From recomb-cg at engr.uconn.edu Sun Aug 17 16:53:47 2008 From: recomb-cg at engr.uconn.edu (RECOM-CG 08) Date: Sun, 17 Aug 2008 16:53:47 -0400 (EDT) Subject: [BiO BB] RECOMB-CG 2008 Call for Posters and Registration In-Reply-To: References: Message-ID: CALL FOR POSTERS AND REGISTRATION It is our pleasure to announce the Sixth Annual RECOMB Satellite Meeting on Comparative Genomics and issue this call for submissions. We are looking forward to another great meeting, this year in Paris, France. We have an exciting group of confirmed keynote speakers, and anticipate a vibrant series of "late breaking talks" selected from the paper and poster submissions. Please consider submitting your own work for papers, posters, and talks. Submission details can be found below and on the conference website: http://igm.univ-mlv.fr/RCG08 --------------------------------------------------------------------------- UPDATES: - Registration is open https://igm.univ-mlv.fr/RCG08/?lang=en&cat=registration - The list of accepted papers is available here http://igm.univ-mlv.fr/RCG08/?lang=en&cat=program --------------------------------------------------------------------------- Sixth Annual RECOMB Satellite Meeting on Comparative Genomics October 13-15, 2008 Ecole Normale Sup?rieure, Paris, France http://igm.univ-mlv.fr/RCG08 THEME AND SCOPE Rapid DNA sequencing technologies have fueled an explosion in genome level data. RECOMB-CG is devoted to the development and utilization of computational methods for the comparative exploration of genome structure, function, and evolution. Both theoretical and applied contributions are welcome, and papers that combine new techniques with new knowledge derived from their application are highly encouraged. Submissions should include genome wide analyses informed by comparative data. Topics of interest include but are not limited to: Algorithms for comparative genomics Genome rearrangements Ancestral genome reconstruction Multiple genome alignment Genome sequence comparison Modeling genome evolution Identification, classification, and evolution of non-coding motifs Comparative genomics for genome annotation Gene and genome duplication Evolution of gene families Identification of highly conserved and rapidly evolving sequences Gene tree reconciliation Comparative genomics and epigenetics Comparative genomics and proteomics Comparative genomics and gene expression Comparative genomics and adaptation CALL FOR POSTER PRESENTATIONS We invite you to apply for poster presentations on topics of relevance to the workshop. Each poster presentation should be described in a 1 page summary and be submitted by September 22, 2008 via the Easychair submission system: http://www.easychair.org/conferences/?conf=recombcg08 PROGRAM The lists of invited speakers and accepted papers are available here https://igm.univ-mlv.fr/RCG08/?lang=en&cat=program KEY DATES June 18, 2008 Paper submission deadline July 14, 2008 Notification of paper acceptance July 24, 2008 Final manuscript due Early registration is through September 15, 2008 Late registration will begin September 16, 2008 September 22, 2008 Poster submission deadline October 13-15, 2008 Workshop INVITED SPEAKERS Olga Troyanskaya (Princeton University) Aviv Regev (Broad Institute) Trisha Wittkop (University of Michigan) Chris Ponting (University of Oxford) Laurent Duret (Universit? Claude Bernard) CONFERENCE CHAIRS Craig E. Nelson (Molecular & Cell Biology - Univ. of Connecticut, USA) Stephane Vialette (IGM - Univ. Paris-Est, France) STEERING COMMITTEE Jens Lagergren (Stockholm Bioinformatics Centre and CSC, KTH, Sweden) Aoife McLysaght (University of Dublin, Ireland) David Sankoff (University of Ottawa, Canada) PROGRAM COMMITTEE Lars Arvestad (Royal Institute of Technology, Sweden) Veronique Barriel (Museum national d'histoire naturelle, France) Anne Bergeron (Universite du Quebec a Montreal, Canada) Guillaume Blin (Universite Paris-Est, France) Guillaume Bourque (Genome Institute of Singapore, Singapore) Jeremy Buhler (Washington University in Saint Louis, USA) Pierre Capy (Universite Paris-Sud, France) Cedric Chauve (Simon Fraser University, Canada) Avril Coghlan (Sanger Institute, UK) Miklos Csuros (Universite de Montreal, Canada) Aaron Darling (University of Queensland, Australia) Bernard Dujon (Institut Pasteur, France) Dannie Durand (Carnegie Mellon University, USA) Nadia