GDR-LIST

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336 discussions

by Nnadozie Oraguzie

Got it. Many thanks. Nnadozie -----Original Message----- From: Charles-Eric Durel [mailto:Charles-Eric.Durel@angers.inra.fr] Sent: Monday, March 09, 2009 1:40 AM To: Nnadozie Oraguzie Cc: gdr-list(a)bioinfo.wsu.edu Subject: Re: [GDR] RosBREED M-TA table update Hi Nnadozie, Another paper on apple : fire blight resistance QTL in wild/ornamental Malus. Best regards, CE Nnadozie Oraguzie a écrit : > > Hi folks, > > Its that time of the year again for SCRI grant proposals! We would > like to update the Rosaceae marker-trait association (M-TA) table > prepared last year for the RoseBREED proposal. We are particularly > interested in any new QTLs, major gene loci, genes and linked markers > that may have been discovered and probably published since the last > table was created. Please provide the information using the format in > the last table which you will find at the following links: > > Full information: > http://www.hrt.msu.edu/faculty/Iezzoni/Links/TABLE%20of%20M-T%20associations %20for%20website_Sept2008.pdf > > > Summary Table: > http://www.hrt.msu.edu/faculty/Iezzoni/Links/Summary%20Table%20of%20MT%20Ass ociations.pdf > > That is, the information should follow the sequence: species, trait, > QTL, major trait locus, genes (including LGs for genes/major loci and > LGs, LOD score, percentage of variation explained for QTLs), > source/population, linked markers, references, use in MAPS (i.e., > marker-assisted parent selection) and MASS (marker-assisted seedling > selection). I would appreciate if you could include the full citation > details for all references in the full information table. Please send > the information to me by the 25^th of March 2009. > > Thank you so much for your assistance. > > Nnadozie > > Nnadozie Oraguzie > > Associate Professor > > Prunus Breeding, Genetics & Genomics > > Department of Horticulture & Landscape Architecture > > Washington State University-IAREC > > 24106 N Bunn Road Prosser > > WA 99350 USA > > Tel: 1 509 786 9271 > > Fax: 1 509 786 9370 > > E-mail:noraguzie@wsu.edu > > ------------------------------------------------------------------------ > > _______________________________________________ > Main Bioinformatics Laboratory > GDR-LIST mailing list > GDR-LIST(a)mail.bioinfo.wsu.edu

17 years, 7 months

Re: [GDR] RosBREED M-TA table update

by Nnadozie Oraguzie

Hi folks, It's that time of the year again for SCRI grant proposals! We would like to update the Rosaceae marker-trait association (M-TA) table prepared last year for the RoseBREED proposal. We are particularly interested in any new QTLs, major gene loci, genes and linked markers that may have been discovered and probably published since the last table was created. Please provide the information using the format in the last table which you will find at the following links: Full information: http://www.hrt.msu.edu/faculty/Iezzoni/Links/TABLE%20of%20M-T%20associations %20for%20website_Sept2008.pdf Summary Table: http://www.hrt.msu.edu/faculty/Iezzoni/Links/Summary%20Table%20of%20MT%20Ass ociations.pdf That is, the information should follow the sequence: species, trait, QTL, major trait locus, genes (including LGs for genes/major loci and LGs, LOD score, percentage of variation explained for QTLs), source/population, linked markers, references, use in MAPS (i.e., marker-assisted parent selection) and MASS (marker-assisted seedling selection). I would appreciate if you could include the full citation details for all references in the full information table. Please send the information to me by the 25th of March 2009. Thank you so much for your assistance. Nnadozie Nnadozie Oraguzie Associate Professor Prunus Breeding, Genetics & Genomics Department of Horticulture & Landscape Architecture Washington State University-IAREC 24106 N Bunn Road Prosser WA 99350 USA Tel: 1 509 786 9271 Fax: 1 509 786 9370 E-mail:noraguzie@wsu.edu

17 years, 7 months

remove email

by Neil Nagata

Please remove me

17 years, 7 months

Postdoctoral Fellow and Software Developer Positions in Comparative Genomics and Systems Biology

