GDR-LIST

gdr-list@bioinfo.wsu.edu

328 discussions

by Sook Jung

Dear Rosaceae researchers, Gene Naming Guideline has been put together by Rosaceae Gene Name Standardization Subcommittee of RosEXEC/RosIGI and is available in GDR. This information is found on the main menu at 'Help' ->'Gene Naming Guideline'. http://www.rosaceae.org/nomenclature/gene We recommend authors to refer to the list of gene class symbols in Rosaceae and gene naming guidelines and submit the gene/gene class data. As in the guideline, the data can be submitted in the template available from the page below. http://www.rosaceae.org/data/submission *If you are working on Rosaceae genes, we would like to ask you to submit your gene data using the guideline and give us any feedback. If you know of any researchers who are actively working on genes, please forward this email.* The gene data includes gene name, gene symbol, species, gene model ID, evidence code, etc. After getting enough feedback from the community researchers, we will work with editors of journals to check whether the authors are following the nomenclature guidelines and make sure that novel gene names have been submitted to NCBI and/or GDR before accepting a paper as publishable. Unlike, NCBI, GDR will accept genes that do not come from single molecule sequencing with appropriate evidence code. Sincerely, GDR team ------------------------------------------ Sook Jung, PhD Assistant Research Professor of Bioinformatics Dept of Horticulture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: sook_jung(a)wsu.edu ------------------------------------------- Follow GDR on Twitter! <https://twitter.com/GDR_news>

9 years, 10 months

GDR Newsletter April 2015

by Main, Doreen

Dear Rosaceae Community Members, Please find attached a newsletter describing what's new in GDR* over the last several months. If you have any comments/suggestions/needs for GDR, please let us know. We will be meeting with our Advisory Board (RosEXEC) in 2 weeks and will be discussing our plan of work and community needs at that meeting. As always, we thank you for your continued support of GDR. Cheers Dorrie * GDR is supported by grants from the USDA SCRI Program, NIFA NRSP, the Washington Tree Fruit Research Commission, as well as principal investigator support from Washington State University, Clemson University and the University of Florida. Dorrie Main, PhD Associate Professor of Bioinformatics Department of Horticulture Washington State University 45 Johnson Hall Pullman, WA 99164-6414 Tel: 509-335-2774 (office) Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu> URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>

9 years, 11 months

Dorrie Main looking for applicants for 3 positions

by Humann, Jodi Lynn

Hello everyone, Attached is a PDF with the descriptions of three positions in the Main Bioinformatics Lab at Washington State University. Please forward this to anyone you know who is qualified and interested. The descriptions can also be viewed at: http://www.bioinfo.wsu.edu/node/153. Thanks, Jodi Jodi Humann, Ph.D. Main Lab Bioinformatics Project Coordinator Department of Horticulture Washington State University PO Box 646414 Pullman, WA 99164-6414 509-335-3206 jhumann(a)wsu.edu

10 years, 1 month

Genomics and Bioinformatics position at Oregon State University- Closing January 25, 2015

by Bassil, Nahla

Dear Colleagues, The Department of Horticulture at Oregon State University invites applications for a full-time (1.0 FTE), 9-month, tenure-track Assistant Professor position. This position will conduct research on genomics of economically important crop plants. Two months of summer salary will be provided on a fixed-term, recurring basis for three years. Thereafter, the faculty member will be expected to generate two months of summer salary. The incumbent will be responsible for writing grants and securing the funds for summer salary and operating expenses. The person in this position is responsible for developing a comprehensive program in research teaching and outreach in applied genomics and bioinformatics for economically important staple and specialty crops of Oregon. The person in this position is expected to develop and implement collaborative and independent research, to discover new knowledge and/or creative solutions to problems related to genomics and bioinformatics of economically important crops. The research discoveries and impacts are to be communicated to peers, practitioners and citizens. College of Agricultural Sciences faculty are committed to enhancing student success by engaging students in quality academic, research, internships, global studies, and other experiential learning opportunities. Positions with primary responsibility for extension and outreach are likewise committed to learner success through programming appropriate for diverse audience. The Department of Horticulture is a comprehensive department with active research, Extension, and resident instruction missions. The department serves a diverse and changing horticultural industry and strives to serve the horticultural needs of all citizens in Oregon. To meet these missions, the department has approximately 60 statewide faculty. The faculty are approximately equally split between on-campus and off-campus locations. Off-campus research faculty are located at Experiment Stations and County Extension offices throughout the state. The Department of Horticulture faculty also collaborate with the USDA-Agricultural Research Service in the Corvallis area. To review the full position announcement, qualifications and to apply, go to https://jobs.oregonstate.edu/applicants/Central?quickFind=65022 or http://oregonstate.edu/jobs, Posting #0013285; Closes January 25, 2015. OSU is an AA/EOE. For further information, please contact Search Committee Chair Shawn.Mehlenbacher(a)oregonstate.edu or Department Head Bill.Braunworth(a)oregonstate.edu Detailed information is in the attachment- Best regards, Nahla Nahla V. Bassil Plant Molecular Geneticist USDA-ARS National Clonal Germplasm Repository 33447 Peoria Rd. Corvallis, OR 97333-2521 Tel: (541) 738-4214 Nahla.bassil(a)ars.usda.gov<mailto:Nahla.bassil@ars.usda.gov> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

