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July 16, 2014

03:03
The National Center for Ecological Analysis and Synthesis (NCEAS) is co-sponsoring Open Science Codefest 2014, which aims to bring together researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate on coding projects of mutual interest. This conference may be of interest to the EvolDir network. Cheers, Morgan Visalli Are you a researcher with a coding project that needs some help? Are you developing software for the earth sciences and would like some feedback and collaboration from a diverse group of scientists? Open Science Codefest September 2-4, 2014 Santa Barbara, CA Open Science Codefest will gather researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate on coding projects of mutual interest. Design. Code. Discuss. Learn more on the Codefest website: http://bit.ly/W9D3gl Inspired by hack-a-thons and organized in the participant-driven, unconference style, the Open Science Codefest is for anyone with an interesting problem, solution, or idea that intersects environmental science and computer programming. This is the conference where you will actually get stuff done — whether that’s coding up a new R module, developing an ontology, working on a data repository, creating data visualizations, dreaming up an interactive eco-game, discussing an idea, or any other concrete collaborative goal that interests a group of people. Open Science Codefest 2014 will be held in *Santa Barbara on September 2-4, 2014* at the Fess Parker Santa Barbara Hotel. Registration is *free*. Register at http://bit.ly/W9D3wC. Suggest a session topic or review proposed sessions in the Open Science Codefest Github project . To suggest a session, create a “New Issue” and apply the “proposed session” label. Alternatively, email the Codefest team at codefest@nceas.ucsb.edu. Forward this invite and spread the word about Open Science Codefest 2014. People from a wide variety of disciplines, geographic regions, and skill levels are encouraged to attend! Follow us on Twitter #OSCodefest Contact Open Science Codefest at codefest@nceas.ucsb.edu Morgan Visalli via Gmail
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—_000_BD21BECB2AF1994DA91AA9D93CD88DF49E1D49ACShempintraecued_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable East Carolina University ASSISTANT PROFESSOR OF CONSERVATION BIOLOGY Position Number: 934002 The Department of Biology at East Carolina University, Greenville, NC, the third largest campus in the University of North Carolina system, invites applications for a nine-month tenure-track position at the Assistant Professor level with expertise in Conservation Biology, to begin August 17, 2015. We seek a broadly trained individual with a successful, innovative research program involving the development and application of ecological and evolutionary principles to address fundamental questions in conservation biology. In support of ECU’s strategic emphasis in coastal research, we seek applicants whose research programs can be applied to aquatic or terrestrial ecosystems of coastal areas, including offshore, nearshore or adjacent onshore physiographic provinces. The successful candidate will be expected to establish a vigorous, externally funded research program that involves work in a coastal area, teach undergraduate and graduate-level courses in conservation biology and related disciplines, mentor students in the M.S. and Ph.D. programs, be an active member of ECU’s Center for Biodiversity and engage in university, community and professional service. Collaborative opportunities exist in Biology as well as other University departments and centers, including the Institute for Coastal Science and Policy and the Center for Sustainability. Departmental resources include computational facilities, a central environmental lab, next generation sequencing, university-owned natural areas and field vehicles and vessels. East Carolina University is in close proximity to the Croatan National Forest, the coast, and North Carolina’s Research Triangle. Please visit our website at http://bit.ly/1t2kZzB for more information on the depar tment. Appointment at the Associate Professor or Professor level may be considered for a candidate with a well-established record of teaching and research. Qualifications: A Ph.D. in Biology or Biology-related fields with training in conservation biology and at least one year of postdoctoral research experience are required. Qualifying degrees must be received from appropriately accredited institutions. Applicants must complete a candidate profile and submit a cover letter, curriculum vitae, a list of three references (including contact information), and statements of research interests and teaching experience/philosophy online at www.jobs.ecu.edu using the position number 934002 -Assistant Professor of Conservation Biology. We will ask short-listed candidates to have three reference letters sent to the Search Committee Chair via email within 7 days of short-list notification. Official transcript and original hard-copy reference letters are required upon employment. Inquiries may be directed to Dr. David Chalcraft (chalcraftd@ecu.edu), Search Committee Chair. Review of applications will begin on September 2, 2014 and continue until the position is filled. East Carolina University is an Equal Opportunity/Affirmative Action Employer. Visit this job posting at http://bit.ly/1t2kYvh. —_000_BD21BECB2AF1994DA91AA9D93CD88DF49E1D49ACShempintraecued_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable
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*Description of Work:* The Division of Public Health Informatics and Analytics (DPHIA) within the Center for Food Safety and Applied Nutrition (CFSAN) at the US Food and Drug Administration seeks a creative and enthusiastic research fellow to assist in the analysis of next-generation DNA sequencing data. The primary focus of the research fellow will be the analysis of whole genome sequence data from food-borne pathogens. The fellow is expected to be proficient with 1) algorithms and programs to perform whole genome assembly, 2) software for detection of variant nucleotide positions with respect to a reference genome, and 3) the construction and interpretation of phylogenies based on next-generation sequence data. The fellow would also serve as a genome database specialist to help curate genomic sequence data generated both at CFSAN and externally. As part of the curation work, the fellow will contribute to improving the entire process of formatting, loading, and vetting both genomic data and associated meta-data from food borne pathogens. The production of reference data sets for the evaluation of analysis methodologies will be an important aspect of this work, as will be the use of statistical and bioinformatics analysis tools to explore analysis methodologies. The curation work and associated analysis methodology work is expected to play an important role in providing faster and better traceback information for bacterial isolates during outbreak investigations. The fellow is also encouraged to develop an independent research project that furthers the mission of the FDA and the analytics group within CFSAN. Examples of such a project include the development of novel genomic analyses, evaluating alternative strategies for identifying variant sites, and the visualization and extraction of information contained in large whole genome sequence datasets and associated phylogenies. CFSAN and the Biostatics Branch is a vibrant community of specialists from a number of different disciplines (e.g., epidemiologists, chemists, microbiologists, biostatisticians, and bioinformaticians). Applicants should email Dr. James Pettengill at james.pettengill(at)fda.hhs.gov with questions about the position. *Desired Skills:* Educational background (PhD or MS) in microbiology, genetics/genomics, phylogenetics, bioinformatics, statistics and/or computer science. Familiarity with next-generation sequence data (e.g., fastq format). Proficient at running de novo assembly algorithms (e.g., Velvet, SPADES, SOAPdenovo) and reference based mapping programs (e.g., Bowtie2, BWA). Proficient in a computer language such as R, Python, or Perl. Skilled in the management, organization, and querying of large files/databases. *Application Materials:* Cover letter describing previous and future research interests CV/Resume Contact information for three references To be mailed as a single pdf to james.pettengill(at)fda.hhs.gov *Duration:* 2 years *Location:* FDA, Center for Food Safety and Applied Nutrition 5100 Paint Branch Parkway College Park, MD 20740-3835 USA *Salary/Benefits:* The position is offered through the Oak Ridge Institute for Science and Education. The position does not include funds to offset moving. The position does not include benefits. ORISE offers a plan or the fellow can have her/his own but proof of insurance is required before beginning the position. However, funds are available for travel to conferences/workshops. Stipend: $6,091.67/month x 12 months $73,100.00 per year fixtgear@gmail.com via Gmail

