BigData 2020 - Revision history

imported>Weigang: /* Schedule */

2020-07-15T21:06:14Z

Schedule

← Older revision		Revision as of 21:06, 15 July 2020
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	* 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])		* 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])
	* 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx\|thumbnail]] & Handouts [[File:Pretest.pdf\|thumbnail]]		* 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx\|thumbnail]] & Handouts [[File:Pretest.pdf\|thumbnail]]
	* 11:05 - 12: [http://phylogeny.fr Build molecular phylogeny online]		* 11:05 - 12: [http://www.phylogeny.fr Build molecular phylogeny online]

	==Exercises & Challenges==		==Exercises & Challenges==

imported>Weigang: /* Schedule */

2020-07-15T21:05:40Z

Schedule

← Older revision		Revision as of 21:05, 15 July 2020
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	* 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])		* 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])
	* 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx\|thumbnail]] & Handouts [[File:Pretest.pdf\|thumbnail]]		* 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx\|thumbnail]] & Handouts [[File:Pretest.pdf\|thumbnail]]
	* 11:05 - 12: ~~Demo~~: ~~[[Mini-Tutorals#ospC_amplicon_identification\|identification of genomic mutations associated with antibiotic resistance]~~]		* 11:05 - 12: [http://phylogeny.fr Build molecular phylogeny online]

	==Exercises & Challenges==		==Exercises & Challenges==

imported>Weigang: /* Schedule */

2020-07-15T21:00:59Z

Schedule

← Older revision		Revision as of 21:00, 15 July 2020
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	==Schedule==		==Schedule==
	* 9:00 - 9:25: Introduction; [http://rstudio.org Install R & R Studio]; Download fasta file & save as "~~ospC-pep~~.fasta" : [[File:~~OspC-pep~~.txt\|thumbnail]]		* 9:00 - 9:25: Introduction; [http://rstudio.org Install R & R Studio]; Download fasta file & save as "spike.fasta" : [[File:Spike2.txt\|thumbnail]]
	* 9:30 - 10:00: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1 Part I. Unix Basics])		* 9:30 - 10:00: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1 Part I. Unix Basics])
	* 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])		* 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])
	* 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx\|thumbnail]] & Handouts [[File:Pretest.pdf\|thumbnail]]		* 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx\|thumbnail]] & Handouts [[File:Pretest.pdf\|thumbnail]]
	* 11:05 - 12: Demo: [[Mini-Tutorals#ospC_amplicon_identification\|identification of genomic mutations associated with antibiotic resistance]]		* 11:05 - 12: Demo: [[Mini-Tutorals#ospC_amplicon_identification\|identification of genomic mutations associated with antibiotic resistance]]
	** Slides on background
	** Demo (on wallace lab server)

	==Exercises & Challenges==		==Exercises & Challenges==

imported>Weigang: /* Textbooks for genome evolution */

2020-07-15T20:56:39Z

Textbooks for genome evolution

← Older revision		Revision as of 20:56, 15 July 2020
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	* Familiarity with a programming language (e.g., Python or Perl)		* Familiarity with a programming language (e.g., Python or Perl)
	* Data visualization & statistical analysis (e.g., JavaScript; the R statistical computing environment)		* Data visualization & statistical analysis (e.g., JavaScript; the R statistical computing environment)

	~~==Textbooks for genome evolution==~~
	* Graur, 2016, Molecular and Genome Evolution, First Edition, Sinauer Associates, Inc. ISBN: 978-1-60535-469-9. [http://www.sinauer.com/molecular-and-genome-evolution.html Publisher's Website]
	* Baum & Smith, 2013. Tree Thinking: an Introduction to Phylogenetic Biology, Roberts & Company Publishers, Inc.