10 years, 2 months

RosEXEC and RosIGI meetings at PAG 2015 on Sunday Jan 11, 2015

by Volk, Gayle

We will be having a U.S. RosEXEC meeting at PAG, 2015, scheduled for the Stratford Room at the Town and Country Hotel, Sunday Jan 11, 2015 from 8-10 am. This will be followed by the RosIGI meeting from 10-11 am (chaired by Dorrie Main) in the same room. As members of the Rosaceae community, you are invited to join us. If you are unable to attend the meetings, Dorrie Main will make both the RosEXEC and RosIGI meetings available via Skype. Her address is dorrie.s.main For more information about U.S. RosEXEC and RosIGI, please see the following websites: http://www.rosaceae.org/community/us_rosexec http://www.rosaceae.org/community/rosgi Gayle Volk (soon-to-be RosEXEC Chair) USDA-ARS-NCGRP 1111 S. Mason St. Fort Collins, CO 80521 970-495-3205 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

10 years, 2 months

New Postdoc Positions with RosBREED Project

by Ksenija Gasic

Postdoc Opportunities in U.S. with RosBREED Project Application window is closing at Christmas! We are seeking postdoctoral associates for key positions in the newly funded RosBREED project (www.rosbreed.org). RosBREED is a U.S-wide collaboration among breeders, geneticists, physiologists, pathologists, and socio-economists of Rosaceae crops. This project seeks to develop and apply modern DNA-based diagnostic tools to help deliver new cultivars with superior horticultural quality and disease resistance. We are seeking two postdocs to begin 1 January 2015. The Prunus Postdoc will be based at Clemson University under the guidance of Dr. Ksenija Gasic and will focus on Prunus crops, primarily peach but not cherry. The Apple & Cherry Postdoc will be based at Washington State University under the guidance of Dr. Cameron Peace and will focus on apple, sweet cherry, and tart cherry. A third postdoc focusing on strawberry, blackberry, rose, and pear will later be sought to begin from 1 September 2015, to be based at USDA-Corvallis. All positions are funded through to 31 August 2019 - i.e., at least four years. Activities: All postdocs will conduct genetic research in QTL discovery, DNA test development both locus-specific and genome-wide, and applied marker-assisted breeding (MAB). These research associates will be the primary liaisons helping U.S. Rosaceae crop breeders to convert new DNA information and other project advances into breeding impact, using cutting-edge technologies, software, and knowledge. Two six-month internships with project partners outside the U.S. (e.g., in Europe, New Zealand, & Australia) are expected for each postdoc during the project's duration. Qualifications: Active research communication is expected in the form of scientific publications, extension articles, participation in conferences and project meetings, and networking across breeding programs and allied science programs both U.S-wide and internationally. Applicants must have a Ph.D. in Plant Breeding, Horticultural Genetics, or a closely related field. The successful candidate will be a highly motivated team player with excellent communication skills and extensive experience in statistical genetics and linkage analysis. Preference will be given to candidates with evidence of successful management of large datasets, substantial research productivity, a strong publication record, experience with perennial, clonally propagated crop genetics, and a commitment to practical application. Familiarity with Rosaceae crop breeding germplasm and Pedigree-Based Analysis software are also advantageous. Applying: If you are interested in the Prunus Postdoc or the Apple & Cherry Postdoc position, please email a cover letter highlighting your qualifications, your current CV, copies of graduate degree transcripts, and contact information (phone number and email address) of three referees to either: Prunus: Dr. Ksenija Gasic at kgasic(a)clemson.edu or Apple & Cherry: Dr. Cameron Peace at cpeace(a)wsu.edu Please direct questions on either position to the same email addresses. Consideration of applications will begin immediately and will continue until the positions are filled.

