From Carolyn.Lawrence from ARS.USDA.GOV Wed Jul 1 11:49:28 2009 From: Carolyn.Lawrence from ARS.USDA.GOV (Carolyn Lawrence) Date: Wed Jul 1 13:33:07 2009 Subject: [Maize] Three new things at MaizeGDB! Message-ID: Greetings, Maize-o-philes! We have three items at MaizeGDB that you should check out. 1. The Mo17 SNP are in the Genome Browser! Visit http://gbrowse.maizegdb.org/ to view those aligned SNP and other variations contributed by the DOE's JGI. 2. Curious about how B73 is being sequenced? Want to know more about what you're seeing when you work with sequence at MaizeGDB? Check out the "Featured MaizeGDB Tutorials" at http://www.maizegdb.org/tutorial. The movie "B73 Genome Caveats" is available in both QuickTime and FLASH formats via links to the right of the "View Area" toward the top of that page. This movie will be updated over time as the Maize Genome Sequencing Project progresses and as MaizeGDB's representation of the genome improves. 3. Trying to find all the maize projects on a particular topic? Browse POPcorn! POPcorn (http://www.maizegdb.org/POPcorn/) currently has 42 projects and 76 resources. Let us know what we're missing - we want this to be a comprehensive list of projects and soon will implement the ability to BLAST cooperating projects' sequence-indexed data from one place. Thanks for your continued help and suggestions! We owe a special thanks to the Maize Genome Sequencing Project personnel for their help in making the B73 movie accurate. Sincerely, The MaizeGDB Team From jaiswalp from science.oregonstate.edu Thu Jul 2 15:02:11 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Thu Jul 2 15:27:04 2009 Subject: [Maize] Job Opening: Plant Ontology Project Coordinator Message-ID: <4A4D1243.906@science.oregonstate.edu> Deadline extended until July 31st. Also, if you are attending the following meetings please feel free to contact us to learn more about this position and the project: ASPB-Plant Biology 2009 : Contact Pankaj Jaiswal BSA Botany & Mycology 2009: Contact Aaron Liston Position Title: Research Associate (Senior Postdoc) / Research Associate (Postdoc) Working Title: Plant Ontology Project Coordinator The Plant Ontology Consortium (www.plantontology.org) is seeking applicants for a full-time position of scientific curator who will coordinate the Consortium’s efforts. The Plant Ontology Consortium is a collaboration among researchers at Oregon State University, Cornell University and New York Botanical Garden. The project is funded by the National Science Foundation. The Consortium also collaborates with the curators of many model organism databases including rice, Arabidopsis, maize, grasses, legumes, Solanaceae, Bryophytes, Rosaceae and plant phylogenomics. The project aims to develop shared vocabularies on plant anatomy and growth and developmental stages, to describe patterns of phenotype(s) and gene expression. For more details on the project please see the publications (PubMed IDs:18194960, 17142475, 16905665, 18629207) How to Apply: To review the position description in detail and apply, go to posting #0004322 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a cover letter citing your interest in the position and your experience, and a CV/resume including 3 references. Closing date 7/31/09. Required qualifications: Ph.D. in an aspect of plant biology (e.g. Development, Physiology, Biochemistry, Genetics, Plant Pathology, Systematics) and/or genomics, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Available immediately to start working on the project. Demonstrated ability for independent, critical thinking and excellent communication, networking and teamwork skills. -- 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 From baskin from bio.umass.edu Mon Jul 6 17:42:46 2009 From: baskin from bio.umass.edu (Tobias Baskin) Date: Mon Jul 6 20:30:11 2009 Subject: [Maize] postdoc position open Message-ID: A postdoctoral position is available to study the relation between cell wall structure and morphogenesis. The project uses the emerging model grass, Brachypodium distachyon, and both forward and reverse genetic approaches. The forward genetic approach will be a screen for mutants with aberrant root morphology; the reverse genetic approach will be to inactivate genes that are known to be important in other species. The position requires a Ph.D. in a relevant area of biology and preference will be given to candidates having experience with any of the following: developmental genetics; cell wall analysis; microscopy. The Baskin lab participates actively in the University of Massachusetts-Amherst Interdisciplinary Program in Plant Biology and also in a new cluster of scientists on campus working on B. distachyon. The University of Massachusetts is an Equal Opportunity Employer and I encourage all qualified persons to apply. To apply, please send your cv to baskin@bio.umass.edu. Check http://www.bio.umass.edu/biology/baskin/ for (somewhat outdated) information about my lab and feel free to contact me for more information. -- _ ____ __ ____ / \ / / \ / \ \ Tobias I. Baskin / / / / \ \ \ Biology Department /_ / __ /__ \ \ \__ 611 N. Pleasant St. / / / \ \ \ University of Massachusetts / / / \ \ \ Amherst, MA, 01003 / / ___ / \ \__/ \ ____ www.bio.umass.edu/biology/baskin Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243 From jacksond from cshl.edu Tue Jul 7 10:03:02 2009 From: jacksond from cshl.edu (Jackson, David) Date: Tue Jul 7 10:44:03 2009 Subject: [Maize] CSHL Cereal Genomics Workshop- deadline approaching Message-ID: ********************************* APPLICATION DEADLINE APPROACHING: A WORKSHOP IN CEREAL GENOMICS October 13 - 19, 2009, Cold Spring Harbor Laboratory. Application deadline - July 15, 2009 ********************************* Workshop Instructors: David Jackson & Doreen Ware, Cold Spring Harbor Laboratory Sarah Hake, USDA/UC Berkeley Plant Gene Expression Center This one-week workshop in Cereal Genomics will enable participants to take advantage of emerging genetic tools and the completed cereal genome sequences of rice and maize, and emerging sequences of other species. The workshop will feature morning and evening lectures with afternoon computer lab exercises. The workshop will also provide hands-on lab work in the comparative anatomy, phenotype and QTL sections in which participants will examine samples and make measurements for statistical analysis to illustrate the power of maize genetics and its relation to genomics. The faculty (instructors and invited lecturers) are active researchers in cereal genetics and genomics who have made significant contributions to the field, ensuring that the latest techniques and ideas will be presented. The course will be structured to provide time for informal discussions and exchange with leaders in the field. Students from academic institutions are eligible to apply for partial scholarships. Topics: The rice, maize and other cereal genomes, and their annotation; Genetic mapping: linking physical and genetic maps; Classical maize genetics and tools; Comparative anatomy of the cereals; Comparative genomics; Cereals databases; Quantitative trait locus mapping, association analysis and evolution; Genome wide expression analysis- ESTs, microarrays and Solexa transcript profiling. Confirmed speakers: Lisa Harper, Toby Kellogg, Ed Buckler, Torbert Rocheford, Blake Meyers, Matt Hudson, Jeff Bennetzen, Katrien Devos, Karen Koch, Scott Tingey, Jean Philippe Vielle Caldaza. This workshop is supported with funds provided by the National Science Foundation, and students from US academic institutions are eligible to apply for partial scholarships. From jaiswalp from science.oregonstate.edu Wed Jul 15 13:25:21 2009 From: jaiswalp from science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Wed Jul 15 13:31:49 2009 Subject: [Maize] Research Associate (Post Doc) at Oregon State Univ. Message-ID: <4A5E1F11.4070400@science.oregonstate.edu> Please post. Position Title: Research Associate (Post Doc) The Department of Botany and Plant Pathology has an immediate opening for a Research Associate (Post Doc) to work on a cereal plant genome wide gene expression analysis. This is a full-time, (1.0 FTE), 12-month, fixed-term position working in Dr. Pankaj Jaiswal's lab (http://www.science.oregonstate.edu/bpp/). How to Apply: To review the position description and apply, go to posting #0004455 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a Letter of Intent, and a Curriculum Vitae (including 3 references). For full consideration, apply by 07/31/09 when review of applications will begin. This position is required to develop a comprehensive gene expression catalog of rice and other cereal plant genes in various the plant development stages. The project includes histological studies, whole genome transcriptome and proteome data generation and analysis. The incumbent will be responsible for designing microarray and whole genome transcriptome/digital gene expression experiment(s) using newer high throughput sequencing technologies developed by Illumina, 454-LifeSciences, etc. Development of methods suitable to the experimental conditions and plant material being investigated, carrying out the experiments on analysis of anatomical samples using microscopy and whole genome transcriptome, data analysis and publication of the results in peer reviewed journals and submission to major data repositories. Besides this, the incumbent will also participate in lab's outreach activities, help in mentoring undergraduates and graduate students. Successful candidate will work with existing lab personnel and various collaborators that includes project PIs, faculty, highly trained PhD. level bioinformatics specialists, software developers and the department's fellow postdoc and graduate students. Required qualifications: - PhD in Plant Biology, Molecular Biology, Genetics, Biochemistry, Biological Chemistry, Metabolomics, or related field. - Worked previously on gene expression data generation and analysis in their PhD studies or postdoctoral training. Demonstrated expertise in studying plant development, anatomy, histology, microarrays, gene expression, proteomics, genetics and general understanding of plant biochemistry and gene regulation. - Demonstrated ability for independent and critical thinking, excellent communication skills in oral and written presentations in English and ability to work in teams. Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA