Comments for The Hyphal Tip http://fungalgenomes.org/blog Digesting the fungal genomes Fri, 17 May 2013 23:10:39 +0000 hourly 1 http://wordpress.org/?v= Comment on Basidiobolus! – genus of the month at ATCC by Jason Stajich http://fungalgenomes.org/blog/2013/04/basidiobolus-genus-of-the-month-at-atcc/comment-page-1/#comment-21146 Jason Stajich Fri, 17 May 2013 23:10:39 +0000 http://fungalgenomes.org/blog/?p=3958#comment-21146 The JGI will archive data in GEO and SRA and the assembly/genome archive on their timeframe.
We will keep announcing genome on the 1000.fungalgenomes.org site.
Downloading all data in batches will be available through the JGI site and as we prepare publications the bundles of data will be made available as a single download I expect to enable large scale analysis

]]> Comment on Basidiobolus! – genus of the month at ATCC by Mark Voorhies http://fungalgenomes.org/blog/2013/04/basidiobolus-genus-of-the-month-at-atcc/comment-page-1/#comment-21145 Mark Voorhies Wed, 15 May 2013 21:54:05 +0000 http://fungalgenomes.org/blog/?p=3958#comment-21145 Thanks for the pointer. I see that the transcriptome project is marked public/complete, but I don’t see a download link and it doesn’t appear to be in GEO. Do you know of a good gateway for downloading data from the 1000 genomes project and/or setting a watch for the release of a particular project?

]]> Comment on Basidiobolus! – genus of the month at ATCC by Daniel Henk http://fungalgenomes.org/blog/2013/04/basidiobolus-genus-of-the-month-at-atcc/comment-page-1/#comment-21144 Daniel Henk Wed, 15 May 2013 10:08:30 +0000 http://fungalgenomes.org/blog/?p=3958#comment-21144 Nice one. Basidiobolus phylogenomics should be on the horizon. I wonder where we’ll find all the Basidiobolus species?

]]> Comment on Fungal conferences abstract wordle by Posters for Fungal Genetics Conference | The Hyphal Tip http://fungalgenomes.org/blog/2010/12/abstract-wordle/comment-page-1/#comment-21139 Posters for Fungal Genetics Conference | The Hyphal Tip Sun, 03 Mar 2013 18:56:13 +0000 http://fungalgenomes.org/blog/?p=1819#comment-21139 [...] other memorable data viz. The abstract book should be released soon and I hope to get a Wordle up like from years past. I’m curious to see what topics are trending and if it belies how the fields are changing [...]

]]> Comment on Fungal conferences abstract wordle by Poster sizes for Fungal Genetics Conference | The Hyphal Tip http://fungalgenomes.org/blog/2010/12/abstract-wordle/comment-page-1/#comment-21138 Poster sizes for Fungal Genetics Conference | The Hyphal Tip Sun, 03 Mar 2013 18:55:36 +0000 http://fungalgenomes.org/blog/?p=1819#comment-21138 [...] other memorable data viz. The abstract book should be released soon and I hope to get a Wordle up like from years past. I’m curious to see what topics are trending and if it belies how the fields are changing [...]

]]> Comment on Twitter Weekly Updates for 2009-04-27 by Jeremy Semeiks http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/comment-page-1/#comment-21133 Jeremy Semeiks Wed, 23 Jan 2013 14:52:53 +0000 http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/#comment-21133 OK, here is the Stachybotrys umbrella project: http://www.ncbi.nlm.nih.gov/bioproject/186748

That page links to the projects of all four strains that I sequenced (IBT 40285, 40288, 40293, and 7711).

Data upload pending.

]]> Comment on Twitter Weekly Updates for 2009-04-27 by Jeremy Semeiks http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/comment-page-1/#comment-21122 Jeremy Semeiks Thu, 17 Jan 2013 16:20:23 +0000 http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/#comment-21122 We are currently working with NCBI to reorganize our four Stachy Bioprojects under a single umbrella project. I will post the new link here when everything is sorted out.

]]> Comment on Twitter Weekly Updates for 2009-04-27 by Jason Stajich http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/comment-page-1/#comment-21120 Jason Stajich Wed, 16 Jan 2013 06:18:22 +0000 http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/#comment-21120 It looks like there are two S. chartarum strains in progress – your link to Bioprojects wasn’t working.
http://www.ncbi.nlm.nih.gov/bioproject/?term=Stachybotrys

We are trying to get all of these recorded in the JGI site but it isn’t let me curate in progress genome listings yet.

]]> Comment on Nominate genomes for F1000 project by cwvhogue http://fungalgenomes.org/blog/2012/12/nominate-genomes-for-f1000-project/comment-page-1/#comment-21116 cwvhogue Thu, 03 Jan 2013 07:12:02 +0000 http://fungalgenomes.org/blog/?p=3800#comment-21116 @fungalgenomes Was going to nominate some of the thermophiles but see they were done already in 2011. :)

]]> Comment on Nominate genomes for F1000 project by MarcelGutCo http://fungalgenomes.org/blog/2012/12/nominate-genomes-for-f1000-project/comment-page-1/#comment-21108 MarcelGutCo Mon, 31 Dec 2012 03:38:14 +0000 http://fungalgenomes.org/blog/?p=3800#comment-21108 @fungalgenomes An interesting idea

]]> Comment on 2012 Fungal Genomes: a review of mycological genomic accomplishments by Jason Stajich http://fungalgenomes.org/blog/2012/12/fungal-genomes-in-review/comment-page-1/#comment-21106 Jason Stajich Fri, 28 Dec 2012 20:43:20 +0000 http://fungalgenomes.org/blog/?p=3769#comment-21106 Thanks Nicolas – I’ve added the Dothideomycetes genomes paper link in the collection and the post.

