list_of_papers

Here a list of papers to capture new homology information not yet annotated in similarity.tsv :

The Origin of Vertebrate Gills http://www.cell.com/current-biology/fulltext/S0960-9822(17)30023-4 Current Biology Available online 9 February 2017 In Press, Corrected Proof — Note to users [marcrr by slack, February 10 2017]

--> ANN, done February 13, 2017, but as pull request to be pushed by FBB

https://github.com/BgeeDB/anatomical-similarity-annotations/pull/23

www.pnas.org/content/early/2016/02/29/1522434113.full [MRR 02-03-2016 : "Fuxianhuiid ventral nerve cord and early nervous system evolution in Panarthropoda]]

--> ANN, done May 2, 2016

http://rstb.royalsocietypublishing.org/content/370/1684.toc [MRR 10-11-2015 : "à mettre de coté pour l’annotation future de systèmes nerveux d’animaux divers"]

http://www.sciencemag.org/news/2015/10/penis-only-evolved-once-suggests-study-reptile-embryos AND http://rsbl.royalsocietypublishing.org/content/11/10/20150694 [MRR 28-10-2015 : "homology of Amniote penises"]

--> ANN, done May 2, 2016

http://www.nature.com/articles/srep11487 [MRR 26-06-2015 : "Molecular and neuronal homology between the olfactory systems of zebrafish and mouse"]

--> ANN, done May 2, 2016

http://www.nature.com/nature/journal/v523/n7558/full/nature14573.html [MRR 25-06-2015 : "homology of mouthparts"]

http://www.ncbi.nlm.nih.gov/pubmed/25829018 also for invertebrate jaws and pharyngeal teeth

http://www.ncbi.nlm.nih.gov/pubmed/26966045 [JR 14-03-2016]

http://www.reptilian-transcriptomes.org/reptilian-transcriptomes/brain_data_download.html AND http://www.ncbi.nlm.nih.gov/pubmed/25963196 [MRR 20-05-2015 - with expresssion data files]

• new term request: skin (or cutaneous) appendage placode

        https://github.com/obophenotype/uberon/issues/1266
  

http://www.nature.com/nature/supplements/insights/origin_of_vertebrates/index.html [MRR 29-04-2015 : "Nature Insight: Origin of vertebrates" : 6 reviews in contents]

1.- Scenarios for the making of vertebrates

http://www.ncbi.nlm.nih.gov/pubmed/25903626

• annotation of primary nerve cord

--> ANN, done April 30, 2015

• annotation of stomochord

--> ANN, done August 29, 2016

2.- A new heart for a new head in vertebrate cardiopharyngeal evolution

http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html

• annotation of cranial placodes (adenohypophyseal, olfactory and otic)

• Uberon new term request: Cardiopharyngeal field

• This evolutionary scenario implies that the amphioxus orovelar muscles and urochordate oral siphon muscles may be homologous to the cyclostome orovelar muscles and gnathostome mandibular muscles, which could potentially explain why these muscles are derived from the CPF only in vertebrates.

--> currently annotated via UBERON:0011648 jaw muscle, non-traceable author statement, on Chordata

https://github.com/obophenotype/uberon/issues/1263

https://github.com/obophenotype/uberon/issues/1264

https://github.com/obophenotype/uberon/issues/1265

--> ANN, done September 05, 2016

3.- Facts and fancies about early fossil chordates and vertebrates

http://www.nature.com/nature/journal/v520/n7548/full/nature14437.html

4.- The deuterostome context of chordate origins

http://www.nature.com/nature/journal/v520/n7548/full/nature14434.html

5.- Evolution of vertebrates as viewed from the crest

http://www.nature.com/nature/journal/v520/n7548/full/nature14436.html

6.- The origin and early phylogenetic history of jawed vertebrates

http://www.nature.com/nature/journal/v520/n7548/full/nature14438.html

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19322.html [MRR 22-08-2016 : "Digits and fin rays share common developmental histories"]

--> ANN, done August 29, 2016

Nucleus Ruber of Actinopterygians. http://www.ncbi.nlm.nih.gov/pubmed/27505060 Brain Behav Evol. 2016 Aug 10. [Epub ahead of print] abstract only so far