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| <center>[http://bigdata.citytech.cuny.edu/ City Tech/Cornell BioMedical Big Data Week 2020]: '''Pathogen Evolutionary Genomics'''</center>
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| <center>Wed, July 22, 2020, 9 am - 12 noon</center>
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| <center>'''Instructor:''' Dr Weigang Qiu, Professor, Department of Biological Sciences </center>
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| <center>'''Office:''' B402 Belfer Research Building</center>
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| <center>'''Email:''' weigang@genectr.hunter.cuny.edu</center>
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| <center>'''Lab Website:''' http://diverge.hunter.cuny.edu/labwiki/</center>
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| <center>
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| {| class="wikitable"
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| ! Lyme Disease (Borreliella) !! CoV Genome Tracker !! Coronavirus evolutuon
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| | [[File:Lp54-gain-loss.png|300px|thumbnail| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] ||
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| [[File:Cov-screenshot-1.png|300px|thumbnail| [http://cov.genometracker.org/ Haplotype network] ]]
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| [[File:Cov-screenshot-2.png|300px|thumbnail| Spike protein alignment ]]
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| |}
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| </center>
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| ----
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| ==What is evolutionary genomics?==
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| 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).
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| 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).
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| 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".
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| 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.
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| ==Case studies from Qiu Lab==
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| * [http://borreliabase.org Comparative genomics of worldwide Lyme disease pathogens]
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| * [http://cov.genometracker.org Covid-19 Genome Tracker]
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| ==Essential bioinformatics skills==
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| * Linux command-line interface (e.g., BASH shell)
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| * Familiarity with a programming language (e.g., Python or Perl)
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| * Data visualization & statistical analysis (e.g., JavaScript; the R statistical computing environment)
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|
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| ==Learning Goals==
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| * Be able to compare evolutionary relationships using phylogenetic trees
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| * Be able to use command-line tools for batch-processing of genome files
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| * Be able to perform genome-wide association analysis on the R platform
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|
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| ==Schedule==
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| * 9:00 - 9:25: Introduction; [http://rstudio.org Install R & R Studio]; Download fasta file & save as "spike.fasta" : [[File:Spike2.txt|thumbnail]]
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| * 9:30 - 10:00: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1 Part I. Unix Basics])
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| * 10:05 - 10:30: Unix Tutorial ([http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Part II Advanced Unix])
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| * 10:35 - 11:00: Tree-thinking Quizzes: Slides [[File:Big-data-phylogeny.pptx|thumbnail]] & Handouts [[File:Pretest.pdf|thumbnail]]
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| * 11:05 - 12: [http://www.phylogeny.fr Build molecular phylogeny online]
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| ==Exercises & Challenges==
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| * Finish Tree Thinking Quizzes
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| * Unix exercises:
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| ** count the number of sequences using "grep -v" or "wc"
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| ** display the first 5 lines of a file
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| ** display the last 5 lines of a file
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| ** change upper-cases to lower-cases
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| ** change "|" to "_"
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| ** replace strings
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