02:35
University of North Carolina at Charlottes Plant Population Genomics and Biotic Stress A postdoctoral position is available in the laboratory of Bao-Hua Songs lab at University of North Carolina at Charlotte to study wild soybean biotic stress. The primary research involves identifying genes that are responsible for wild soybean biotic stress. Specific tasks include stress resistance/tolerance assays, genomic analysis of diverse ecotypes, transcriptome analysis and candidate gene selection. The candidate must be passionate and hard working, able to create an environment that fosters diversity, and ability to work in a multi-cultural setting. The position is full-time for two years subject to satisfactory performance in the first year. The position is available immediately and will remain open until filled. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to bsong5@uncc.edu. Please also arrange to have two letters of recommendation sent directly by the letter writer to the above email address as well. The University of North Carolina at Charlotte is an EOE/AA employer and an ADVANCE Institution that strives to create an academic climate in which the dignity of all individuals is respected and maintained. Therefore, we celebrate diversity that includes, but is not limited to ability/disability, age, culture, ethnicity, gender, language, race, religion, sexual orientation, and socio-economic status. “Song, Bao-Hua” via Gmail
02:35
Faculty Position in Microbiology Texas A&M University The Department of Biology at Texas A&M University (TAMU) invites applications for a tenure-track Assistant Professor position in microbiology. We will consider candidates pursuing innovative research in all disciplines of microbiology, including, but not limited to, bacteriology, mycology, virology, immunology, host-pathogen/parasite interactions, developmental-, environmental-, evolutionary- or behavioral microbiology, genetic mechanisms and genomics, synthetic biology and biotechnology. The criteria for selection will be uniqueness, creativity and excellence in research and scholarship. We strongly encourage applications from candidates who will increase the exposure of our students to a diverse culture. The successful candidate will be expected to develop an externally funded research program and to teach undergraduate and graduate courses. We offer an interactive and collegial research environment, a modern infrastructure, and a competitive startup package. More information about our department can be found at www.bio.tamu.edu. For full consideration, applicants should email a letter of intent, curriculum vitae, statement of research and teaching interests, and three letters of recommendation by October 1, 2014 to microsearch@bio.tamu.edu If you have questions about this search, please direct e-mails to Dr. L. Rene Garcia, Chair of the Search Committee, at microsearch@bio.tamu.edu Texas A & M University is an Equal Opportunity/Affirmative Action employer that is dedicated to the goal of building a culturally diverse and pluralistic faculty and staff who are committed to teaching and working in a multicultural environment. We strongly encourage applications from women, minorities, veterans, and individuals with disabilities. In addition, the University is responsive to the needs of dual career couples. Gil Rosenthal via Gmail
02:35

