From rpwise from iastate.edu Fri Jan 4 18:34:36 2008 From: rpwise from iastate.edu (Roger Wise) Date: Fri Jan 4 18:40:16 2008 Subject: [Maize] Postdoctoral Position - Bioinformatics Message-ID: Postdoctoral Position - Bioinformatics/Computational Biology USDA-ARS / Iowa State University Functional Genomics of Plant Disease Defense A postdoctoral research position is available immediately in the Crop Genomics and Informatics Laboratory (CGIL), a collaborative effort of ARS and Iowa State University scientists. The overall goals of the "Functional Genomics of Plant Disease Defense" project are to utilize genomics tools and resources to accelerate comparative analysis of disease defense pathways important in agriculture (http://nsf.gov/awardsearch/showAward.do?AwardNumber=0500461). The candidate will work with a team responsible for molecular, genetic, and functional characterization of genes associated with and required for R-gene mediated resistance responses using barley powdery mildew and barley stem rust as model systems. The candidate will work with GeneNetwork [http://www.genenetwork.org/] to integrate eQTL analysis modules into the multi-crop plant expression database, PLEXdb [http://plexdb.org/] to enable visualization and analysis of quantitative gene expression- and trait data collected from segregating populations and diversity panels. Biologically relevant co-expression networks will be extracted and tested for function in disease defense. Recent Ph.D. in Bioinformatics/Computational Biology or a closely related field is required. Knowledge of Genetics/Cell Biology/Pathology/Biochemistry are desirable. Salary starts at $54,494 (GS-11). Funding is available for two years with possibility of extension. INFORMATION ON SALARY AND APPLICATION PROCEDURES is available at: http://www.afm.ars.usda.gov/divisions/hrd/hrdhomepage/vacancy/pd962.html Citizenship limitations may apply; see http://www.afm.ars.usda.gov/hrd/jobs/VISA/countries.htm INFO ON EMPLOYEE BENEFITS is available at: http://www.usajobs.opm.gov/ei61.asp Highly motivated individuals should send curriculum vitae, research interests, and reprints to the address below (Include name, e-mail, address, phone, and fax no. of three references) Dr. Roger Wise, USDA-ARS Department of Plant Pathology 351 Bessey Hall Iowa State University, Ames, IA 50011-1020 USA Phone: 515-294-9756 Fax: 515-294-9420 E-mail: rpwise@iastate.edu http://wiselab.org/ http://plexdb.org/ http://barleygenome.org/ Refer to Announcement No. RA-07-016H From rpalanivelu from hotmail.com Wed Jan 9 02:37:21 2008 From: rpalanivelu from hotmail.com (Ravi Palanivelu) Date: Thu Jan 10 00:46:56 2008 Subject: [Maize] Frontiers in Sexual Plant Reproduction III conference announcement Message-ID: <5ee2dc26-2b35-4d80-a708-b286e28d2200@e6g2000prf.googlegroups.com> Dear colleagues, We are pleased to announce an upcoming conference in the field of plant reproductive biology, "Frontiers in Sexual Plant Reproduction III" (http://www.cals.arizona.edu/FSPRIII), that will be held in Tucson, Arizona on October 17-19, 2008 in the Tucson Marriott University Park. We would like to invite you to participate in this meeting and share your most recent research with your colleagues. Participants are encouraged to submit an abstract and present a poster. Abstracts presented before May 31, 2008 will be considered for an oral presentation. Six major sessions have been planned for the conference: Male gametophyte development and function, Female gametophyte development and function, Endosperm development and imprinting, Compatible and incompatible pollen-pistil interactions, Evolution of plant reproduction, Systems biology of plant reproduction and emerging technologies Preliminary program and information on registration, abstracts, lodging and travel is posted at the FSPR III conference website: http://www.cals.arizona.edu/FSPRIII. Previous meetings in this series, FSPR I (2000) and FSPR II (2004), were held in SUNY, Albany to review progress, discuss challenges, debate strategies and devise effective solutions for various unanswered questions in the field of plant reproductive biology. These meetings were filled to capacity with many leading experts in the field and enthusiastic partcipants. As a follow up to these highly successful meetings, we are pleased to organize FSPR III in 2008 to serve as an international forum to review and discuss the state of the art in the plant sexual reproduction research, from multiple viewpoints: classical plant physiology, molecular biology, evolution, cell biology, biochemistry, biophysics, genetics, functional genomics and proteomics. We look forward to seeing you in Tucson in October 2008 for an exciting scientific meeting on plant reproduction. Sincerely, The