	==Learning Goals==		==Learning Goals==

imported>Weigang: /* Bioinformatics workflow for comparative analysis of bacterial pathogen genomes */

2020-07-15T20:56:20Z

Bioinformatics workflow for comparative analysis of bacterial pathogen genomes

← Older revision		Revision as of 20:56, 15 July 2020
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	* [http://cov.genometracker.org Covid-19 Genome Tracker]		* [http://cov.genometracker.org Covid-19 Genome Tracker]

	~~==Bioinformatics workflow for comparative analysis of bacterial pathogen genomes==~~
	* Pathogen isolation -> DNA extraction -> Library preparation -> High-through sequencing
	* De novo genome assembly (canu; velvet; etc)
	* Identify reference genome from NCBI database (kraken)
	* Variant call (bwa; cortex_var; samtools mpileup)
	* Infer genome phylogeny (muscle; reXML)
	* Annotation (PATRIC)
	* Custom genome browser (JavaScript; D3 library for interactive graphics)

	==Essential bioinformatics skills==		==Essential bioinformatics skills==
	* Linux command-line interface (e.g., BASH shell)		* Linux command-line interface (e.g., BASH shell)

imported>Weigang at 20:45, 15 July 2020

2020-07-15T20:45:41Z

← Older revision		Revision as of 20:45, 15 July 2020
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	\|-		\|-
	\| [[File:Lp54-gain-loss.png\|300px\|thumbnail\| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] \|\|		\| [[File:Lp54-gain-loss.png\|300px\|thumbnail\| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] \|\|
	[[File:Cov-screenshot-1.png\|300px\|thumbnail\| Haplotype network ]]		[[File:Cov-screenshot-1.png\|300px\|thumbnail\| [http://cov.genometracker.org/ Haplotype network] ]]
	\|\|		\|\|
	[[File:Cov-screenshot-2.png\|300px\|thumbnail\| S protein alignment ]]		[[File:Cov-screenshot-2.png\|300px\|thumbnail\| Spike protein alignment ]]
	\|}		\|}
	</center>		</center>
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	==Case studies from Qiu Lab==		==Case studies from Qiu Lab==
	* [http://borreliabase.org Comparative genomics of worldwide Lyme disease pathogens]		* [http://borreliabase.org Comparative genomics of worldwide Lyme disease pathogens]
	* Evolutionary origin of coronaviruses
	* [http://cov.genometracker.org Covid-19 Genome Tracker]		* [http://cov.genometracker.org Covid-19 Genome Tracker]

imported>Weigang at 20:43, 15 July 2020

2020-07-15T20:43:47Z

← Older revision		Revision as of 20:43, 15 July 2020
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Lyme Disease (Borreliella) !! ~~Coronaviruses~~ !! ~~SARS-CoV-2~~		! Lyme Disease (Borreliella) !! CoV Genome Tracker !! Coronavirus evolutuon
	\|-		\|-
	\| [[File:Lp54-gain-loss.png\|300px\|thumbnail\| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] \|\|		\| [[File:Lp54-gain-loss.png\|300px\|thumbnail\| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] \|\|
	[[File:~~GeneExp2~~.~~jpeg~~\|300px\|thumbnail\| ~~p-value (y-axis) vs. fold change (x-axis)~~]]		[[File:Cov-screenshot-1.png\|300px\|thumbnail\| Haplotype network ]]
	\|\|		\|\|
	[[File:~~GeneExp3~~.~~jpeg~~\|300px\|thumbnail\| ~~genes significantly down or up-regulated (at p<1e-4)~~]]		[[File:Cov-screenshot-2.png\|300px\|thumbnail\| S protein alignment ]]
	\|}		\|}
	</center>		</center>

