UVM Genetics & Genomics Wiki

==Welcome to the 2012 UVM Genetics & Genomics Wiki==
Class wiki for the Genetics and Genomics course in the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington VT USA. John Burke is the course instructor, and can be reached at john.burke@uvm.edu or @JohnBTV. The Twitter hashtag for the course is #uvmgg. Comments, questions and suggestions are welcome. Use the comments section on the relevant page, or John's Wikia wall, or Twitter as appropriate.
==About the Course==
This course is being offered for the first time in the 2012 fall semester, and is intended for both graduate students and advanced undergraduates. It will be a highly collaborative and open course in which students will have the backing of an excellent textbook and an experienced instructor, while learning how to cope with a vast flow of new information. Students will generate, evaluate, and collaboratively edit content and will primarily be evaluated by the quality of their contributions and collaborations in class and on this wiki.
==Getting Started==
==Expectations for Enrolled Students==
==Editing work of class participants==
| ChavenVT | John Mackenzie Burke | Lisz Graves | Lorantes | LoriUVM | Meghan.mckeown | RachaelChi | ShruthiUvm | Tereza Pos |
==WIKI CONTENT (required sections)==
===Class Notes===
*AUGUST | 2012 August 27 | 2012 August 29 |
*SEPTEMBER | 2012 September 5 | 2012 September 10 | 2012 September 12 | 2012 September 17 | 2012 September 19 | 2012 September 24 | 2012 September 26 |
*OCTOBER | 2012 October 1 | 2012 October 3 | 2012 October 8 | 2012 October 10 | 2012 October 15 | 2012 October 17 | 2012 October 22 | 2012 October 24 | 2012 October 29 | 2012 October 31 |
*NOVEMBER | 2012 November 5 | 2012 November 7 | 2012 November 12 | 2012 November 14 | 2012 November 26 | 2012 November 28 |
*DECEMBER | 2012 December 3 | 2012 December 5 |
===Concepts and Jargon===
====A B C====
*| Allele | Alternative splicing | Annotation | Assembly | BAC Clones | Barr Body | Biochemistry | Biodiversity | Bioinformatics | BLAST | Cancer genome | Candidate gene study | CGH | Chimera | Chloroplast DNA| Chromatin immunoprecipitation (ChIP) | Chromosome banding  |  Classical Genetics | Clone | COGs | Combinatorial | Common ancestor | Complementation | Complex phenotypes | Conditional mutant | Contig | Copy number variation | Coverage | Curation | Current Phylogenetic Programs | Cis-Trans Test|
====D E F====
*Deletion | Deletion mapping | De novo sequencing | Diploid | DIY biology | DNA Barcode | DNAseq: 454 pyrosequencing | DNAseq: Illumina | DNAseq: Ion Torrent | DNAseq: Maxam-Gilbert | DNAseq: Oxford Nanopore | DNAseq: Pacific Biosciences | DNAseq: RAD-seq | DNAseq: Sanger dideoxy | DNAseq: SOLiD | Dominance | Dosage Compensation | Duplex | Dysbiosis | EBI | ENCODE | Endosymbiosis | Enrichment | Epigenetics | Epistasis | EST | Euchromatin | Exome Sequencing | FASTA | FISH | Forward genetics | Functional genomics | Fusion |
====G H I====
*| GenBank | Gene | Gene chip | Gene cluster | Gene duplication | Gene synthesis | Gene therapy | Genetic Counseling | Genetic drift | Genetic information | Genetic map | Genetics | Genetics Home Reference | Genome | Genome browser | Genomics | Genotype | GFP | GMO | GWAS | Haploid | Haplotype | Heterochromatin | High-throughput sequencing | Homolog | Horizontal gene transfer | Human genome | Huntington's disease | Indel | In vitro selection |
====J K L====
*| Karyotype | KEGG (Kyoto Encyclopedia of Genes and Genomes) | Knockout | Knock-in | Landscape Genomics | Linkage | Linkage disequilibrium | Linnaean classification |
====M N O====
*| Marker | Mating | MESQUITE | Metagenome | Metagenomics linkage group | Methylated DNA immunoprecipitation | Microarray | Mitochondrial DNA | Missing heritability | Mobile genetic element | Model organism | Molecular cloning | Morgan (unit of measurement) | Mosaic | Mutagen | Mutant | Mutation | NCBI | ncRNA | Null mutation | Next-gen sequencing | NEXUS | Noncoding DNA | Noncoding RNA | Nonsense mutation | Nonsense suppressor tRNA | Northern blot | Null mutant | OMIM (Online Mendelian Inheritance in Man) | Oncogene | Ortholog |
====P Q R====
*| Pan-genome | Paralog | Partial diploid | Personal genomics | Pfam |PFGE | Phenotype | Physical map | Plasmid | Polar mutation | Polyploids | Protein | Proteome | Pseudogene | RAD-seq | Read | Read length | Recombination | Reference genome | Regulatory DNA | REFSEQ | Resequencing | Restriction map | Reverse genetics | Reverse transcription | Rfam | RFLP | RNA editing | RNAi (miRNA) | RNA-seq |
====S T U====
*| Scaffold | Screening | Selection | Selective pressure | Sexual reproduction | Sickle cell disease | Silencing | Site-directed mutagenesis | SNP | Species | SSH | Statistical Methods | STRP | Synthetic biology | Temperature-sensitive mutant | Trait | Transgene | Transgenic Organism | Translocation | Trinucleotide repeat |
====V W X Y Z====
*| VNTR | Wild-type | Wreck-and-check | YAC | Yeast two-hybrid |
===Student Projects===
====YFG: Your Favorite Gene====