El-Mabrouk (Universite de Montreal, Canada) Niklas Eriksen (Goteborg University, Sweden) Guillaume Fertin (Universite de Nantes, France) Olivier Gascuel (Universite de Montpellier II, France) Henri Grosjean (Universite Paris-Sud, France) Matthew Hahn (Indiana University, USA) Tao Jiang (University of California - Riverside, USA) Jens Lagergren (Stockholm Bioinformatics Centre and CSC, KTH, Sweden) Emmanuelle Lerat (Universite Claude Bernard, France) Aoife McLysaght (University of Dublin, Ireland) Bernard Moret (Ecole Polytechnique Federale de Lausanne, Switzerland) Craig Nelson (Co-Chair, University of Connecticut, USA) Michal Ozery-Flato (University of Tel-Aviv, Israel) Pierre Pontarotti (Universite de Provence, France) Eduardo Rocha (Universite Paris 6 et Institut Pasteur, France) Hugues Roest-Crollius (Ecole Normale Superieure, France) Antonis Rokas (Vanderbilt University, USA) Marie-France Sagot (INRIA Rh?ne-Alpes, France) David Sankoff (University of Ottawa, Canada) Cathal Seoighe (University of Cape Town, South Africa) Jens Stoye (Bielefeld University, Germany) Chuan-Yi Tang (National Tsing Hua University, Taiwan) Eric Tannier (INRIA Rh?ne-Alpes, France) Glenn Tesler (University of California - San Diego, USA) Stephane Vialette (Co-Chair, Universite Paris-Est, France) Louxin Zhang (National University of Singapore, Singapore) LOCAL ORGANIZING COMMITTEE Severine Berard (Universite de Montpellier II, France) Guillaume Blin (Universite Paris-Est, France) Maxime Crochemore (Universite Paris-Est, France) Hugues Roest Crollius (Ecole Normale Superieure, France) Guillaume Fertin (Universite de Nantes, France) Eric Tannier (INRIA Rh?ne-Alpes, France) Jean-Stephane Varre (INRIA Futurs - Universite de Lille, France) Stephane Vialette (Universite Paris-Est, France) -------------- next part -------------- _______________________________________________ RECOMB-CG mailing list RECOMB-CG at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/recomb-cg From phdsymposium2008ad at googlemail.com Tue Aug 19 05:07:25 2008 From: phdsymposium2008ad at googlemail.com (PhD Student) Date: Tue, 19 Aug 2008 11:07:25 +0200 Subject: [BiO BB] EMBL 10th International PhD Student Symposium Message-ID: <678cd5320808190207x3c05cf19jfd331b879030ec5d@mail.gmail.com> Dear Subscribers, The 2008 EMBL PhD Symposium held at EMBL Heidelberg from October 23rd to 25th calls for applications from PhD students and young scientists. The symposium is the 10th in a series of very successful international conferences for young scientists, organized by PhD students of the European Molecular Biology Laboratroy - EMBL. The topic of this year's symposium is ?Decision Making in Biology ? Nature at the Crossroads". Four sessions will adress decisions at different levels of complexity, moving from cells to populations and from molecules to the animal mind. Confirmed Speakers include Nobel Prize Laureate Tim Hunt (Cambridge University), Baroness Susan Greenfield (Oxford University), Nenad Ban (ETH Zuerich) and Hans Schoeler (MPI Muenster). Beside excellent lectures, the symposium offers an interactive environment which is acclaimed by both the junior and the senior scientists. Online registration closes 31st August, we strongly encourage submission of poster abstracts and applications for participant talks. The speakers will choose a poster prize winner. Registration fee is 100 Euros and includes accomodation and meals. Selected participants, e.g. the winner of the poster prize, are refunded their registration fee. Attached to this email, you find the Symposium poster. We would appreciate if you can forward it to all young researchers at your institute and post a printout of the poster at frequented locations. For further information about Heidelberg, the EMBL and the symposium itself, please visit the symposium website at http://phdsymposium.embl.org Thank you for your help. Yours sincerely, The PhD Student Symposium Organising Committee This conference is supported by the European Commission's Marie Curie SCF (Series of Conferences & Training Courses) Action, under the Sixth Framework Programme (FP6). From skhadar at gmail.com Tue Aug 19 09:18:52 2008 From: skhadar at gmail.com (Shameer Khadar) Date: Tue, 19 Aug 2008 18:48:52 +0530 Subject: [BiO BB] Human GO Annotations Message-ID: Hi all, I want to know from which database I can access human gene ontology