Terrestrial Invasive Plant Species II: Pre-Conference Registration Deadline July 20 ============================================================= The Terrestrial Invasive Plant Species II meeting will be held at the University of Toronto Mississauga on 6-8 August 2014, with major support from the Invasive Species Centre (Ontario) and the University of Toronto. A draft schedule is now available on-line; please visit our website (http://bit.ly/1kz0M1Y) for details. The pre-conference registration deadline is July 20. Please see http://bit.ly/1kz0M1Y for on-line registration information. Program and Invited Speakers: A draft schedule is now available on the website (http://bit.ly/1m5bQSs), including many exciting presentations. Our keynote speakers are Spencer Barrett from the University of Toronto, and Kirsten Prior from the University of Florida. We also are organizing a special session devoted to biocontrol of invasive plants; confirmed speakers to date include Bernd Blossey (Cornell University), Rob Bourchier (Agriculture and AgriFood Canada), Richard Casagrande (University of Rhode Island), John Gaskin (USDA-ARS), Hariet Hinz (CABI Switzerland), Lindsey Milbrath (USDA-ARS) and Richard Shaw (CABI UK). We still have space for late-breaking posters and 2-minute talks. Field Trips: We are offering a pre-conference field trip on August 6, at a modest additional cost: the Carden Plain Alvar (http://bit.ly/1kz0Mic). If you would like to participate, please submit your payment with your conference registration; see our registration page for details. If you already have registered, or wish to add a field trip at a later date, please contact Antonia Maughn (antonia.maughn@utoronto.ca) for instructions. There also will be a lunchtime walk from the conference venue into the Credit River valley on August 8. See you in August! TIPS II Organizing Committee: Peter Kotanen, University of Toronto Mississauga (lead organizer) Sandy Smith, University of Toronto (St. George) Roberta Fulthorpe, University of Toronto Scarborough Ben Gilbert, University of Toronto (St. George) Marc Cadotte, University of Toronto Scarborough Pedro Antunes, Algoma University Colin Cassin, University of Toronto Mississauga (student member) via Gmail

01:40
Graduate Students (MSc and PhD) and postdoctoral position in Fisheries Genomics and Evolutionary Ecology - Halifax, NS, Canada Positions: Graduate student positions and a postdoctoral fellow position are available at Dalhousie University and Fisheries and Oceans Canada (Halifax, NS) working on the ecology, evolution, and conservation genomics of fishes and invertebrates. Species of primary interest are Atlantic salmon and Atlantic cod, but current projects include other anadromous fish and species of marine invertebrates as well. The labs research is broadly concerned with resolving adaptation and how it may influence both the geographic and genomic scale of divergence among allopatric and sympatric populations. (seefor more details). The specific projects willinvolve using next generation sequencing approaches to resolve signatures of adaptation across genomes and populations and the use of molecular tools in mixture analysis and individual assignment. Themes include adaptation to climate, invasive species, and the impact of escaped farmed salmon on natural populations. These multidisciplinary projects represent training in state of the art genomic tools and techniques while experiencing both university and government laboratory environments. Graduate students will have access to technical support both in the field and laboratory through DFO staff and expertise and be part of the Marine Gene Probe Laboratory (Dal). Qualifications: Honours degree or equivalent in biology (for a MSc position) and a MSc or equivalent (for a PhD position), and strong interests in evolutionary ecology, molecular ecology, and conservation biology. Application: Please email (ibradbur@me.com) (1) a letter describing your interests in this position and your previous research experience, (2) a recent CV. Ian Bradbury Ian Bradbury via Gmail
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Please note the following DEADLINES: Registration and abstract submission:4 August, 2014 Accommodation:availability cannot be guaranteed after 28 July, 2014 The United Kingdom is home to exceptional evolutionarybiologists. However, compared to the number of evolutionaryzoologists, the number of their botanical counterparts is few. In many cases, U.K. plant evolutionary biologists are in small numbers at any one institution, and such isolation hinders progress. The Royal Botanic Gardens, Edinburgh will host a conference on 8, 9 September, 2014 to help address this situation. The conference will showcase evolutionary research on plants by UK researchers to foster new collaborations. The conference will also hold a workshop, where discussion will identify challenges faced and suggest strategies to overcome them. We see this as a first step towards developing a longer-terms strategy for strengthening the UK community of plant evolutionary biologists. The conference will include a poster and networking session, open speaking slots (both standard and “lightning” talks), as well as an exciting lineup of invited speakers. For more information and to register, please visit the website at: http://bit.ly/1h7xbNN Invited speakers: Mating system: Dr. Mario Vallejo-Marin Speciation: Dr. Richard Buggs Ecological Speciation: Dr. Patrik Nosil Evo-Devo: Dr. Beverley Glover Phylogeny: Dr. Toby Pennington Polyploidy: Dr. Barbara Mable Biogeography: Dr. Bill Baker Population Genetics (Molecular ecology): Dr. Simon Hiscock Population Genetics (Genomics): Dr. Rob Ness International Speaker: Dr. Spencer Barrett (University of Toronto) via Gmail

