BioMed-R-2021 - Revision history

imported>Weigang: /* May 15, 2020 */

2021-05-02T02:12:55Z

May 15, 2020

← Older revision		Revision as of 02:12, 2 May 2021
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	===May 15, 2020===		===May 15, 2020===
	* Consultation by appointment (no live session)		* Consultation by appointment (no live session)
	** '''Submit your Teacher's Evaluation''', using either:		* '''Submit your Teacher's Evaluation''', using either:
	** Personal computer at [http://www.hunter.cuny.edu/te www.hunter.cuny.edu/te]; or,		** Personal computer at [http://www.hunter.cuny.edu/te www.hunter.cuny.edu/te]; or,
	** Smartphone at [http://www.hunter.cuny.edu/mobilete www.hunter.cuny.edu/mobilete]		** Smartphone at [http://www.hunter.cuny.edu/mobilete www.hunter.cuny.edu/mobilete]

imported>Weigang: /* May 15, 2020 */

2021-05-02T02:12:43Z

May 15, 2020

← Older revision		Revision as of 02:12, 2 May 2021
Line 192:		Line 192:
	===May 15, 2020===		===May 15, 2020===
	* Consultation by appointment (no live session)		* Consultation by appointment (no live session)
			** '''Submit your Teacher's Evaluation''', using either:
			** Personal computer at [http://www.hunter.cuny.edu/te www.hunter.cuny.edu/te]; or,
			** Smartphone at [http://www.hunter.cuny.edu/mobilete www.hunter.cuny.edu/mobilete]

	===May 22, 2020===		===May 22, 2020===

imported>Weigang: /* May 15, 2020 */

2021-05-02T02:10:43Z

May 15, 2020

← Older revision		Revision as of 02:10, 2 May 2021
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	===May 15, 2020===		===May 15, 2020===
	* ~~No class~~		* Consultation by appointment (no live session)

	===May 22, 2020===		===May 22, 2020===

imported>Weigang: /* May 8, 2020 */

2021-05-02T02:10:23Z

May 8, 2020

← Older revision		Revision as of 02:10, 2 May 2021
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	===May 8, 2020===		===May 8, 2020===
	* ~~Group presentation #4. Conclusions & Knit into final report~~		* Consultation by appointment (no live session)

	===May 15, 2020===		===May 15, 2020===

imported>Weigang: /* Course Schedule */

2021-04-23T16:28:02Z

Course Schedule

← Older revision		Revision as of 16:28, 23 April 2021
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	===April 17, 2020===		===April 17, 2020===
	* ~~Consultation~~		* Group presentation #1. Summary slides
	* Case study 2: identify genes/proteins/metabolites associated with tissue regeneration
	** [https://www.~~pnas.org/content/114/5/E717 Article link] (submission by Jenifer)~~
	** Tutorial: [http://diverge.hunter.cuny.edu/~weigang/Case-study-for-final.html Tutorial for case study]

	===April 24, 2020===		===April 24, 2020===
	* ~~Consultation~~		* Group presentation #2. R Markdown & Data import
			* I will hear group presentation Round #2. I will grade individual performance by the following rubric:
			** Biologist: Be prepared to answer my questions regarding the study background, question, and significance
			** Writer: Be prepared to show R Markdown (in R Studio) that included ALL sections from the last week's slide
			** Data Scientist: Be prepared to show data table that has been read into R Studio & show a preliminary graph & visualization
			** Statistician: Be prepared to answer questions on what is the statistical null hypothesis and what test to perform

	===May 1, 2020===		===May 1, 2020===
	* ~~Consultation~~		* Group presentation #3. R Markdown & Data analysis

	===May 8, 2020===		===May 8, 2020===
	* ~~Presentation: Groups 1-3~~		* Group presentation #4. Conclusions & Knit into final report

	===May 15, 2020===		===May 15, 2020===
	* ~~Presentation: Groups 4 & 5~~		* No class