organizers: Dr. Ravi Palanivelu, University of Arizona (rpalaniv@ag.arizona.edu) Dr. Dmitry Belostotsky, University of Missouri, Kansas City. From r.k.varshney from CGIAR.ORG Wed Jan 9 13:08:30 2008 From: r.k.varshney from CGIAR.ORG (Varshney, Rajeev) Date: Thu Jan 10 00:47:00 2008 Subject: [Maize] Genomics Assisted Breeding workshop in PAG (14th Jan, 5.40 pm- 7.50 pm) Message-ID: Dear all, Greetings! This mail is an invitation to participate in the "Genomics-Assisted Breeding" workshop that is scheduled in the evening (5.40 pm to 7.50 pm ) of 14 January, 2008 (Monday) during the XVIth PAG Conference in San Diego (USA). Having a panel of eminent scientists for the workshop, we hope to have fruitful discussions on the strategies and applications of genomics research in practical breeding. The details on the workshop can be found at http://www.intl-pag.org/16/16-gen-breeding.html and the programme is pasted below. In view of above, I request you to please mark your calendar for participating in the workshop. Looking forward to see you in PAG and Genomics Assisted Breeding workshop (Town and Country Room). Thanking you. With kind regards, Rajeev +++++++++++++++++++++++++++++++ Speakers: 5.40 pm Introduction Rajeev Varshney, ICRISAT (r.k.varshney@cgiar.org) 1. 5.50 pm Anker Sorensen , Keygene, Wageningen, The Netherlands (anker.sorensen@keygene.com) "Sequence Based Breeding! How Markers Turn into Sequence Alleles" 2. 6.10 pm Eduard Akhunov , Kansas State University, Manhattan, USA (edakhunov@ucdavis.edu) "High-throughput SNP Genotyping of Polyploid Wheat: Resources and Technologies" 3. 6.30 pm Perry Cregan , USDA-ARS, Beltsville, USA (perry.cregan@ars.usda.gov) "SNP Analysis for QTL Discovery and Whole Genome Analysis in Soybean" 4. 6.50 pm Antoni Rafalski, DuPont Co. Crop Genetics, Wilmington,USA (j-antoni.rafalski@cgr.dupont.com) "Genome Scan Mapping Of Complex Traits In Maize" 5. 7.10 pm Peter Langridge , Australian Centre for Plant Functional Genomics (ACPFG), Adelaide, Australia (peter.langridge@acpfg.com.au) "Tackling Tolerance To Drought In Barley And Wheat" 6. 7.30 pm Abdel Ismail , International Rice Research Institute (IRRI), Las Banos, Philippines (abdelbagi.ismail@cgiar.org) "Introgression of QTLs associated with tolerance to abiotic stresses in rice using marker-assisted breeding" *************************************************************************** Rajeev K. Varshney, Ph.D. Senior Scientist (Applied Genomics) International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Leader, Sub Programme 2: Comparative Genomics and Gene Discovery Generation Challenge Programme (GCP, www.generationcp.org) Mailing Address: Applied Genomics Laboratory, GT- Biotechnology, ICRISAT PATANCHERU- 502 324, Greater Hyderabad, INDIA Off: Tel: 0091 40 30713305; Fax: 0091 40 3071 3074/ 3075 e-mail: r.k.varshney@cgiar.org /varshney.raj@gmail.com **************************************************************************** From pj37 from cornell.edu Wed Jan 9 14:05:26 2008 From: pj37 from cornell.edu (Pankaj Jaiswal) Date: Thu Jan 10 00:47:03 2008 Subject: [Maize] International PAG Ontology Workshop 14 January 2008 Message-ID: <47851AF6.8080403@cornell.edu> Dear All, If you are attending the 16th International Plant and Animal Genome meeting to be held in San Diego (USA), everyone is cordially invited to attend the “Biological Ontologies and Applications” workshop that is scheduled for Monday Afternoon, 14 January 2008 12:50 pm - 3:00 pm. We have a great panel of talks scheduled for this year's workshop, and look forward to see you at the meeting. Thanks Pankaj http://intl-pag.org/16/16-ontology.html Monday Afternoon, 14 January 2008 --- 12:50 pm - 3:00 pm Biological Ontologies and Applications - Royal Palm Salon 1, 2, and 3 Organizer: Pankaj Jaiswal,Cornell University (pj37@cornell.edu) Workshop Background: The use of various ontologies for biology has been clearly demonstrated in several biological domains e.g., Gene Ontology and Plant Ontology. An Ontology is a common, structured and controlled vocabulary for describing the concepts that exist in an area of knowledge and the relationships that exist between them. Over the last few years a number of ontologies have been developed and implemented for use in the biological databases. However, among the researchers, the enthusiasm for ontologies has been accompanied by a general lack of awareness of what exactly ontologies are and how to use them. In this workshop we are trying to promote awareness and interaction among the researchers (audiences) and the developers of various ontology and/or those developing computational tools for using these ontologies in large/small scale analysis of genomics and genetics datasets. Useful link: OBO Foundry