00:06

Description of Work: The Division of Public Health Informatics and Analytics (DPHIA) within the Center for Food Safety and Applied Nutrition (CFSAN) at the US Food and Drug Administration seeks a creative and enthusiastic research fellow to assist in the analysis of next-generation DNA sequencing data. The primary research focus of the fellow will be on the analysis of metagenomic datasets as a means to (1) better quantify the microbial diversity associated with foodborne pathogens and (2) evaluate the utility of metagenomics as a culture-independent method for pathogen detection (e.g., of Salmonella Montevideo, Salmonella Enterititidis, Salmonella Heidelberg, and Listeria monocytogenes). The fellow will also support microbiologists in the analysis of data from sequencing projects of bacterial pathogens (e.g., whole genome sequencing, RNA-Seq). The projects using whole genome sequence data from bacterial pathogens include samples collected from foodborne outbreaks, and the research will include the construction of phylogenies from whole genome sequence data, gene specific analyses, and identification of mobile elements. The fellow is also encouraged to develop an independent research project that furthers the mission of the FDA and the analytics group within CFSAN. Examples of such a project include the development of novel metagenomic analyses, evaluating alternative strategies for assigning taxonomy to reads, and the visualization and extraction of information contained in large metagenomic datasets. CFSAN and the Biostatics Branch is a vibrant community of specialists from a number of different disciplines (e.g., epidemiologists, chemists, microbiologists, biostatisticians, and bioinformaticians). Applicants should email Dr. James Pettengill at james.pettengill(at)fda.hhs.gov with questions about the position. Desired Skills: • Educational background (PhD or MS) in microbiology, genetics/genomics, phylogenetics, bioinformatics, statistics and/or computer science • Familiarity with next-generation sequence data (e.g., fastq format) • Proficient at running programs for the analysis of metagenomic data (e.g., mother, QIIME) • Proficient at running de novo assembly algorithms (e.g., Velvet, SPADES, SOAPdenovo) and reference based mapping programs (e.g., Bowtie2, BWA) • Proficient in a computer language such as R, Python, or Perl. • Skilled in the management, organization, and querying of large files/databases Application Materials: • Cover letter describing previous and future research interests • CV/Resume • Contact information for three references • To be mailed as a single pdf to james.pettengill(at)fda.hhs.gov Duration: 2 years Location: FDA, Center for Food Safety and Applied Nutrition 5100 Paint Branch Parkway College Park, MD 20740-3835 USA Salary/Benefits: The position is offered through the Oak Ridge Institute for Science and Education. The position does not include funds to offset moving. The position does not include benefits. ORISE offers a plan or the fellow can have her/his own but proof of insurance is required before beginning the position. However, funds are available for travel to conferences/workshops. Stipend: $6,091.67/month x 12 months $73,100.00 per year fixtgear@gmail.com via Gmail

00:06

Postdoctoral position in NGS population genomics University of Vigo, Spain DESCRIPTION: A postdoctoral position is available to work on an ongoing research project on the evolution of marine snails in the Cape Verde archipelago, in David Posada’s lab at the University of Vigo, Spain (http://bit.ly/1rfGm2C). The appointment will start as soon as October 2014 and will end no sooner than December 2015. Gross annual salary including benefits will be 25,000-30,000 Euros, commensurate with experience. Starting date is negotiable. MINIMUM REQUIREMENTS: Candidates should have a doctoral degree in Science, advanced programming skills and demonstrable experience with NGS data analysis. DESIRABLE REQUIREMENTS: Background in population and/or evolutionary genomics, and statistical skills. APPLICATION: Please send a single pdf including a letter of interest, C.V., and the names and contact details of two referees to xb5lab@gmail.com, indicating postdoc conus application in the subject of the email. Questions and requests for additional information should be directed to the same email address. Review of applications will begin immediately, and continue until the position is filled. David Posada Facultad de Biologa Campus Universitario Universidad de Vigo 36310 Vigo Spain Phone: +34 986 812038 Cell: +34 647 343300 Fax: +34 986 812556 Email: dposada@uvigo.es Web: http://bit.ly/1rfGm2C dposada@uvigo.es via Gmail

00:06

The Department of Biology at the University of Virginia invites applications for a Bioinformatics Research Analyst position to provide bioinformatics support for population and quantitative genomics projects in the Blackman laboratory. The research of the Blackman laboratory focuses on the genetic basis of domestication and adaptation, the ecology and evolution of plant development, and mechanisms of gene-environment interaction. Using sunflower and monkeyflower as study systems, current work is focused on reconstructing the genetic history of domestication through paleogenomics as well as the genetic changes and ecological pressures contributing to natural variation in developmental responses to daily and seasonal environmental cues. The analyst will work closely with the PI, collaborators, and lab personnel to design and/or implement algorithms and computational pipelines to process high-throughput sequencing datasets for population and quantitative genetics analysis or plant genome assembly. The position may also involve developing and/or running tools for phenotype scoring by automated image analysis. The analyst will also be responsible for building and maintaining databases for management of biological samples, sequencing, and phenotype data. The position also involves writing reports, presenting research results at lab meetings and conferences, data management and dissemination, administration and maintenance of computational infrastructure, mentoring graduate and undergraduate students, and related tasks in support of research projects. The position requires a Bachelor’s degree in Evolutionary Biology, Genetics, Bioinformatics, Computer Science or related field. At least 8 years related lab experience, or the equivalent combination of advanced education and experience, with a minimum of two of those years of experience with bioinformatics programming tools for analysis of next generation sequencing data is required. The incumbent will demonstrate the ability to integrate across biological disciplines, identify and troubleshoot promising new methodologies independently, and be able to coordinate with multiple research staff concurrently to pursue diverse questions or types of analysis. Demonstrated expertise in programming and scripting (such as Unix and Perl and/or Python), a good understanding of high performance computing, and knowledge of probability theory are essential. Proficiency in C/C++, Javascript, R, Matlab, and/or SQL is preferred. Experience with statistical analysis, morphometrics, cluster computing, IT support, and development of web applications is highly desirable. Preferred start date is August 2014. This position is estimated to last for a year with the option of renewal contingent on the availability of funding and satisfactory performance. To apply, please submit a staff application through Jobs@UVA (http://bit.ly/1ccxWRu) and electronically attach: curriculum vitae, a cover letter that summarizes research interests and professional goals, and contact information for three (3) references; search on posting number 0614596. Review of applications will begin July 24, 2014; however, the position will remain open until filled. Questions regarding this position should be directed to: Dr. Benjamin Blackman 812-369-5045 bkb2f@virginia.edu http://bit.ly/1aYcQ6g Questions regarding the Staff application process or Jobs@UVA should be directed to: Rich Haverstrom rkh6j@virginia.edu The University of Virginia is an Equal Opportunity/Affirmative Action Employer. Women, Minorities, Veterans and Persons with Disabilities are encouraged to apply. bkb2f@virginia.edu via Gmail

