data using a fluid, fast, and intuitive interface that just "made sense." Recent updates to GenomeBrowse, including support for VCF files and BED files and the ability to export tables of data extracted from viewable annotation tracks, further improved the product and created new synergy with Golden Helix SNP & Variation Suite (SVS).
This webcast will demonstrate the ability of GenomeBrowse to stream sequence alignment data from the Amazon Cloud, seamlessly transitioning between whole genome views and base-pair resolution in the context of both public and custom annotation tracks. We will show how GenomeBrowse can be used in conjunction with SVS to highlight false variant calls, confirm the inheritance pattern of putative functional variants, and aid in the interpretation of a variant's impact. Examples of RNA-seq expression analysis, somatic variation in cancer, and family-based DNA-seq analysis will be included.
Single-cell RNA sequencing workshop given at the Ottawa Hospital Research Institute in 2018. Note that slides contain animations that won't be viewed in the slidehsare
How to sequence a large eukaryotic genome - and how we sequenced the cod genome. A seminar I gave for the Computational Life Science (Univ. of Oslo) seminar series, September 28, 2011
The genome assembly is simply the genome sequence produced after chromosomes have been fragmented, those fragments have been sequenced, and the resulting sequences have been put back together. Genome assembly has been metaphorically described as the process of assembling a jigsaw puzzle from the individual reads.
Genome assembly software (BySS, AMOS, Arapan-M, Arapan-S, Cortex, DNA Baser, DNAnexus etc.) combines the read into larger regions called contigs.
Presentation at 2019 ASHG GRC/GIAB workshop describing history of the human reference genome, current curation efforts and future plans, and the relationship of all 3 to efforts to produce a human pan-genome.
Platform presentation at ASHG 2019 describing recent updates to the human reference genome assembly (GRCh38) and future plans with relevance to pan-genomic representations.
Presentation at 2019 ASHG GRC/GIAB workshop describing features and recent updates to the vg toolkit, including examples of comparisons to other methods used for alignment and variant detection.
Presentation at 2019 ASHG GRC/GIAB workshop describing recent updates to the MANE project, which aims to provide matched annotation from RefSeq and GENCODE.
Presentation at PanGenomics in the Cloud Hackathon, run by NCBI at UCSC (https://ncbiinsights.ncbi.nlm.nih.gov/2019/02/06/pangenomics-cloud-hackathon-march-2019/). Presents points to consider about the adoption of a pangenome reference, emphasizing aspects for long-term data management and wide-spread adoption.
Presentation by Valerie Schneider at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on updates to the human reference assembly, GRCh38.
Presentation by Tina Graves-Lindsay at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on production of reference grade assemblies for various human populations.
Presentation by Fritz Sedlazeck at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on characterizing human structural variation.
Presentation by Justin Zook at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on benchmarks for indels and structural variants.
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.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
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.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
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.
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.
Richard's aventures in two entangled wonderlandsRichard 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.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
Salas, V. (2024) "John of St. Thomas (Poinsot) on the Science of Sacred Theol...Studia Poinsotiana
I Introduction
II Subalternation and Theology
III Theology and Dogmatic Declarations
IV The Mixed Principles of Theology
V Virtual Revelation: The Unity of Theology
VI Theology as a Natural Science
VII Theology’s Certitude
VIII Conclusion
Notes
Bibliography
All the contents are fully attributable to the author, Doctor Victor Salas. Should you wish to get this text republished, get in touch with the author or the editorial committee of the Studia Poinsotiana. Insofar as possible, we will be happy to broker your contact.
2. Cost per Genome Dilemma
2
Sequencing cost is down for sure, but getting a de novo human genome that has the
same scientific standard as the initial work does NOT follow Moore’s law.
PacBio® CHM1: 4378 kb
from just single random fragment
library
HGP, N50 ~100kb
NCBI-34
Contig N50 29Mb
HuRef: 107kb
BGI YH: 7.4kb
KB1: 5.5kb
NA12878: 24kb
CHM1: 144kb
RP11: 127kb
According to the NHGRI
website, the definition of
“sequencing a genome”
changed in 2008.
The 1000 Genomes Project
starts in 2008, too.
3. Question Asked!!
• Since the 1000 Genomes
Project, we have learned a lot
of about point mutations. Can
we go beyond that?
• What if we have 50, 100 or
more human assemblies so we
can address all genetic
variations as much as
possible?
• Will one day all human genome
sequencing be done in de novo
fashion?
– If so, how can we get ready
for that as bioinformatists?
3
Evan Eichler , In Future Opportunities
for Genome Sequencing and Beyond,
July 28-29, 2014
4. Where We Are Now
• One PacBio® human data set is publicly available, more are likely to
come
• Multiple groups have successfully assembled the public CHM1 data
set independently with new algorithms from raw data
• With new alignment/assembly tools from Gene Myers:
one can assemble a genome in ~ 20,000 CPU-hours. (20X faster
than 400,000+ CPU-hours from previous effort.)