	===May 22, 2020===		===May 22, 2020===

imported>Weigang: /* A sample of original NGS paper with data sets */

2021-04-16T04:34:16Z

A sample of original NGS paper with data sets

← Older revision		Revision as of 04:34, 16 April 2021
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	==A sample of original NGS paper with data sets==		==A sample of original NGS paper with data sets==
	* [[ https://doi.org/10.1128/mSystems.00939-20\|de la Cuesta-Zuluaga J, Spector TD, Youngblut ND, Ley RE. 2021. Genomic insights into adaptations of trimethylamine-utilizing methanogens to diverse habitats, including the human gut. mSystems 6:e00939-20.]]		* [https://doi.org/10.1128/mSystems.00939-20 de la Cuesta-Zuluaga J, Spector TD, Youngblut ND, Ley RE. 2021. Genomic insights into adaptations of trimethylamine-utilizing methanogens to diverse habitats, including the human gut. mSystems 6:e00939-20.]
	* [https://doi.org/10.1128/mSystems.00033-21 Reiter et al. 2021. Transcriptomics provides a genetic signature of vineyard site and offers insight into vintage-independent inoculated fermentation outcomes. mSystems 6:e00033-21]		* [https://doi.org/10.1128/mSystems.00033-21 Reiter et al. 2021. Transcriptomics provides a genetic signature of vineyard site and offers insight into vintage-independent inoculated fermentation outcomes. mSystems 6:e00033-21]
	* [https://doi.org/10.1128/mSystems.01350-20 Renninger et al (2021). Indoor dust as a matrix for surveillance of COVID-19. mSystems 6:e01350-20.]. [https://datadryad.org/stash/dataset/doi:10.5061/dryad.rn8pk0p8t Data available at Dryad]		* [https://doi.org/10.1128/mSystems.01350-20 Renninger et al (2021). Indoor dust as a matrix for surveillance of COVID-19. mSystems 6:e01350-20.]. [https://datadryad.org/stash/dataset/doi:10.5061/dryad.rn8pk0p8t Data available at Dryad]

imported>Weigang: /* A sample of original NGS paper with data sets */

2021-04-16T04:33:21Z

A sample of original NGS paper with data sets

← Older revision		Revision as of 04:33, 16 April 2021
Line 32:		Line 32:

	==A sample of original NGS paper with data sets==		==A sample of original NGS paper with data sets==
			* [[ https://doi.org/10.1128/mSystems.00939-20\|de la Cuesta-Zuluaga J, Spector TD, Youngblut ND, Ley RE. 2021. Genomic insights into adaptations of trimethylamine-utilizing methanogens to diverse habitats, including the human gut. mSystems 6:e00939-20.]]
	* [https://doi.org/10.1128/mSystems.00033-21 Reiter et al. 2021. Transcriptomics provides a genetic signature of vineyard site and offers insight into vintage-independent inoculated fermentation outcomes. mSystems 6:e00033-21]		* [https://doi.org/10.1128/mSystems.00033-21 Reiter et al. 2021. Transcriptomics provides a genetic signature of vineyard site and offers insight into vintage-independent inoculated fermentation outcomes. mSystems 6:e00033-21]
	* [https://doi.org/10.1128/mSystems.01350-20 Renninger et al (2021). Indoor dust as a matrix for surveillance of COVID-19. mSystems 6:e01350-20.]. [https://datadryad.org/stash/dataset/doi:10.5061/dryad.rn8pk0p8t Data available at Dryad]		* [https://doi.org/10.1128/mSystems.01350-20 Renninger et al (2021). Indoor dust as a matrix for surveillance of COVID-19. mSystems 6:e01350-20.]. [https://datadryad.org/stash/dataset/doi:10.5061/dryad.rn8pk0p8t Data available at Dryad]

imported>Weigang: /* A sample of original NGS paper with data sets */

2021-04-16T04:20:12Z

A sample of original NGS paper with data sets

← Older revision		Revision as of 04:20, 16 April 2021
Line 32:		Line 32:

	==A sample of original NGS paper with data sets==		==A sample of original NGS paper with data sets==
			* [https://doi.org/10.1128/mSystems.00033-21 Reiter et al. 2021. Transcriptomics provides a genetic signature of vineyard site and offers insight into vintage-independent inoculated fermentation outcomes. mSystems 6:e00033-21]
	* [https://doi.org/10.1128/mSystems.01350-20 Renninger et al (2021). Indoor dust as a matrix for surveillance of COVID-19. mSystems 6:e01350-20.]. [https://datadryad.org/stash/dataset/doi:10.5061/dryad.rn8pk0p8t Data available at Dryad]		* [https://doi.org/10.1128/mSystems.01350-20 Renninger et al (2021). Indoor dust as a matrix for surveillance of COVID-19. mSystems 6:e01350-20.]. [https://datadryad.org/stash/dataset/doi:10.5061/dryad.rn8pk0p8t Data available at Dryad]
	* [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1133-7 Litzenburger et al. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol 18, 15 (2017).]		* [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1133-7 Litzenburger et al. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol 18, 15 (2017).]

imported>Weigang: /* A sample of original NGS paper with data sets */

2021-04-16T04:07:23Z

A sample of original NGS paper with data sets

← Older revision		Revision as of 04:07, 16 April 2021
Line 32:		Line 32:

	==A sample of original NGS paper with data sets==		==A sample of original NGS paper with data sets==
			* [https://doi.org/10.1128/mSystems.01350-20 Renninger et al (2021). Indoor dust as a matrix for surveillance of COVID-19. mSystems 6:e01350-20.]. [https://datadryad.org/stash/dataset/doi:10.5061/dryad.rn8pk0p8t Data available at Dryad]
	* [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1133-7 Litzenburger et al. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol 18, 15 (2017).]		* [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1133-7 Litzenburger et al. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol 18, 15 (2017).]
	* [https://science.sciencemag.org/content/361/6409/1380 Cao et al. Single-cell chromatin and RNA analysis. Science (2018)]		* [https://science.sciencemag.org/content/361/6409/1380 Cao et al. Single-cell chromatin and RNA analysis. Science (2018)]

imported>Weigang: /* Course Schedule */

2021-04-09T14:01:18Z

Course Schedule

← Older revision		Revision as of 14:01, 9 April 2021
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	===April 10, 2020===		===April 10, 2020===
	* Paper assignments & break into project groups		* Paper assignments & break into project groups
			* For final presentation (10 pts)
			** Each member will present his or her part
			* For final report (90), you are required to:
			** Read the paper and identify a dataset to replicate
			** Create an R markdown file to record your work
			** Produce a final WORD or PDF file as final report
	* Case study 1: Restriction/Modification system in Lyme pathogen: [https://jb.asm.org/content/200/24/e00395-18 Casselii et al (2018)]		* Case study 1: Restriction/Modification system in Lyme pathogen: [https://jb.asm.org/content/200/24/e00395-18 Casselii et al (2018)]

			===April 17, 2020===
			* Consultation
	* Case study 2: identify genes/proteins/metabolites associated with tissue regeneration		* Case study 2: identify genes/proteins/metabolites associated with tissue regeneration
	** [https://www.pnas.org/content/114/5/E717 Article link] (submission by Jenifer)		** [https://www.pnas.org/content/114/5/E717 Article link] (submission by Jenifer)
	** Tutorial: [http://diverge.hunter.cuny.edu/~weigang/Case-study-for-final.html Tutorial for case study]		** Tutorial: [http://diverge.hunter.cuny.edu/~weigang/Case-study-for-final.html Tutorial for case study]

	~~===April 17, 2020===~~
	* Consultation
	** Biological question
	** Experimental design: samples, sample sizes, controls
	** Experimental techniques/measurements
	** Data set description, column by column
	** Visualization to be made
	** Statistical tests to be performed

	===April 24, 2020===		===April 24, 2020===
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	===May 1, 2020===		===May 1, 2020===
	* ~~Self study (no live session)~~		* Consultation
	* Tutorial: [http://diverge.hunter.cuny.edu/~weigang/Case-study-for-final.html Tutorial for case study]
	* For final report, you are required to:
	** Read the paper and identify a dataset to replicate
	** Create an R markdown file to record your work
	** Produce a final WORD or PDF file as final report
	* '''Your final report (100 pts) should include the following required components''':
	** (10 pts) Section 1. Background & Objectives. Describe (a) the overall goal of the study; (b) the specific question to be addressed by your dataset
	** (20 pts) Section 2. Material & Methods. Describe experimental design, i.e., how your assigned data set was generated, including the nature of the biological samples, sample size, number of replicates (biological & technical), controls (if any), sequencing technologies. Hint: Fig S1
	** (40 pts) Section 3. R codes & graphs. Show R codes with comments for individual commands. Graphics should be as close to the published figure as possible (e.g., with proper axis labels)
	** (10 pts) Section 4. Statistical analysis. Show mull hypothesis and p-value. Draw statistical conclusion
	** (10 pts) Section 5. Conclusion. Draw biological conclusions of your analysis
	** (10 pts) Section 6. Citations/source/URL to paper, your dataset, and methods

	===May 8, 2020===		===May 8, 2020===
	* ~~Consultation (no mandatory participation)~~		* Presentation: Groups 1-3

	===May 15, 2020===		===May 15, 2020===
	* ~~Consultation (no mandatory participation)~~		* Presentation: Groups 4 & 5

	===May 22, 2020===		===May 22, 2020===
	* Friday, 5pm: Final report Due (Blackboard submission)		* Friday, 5pm: Final report Due (Blackboard submission)
			* '''Your final report (100 pts) should include the following required components''':
			** (10 pts) Section 1. Background & Objectives. Describe (a) the overall goal of the study; (b) the specific question to be addressed by your dataset
			** (20 pts) Section 2. Material & Methods. Describe experimental design, i.e., how your assigned data set was generated, including the nature of the biological samples, sample size, number of replicates (biological & technical), controls (if any), sequencing technologies. Hint: Fig S1
			** (40 pts) Section 3. R codes & graphs. Show R codes with comments for individual commands. Graphics should be as close to the published figure as possible (e.g., with proper axis labels)
			** (10 pts) Section 4. Statistical analysis. Show mull hypothesis and p-value. Draw statistical conclusion
			** (5 pts) Section 5. Conclusion. Draw biological conclusions of your analysis
			** (5 pts) Section 6. Citations/source/URL to paper, your dataset, and methods