July 15, 2014

02:13

Annual Cornell Lab of Ornithology Postdoctoral Competition The Cornell Lab of Ornithology encourages applications to our competitive postdoctoral program (http://bit.ly/U6qXCS) that supports innovative, independent research by early career scholars of exceptional promise. Two or more named positions are available annually, with applications due on September 8. These postdoctoral opportunities support individuals pursuing cutting-edge scholarship, while fostering intellectual interaction with two or more of the Lab’s programs. Any area of inquiry related to the Lab’s mission “to interpret and conserve the earth’s biological diversity through research, education, and citizen science focused on birds” may be appropriate. Potential applicants are encouraged to learn more about our activities and opportunities, including our formal programs in Bioacoustics, Bird Population Studies (avian ecology), Citizen Science, Conservation Science, Communication, Education, Evolutionary Biology, Information Science, Macaulay Library (animal behavior), Multimedia Productions, and Public Engagement in Science. Research or activities involving several of these areas are particularly appropriate, and therefore each postdoctoral scholar may be co-mentored by two senior Cornell scholars. Potential applicants are encouraged to contact relevant faculty and staff at the Lab to brainstorm about areas of mutual interest and synergistic projects. We are especially interested in supporting the independent research of individuals who can bring new ideas and approaches to the Lab, while simultaneously leveraging our existing tools, data, and expertise in science, education, and communication. Each Postdoctoral Scholar will hold a two-year appointment at the Lab. Located at the Imogene Powers Johnson Center for Birds and Biodiversity in the 220-acre Sapsucker Woods sanctuary, the Cornell Lab of Ornithology is a vibrant unit within Cornell’s University’s College of Agriculture & Life Sciences. More than 200 faculty and staff work at the Lab within our 10 mission-driven programs. Our management and staff are committed to the highest standards of ethics and excellence in all areas of our work, and our Board leadership includes faculty from Cornell and other universities, successful entrepreneurs and managers from the business and non-profit sectors, and conservation-minded citizens from the United States and beyond. These appointments provide a competitive salary, standard Cornell health and other benefits, and funds to help support the Scholar’s research and professional travel needs. Start dates are flexible between February and September of the year following the application. The application package consists of a cover letter, CV, two page research proposal, pdfs of up to three representative publications, and names and contact information for three references. Postdoctoral Scholars must have received their PhD before beginning their postdoctoral appointment at Cornell. Application materials should be sent as a single pdf file to the attention of Sue Taggart (SET2@cornell.edu). Applications for the two positions available in 2014 will be accepted until September 8. The selection committee is chaired by Dr. Irby Lovette (IJL2@cornell.edu), Professor and Associate Director for Academic Affairs at the Lab. Cornell University is an innovative Ivy League university and a great place to work. Our inclusive community of scholars, students and staff impart an uncommon sense of larger purpose and contribute creative ideas to further the university’s mission of teaching, discovery and engagement. Located in Ithaca, NY, Cornell’s far-flung global presence includes the medical college’s campuses on the Upper East Side of Manhattan and in Doha, Qatar, as well as the new Cornell Tech campus to be built on Roosevelt Island in the heart of New York City. Diversity and inclusion have been and continue to be a part of our heritage. Cornell University is a recognized EEO/AA employer and educator. via Gmail

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—_000_3FDD755888F55C40A52B84684E43FA3F338D1DE8ORANGECOUGARSIN_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable The unPAK project (undergraduates Phenotyping Arabidopsis Knockouts - http://bit.ly/W63Xp6) seeks a project manager to coordinate activities across 10 participating institutions. The unPAK project is collecting phenotypic information associated with Arabidopsis thaliana T-DNA insertion mutants and includes extensive involvement of undergraduate researchers. This project addresses broad questions in ecological genomics and is developing a phenotypic resource for the Arabidopsis and evolutionary genomic communities. The project manager will be responsible for communication between institutions, seed stock production, seed distribution, data curation, and management of participating undergraduates. The position will be located at the College of Charleston, and will involve travel to other participating institutions. We seek a candidate who is organized, energetic, and has strong communication skills. A successful candidate will have professional, diplomatic and leadership qualities. Ideally the candidate will bring experience working in a field or laboratory setting with plants. The position has ample opportunities for developing management skills and for publishing research. Interested individuals with undergraduate, master’s or doctoral degrees are welcome to apply. Specific responsibilities - distribution of protocols to new partner schools - travel to institutions to train participants in phenotyping and data management - grow plants with student help to bulk seeds for distribution - maintain seed-stock records - coordinate seed stocks to be shipped. - maintain of tissue and genotype records - assist PI and CoPIs with maintaining CURE (course-based undergraduate research experience) plants - format datasheets for downstream bioinformatics analyses - upkeep experiment log - maintain an already existing cyber-presence including the project website and the - project google wiki site - maintain contact information for all participants - initial training of students in lab procedures - contribute to newsletters, organize joint meetings (both virtual and in person) - podcast and vodcast development For more information about the position, please contact us at: Matt Rutter (rutterm@cofc.edu) Courtney Murren (murrenc@cofc.edu) Allan Strand (stranda@cofc.edu) Department of Biology College of Charleston Charleston SC USA —_000_3FDD755888F55C40A52B84684E43FA3F338D1DE8ORANGECOUGARSIN_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable

01:24

*Postdoctoral Position in Mathematical Modeling of Microbial Evolution* A postdoctoral researcher position is available in the lab of Olga Zhaxybayeva at the Biological Sciences Department of Dartmouth College in Hanover, NH to study evolution of gene transfer agents via mathematical modeling. This is a 5-year project funded through the Simons Foundation program in Mathematical Modeling of Living Systems. Qualified applicant must have a Ph.D. in bioinformatics, applied mathematics, computer science, statistics, biology, microbiology, or a related field with strong interest in molecular evolution, prior research experience in computational sciences and some programming skills. The successful candidate will join a vibrant research and educational environment of Dartmouth College. Zhaxybayevas lab uses computational approaches to study how microbes evolve and adapt to their environments. Ongoing projects fall into the following broad areas: 1) Studying impact of horizontal gene transfer on microbial populations; 2) Characterization of microbial communities; and 3) Deciphering genomic signatures of microbial adaptations. More information about Zhaxybayevas lab is available at http://bit.ly/17izh1S. Review of applications will begin immediately and continue until the position is filled. Start date is negotiable. Interested applicants should send a single PDF file containing CV, one-page statement of research interests and contact information of three referees to Olga Zhaxybayeva at ECGLabJobs@gmail.com. Dartmouth offers competitive salary and benefits along with the opportunity to live in a picturesque rural region that offers year-round recreational activities and is located near cities of Boston, Montreal, and New York. Dartmouth College is an equal opportunity/affirmative action employer that has a strong commitment to diversity. via Gmail