10 years, 2 months

Special Issue on New approaches to fruit tree transcriptome analysis

by Sook Jung

Dear All, Please see the message from Dr. Ariel Lopez below about the Special Issue on New approaches to fruit tree transcriptome analysis. Thanks! Sook -------------------------- *Special Issue on New approaches to fruit tree transcriptome analysis* Dear Sook: I would appreciate your help on disseminating the information at GDR regarding an special issue on “new approaches to fruit tree transcriptome analyses”. This is part of a Research Topic from Frontiers in Plant Science. I would like to encourage the members of the Rosaceae community to consider the submission of manuscripts on this topic. Further information can be found at the following link http://journal.frontiersin.org/ResearchTopic/3325#impact Thanks! Best wishes Ariel ------------------------------------------ Sook Jung, PhD Assistant Research Professor of Bioinformatics Dept of Horticulture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: sook_jung(a)wsu.edu ------------------------------------------- Follow GDR on Twitter! <https://twitter.com/GDR_news>

10 years, 3 months

Two postdoc opportunities to study tree architecture at Cornell University, Geneva, NY and at the USDA ARS Appalachian Fruit Research Station, Kearneysville, WV

by Sook Jung

*Two postdoc opportunities to study tree architecture at Cornell University, Geneva, NY and at the USDA ARS Appalachian Fruit Research Station, Kearneysville, WV * We are seeking two postdoctoral scientists to study molecular and genetic aspects of tree architecture as part of a project newly funded by NSF Plant Genome Research Program. The aims of this project are to uncover the molecular mechanisms underlying a phenomenon called apical control that regulates tree structures. Both positions will be hired through Cornell University and are anticipated to begin as early as February 2015 and are funded for a period of at least 3 years. A postdoc specializing in apple will be based at Cornell University, Geneva, NY under the guidance of Dr. Kenong Xu. A postdoc specializing in Prunus species (peach and plum) will be based at the USDA ARS Appalachian Fruit Research Station, Kearneysville WV under the guidance of Dr. Chris Dardick. The postdocs will conduct genetic analyses to identify causative genes responsible for mutant growth habits, perform yeast two-hybrid screens, create transgenic apple or Prunus knock-down and over-expression lines, and carry out image-based phenotyping and transcriptional profiling studies of wild type and mutant apple or Prunus meristems. As part of the research program, both postdocs will be expected to interact with the entire research team as well as with growers and industry leaders to communicate the practical applications of their findings. Successful candidates should have a background in plant development and be skilled in molecular techniques. Specific experience in horticultural crops is desired but not necessary as candidates with complementary experience in model plant systems are strongly encouraged to apply. Candidates should be able to work independently, devise appropriate hypotheses and experiments, and learn new skills as appropriate. Strong writing and communication skills are also required. Applicants must have a Ph.D. in plant genetics, molecular biology, development, or a related field. Qualified minority candidates are strongly encouraged to apply. Applying: Interested applicants should send a cover letter highlighting your qualifications and research interests, your current CV, copies of graduate degree transcripts, and contact information for three references to both project leaders: Apple: Dr. Kenong Xu at kx27(a)cornell.edu and Prunus: Dr. Chris Dardick at chris.dardick(a)ars.usda.gov Review of applications will begin at the time they are received and will continue until both positions are filled. Employment information can be accessed at http://www.rosaceae.org/community/employment ------------------------------------------ Sook Jung, PhD Assistant Research Professor of Bioinformatics Dept of Horticulture Washington State University 45 Johnson Hall, Pullman, WA 99164-6414 Email: sook_jung(a)wsu.edu ------------------------------------------- Follow GDR on Twitter! <https://twitter.com/GDR_news>