Ontologies Speakers: 12:50pm Michael Ashburner, Department of Genetics, University of Cambridge, UK (ma11@gen.cam.ac.uk) "GAZ an ENVO: Two new ontologies to help tame data." 1:20pm Bjoern Peters, La Jolla Institute for Allergy and Immunology, USA (bpeters@liai.org) "OBI: Ontology for Biomedical Investigations" 1:45pm Ken Ichiro Fukuda, National Institute of Advanced Industrial Science and Technology, Japan (fukuda-cbrc@aist.go.jp) "Inoh Pathway Event Ontology" 2:10pm Jayesh Pandey, Dept. of Computer Science, Purdue University, USA (jpandey@cs.purdue.edu) "Functional Characterization Of Pathways In Interaction Networks" 2:35pm Neil Sarkar, Encyclopedia of Life, Marine Biological Laboratory, USA (sarkar@mbl.edu) "Towards Developing Practical Taxonomic Ontologies" From cer17 from cornell.edu Thu Jan 10 12:27:41 2008 From: cer17 from cornell.edu (Claire Hebbard) Date: Thu Jan 10 20:57:24 2008 Subject: [Maize] Plant Databases booth at PAG Message-ID: Schedule some time to visit Booth #318 at the PAG conference January 13-16, 2008. Ten plant database projects are working together to provide users with an opportunity to visit with them to get an introduction or to ask questions about using the databases. A representative from each database will be available for a period of time during the opening reception, and again during the poster sessions. Representatives will also be available throughout the convention as scheduled (See the schedule below). For more information visit the booth for the daily schedule, or contact your favorite databases to schedule a time to meet with them. Databases that will be represented include: MaizeGDB (www.maizegdb.org) - the community database for genetic and genomic information about maize and its close relatives. Maizesequence.org - (www.maizesequence.org) provides sequence and annotation of the Zea mays ssp. mays genome resulting from the Maize Genome Sequencing Project. Gramene (www.gramene.org) - resource for comparative genome analysis in plants using model genomes from rice, maize, and Arabidopsis. TAIR (www.arabidopsis.org)- database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. GrainGenes (www.graingenes.org) - a compilation of molecular and phenotypic information for the Triticeae and Avena species. This includes wheat, barley, rye, oats, and other closely related species. SGN (www.sgn.cornell.edu) - The SOL Genomics Network is a Clade Oriented Database (COD) containing genomic, genetic and taxonomic information for species in the Euasterid clade, including the families Solanaceae (e.g. tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). PLEXdb (Plant Expression Database) (www.plexdb.org) - a unified public resource for large-scale plant gene expression for comparative functional genomics. VPhenoDBS (www.phenomicsworld.org) - a search engine and database for visually observed phenotypes of Maize mutant and diseases. It features query by images, query by semantics, and browsing through ontological structures. SoyBase (http://soybase.org) - database of genetic, phenotypic, and other information about soybean. LIS (http://comparative-legumes.org) - resource that integrates genetic and molecular data from multiple legume species and enables cross-species genomic, transcript and map comparisons. PLANTS DATABASES CONSORTIUM - PAG XVI, JAN 12-16, 2008 Exhibit Booth #318 SUNDAY 645-655 (Reception) MEET AND GREET, GET REFRESHMENTS 6:55-7:15 SoyBase SGN TAIR 7:15-7:35 PlexDB LIS VPhenoDB 7:35-7:55 GrainGenes MaizeGDB 7:55-8:15 Gramene MaizeSequence MONDAY 9:30-10:45(Coffee break) GrainGenes MaizeSequence 10:45-11:30 BREAK 11:30-12:50 LUNCH 12:50-2:55 WORKSHOPS 3:00-3:45 (Posters) MaizeGDB TAIR GrainGenes 3:45-4:30 (Posters) SoyBase PlexDB 4:30-5:15 (Posters) Gramene VPhenoDB MaizeSequence 5:15-6:00 Posters) LIS SGN TUESDAY 9:30-10:15(Coffee @10) SGN MaizeGDB PlexDB 10:15-11:00 (Coffee) Gramene LIS TAIR 11-12:40 (workshops) 12:40-1:30 LUNCH 1:30 -3:00 workshops 3:00-4:00 (coffee break) MaizeGDB VPhenoDB MaizeSequence 4:00- 5:40 (workshops) 5:40-6:40 (Coffee break) SoyBase SGN GrainGenes Wednesday 9:30-10:15 TAIR PlexDB VPhenoDB 10:15-11:00 SoyBase LIS Gramene 11-12:00 (break) 12:00-1:30 (LUNCH) 1:30-2:00 2PM CLOSED -- ******************************************* Claire Hebbard Gramene Outreach Coordinator G15 Bradfield Hall Ithaca, NY 14853 www.gramene.org ph: 607-255-4199 ******************************************* From cer17 from cornell.edu Thu Jan 10 12:45:19 2008 From: cer17 from cornell.edu (Claire Hebbard) Date: Thu Jan 10 20:57:32 2008 Subject: [Maize] Meet with Gramene At PAG Message-ID: We are pleased to inform you that you will have various opportunities to meet with a Gramene representative during the PAG Conference (Plant & Animal Genome XVI (PAGXVI), San Diego, CA.), as indicated below. We hope to see you there! 