4
New Assembly Statistics done
With Daligner:
#Seqs
5,058
Mean
562,695
Max
27,292,514
n50
5,265,098
Total
2,846,115,586
http://dazzlerblog.wordpress.com
5. What Can We Learn from High-contiguity
De Novo Human Assemblies?
5
6. What Can We Learn from High-contiguity Human
Assemblies?
• Low-hanging Fruits
– Calling SNPs (assembly not needed, but it helps)
– Calling structure variants with whole-genome alignment
approaches
– Inferring repeats by coverage analysis
• Assembly graph can provide information for understanding
more complicated polymorphisms
6
8. Call Structure Variation By Whole-genome Alignment
• Whole-genome alignments ( ~ 1 hr in a 32-core machine)
– With multi-threaded Mummer
– Clustering the hits with Mgaps and identified “gaps” in the alignments,
convert to bed format for visualization
8
Structure Variants Called in Chromosome 1
9. Distribution of The Structure Variation Sizes
• Number of insertions/deletions: 13796 SV calls (for insertion or deletion >
100 bp against hg19)
9
11. Assembly Graph
11
Each edge is associated with a sequence.
Every path is a candidate of a model of part
of the genome.
From Gene Myers’ ISMB 2014 Keynote talk
12. Dissect a Contig from a String Graph
The autonomy of a contig from a string graph layout
12
A contig: a linear non-branching path
Each node: the begin (5’) or end (3’)
of a read
Each edge: a continuous sub-
sequence from one read
Ek:
(V1,
V2,
Read,
Range)
=
(
00099576_1:B,
00101043_0:B,
00101043_0,
1991-‐0
)
Read
1:
00099576_1,
Read
2:
00101043_0
In practice, we might just encode the paths in a contig rather than each single
edge:
C
=
(Ek,
Ek+1,
Ek+2,
Ek+2)
=
(Pj
Pj+1)
V1 V2 V3 V4 V5
Ek Ek+1 Ek+2 Ek+3
V1 V3 V5
Pj Pj+1
C =
=
13. Assembly String Graph of CHM1 Genome
• Largest connect component: 31998 nodes, 39399 edges, ~36.5%
(~1Gbp) of the human genome (total: 87572 nodes, 94530 edges)
13
Centromere?
Casey Bergman:
“it almost looks like an
electron micrograph of
the nucleus”
#convergence
14. Polymorphism Structure vs. Local Assembly Graph
Structure
14
SNPs
SNPs SNPs
SVsSVs
Diploid Genome
Segmental Duplication
Similar String Graph
15. Identify Contigs: A New Proposal
SNPs
SNPs SNPs
SVs
SVs
Associated
contig 1
Associated
contig 2
Primary
contig
1 full length contig + 2 associated contigs
Keep the long-range information
while maintaining the relations of
the alternative alleles.
22. Contig Coverage Analysis
22
18.5 X
2 * 18.5 X
3 * 18.5 X
High coverage long contigs
40 contigs > 100kbp
> 2.5 * 18.5 X
Poor assemblies,
alignment artifacts,
or sequence errors?
High repeat elements
23. Checking the Complexity of the High-coverage Contigs
23
Contig 4006, 687kb, 53x coverage
Contig 4235, 453k, 59x coverage
Contig 3842, 235k, 54x coverage
Warning: These contigs may not be 100% correctly assembled due to
some nasty repeats. However, the local graphs give hints about the
true genome structures.
24. How does the High-coverage Contig Look?
24
>2000X in this region
25. How does The High-coverage Contig Look?
25
High-coverage
Region
Alpha satellites?
26. For Research Use Only. Not for use in diagnostic procedures.
Extreme Repeats
26
27. Identify Centromere Alpha-satellite Structure
• Most of the nasty contig graphs are around the centromere.
Currently, it remains hard to get long contigs around those very long
tandem repeats.
• However, we can still learn many useful things from long-read data
• Tool In Development: α-Centauri for identifying different high-order
repeat structures (https://github.com/volkansevim/alpha-CENTAURI,
Volkan Sevim, Ali Bashir & Karen Miga )
27
29. Example: A Read Reconstructs a 24-mer HOR
29
Align monomer to each other to
identify near identical mon0mers
Identify HOR with the monomer
IDs and positions
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
171819
20
21
22
23
24
30. Many Other Open Topics
• Low-coverage assembly: cost vs. quality analysis
• Phasing for haplotypes
• Crowd-sourcing infrastructure for examining / annotating / correcting
genome assemblies
• Evaluation about SNPs calling with short reads on better assembly
• Large-scale comparative genomes with de novo assemblies
• Assembly-graph data format
• Visualization Techniques
• Combining other data types, e.g. optical mapping
30
It is a very exciting time. We still need more tools to harvest
information to generate new knowledge.
31. For Research Use Only. Not for use in diagnostic procedures. Pacific Biosciences, the Pacific Biosciences logo, PacBio, SMRT, SMRTbell and Iso-Seq
are trademarks of Pacific Biosciences in the United States and/or other countries. All other trademarks are the sole property of their respective owners.
31