01:23
Please consider the following job opening for EvolDir: Utrecht University$B!G(Bs Ecology & Biodiversity Group investigates the mechanisms that regulate biodiversity and allow for the maintenance of ecosystem functioning in our changing world. We pay special attention to above- and belowground species interactions, spatial processes from local to landscape scales and community assembly following dispersal and colonization. We seek to obtain process-based, mechanistic understanding of species interactions and functional responses in order to predict the future impacts of climate and land-use changes on biodiversity and ecosystem functions such as carbon sequestration and biogeochemical cycling. The integrated research mission of the Ecology and Biodiversity group is $B!H(BUnderstanding and predicting biodiversity and ecosystem functioning in a changing world.$B!I(B The Ecology & Biodiversity research group looks to advance its integrated research program (http://bit.ly/1mF8Wax) with the appointment of an enthusiastic and dedicated: Assistant/Associate Professor Plant Ecology For a more detailed job description and online application forms, please visit www.uu.nl/vacancies Application deadline: July 27th, 2014 Kind regards, and thank you, Merel Soons Dr. M.B. Soons Associate Professor in Ecology and Biodiversity Institute of Environmental Biology Utrecht University Padualaan 8 3584 CH Utrecht m.b.soons@uu.nl +31-(0)30-253 6837 www.uu.nl/science/eb http://bit.ly/1kYeW9Pwww.uu.nl/vacancies Application deadline: July 27th, 2014 Kind regards, and thank you, Merel Soons Dr. M.B. Soons Associate Professor in Ecology and Biodiversity Institute of Environmental Biology Utrecht University Padualaan 8 3584 CH Utrecht m.b.soons@uu.nl +31-(0)30-253 6837 www.uu.nl/science/eb http://bit.ly/1kYeW9P “Soons, M.B. (Merel)” via Gmail
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ECCB’14 - Tutorial T05 “Protein Evolution Analysis: on the Use of Phylogenetic Trees” Tutorial of ECCB 2014, Strasbourg, France. September 7th, 2014 Website: http://bit.ly/1mF8VTX Important dates: - ECCB/Tutorial Early registration: May 12 - August 1st, 2014 - ECCB/Tutorial Late registration: August 2 - August 29, 2014 - Tutorial date: Sunday, September 7th, 2014. Motivation Homologous proteins, that share a common ancestor, can be classified into families. These homologs can be orthologs, that were separated by a speciation event, or paralogs, that were separated by a duplication event. Within a protein family, all members are related by a phylogenetic tree, which consists of a root (the last common ancestor of the protein family), nodes (which are speciation/duplication events), branches (whose lengths correspond to the number of substitutions) and tips (which correspond to modern sequences). The tree is helpful for inferring the evolutionary history of the protein family. For example, we can reconstruct the ancestral sequences at each node of the tree. These ancestral sequences can be used for homology modelling, to reveal the ancestral 3D structures, or synthesised in vitro. Or we can compare trees to reveal similar evolutionary history between protein families (co-evolution). Manipulating tree topologies are complex operations that require tools to perform operations such as reading, pruning, collapsing, rerooting. These operations can be done with programs with graphical user interfaces (GUI). However, in the area of large-scale data, in which hundreds or thousands of trees may be manipulated, it is impractical to use such programs. To this end, new software/libraries have been developed to deal with such large data sets in an automated manner. Goal This tutorial will present recent concepts regarding the evolution and adaptation of protein sequences. It will be divided into three sections, in which we will present methods relating to the use of phylogenetic trees to infer protein function. These sections will be 1) using scripts to manipulate trees, 2) using ancestral sequence reconstruction to infer history of a protein family and 3) the detection of coevolution between protein families. Each section will have an introduction explaining the concepts underlying any analysis methods, and a discussion of the power and limitations of different methods and tools used to explore these concepts and which participants will learn how to use during the practical for that section. Outline The first part will focus on tools to detect adaptation in protein sequences. It will start with a brief introduction on multiple alignment and phylogenetic trees followed by a more detailed presentation of tools available to estimate selective pressures and detect adaptation in protein sequences with CodeML / PAML. The second part will focus on the reconstruction of ancestral sequences and ancestral structures by homology modelling. The third part will focus on the identification of co-evolution between protein families. The organiser will provide protein datasets, or participants can bring their own sequences. Then, they will be able to use the different programs/libraries in a practical way. This tutorial will be in three parts (more info on the website): 1) Performing phylogenetic analyses with Biopython 2) Ancestral sequence reconstruction and homology modelling 3) Studying molecular co-evolution Level: Introductory Schedule (Sunday, September 7th): Morning session: Performing phylogenetic analyses with Biopython. 9:00 Talk (45min): Performing phylogenetic analyses with Biopython (B. Invergo, EBI) 9:45 Practical (30min): Performing phylogenetic analyses with Biopython (B. Invergo, EBI) 10:15 Coffee break 10:45 Practical (1h30): Performing phylogenetic analyses with Biopython (B. Invergo, EBI) 12:15 Lunch Afternoon session: ancestral sequence reconstuction and molecular co-evolution. 13:15 Talk (30min): Ancestral sequence reconstruction (R. Studer, EBI) 13:45 Practical (1h30): Ancestral sequence reconstruction (R. Studer, EBI) 15h:15: Coffee break 15h45: Talk (30 min): Studying molecular co-evolution (D. Ochoa, EBI) 16h15: Practical (45min): Studying molecular co-evolution (D. Ochoa, EBI) 17:00 End Intended audience: - Evolutionary biologists, biochemists, computational biologists, structural biologists. Possible prerequisites: - Unix command line. - We strongly encourage participants to learn the basics of the Python programming language. Organisers: Brandon Invergo - EMBL-EBI, Cambridge, UK (invergo [at] ebi.ac.uk) David Ochao - EMBL-EBI, Cambridge, UK (ochoa [at] ebi.ac.uk) Romain Studer - EMBL-EBI, Cambridge, UK (rstuder [at] ebi.ac.uk) via Gmail

