Papers to read - Githubissues

MManee commented 8 years ago

Keightly 2005:
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240079/
- intro explains some of the problems associated with identifying conserved noncoding elements (CNEs)
Siepel 2005:
- http://www.ncbi.nlm.nih.gov/pubmed/16024819/
- this explains phastCons CNE detection method
Bergman 2002:
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151188/
- this mentions the spacing regions (spacers) between CNEs

MManee commented 7 years ago

Papers about conservation and side-effects

Side Effects: Substantial Non-Neutral Evolution Flanking Regulatory Sites
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667769/
Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences
- http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003512
Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura
- http://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-7-r67
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
- http://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-2-r15
Dynamic Epigenetic Control of Highly Conserved Noncoding Elements
- http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109326

atalgarni commented 7 years ago

Good paper about metagenomics ((Highly Recommended))

The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet
- https://www.ncbi.nlm.nih.gov/books/NBK54001/

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