data ? Is it GO Annotations @ EBI or Ensembl ? If it is Ensembl, where to download this ? any url for the download ? I downloaded GO data for following organisms from its respective databases. Fly -> Flybase Worm -> WormBase Arabidopsis -> TAIR Like this, I was not able to find a dedicated resource for human ! Purpose : I have a set of human Ensembl ids, I need GO annotations for each of this. Eagerly waiting for your response, -- K Shameer ========================================= | Indulge | Innovate | Inspire | From marty.gollery at gmail.com Tue Aug 19 13:02:51 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Tue, 19 Aug 2008 10:02:51 -0700 Subject: [BiO BB] Human GO Annotations In-Reply-To: References: Message-ID: Hi Shameer, Go to http://www.geneontology.org/GO.current.annotations.shtml and scroll down to Homo sapiens. There you will find the appropriate link. Cheers, Marty On Tue, Aug 19, 2008 at 6:18 AM, Shameer Khadar wrote: > Hi all, > > I want to know from which database I can access human gene ontology data ? > Is it GO Annotations @ EBI or Ensembl ? If it is Ensembl, where to download > this ? any url for the download ? > I downloaded GO data for following organisms from its respective databases. > Fly -> Flybase > Worm -> WormBase > Arabidopsis -> TAIR > Like this, I was not able to find a dedicated resource for human ! > > Purpose : I have a set of human Ensembl ids, I need GO annotations for each > of this. > > Eagerly waiting for your response, > -- > K Shameer > ========================================= > | Indulge | Innovate | Inspire | > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif North America Toll Free (877) 222-9543 ext. 6 Direct (760) 431-1263 ext. 6 From drjohn08318 at yahoo.com Tue Aug 19 13:21:44 2008 From: drjohn08318 at yahoo.com (drjohn08318 at yahoo.com) Date: Tue, 19 Aug 2008 17:21:44 +0000 Subject: [BiO BB] Human GO Annotations Message-ID: <1152068219-1219166565-cardhu_decombobulator_blackberry.rim.net-733057157-@bxe017.bisx.prod.on.blackberry> www.genome.jp/kegg ------Original Message------ From: Shameer Khadar Sender: To: General Forum at Bioinformatics.Org To: General Forum at Bioinformatics.Org ReplyTo: General Forum at Bioinformatics.Org Sent: Aug 19, 2008 09:18 Subject: [BiO BB] Human GO Annotations Hi all, I want to know from which database I can access human gene ontology data ? Is it GO Annotations @ EBI or Ensembl ? If it is Ensembl, where to download this ? any url for the download ? I downloaded GO data for following organisms from its respective databases. Fly -> Flybase Worm -> WormBase Arabidopsis -> TAIR Like this, I was not able to find a dedicated resource for human ! Purpose : I have a set of human Ensembl ids, I need GO annotations for each of this. Eagerly waiting for your response, -- K Shameer ========================================= | Indulge | Innovate | Inspire | _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb Sent via BlackBerry by AT&T From rajju1234 at gmail.com Tue Aug 26 07:36:14 2008 From: rajju1234 at gmail.com (rajju rajju) Date: Tue, 26 Aug 2008 17:06:14 +0530 Subject: [BiO BB] Protein structure for BPSS1528 Message-ID: <40435bd90808260436r4ca85fe0l13e2fe116254f452@mail.gmail.com> HI all can any one tell me how to get protein for BPSS1528.ITS ORAGANISM NAME IS B. pseudomallei.I tried to all possible way to finf out the protein and get the structure for that above mentioned gene but i m not able to find out.isthere any site or database which can give me protein stucture n function for BPSS1528 gene. please help me thanks -- Raj GeneFlux Biosciences pvt ltd 9739396049 From christoph.gille at charite.de Thu Aug 28 14:22:08 2008 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 28 Aug 2008 20:22:08 +0200 (CEST) Subject: [BiO BB] BPSS1528 Message-ID: <0830a146b00a674e16576b2aa44db6f1.squirrel@webmail.charite.de> There is no close Blast match of UNIREF:A3NLD1 Putative uncharacterized protein with PDB The top blast hit is attributed to composition and does not prove homology. Forget the low E-value. There is lots of Proline which is a strong attractor in sequence alignments. 1> PDB:1Y0F_A mol:protein length:1054 COLLAGEN I ALPHA 1 (NEW) Score = 135 (52.599998474121094), Expect = 1.7999999499807018E-6 Identities = 30/258, Positives = 36/258 Therefore one could try http://tardis.nibio.go.jp/fugue/ Hope this helps Christoph