1 - Gramene workshop http://www.intl-pag.org/16/16-gramene.html Title: Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses. Date: Tuesday Afternoon - January 15, 2008 Time: 3:50 pm - 6:00 pm Place: California Room 2 - Poster number: P841 http://www.intl-pag.org/16/abstracts/PAG16_P08a_841.html Monday Afternoon, 3:-3:40 January 14, 2008 3 - Exhibit Booth #318 - Plant Genome DB Outreach Consortium Sunday 7:55 - 8:15 PM Monday 4:30 - 5:15 PM Tuesday 10:15 - 11:00 AM Wednesday 10:15 - 11:00 AM -- ******************************************* Claire Hebbard Gramene Outreach Coordinator G15 Bradfield Hall Ithaca, NY 14853 www.gramene.org ph: 607-255-4199 ******************************************* From gebee from psb.ugent.be Thu Jan 17 10:20:59 2008 From: gebee from psb.ugent.be (Gerrit Beemster) Date: Thu Jan 17 10:55:51 2008 Subject: [Maize] 3 post-doctoral positions on identification of molecular networks for yield increase in Maize Message-ID: <3953B774-C475-45CC-A694-9A37DAA6EAA4@psb.ugent.be> Dear maize community, The Department of Plant Systems Biology has an exciting opportunity for three Postdoctoral Scientists for gene discovery and functional analysis projects in maize using an integrated Systems Biology approach based on transcriptome analysis involving experimental and bio-informatics groups. The three (3-year) projects include leaf and ear development under stress conditions (cold and drought) and lateral root initiation. The work is supported by related projects on Arabidopsis and maize in the Research Groups Organ Growth Regulation and Root development and situated in the context of an industrial collaboration with CropDesign, a leading Biotechnology company in trait discovery and development. The Department of Plant Systems Biology, directed by Prof. Dr. D. Inz?, offers excellent opportunities to develop multidisciplinary projects in life sciences. Located in a brand new spacious facility with state-of-the-art equipments and a staff of 170, it is a leading research institution in the areas of plant and systems biology. Our campus is ideally positioned at the interface between academia and industry and is one of the largest plant biotechnology centres in Europe. The department is located in Ghent, one of the most vivid and international cities in Flanders. Profile q PhD with relevant expertise in plant cell and/or molecular biology. q Expertise in Maize is a plus. q An excellent command of English is a must. Contact Please apply by e-mail preferentially before March 1th, 2008, including your CV and coordinates of two references to Prof. Dr. D. Inz? Department of Plant Systems Biology VIB-University of Ghent Technologiepark 927 B-9052 Ghent, Belgium Phone: +32 (0)9 3313806 dirk.inze@psb.ugent.be www.psb.ugent.be -- ================================================================== Gerrit Beemster Tel:+32 (0)9 33 13971 fax:+32 (0)9 3313809 Mobile: +32 (0) 498 53 9091 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM gebee@psb.ugent.be http://www.psb.ugent.be ================================================================== From r.k.varshney from CGIAR.ORG Wed Jan 23 15:58:27 2008 From: r.k.varshney from CGIAR.ORG (Varshney, Rajeev) Date: Wed Jan 23 16:42:05 2008 Subject: [Maize] Genomics Assisted Crop Improvement volumes published Message-ID: Two volumes of Genomics-Assisted Crop Improvement (GACI) have been recently published by Springer. Volume 1, entitled "Genomics Approaches and Platforms", presents state-of-the-art genomic resources and platforms and also describes the strategies and approaches for effectively exploiting genomics research for crop improvement (http://www.springer.com/east/home?SGWID=5-102-22-173739833-0 ). Volume 2, entitled "Genomics Applications in Crops", presents a number of case studies of important crop and plant species that summarize both the achievements and limitations of genomics research for crop improvement (http://www.springer.com/dal/home?SGWID=1-102-22-173739832-0 ). More than 90 authors, representing 16 countries from five continents have contributed 16 chapters for Volume I and 18 chapters for Volume II. Each article shows how structural and/or functional genomics can improve our capacity to unveil and deploy natural and artificial allelic variation for the benefit of plant breeders. Editors (Rajeev Varshney, ICRISAT and Roberto Tuberosa, Uni Bologna) hope that these two volumes, while providing new ideas and opportunities to those working in crop breeding, will help graduate students and teachers to develop a better understanding of the applications of crop genomics to plant research and breeding. For details contact: Rajeev Varshney (rkvarshney@cgiar.org).