genome compression

https://en.wikipedia.org/wiki/Compression_of_Genomic_Re-Sequencing_Data

Number theory, data compression for NGS data

Can RSA or other methods be used for NGS sequence compression?

Editing Genomes to Record Cellular Histories

Whole organism lineage tracing by combinatorial and cumulative genome editing

http://science.sciencemag.org/content/early/2016/05/25/science.aaf7907


http://www.the-scientist.com/?articles.view/articleNo/46173/title/Editing-Genomes-to-Record-Cellular-Histories/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=30023521&_hsenc=p2ANqtz-_R1n6GFzmrTt34_hkUqUVfwahxXsR3FIUKRDnqbJEghIVaQfXQ6FAd2sYy_HyvmbyFGoI2o9ihE5P2eTgED-mCTiOXyA&_hsmi=30023521

Yeast Resource Center at U W Seattle

Provided genomes, mass spec, RNA seq data. Description of the experimental conditions are not clear.

http://www.yeastrc.org/g2p/about.do

Funded by P41 GM103533

Genome annotation, metascape

http://metascape.org/gp/index.html#/main/step1

Strope 2015 Genome Research, 100 S. cerevisiae genomes, McCusker lab

http://genome.cshlp.org.proxy.library.emory.edu/content/25/5/762/suppl/DC1

Strope PK,  McCusker group at Duke
Genome Res. 2015 May;25(5):762-74. doi: 10.1101/gr.185538.114. Epub 2015 Apr 3.

Strope15GR used its own strain nominations, even though the strains are obtained from others. This is quite annoying. 

I recognize M22, M1-2, YPS163

Strains are explained in Table S1, accession numbers are explained in table_S19. 

IGV, integrated genome viewer

http://www.broadinstitute.org/software/igv/?q=download

Genolevures, notes

Genolevures and the Saccharomycodtina

Gene orders are apparently randomly shuffled in yeast genomes.

*** Yeast genomic data resources for network and robustness (in progress)

Seattle Yeast Resource Center
Provided genomes, mass spec, RNA seq data. Description of the experimental conditions are not clear.
http://www.yeastrc.org/g2p/about.do

GenAge

Yeast rDNA Stability DataBase, YRSD at http://lafula-com.info/kobayashiken/geldata/index.php.

Expression data from S. cerevisiae under serial stresses, including H2O2 time course
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15936



Yeast

fitness Giaever lab, 2002 Nature
http://www.nature.com/nature/journal/v418/n6896/extref/nature00935-s1.htm
http://genomics.lbl.gov/YeastFitnessData/websitefiles/cel_index.html
(The site provide .cel files, but I did not locate the fitness files?! How did He14Ibuprofen obtain their fitness values?).


yeast resources pages
http://yeast.uni-graz.at/index.php?item=research
http://www.yeastgenome.org/download-data/sequence


Yeast essential and non-essential genes
 /data_download/literature_curation/phenotypes.tab  #contain this information in an irregular way.
 Winzeler99Science and yeast deletion database also provide these information (cited by Hwang, Lin, Chang, Mori, Juan, Huang, 2009 Molecular Biosystems, Predicting essential genes based on network and sequence analysis)

Yeast RLS and CLS data
  Kaeberlein and Kennedy labs.

bipixe
http://downloads.yeastgenome.org/published_datasets/Myers_2004_PMID_16420673/README
http://www.yeastgenome.org/download-data/published-datasets

Yeast CV GFP  from Alon's paper


http://www.ncbi.nlm.nih.gov/pubmed/?term=zakrzewska+robustness

http://www.yeastgenome.org/cache/genome-wide-analysis.html

CV of GEO expression data

Genetic network (Costanzo2009).

PPI

LOH screen by Gottschling lab

Phenotypic capacitance, The phenotypic capacitance was used directly from the Levy & Siegal study (S28) and captures variability across a range of morphological phenotypes upon deletion of each of
the non-essential genes

Yeast morphology Database

Princeton genomics
http://genomics-pubs.princeton.edu/
BYxRM
http://genomics-pubs.princeton.edu/YeastCross_BYxRM/data/BYxRM_PhenoData.txt


Predicted prions
http://www.utsouthwestern.edu/labs/halfmann/publications/


ChEMBL, chemical database

https://www.ebi.ac.uk/chembl/

• Hellenmyer 2008 science chemical screen
• Rugly 2006 JB, literacture curated PIN dataset (I did not find it in Biogrid publication download)
• Lipson 2009 NBT, single molecular sequencing on trancriptome, supplment table 2 provide stddev and mean that can be used for CV=stddev/mean.
• CV of microarray based gene expression
• Gasch 2000
• Genetic network, Costanzo 2010
• PPI
• http://www.yeastract.com/
• Power06 CLS life span
• LevySegel08 phenotypic potential
• CLS, Fabrio 2010 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001024#s5
• http://spell.yeastgenome.org/
• Yeast GFP CV data, Newman et al
• Supplementary information From the following article  Quantification of the yeast transcriptome by single-molecule sequencing  Doron Lipson, Tal Raz, Alix Kieu, Daniel R Jones, Eldar Giladi, Edward Thayer, John F Thompson, Stan Letovsky, Patrice Milos & M
• 
  

Yeast human gene homologs 
http://yeastmine.yeastgenome.org/yeastmine/bagDetails.do?scope=all&bagName=Human+genes+with+yeast+homologs