]]> Comment on 2012 Fungal Genomes: a review of mycological genomic accomplishments by Nicolas Feau http://fungalgenomes.org/blog/2012/12/fungal-genomes-in-review/comment-page-1/#comment-21105 Nicolas Feau Fri, 28 Dec 2012 17:27:05 +0000 http://fungalgenomes.org/blog/?p=3769#comment-21105 Nice review, the focus made this year on wood decay fungi was impressive. One work maybe missing is the joint publication of 18 Dothideomycete fungi http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003037

]]> Comment on 2012 Fungal Genomes: a review of mycological genomic accomplishments by Ken http://fungalgenomes.org/blog/2012/12/fungal-genomes-in-review/comment-page-1/#comment-21102 Ken Thu, 27 Dec 2012 08:01:27 +0000 http://fungalgenomes.org/blog/?p=3769#comment-21102 Nice work. I don’t know how I missed the Eukaryotic Cell Genome Announcements. This approach makes a lot of sense. I remember when the (jokingly) dogma was one-gene one -paper. Now we are at a point where one-genome may not be a paper. amazing.

]]> Comment on Announcing FungiDB 2.1 release by Allen Henderson http://fungalgenomes.org/blog/2012/11/fungidb-2-1-release/comment-page-1/#comment-21083 Allen Henderson Tue, 13 Nov 2012 15:35:44 +0000 http://fungalgenomes.org/blog/?p=3640#comment-21083 Woo hoo! Thanks for all your hard work. This is really helpful.

]]> Comment on Fungal Genome Tools discussion as Asilomar by emiliano http://fungalgenomes.org/blog/2011/02/fungal-genome-tools-discussion-as-asilomar/comment-page-1/#comment-21062 emiliano Tue, 11 Sep 2012 15:42:58 +0000 http://fungalgenomes.org/blog/?p=1881#comment-21062 Dear Sir/Madam,
I was a user of the FOLY database. Unfortunately I cannot
find it anymore. Does it has a new website?

Yours Sincerely,

Ing. Agr. Emiliano Jozami
Cátedra de Biología,
Parque Villarino, Zavalla, Santa Fe
Facultad de Ciencias Agrarias,
Universidad Nacional de Rosario

]]> Comment on Twitter Weekly Updates for 2009-04-27 by Jeremy Semeiks http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/comment-page-1/#comment-21061 Jeremy Semeiks Fri, 31 Aug 2012 21:30:41 +0000 http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/#comment-21061 Yes. Here is the BioProject stub:

http://www.ncbi.nlm.nih.gov/bioproject/170468

]]> Comment on Approaching 100% coverage for GO assignments in S.pombe by Jason Stajich http://fungalgenomes.org/blog/2007/03/approaching-100-coverage-for-go-assignments-in-spombe/comment-page-1/#comment-21058 Jason Stajich Sun, 19 Aug 2012 20:47:58 +0000 http://fungalgenomes.org/blog/2007/03/approaching-100-coverage-for-go-assignments-in-spombe/#comment-21058 Hi Margarita –
Paul Young’s lab website (see image A)

]]> Comment on Approaching 100% coverage for GO assignments in S.pombe by Margarita Schlackow http://fungalgenomes.org/blog/2007/03/approaching-100-coverage-for-go-assignments-in-spombe/comment-page-1/#comment-21057 Margarita Schlackow Sun, 19 Aug 2012 20:07:29 +0000 http://fungalgenomes.org/blog/2007/03/approaching-100-coverage-for-go-assignments-in-spombe/#comment-21057 Dear Prof. Stajich,

I am a doctorate student from University of Oxford. I am currently working on a web site for S. pombe and I would like to include the picture above in my banner. I am wondering what the source of that image is, as I cannot find it anywhere else. If it is your image, would it be ok for me to use it? How should I cite it? I would be very greatful if you would help me out!

All the best wishes,

Margarita

]]> Comment on Tripartate symbioses with fungi by The superpowers of endophytes | The Hyphal Tip http://fungalgenomes.org/blog/2007/01/tripartate-symbioses-with-fungi/comment-page-1/#comment-21056 The superpowers of endophytes | The Hyphal Tip Tue, 31 Jul 2012 21:26:46 +0000 http://fungalgenomes.org/blog/2007/01/tripartate-symbioses-with-fungi/#comment-21056 [...] and grass also has additional player in the form of a mycovirus that infects the fungus which we’ve talked about before. The article doesn’t seem to reference any recently published papers but mainly the ongoing [...]

]]> Comment on Twitter Weekly Updates for 2009-04-27 by Jason Stajich http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/comment-page-1/#comment-21055 Jason Stajich Tue, 31 Jul 2012 20:48:21 +0000 http://fungalgenomes.org/blog/2009/04/twitter-weekly-updates-for-2009-04-27/#comment-21055 I assume it will be in GenBank upon publication and that it will show up as a BioProject in NCBI? We will try and keep track of these in the F1000 project

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