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—_000_1D503F5375C52140A2C24AB93B2DD09BA1C50B77zivexdag2wwude_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable Dear all, please find below an announcement for 2 PhD positions. 2 PhD positions for international (non-German) students within the interdisciplinary “Muenster Graduate School of Evolution”: PhD projects in Biology, Medicine, or Philosophy The “Muenster Graduate School of Evolution” (MGSE) offers 2 PhD positions funded by DAAD- stipends for international (non-German) students within the stimulating environment of the University of Muenster, Germany. As an interdisciplinary graduate school, the MGSE uses the unifying concept of evolution to bridge the faculties of biology, medicine, geosciences, mathematics, and philosophy. PhD students work on their diverse disciplinary projects in one of the involved institutes and benefit from interdisciplinary curricular activities as well as a structured supervision and support throughout their PhD. The MGSE is based in the stimulating city of Muenster in a historical building opposite the Muenster castle and offers a family friendly and international atmosphere. Location: Muenster, Germany Working Language: English Start of the PhD: 2015 Duration: 3 years (4 years for students from developing and emerging countries) You can apply for one or several of the following six projects. Each project involves high-quality research and state-of-the-art techniques and is supervised by excellent researchers. 1) The genetic origin of novel protein coding genes in populations and their evolutionary constraints Prof. Erich Bornberg-Bauer (Research Group Evolutionary Bioinformatics), Prof. Matthias Loewe (Institute of Mathematical Statistics), Prof. Juergen Gadau (School of Life Sciences, Arizona State University) 2) Immunogenic males: where sex and immunity meet Dr. Claudia Fricke (Research Group Evolution and Sexual Conflict), Dr. Sophie Armitage (Research Group Animal Evolutionary Ecology) 3) The Concept of Disease in Individualized Medicine Prof. Ulrich Krohs (Research Group Philosophy of Science and of Nature) 4) Interactions of animal personality, social environment and immunity Prof. Joachim Kurtz (Research Group Animal Evolutionary Ecology), Dr. Joern Scharsack (Research Group Animal Evolutionary Ecology), Prof. Norbert Sachser (Department of Behavioural Biology) 5) Functional consequences of evolutionary conservation vs. variability in the influenza virus genome Prof. Stephan Ludwig (Institute of Molecular Virology) 6) Reconstruction of the ancient transcriptome of species Dr. Juergen Schmitz (Institute of Experimental Pathology), Dr. Francesco Catania (Research Group Evolutionary Cell Biology) More information on the projects can be found here: http://bit.ly/1zowANF Highly qualified and motivated candidates all over the world are invited to submit their application. Requirements: - MSc (or an equivalent degree) relevant for the respective project (biology, medicine, mathematics, or philosophy). At the time of application, generally no more than six years should have passed since you gained the last degree. - Excellent academic record, interest to work interdisciplinary, and motivation to actively participate in the structured PhD program of the MGSE. - Fluency in spoken and written English (or willingness to take part in a respective course). - Only international (non-German) applicants can be accepted. At the time of application you should not be living in Germany for more than 15 months. - Applications from women are particularly encouraged. Handicapped candidates with equivalent qualifications will be given preference. Application procedure: You can apply for one or several of the listed projects via the DAAD platform by 1.8.2014: http://bit.ly/1woIOS6 indicate which project(s) you are interested in! >From among the applicants, we will shortlist candidates for (Skype) interviews and subsequently nominate 4-8 applicants. From among the nominees, a DAAD committee will select the two scholarship recipients. In case of questions please contact: (Please don’t send your applications here, instead use the DAAD online application (see above)!) Dr. Rebecca Schreiber (MGSE Coordinator) Email: rebeccaschreiber@uni-muenster.de Telephone: +49-(0)251 / 83-21252 Best regards, Rebecca Schreiber via Gmail
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The Molecular Ecology Group at the Institute of Ecology at Innsbruck University is seeking a full-time laboratory technician as permanent employee. Main tasks: - Conduction of experiments in the molecular lab (nucleic acid extraction, PCR, qRT-PCR, electrophoresis, cloning, preparation of libraries, etc.) - Basic data analyses - Ordering of supplies and maintainance of equipment (PCR machines, near-infrared-spectrometer, centrifuges, microscopes, incubators, etc.). Further duties may include help with rearing of lab organisms (e.g. Drosophila), evolution experiments, collection of samples in the field and general support of the working group. The ideal candidate will have an education as biological/chemical/medical laboratory technician or equivalent. Solid knowledge of basic molecular and microbiological techniques, experience in the use of MS Office, web-based data collections (e.g. NCBI) and basic imaging software, and good knowledge of English are essential. Openness for independent learning and the ability to work as part of a multi-disciplinary team are also important features. Knowledge of the German language may be helpful for everyday life in Innsbruck, but is not required. Please note that for legal reasons applications of candidates holding an MSc or higher degree in biology or related fields cannot be considered. The position can be filled from August 2014. The minimum annual gross salary is EUR 26,096 including health insurance and 5 weeks of annual holidays. The salary will be higher if you have worked in a similar position before. Please apply until July 31 at: http://bit.ly/1mF1WKQ The Molecular Ecology Group uses the exciting opportunities offered by molecular biology to study ecology as a snap-shot of evolving biodiversity. Since the group’s founding in 2009, research has been conducted in integrative biodiversity assessment, rapid evolution, symbiotic interactions, and social evolution, in all instances integrating genetic data with those from other sources (e.g., niche ecology, morphology, behaviour, chemistry). Most of our study organisms are terrestrial animals, often from the Alpine region. Detailed information about the Molecular Ecology Group can be found at http://bit.ly/19cQMBY. Innsbruck is situated in the Alps and very close to Switzerland, Germany and Italy; scenery and outdoor recreation are fantastic. More information needed? Please contact Wolfgang Arthofer via Gmail

July 13, 2014

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This is a multi-part message in MIME format… via Gmail

July 12, 2014

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The Center for Macroecology, Evolution and Climate at the University of Copenhagen invites applications for 7 postdoctoral positions and one PhD position in the following fields: Announcement of eight fixed-term Postdoc/PhD positions (2-3 years): 1. Postdoc in Macroecology 2. Postdoc in Marine Macroecology 3. Postdoc in Comparative Phylogeography 4. Postdoc in Macroevolution 5. Postdoc in Community Ecology 6. Postdoc in Theoretical Community Ecology 7. Postdoc in Experimental and Environmental Economics 8. PhD in Bird Movement Full descriptions of individual positions and relevant contacts are available at http://bit.ly/1oSH3vk We also welcome inquiries from prospective applicants for Marie Curie fellowships. The center (http://bit.ly/1mvlEsp) is a long-term funded center of excellence with an integrated terrestrial and marine research program addressing fundamental questions on the origin, maintenance, conservation and future of life and biological diversity on Earth. Researchers at the center currently represent 14 different nationalities and the working language is English. Candidates should have a track-record of publications, relevant analytical and data handling skills, and an ability to collaborate within an international research team. Competitive salaries and benefits are offered. Applications must be submitted via the link in the position descriptions before 18 August. For inquiries about the program, contact Professor Carsten Rahbek, crahbek@snm.ku.dk. kamarske@snm.ku.dk via Gmail