Posts Tagged ‘cmptxn’

Genomics: Hiding in plain sight : Nature : Nature Publishing Group

August 31, 2014

http://www.nature.com/nature/journal/v512/n7515/full/512374a.html The Nature N&V

YaleNews | Evolution used similar molecular toolkits to shape flies, worms, and humans

August 30, 2014

http://news.yale.edu/2014/08/27/evolution-used-similar-molecular-toolkits-shape-flies-worms-and-humans

2014 Release: Scientists looking across human, fly and worm genomes find shared biology

August 30, 2014

http://www.genome.gov/27558082

GenomeWeb Daily News | Arrays | GenomeWeb

August 27, 2014

http://www.genomeweb.com/arrays/encode-modencode-data-reveal-conserved-regulatory-features-across-model-organism

ModMap – Detecting maps of modules in biological networks

July 17, 2014

http://acgt.cs.tau.ac.il/modmap/

plant phylotypic stage

February 21, 2014

http://www.ncbi.nlm.nih.gov/pubmed/22951968

single cell trascriptomes and WGCNA

January 2, 2014

Nature. 2013 Aug 29;500(7464):593-7. doi: 10.1038/nature12364. Epub 2013 Jul 28.

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.

Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, Liu JY, Horvath S, Fan G.

QT:{{”
…We report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos, using single-cell RNA sequencing…. By weighted gene co-expression network analysis, we find that each developmental stage can be delineated concisely by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation and metabolism, acting in a step-wise fashion from cleavage to morula. Cross-species comparisons with mouse pre-implantation embryos reveal that the majority of human stage-specific modules (7 out of 9) are notably preserved, but developmental specificity and timing differ between human and mouse. Furthermore, we identify conserved key members (or hub genes) of the human and mouse networks.
“}}

This paper mentions finding 350 pseudogenes in C. elegans

August 23, 2013

http://mbe.oxfordjournals.org/content/19/5/728.full.pdf#page=1&view=FitH

The Vast, Conserved Mammalian lincRNome

March 2, 2013

paper comparing human and mouse lncRNAs
The Vast, Conserved Mammalian lincRNome
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002917

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

February 19, 2013

http://www.cell.com/developmental-cell/abstract/S1534-5807%2812%2900142-6

Michal Levin, Tamar Hashimshony, Florian Wagner, and Itai Yanai.
Developmental milestones punctuate gene expression in the
Caenorhabditis embryo. Developmental Cell (May 2012)

Nice disussion of the phylotypic stage .
Figure 4S-E have stage mapping between dmel and celegans