imported>Weigang at 20:46, 14 July 2020

2020-07-14T20:46:50Z

← Older revision		Revision as of 20:46, 14 July 2020
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	<center>[http://bigdata.citytech.cuny.edu/ City Tech/Cornell BioMedical Big Data Week ~~2019~~]: '''Pathogen Evolutionary Genomics'''</center>		<center>[http://bigdata.citytech.cuny.edu/ City Tech/Cornell BioMedical Big Data Week 2020]: '''Pathogen Evolutionary Genomics'''</center>
	<center>Wed, July 22, ~~2019~~, 9-12</center>		<center>Wed, July 22, 2020, 9 am - 12 noon</center>
	<center>'''Instructor:''' Dr Weigang Qiu, Professor, Department of Biological Sciences </center>		<center>'''Instructor:''' Dr Weigang Qiu, Professor, Department of Biological Sciences </center>
	<center>'''Office:''' B402 Belfer Research Building</center>		<center>'''Office:''' B402 Belfer Research Building</center>
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Lyme Disease (Borreliella) !! ~~Volcano plot~~ !! ~~Heat map~~		! Lyme Disease (Borreliella) !! Coronaviruses !! SARS-CoV-2
	\|-		\|-
	\| [[File:Lp54-gain-loss.png\|300px\|thumbnail\| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] \|\|		\| [[File:Lp54-gain-loss.png\|300px\|thumbnail\| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] \|\|
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	==What is evolutionary genomics?==		==What is evolutionary genomics?==
	Genomes differ among individuals and species. Evolutionary genomics studies genome variability and genome changes using evolutionary principles. Typical applications include ~~identification~~ of ~~human genome variations associated with diseases~~ and ~~identification of pathogen~~ virulence ~~genes~~.		Genomes differ among individuals and species. Evolutionary genomics studies genome variability and genome changes using evolutionary principles. Typical applications in pathogen research include molecular epidemiology (e.g., wildlife origin of SARS-CoV-2 & tracking Covid-19 spread), molecular evolution (e.g., identify key genes and protein sequences contributing to virulence and immune escape), and vaccine design (e.g., influenza vaccine based on latest circulating strains).

	Genome changes are studied at two distinct levels: (1) within-species/within-population variations (e.g., ~~human genetic variation~~), and (2) between-species divergence (e.g., ~~human~~-~~mouse comparisons~~).		Genome changes are studied at two distinct levels: (1) within-species/within-population variations (e.g., genomic changes during Covid-19 pandemic), and (2) between-species divergence (e.g., difference between SARS-CoV-1 and SARS-CoV-2).

	The key for analyzing genome variations within species is "population-thinking", the idea that there is no one individual genome that is standard, normal, or ~~disease-free~~.		The key for analyzing genome variations within species is "population-thinking", the idea that there is no one individual genome that is standard, normal, or "wildtype".

	The key for comparing genomes across species is "tree-thinking", the idea that evolution happens by diversification (like a branching tree), not by climbing a ladder. There is no such thing as "advanced" or "primitive" species. All living species have the exact same evolutionary distances/time of divergence since the origin of life.		The key for comparing genomes across species is "tree-thinking", the idea that evolution happens by diversification (like a branching tree), not by climbing a ladder. There is no such thing as "advanced" or "primitive" species. All living species have the exact same evolutionary distances/time of divergence since the origin of life.

	==Case studies from Qiu Lab==		==Case studies from Qiu Lab==
	* ~~Between-sepcies genome comparisons~~: Comparative genomics of worldwide Lyme disease pathogens~~. [http://borreliabase.org/ BorreliaBase~~] ~~(Figure 1)~~		* [http://borreliabase.org Comparative genomics of worldwide Lyme disease pathogens]
	* ~~Within-population genome comparison: Genomic epidemiology~~ of ~~Group B Streptococcus:~~ [http://~~diverge~~.~~hunter~~.~~cuny.edu/~weigang/gbs~~-~~browser/%20 Gene gains & losses associated with Group B Streptococcus virulence~~]		* Evolutionary origin of coronaviruses
	* Within-host genome evolution: Evolution of multi-drug antibiotic-resistance Pseudomonas in cancer patients (Figure 2)		* [http://cov.genometracker.org Covid-19 Genome Tracker]

	==Bioinformatics workflow for comparative analysis of bacterial pathogen genomes==		==Bioinformatics workflow for comparative analysis of bacterial pathogen genomes==

imported>Weigang: Created page with "[http://bigdata.citytech.cuny.edu/ City Tech/Cornell BioMedical Big Data Week 2019]: '''Pathogen Evolutionary Genomics''' Wed, July 22, 2019, 9-12
2020-07-14T20:25:07Z

Created page with "<center>[http://bigdata.citytech.cuny.edu/ City Tech/Cornell BioMedical Big Data Week 2019]: '''Pathogen Evolutionary Genomics'''</center> <center>Wed, July 22, 2019, 9-12</ce..."

