Summer 2018: Difference between revisions
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imported>Weigang (Created page with "=Rules of Conduct= # No eating, drinking, or loud talking in the lab. Socialize in the lobby only. # Be respectful to each other, regardless of level of study # Be on time & r...") |
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# Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585 | # Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585 | ||
=Projects= | =Projects= | ||
==Borrelia genome evolution ( | ==Borrelia genome evolution (Led by Saymon)== | ||
# Goal 1. Estimate time of cross-Atlantic dispersal using core-genome sequences | # Goal 1. Estimate time of cross-Atlantic dispersal using core-genome sequences | ||
# Goal 2. Investigate codon biases with respect to levels of gene expression | # Goal 2. Investigate codon biases with respect to levels of gene expression | ||
==Identification of host species from ticks ( | ==Identification of host species from ticks (Led by Lily [after first-level])== | ||
# Goal 1. Protocol optimization for PCR amplification of host DNA from ticks | # Goal 1. Protocol optimization for PCR amplification of host DNA from ticks | ||
# Goal 2. Protocol development: library construction for MiSeq | # Goal 2. Protocol development: library construction for MiSeq | ||
# Goal 3. Development of bioinformatics protocols and sequence database | # Goal 3. Development of bioinformatics protocols and sequence database | ||
==Pseudomonas Genome-wide Association Studies (GWAS) (Led by Mai | ==Pseudomonas Genome-wide Association Studies (GWAS) (Led by Mai & Yinheng, in collaboration with Dr Xavier of MSKCC)== | ||
# Goal 1. Association of genes/SNPs with biofilm formation and c-di-GMP levels: Manuscript preparation | # Goal 1. Association of genes/SNPs with biofilm formation and c-di-GMP levels: Manuscript preparation | ||
# Goal 2. Association of genome diversity with metabolic diversity | # Goal 2. Association of genome diversity with metabolic diversity | ||
==Machine learning approaches (Led by Oliver & Brian)== | ==Machine learning approaches to evolution (Led by Oliver & Brian)== | ||
# Goal 1. Implement Hopfield network for optimization of protein structure | # Goal 1. Implement Hopfield network for optimization of protein structure | ||
# Goal 2. Neural-net models of OspC | # Goal 2. Neural-net models of OspC | ||
# Goal 3. K-mer-based pipeline for genome classification | # Goal 3. K-mer-based pipeline for genome classification | ||
=Weekly Schedule= | =Weekly Schedule= | ||
==Friday, May 31, 2018. Kickoff== | ==Friday, May 31, 2018. Kickoff== | ||
Revision as of 20:37, 19 May 2018
Rules of Conduct
- No eating, drinking, or loud talking in the lab. Socialize in the lobby only.
- Be respectful to each other, regardless of level of study
- Be on time & responsible. Communicate in advance with the PI if late or absent
Participants
- Dr Oliver Attie, Research Associate
- Brian Sulkow, Research Associate
- Saymon Akther, CUNY Graduate Center, EEB Program
- Lily Li, CUNY Graduate Center, EEB Program
- Mei Wu, Bioinformatics Research Assistant
- Yinheng Li, Informatics Research Assistant
- Christopher Panlasigui, Hunter Biology
- Dr Lia Di, Senior Scientist
- Dr Weigang Qiu, Principal Investigator
- Summer Interns
Readings & Journal Club
- A short introduction to molecular phylogenetics: http://www.ncbi.nlm.nih.gov/pubmed/12801728
- The latest tree of life: http://www.nature.com/articles/nmicrobiol201648
- Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585
Projects
Borrelia genome evolution (Led by Saymon)
- Goal 1. Estimate time of cross-Atlantic dispersal using core-genome sequences
- Goal 2. Investigate codon biases with respect to levels of gene expression
Identification of host species from ticks (Led by Lily [after first-level])
- Goal 1. Protocol optimization for PCR amplification of host DNA from ticks
- Goal 2. Protocol development: library construction for MiSeq
- Goal 3. Development of bioinformatics protocols and sequence database
Pseudomonas Genome-wide Association Studies (GWAS) (Led by Mai & Yinheng, in collaboration with Dr Xavier of MSKCC)
- Goal 1. Association of genes/SNPs with biofilm formation and c-di-GMP levels: Manuscript preparation
- Goal 2. Association of genome diversity with metabolic diversity
Machine learning approaches to evolution (Led by Oliver & Brian)
- Goal 1. Implement Hopfield network for optimization of protein structure
- Goal 2. Neural-net models of OspC
- Goal 3. K-mer-based pipeline for genome classification
Weekly Schedule
Friday, May 31, 2018. Kickoff
- Summer planning
- Lab system tutorial