*| DRACO (synthetic antiviral protein, built from human genes) | F5 (factor V blood coagulation, human gene) | FGFR3 (fibroblast growth factor receptor 3, human gene) | HOXA1 (homeobox developmental control protein, human gene) | GAA (glucosidase alpha acid, human gene) | MTRNR2 (mitochondrial large subunit ribosomal RNA, human gene) | NOG (noggin developmental control protein, human gene) | VRN2 (vernalization, wheat gene) | VSG (variable surface glycoprotein, Trypanosome gene) |
====Genetic Studies====
*| ABCA4 and Stargardt Disease | Agrobacterium tumefaciens | C. elegans and apoptosis | Cre-lox technology | DNA Ligase | Inheritance and the General Nature of the Genetic Code | Familial Alzheimer's | Tet system- Discovery and Uses |
==== Genomic Studies====
Transcriptome analysis of the Vernalization Response in Barley (Hordeum vulgare) Seedlings (Greenup et al. 2011)
Trypanosoma cruzi Genome Project
Extremophiles - Thermophiles
Tetraodon nigroviridis genome
Human susceptibility to Malaria analyzed by GWAS
Epigenetic regulation by long non-coding RNAs in mice
Deinococcus radiodurans R1
====Metagenomic Studies====
Metagenomic-wide association study of gut microbiota in type 2 diabetes
Metagenomics of the leaf-cutter ant fungus-garden
Metagenomics highlighting the complex interplay between diet, gut microbiota and immune response in infants
Metagenomic analysis of the microbiota from the crop of an invasive snail
Metagenomic study of oral microbiota
Metagenomic study of investigation of microbes and viruses in patients with jaw osteonecrosis
CRISPRs
Metagenomic Study of Deinococcus Radiodurans
====Interesting Topics====
HeLa Cells
XNA
Brewing and Diacetyl
ANDi
Kombucha: Exploring the SCOBY
FISH
===Online Resources (databases, web sites, blogs, Twitter feeds)===
*| CDC Genomics and Health Impact Blog | ENCODE | Evernote | Genetics Home Reference | Genomes Unzipped | The Genographic Project | The Personal Genome | Twitter | Wikia |
===Personal Pages===
*| ChavenVT | John Mackenzie Burke | Lisz Graves | Lorantes | LoriUVM | Meghan.mckeown | RachaelChi | ShruthiUvm | Tereza Pos |
===Student-Generated Questions and Proposed Solutions===
*Synonymous mutations change function?
*Huntington's disease and genetic anticipation?
===Textbook Problems and Solutions===
*Ch 1, Introduction to Genomics | Exercises | Problems | Weblems |
*Ch 2, Genomes are the Hub of Biology | Exercises | Problems | Weblems |
*Ch 3, Mapping, Sequencing, Annotation, and Databases | Exercises | Problems | Weblems |
*Ch 4, Comparative Genomics | Exercises | Problems | Weblems |
*Ch 5, Evolution and Genomic Change | Exercises | Problems | Weblems |
*Ch 6, Genomes of Prokaryotes | Exercises | Problems | Weblems |
*Ch 7, Genomes of Eukaryotes | Exercises | Problems | Weblems |
*Ch 8, Genomics and Human Biology | Exercises | Problems | Weblems |
*Ch 9, Microarrays and Transcriptomics | Exercises | Problems | Weblems |
*Ch 10, Proteomics | Exercises | Problems | Weblems |
*Ch 11, Systems Biology | Exercises | Problems | Weblems |
===Wikipedia Page Evaluations===
Polyploid Review
==WIKI CONTENT (optional sections)==
===Biographies of Geneticists and Genome Scientists===
*| Blackburn, Elizabeth | Botstein, David | Church, George | Crick, Francis | Rosalind Franklin | Greider, Carol | Guthrie, Christine | Hood, Leroy | Hopkins, Nancy | Cynthia Kenyon | Lander, Eric | McClintock, Barbara | Morgan, Thomas Hunt | Sanger, Fred | Steitz, Joan | Szostak, Jack | Thornton, Janet | Venter, Craig  | Waddington, Conrad  | Watson, James | Carl Woese
===Book, Film and Video Reviews===
*| GATTACA (film) | Genome: The Autobiography of a Species in 23 Chapters, Ridley | Jurassic Park, Crichton | The Eighth Day of Creation, Judson | The Windup Girl, Bacigalupi | Nothing in Biology Makes Sense Except in the Light of Evolution | 
===Current News in Genetics and Genomics===
*4 October 2012. Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units. Newborn babies in intensive care unit have genomes sequenced in only 50 hours. An interesting read. | BBC News | New York Times | Science Translational Medicine |
*4 October 2012. Huang et al. (2012), A map of rice genome variation reveals the origin of cultivated rice. Nature, published online 3 October 2012. | Nature |
*Gene Therapy aprroved in Europe for a rare genetic disease called glybera where people cannot breakdown lipids. Here is the bbc news link.
*DNA is more stable than we thought it was. Here is an interesting article. Follow the link.
*PHD comics take on "open access" published in 10/24/12. Follow the link
*Two Bowel Cancer Genes identified. More information on this BBC article and Prof Ian Tolinson's homepage at Welcome Trust.
===Humor for Gene Geeks===
* #whatshouldwecallgradschool.
*General Geek Humor: | xkcd | PhD Comics |
===Textbook Issues, Corrections and Updates===
*Textbook Corrections
==Updates, news, plans, questions and announcements==
*Introductory wikia editing tutorial
*Sandbox, where you can practice your editing skills
==Latest activity==
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