New page
<center>[http://bigdata.citytech.cuny.edu/ City Tech/Cornell BioMedical Big Data Week 2019]: '''Pathogen Evolutionary Genomics'''</center>
<center>Wed, July 22, 2019, 9-12</center>
<center>'''Instructor:''' Dr Weigang Qiu, Professor, Department of Biological Sciences </center>
<center>'''Office:''' B402 Belfer Research Building</center>
<center>'''Email:''' weigang@genectr.hunter.cuny.edu</center>
<center>'''Lab Website:''' http://diverge.hunter.cuny.edu/labwiki/</center>
<center>
{| class="wikitable"
|-
! Lyme Disease (Borreliella) !! Volcano plot !! Heat map
|-
| [[File:Lp54-gain-loss.png|300px|thumbnail| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] ||
[[File:GeneExp2.jpeg|300px|thumbnail| p-value (y-axis) vs. fold change (x-axis)]]
||
[[File:GeneExp3.jpeg|300px|thumbnail| genes significantly down or up-regulated (at p<1e-4)]]
|}
</center>
----

==What is evolutionary genomics?==
Genomes differ among individuals and species. Evolutionary genomics studies genome variability and genome changes using evolutionary principles. Typical applications include identification of human genome variations associated with diseases and identification of pathogen virulence genes.

Genome changes are studied at two distinct levels: (1) within-species/within-population variations (e.g., human genetic variation), and (2) between-species divergence (e.g., human-mouse comparisons).

The key for analyzing genome variations within species is "population-thinking", the idea that there is no one individual genome that is standard, normal, or disease-free.

The key for comparing genomes across species is "tree-thinking", the idea that evolution happens by diversification (like a branching tree), not by climbing a ladder. There is no such thing as "advanced" or "primitive" species. All living species have the exact same evolutionary distances/time of divergence since the origin of life.

==Case studies from Qiu Lab==
* Between-sepcies genome comparisons: Comparative genomics of worldwide Lyme disease pathogens. [http://borreliabase.org/ BorreliaBase] (Figure 1)
* Within-population genome comparison: Genomic epidemiology of Group B Streptococcus: [http://diverge.hunter.cuny.edu/~weigang/gbs-browser/%20 Gene gains & losses associated with Group B Streptococcus virulence]
* Within-host genome evolution: Evolution of multi-drug antibiotic-resistance Pseudomonas in cancer patients (Figure 2)

==Bioinformatics workflow for comparative analysis of bacterial pathogen genomes==
* Pathogen isolation -> DNA extraction -> Library preparation -> High-through sequencing
* De novo genome assembly (canu; velvet; etc)
* Identify reference genome from NCBI database (kraken)
* Variant call (bwa; cortex_var; samtools mpileup)
* Infer genome phylogeny (muscle; reXML)
* Annotation (PATRIC)
* Custom genome browser (JavaScript; D3 library for interactive graphics)

==Essential bioinformatics skills==
* Linux command-line interface (e.g., BASH shell)
* Familiarity with a programming language (e.g., Python or Perl)
* Data visualization & statistical analysis (e.g., JavaScript; the R statistical computing environment)

==Textbooks for genome evolution==
* Graur, 2016, Molecular and Genome Evolution, First Edition, Sinauer Associates, Inc. ISBN: 978-1-60535-469-9. [http://www.sinauer.com/molecular-and-genome-evolution.html Publisher's Website]
* Baum & Smith, 2013. Tree Thinking: an Introduction to Phylogenetic Biology, Roberts & Company Publishers, Inc.

==Learning Goals==
* Be able to compare evolutionary relationships using phylogenetic trees
* Be able to use command-line tools for batch-processing of genome files
* Be able to perform genome-wide association analysis on the R platform

==Schedule==
* 9:00 - 9:25: Introduction; [http://rstudio.org Install R & R Studio]; Download fasta file & save as "ospC-pep.fasta" : [[File:OspC-pep.txt|thumbnail]]
* 9:30 - 10:00: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1 Part I. Unix Basics])
* 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])
* 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx|thumbnail]] & Handouts [[File:Pretest.pdf|thumbnail]]
* 11:05 - 12: Demo: [[Mini-Tutorals#ospC_amplicon_identification|identification of genomic mutations associated with antibiotic resistance]]
Slides on background
Demo (on wallace lab server)

==Exercises & Challenges==
* Finish Tree Thinking Quizzes
* Unix exercises:
count the number of sequences using "grep -v" or "wc"
display the first 5 lines of a file
display the last 5 lines of a file
change upper-cases to lower-cases
change "|" to "_"
replace strings