Undergrad Research Experience - Revision history

imported>Weigang: /* Project 1. Covid mutation analysis */

2021-03-14T18:10:19Z

Project 1. Covid mutation analysis

← Older revision		Revision as of 18:10, 14 March 2021
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	==Project 1. Covid mutation analysis==		==Project 1. Covid mutation analysis==
	* [https://www.ncbi.nlm.nih.gov/sars-cov-2/ NCBI Covid genome files]		* [https://www.ncbi.nlm.nih.gov/sars-cov-2/ NCBI Covid genome files]
	* [http://diverge.hunter.cuny.edu/~weigang/~~Covid_mutation~~.html R Markdown file (by Janatul)]		* [http://diverge.hunter.cuny.edu/~weigang/Covid_Mutation.html R Markdown file (by Janatul)]

	<syntaxhighlight lang='python'>		<syntaxhighlight lang='python'>

2021-03-14T18:09:34Z

Project 1. Covid mutation analysis

← Older revision		Revision as of 18:09, 14 March 2021
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	==Project 1. Covid mutation analysis==		==Project 1. Covid mutation analysis==
	# [https://www.ncbi.nlm.nih.gov/sars-cov-2/ NCBI Covid genome files]		* [https://www.ncbi.nlm.nih.gov/sars-cov-2/ NCBI Covid genome files]
			* [http://diverge.hunter.cuny.edu/~weigang/Covid_mutation.html R Markdown file (by Janatul)]

	<syntaxhighlight lang='python'>		<syntaxhighlight lang='python'>
	# Shared Afsana		# Shared Afsana

2021-03-14T18:02:25Z

Project 1. Covid mutation analysis

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 ==Project 1. Covid mutation analysis==
 <syntaxhighlight lang="bash">
 # Shared by Afsana
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 <syntaxhighlight lang='python'>
-# Shared by Eamen
+# Shared by Eamen PYTHON CODE FOR COVID MUTATION COUNTS
-PYTHON CODE FOR COVID MUTATION COUNTSimport re
+import re
 import sys
 gene_name = {}

2021-02-16T23:05:36Z

Reading List

← Older revision		Revision as of 23:05, 16 February 2021
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	**[https://www.nature.com/articles/s41598-018-37288-x Spensley et al (2019). Reverse Immunology. Scientific Report]		**[https://www.nature.com/articles/s41598-018-37288-x Spensley et al (2019). Reverse Immunology. Scientific Report]
	**[https://science.sciencemag.org/content/early/2021/01/11/science.abf6840 Cohen et al (2021). Cocktail approach]		**[https://science.sciencemag.org/content/early/2021/01/11/science.abf6840 Cohen et al (2021). Cocktail approach]
			** [https://asm.org/Articles/2021/February/SARS-CoV-2-Variants-vs-Vaccines an ASM review]
	* Group B Streptococcus (GBS) CC17 Evolution: [https://msystems.asm.org/content/2/5/e00074-17 Almeida et al (2017)]		* Group B Streptococcus (GBS) CC17 Evolution: [https://msystems.asm.org/content/2/5/e00074-17 Almeida et al (2017)]
	* CoV mutation analysis: [https://www.biorxiv.org/content/10.1101/2020.06.20.163188v2 Alouane et al (2020)]		* CoV mutation analysis: [https://www.biorxiv.org/content/10.1101/2020.06.20.163188v2 Alouane et al (2020)]

2021-02-10T15:56:43Z

Reading List

← Older revision		Revision as of 15:56, 10 February 2021
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	==Reading List==		==Reading List==
	* ~~Vaccine design~~:[https://www.nature.com/articles/s41598-018-37288-x Spensley et al (2019). Reverse Immunology. Scientific Report]		* Design of broadly active anti-microbial vaccines:
			** [https://www.nature.com/articles/d41586-021-00340-4 Burton & Topol (2021). A commentary]
			**[https://www.nature.com/articles/s41598-018-37288-x Spensley et al (2019). Reverse Immunology. Scientific Report]
			**[https://science.sciencemag.org/content/early/2021/01/11/science.abf6840 Cohen et al (2021). Cocktail approach]
	* Group B Streptococcus (GBS) CC17 Evolution: [https://msystems.asm.org/content/2/5/e00074-17 Almeida et al (2017)]		* Group B Streptococcus (GBS) CC17 Evolution: [https://msystems.asm.org/content/2/5/e00074-17 Almeida et al (2017)]
	* CoV mutation analysis: [https://www.biorxiv.org/content/10.1101/2020.06.20.163188v2 Alouane et al (2020)]		* CoV mutation analysis: [https://www.biorxiv.org/content/10.1101/2020.06.20.163188v2 Alouane et al (2020)]

2021-02-10T15:52:37Z

Project 1. Covid mutation analysis

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 library(ggrepel)
 ggplot(data=covid, aes(x=Missense,y=Synonymous, label=Gene)) + geom_point() + geom_text_repel() + geom_smooth(method="lm")
 </syntaxhighlight>

2021-02-10T00:43:53Z

Participants

2021-02-04T02:19:06Z

Project 2. Group B STreptoccocus genomics

← Older revision		Revision as of 02:19, 4 February 2021
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	==Project 2. Group B STreptoccocus genomics==		==Project 2. Group B STreptoccocus genomics==
	* GenBank submission of assemblies		* GenBank submission of assemblies
	==Project 3. HIV compartmentalized evolution		==Project 3. HIV compartmentalized evolution==

	==Project 4. DNABERT classification==		==Project 4. DNABERT classification==

2021-02-04T02:18:38Z

Group Reading List

← Older revision		Revision as of 02:18, 4 February 2021
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	* Jmatul: Volunteer		* Jmatul: Volunteer

	==~~Group~~ Reading List==		==Reading List==
	* Vaccine design:[https://www.nature.com/articles/s41598-018-37288-x Spensley et al (2019). Reverse Immunology. Scientific Report]		* Vaccine design:[https://www.nature.com/articles/s41598-018-37288-x Spensley et al (2019). Reverse Immunology. Scientific Report]
	* Group B Streptococcus (GBS) CC17 Evolution: [https://msystems.asm.org/content/2/5/e00074-17 Almeida et al (2017)]		* Group B Streptococcus (GBS) CC17 Evolution: [https://msystems.asm.org/content/2/5/e00074-17 Almeida et al (2017)]
	* CoV mutation analysis: [https://www.biorxiv.org/content/10.1101/2020.06.20.163188v2 Alouane et al (2020)]		* CoV mutation analysis: [https://www.biorxiv.org/content/10.1101/2020.06.20.163188v2 Alouane et al (2020)]
			* HIV compartmentalized eolution: [https://retrovirology.biomedcentral.com/articles/10.1186/s12977-014-0065-0 Evering et al (2014)]

	==Project 1. Covid mutation analysis==		==Project 1. Covid mutation analysis==

2021-02-04T02:17:25Z

Project 2. Group B STreptoccocus genomics

← Older revision		Revision as of 02:17, 4 February 2021
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	==Project 2. Group B STreptoccocus genomics==		==Project 2. Group B STreptoccocus genomics==
	* GenBank submission of assemblies		* GenBank submission of assemblies
			==Project 3. HIV compartmentalized evolution
			==Project 4. DNABERT classification==

	=Fall 2020=		=Fall 2020=