10 years, 3 months

New Postdoc Positions with RosBREED Project

by Peace, Cameron

Postdoc Opportunities in U.S. with RosBREED Project We are seeking postdoctoral associates for key positions in the newly funded RosBREED project (www.rosbreed.org). RosBREED is a U.S-wide collaboration among breeders, geneticists, physiologists, pathologists, and socio-economists of Rosaceae crops. This project seeks to develop and apply modern DNA-based diagnostic tools to help deliver new cultivars with superior horticultural quality and disease resistance. We are seeking two postdocs to begin 1 January 2015. The Prunus Postdoc will be based at Clemson University under the guidance of Dr. Ksenija Gasic and will focus on Prunus crops, primarily peach but not cherry. The Apple & Cherry Postdoc will be based at Washington State University under the guidance of Dr. Cameron Peace and will focus on apple, sweet cherry, and tart cherry. A third postdoc focusing on strawberry, blackberry, rose, and pear will later be sought to begin from 1 September 2015, to be based at USDA-Corvallis. All positions are funded through to 31 August 2019 - i.e., at least four years. Activities: All postdocs will conduct genetic research in QTL discovery, DNA test development both locus-specific and genome-wide, and applied marker-assisted breeding (MAB). These research associates will be the primary liaisons helping U.S. Rosaceae crop breeders to convert new DNA information and other project advances into breeding impact, using cutting-edge technologies, software, and knowledge. Two six-month internships with project partners outside the U.S. (e.g., in Europe, New Zealand, & Australia) are expected for each postdoc during the project's duration. Qualifications: Active research communication is expected in the form of scientific publications, extension articles, participation in conferences and project meetings, and networking across breeding programs and allied science programs both U.S-wide and internationally. Applicants must have a Ph.D. in Plant Breeding, Horticultural Genetics, or a closely related field. The successful candidate will be a highly motivated team player with excellent communication skills and extensive experience in statistical genetics and linkage analysis. Preference will be given to candidates with evidence of successful management of large datasets, substantial research productivity, a strong publication record, experience with perennial, clonally propagated crop genetics, and a commitment to practical application. Familiarity with Rosaceae crop breeding germplasm and Pedigree-Based Analysis software are also advantageous. Applying: If you are interested in the Prunus Postdoc or the Apple & Cherry Postdoc position, please email a cover letter highlighting your qualifications, your current CV, copies of graduate degree transcripts, and contact information (phone number and email address) of three referees to either: Prunus: Dr. Ksenija Gasic at kgasic(a)clemson.edu or Apple & Cherry: Dr. Cameron Peace at cpeace(a)wsu.edu Please direct questions on either position to the same email addresses. Consideration of applications will begin immediately and will continue until the positions are filled.

10 years, 4 months

2015 RosEXEC NOMINATIONS!

by Volk, Gayle

We are seeking US and international scientist nominations for the 2015-2017 term of RosEXEC members. The RosEXEC mission is as follows: · Serve as a communication and coordination focal point for the US Rosaceae genomics, genetics and breeding community. · Define research priorities based on input from the industry and research community. · Facilitate scientific interaction and foster dynamic research teams. · Promote research priorities. · Coordinate educational efforts from the research community to the industry and the public. · Serve as an official steering committee for the Genome Database for Rosaceae The committee seeks to have a diverse representation of scientists from industry, university, and government as well as pome, stone, and rosoid crop groups. Self-nominations are welcome, as are nominations of colleagues in the Rosaceae community. The committee meets annually at the Plant and Animal Genome Conference, and several conference calls are held throughout the year. The current membership of RosEXEC can be viewed at: http://www.rosaceae.org/rosexec_2014 And the RosEXEC page is: http://www.rosaceae.org/community/us_rosexec Five members (Chris Dardick, David Byrne, Thomas Chao, Bob Curtis, and Sook Jung) will be rotating off the committee in January 2015, so five US slots will be filled. International representatives Dan Sargent and Felicidad Fernandez are rotating off the committee, so two international slots will be filled. Scientists rotating off the RosEXEC committee are not eligible for re-nomination for one year. To submit a nomination, please submit 1) a short biography 2) picture 3) e-mail address 4) mailing address to RosEXEC Vice-Chair Gayle Volk (Gayle.Volk(a)ars.usda.gov<mailto:Gayle.Volk@ars.usda.gov>) by November 21, 2014. Elections will be held in December 2014 and new members will begin their assignments at the RosExec meeting to be held at the Plant and Animal Genome Meeting (PAG) in January, 2015. If you have questions, please do not hesitate to contact me. Thank you for your participation. Gayle Volk National Center for Genetic Resources Preservation USDA-ARS 1111 S. Mason Street Fort Collins, CO 80521 970-495-3205 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

10 years, 4 months

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