by Pankaj Jaiswal

Postdoctoral Fellow and Software developer positions in Comparative Genomics and Systems Biology Jaiswal lab at Oregon State University (http://www.oregonstste.edu) is seeking talented and motivated candidates for current and future job openings as postdoctoral fellows and software developers in the systems biology and bioinformatics. The successful candidates are expected to have either or both the experience of working in a biology wet lab and/or bioinformatics, computational biology lab. The successful candidate(s) will collaborate with researchers from Biochemistry, Molecular Biology, Plant Development, Genetics and Systems Biology programs. Postdoctoral applicants must have a Ph.D. (or equivalent degree) in biology, bioinformatics, molecular biology, biochemistry, genetics, computational biology or related fields, and some demonstrated experience in computer science/bioinformatics. For the computational biologists and software developer positions in addition to their experience and interest in biology, expertise in at least one scientific programming language and relational data management system is preferred. Candidates with experience in network analysis methods are encouraged to apply. Candidates with BS/MS degrees are also encouraged to apply for future positions in the lab. Interested individuals should send or email letter of intent/cover letter , CV/Resume with contact info of three references, and a 1-2 page description of previous accomplishments to the following address. E mail is preferred. Pankaj Jaiswal, Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Email: jaiswalp(a)science.oregonstate.edu -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org

17 years, 11 months

Post-doctoral position in Pear Genomics and Biotechnology

by Dhingra, Amit

Post-doctoral position in Pear Genomics and Biotechnology A post-doctoral position is available immediately to study fruit ripening phenomenon in Pear utilizing genomics and biotechnology approaches. The project will focus on understanding the cold-temperature based ripening in certain Pear varieties using transcriptomics. Training in the areas of genomics, genetics and next-generation sequencing technologies and an interest in computational biology and breeding will be preferred. Applicants should have a Ph.D. in plant biology, molecular biology, biotechnology or horticulture. We are looking for a highly enthusiastic, self-motivated and a creative individual who is a critical thinker capable of independent thought and research and is highly desirous of utilizing this opportunity to advance their career. There are additional opportunities to contribute to the ongoing apple genome project in the laboratory. Excellent oral and written communication skills and the ability to work well in a collaborative research environment are essential. The successful candidate is expected to participate in outreach activities, training of graduate and undergraduate students and interact with fruit industry members. The initial appointment will be for one year and reappointment will depend on successful performance and availability of funding. Salary will be commensurate with experience and qualifications. Additional information on horticultural genomics and biotechnology program can be found at www.genomics.wsu.edu <http://www.genomics.wsu.edu/> . Please email your application along with detailed curriculum vitae to Dr. Amit Dhingra (Email: adhingra(a)wsu.edu). Also arrange for three letters of reference to be emailed directly to Dr. Dhingra. WSU employs only U.S. citizens and lawfully authorized non-U.S. citizens. All new employees must show employment eligibility verification as required by the U.S. Citizenship and Immigration Services. AA\EEO\ADA

17 years, 12 months

Associate in Research Position in Horticultural Genomics and Biotechnology lab at WSU

by Dhingra, Amit

Associate in Research Position in Horticultural Genomics and Biotechnology lab at WSU A position for an Associate in Research position is available immediately in the Horticultural Genomics and Biotechnology laboratory at Washington State University. The incumbent will be self-motivated, proactive and a creative individual who can synthesize basic and applied approaches in plant biology research. Our program is sequencing the apple genome and uses high-throughput next-generation genomics platforms to resolve biological questions in horticultural crops grouped in Rosaceae and in grapes. The successful candidate will assist the PI in managing the laboratory, and perform research in various areas related to genomics, genetics, transcriptomics, computational biology and biotechnology. The person will be expected to participate in the laboratory's outreach activities. Excellent organizational and communication skills are required. In addition, computer skills for biological data analysis will be considered favorable. Familiarity with next-generation sequencing technologies will be advantageous. The person is expected to work with an interdisciplinary team and demonstrated ability to interact and work collaboratively with others will be considered favorably. The selected candidate is expected to design and conduct experiments independently, and to help in graduate, undergraduate student training. A MS in plant biology field is required. A Ph.D. in Plant Sciences or related discipline is preferred. A candidate with BS may be considered only if they have over 7 years of experience in a similar position. Good publication record is an advantage. Salary will be commensurate with experience. Additional information on horticultural genomics and biotechnology program can be found at www.genomics.wsu.edu <http://www.genomics.wsu.edu/> . Please email your application along with detailed curriculum vitae to Dr. Amit Dhingra (Email: adhingra(a)wsu.edu). Also arrange for three letters of reference to be emailed directly to Dr. Dhingra. WSU employs only U.S. citizens and lawfully authorized non-U.S. citizens. All new employees must show employment eligibility verification as required by the U.S. Citizenship and Immigration Services. AA\EEO\ADA

17 years, 12 months

2009 Plant and Animal Genome Fruit and Nut Workshop - message from organizer Dr Nahla Bassil

by Main, Doreen

Dear Fruit and Nut Researchers, As organizer to the Fruit and Nut Workshop at the Plant and Animal Genome (PAG) XVII meeting, I am inviting you to e-mail me a title and a description for an oral talk that you would like to present at this workshop on Saturday, January 10th, 2009. I would like to ensure that new research information about the widest possible number of fruits and nuts are presented at this workshop and not status reports that can be presented as posters. Please e-mail me a possible title and a short paragraph describing your presentation by Wednesday, September 24th. Make sure to include: Fruit and Nut Workshop in the subject line. I will e-mail invitations on Friday, September 26th. The deadline for the abstracts is one week later, on Friday, October 3rd. Feel free to e-mail this request to anyone you would think would be interested. Your reply will be instrumental to the success of this workshop. Best regards, Nahla Bassil Plant Geneticist USDA-ARS, NCGR 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Fax: (541) 738-4205 bassiln(a)hort.oregonstate.edu nahla.bassil(a)ars.usda.gov Dorrie Main, PhD Associate Professor of Bioinformatics Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>

18 years, 1 month

RosBREED

by Amy Iezzoni

Dear Colleagues, A few months ago, the US Rosaceae Genetics, Genomics and Breeding Executive Committee, under the leadership of Gennario Fazio, began discussing community initiatives. RosBREED: Enablling marker assisted breeding in Rosaceae, arose from these discussions. As a result of a conference call last week, a small committee was put together to further develop our vision and goals for this community project targeting submission to the fortcoming US Specialty Crop Research Initiative. I agreed to lead the effort at this point and I have tentatively agreed to PI the proposal, depending on the due date. I want to thank the committee, especially Cameron Peace and Jim Olmstead who had a late night last night, for preparing an excellent outline for your review. Our goal was to ground the outline solidly with a vision, mission and justification, yet also provide sufficient detail on the objectives and approach so that you can provide critique. We invite your comments and changes to the attached outline. Please use track changes for your edits etc. Upon reading the outline, you'll notice that under "Strategies to achieve objective 1", our goal is to test the robustness of marker trait associations over a wide range of germplasm (beyond the populations in which they were first discovered). To achieve this objective, I would like to ask for your help in compiling a list of available marker - trait associations. We will use this list as an in-house document from which we can select marker - trait associations for the proposed pipeline. Thank you in advance for your help. Both the outline and table are attached. I began adding to the table to get it started. Unfortunately we are working on a very tight deadline and so we would appreciate your comments, suggestions, and Table additions by next Wed if possible. We look forward to hearing from you and collaborating in any way possible. Best regards, Amy Dr. Amy Iezzoni Professor Department of Horticulture Michigan State University East Lansing, MI 48824 telephone: (517) 355-5191 ext. 391 fax: (517) 353-0890

18 years, 2 months

Warning GDR will be unavailable from 5.30 to 10 PM PST on Monday May 19th

by Main, Doreen

Due to power configuration changes in the IT room housing our servers, GDR will be offline from 5.30 to 10 PM PST on Monday May 19th. I apologize for any inconvenience this may cause. Cheers Dorrie --------------------------------------------------------------------- Dorrie Main, PhD Associate Professor of Bioinformatics Center for Integrated Biotechnology Dept of Horticulture and Landscape Architecture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: dorrie(a)wsu.edu Tel: (509) 335 2774 Fax: (509) 335 8690 ---------------------------------------------------------------------

18 years, 4 months

Plant Ontology Database #0408 Release

by Chih-Wei Tung

Plant Ontology (PO) Consortium is happy to announce the release #0408 of the PO database! http://www.plantontology.org. For detailed release notes, please visit http://www.plantontology.org/docs/release_notes/index.html * Ontology - 1128 PO terms [19 NEW] - 58117 annotations [18572 NEW] * Ontology and annotation browser (http://www.plantontology.org/amigo/ go.cgi) - NEW: Added ~16000 annotations on genes and mutant phenotype germplasm from tomato, tobacco, potato, eggplant, pepper and Hyoscyamus. These annotations are contributed by Solanaceae Genomics Network (SGN; http://sgn.cornell.edu/) - Updated and added new annotations contributed by TAIR (for Arabidopsis) and Gramene (for rice) databases. * Publication - The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Avraham et al. Nucleic Acids Research 2008 36:D449-D454; http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D449 * Ontology requests - We encourage researchers to submit ontology requests at: http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555 * Collaborators - We welcome our new collaborators: Dennis Stevenson: NY Botanical Graden Maria A. Gandolfo: Bailey Hortorium, Cornell University Bioversity International: http://www.bioversityinternational.org Generation Challenge Programme (GCP): http://www.generationcp.org The Plant Ontology Consortium web: http:www.plantontology.org e-mail: po-dev at plantontology.org The project is funded by National Science Foundation, USA, (Grant No. DBI-0703908)

18 years, 5 months

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