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January 24, 2015
Research Faculty Positions (iGEM@Temple) Multiple multi-year research faculty positions (non tenure-track) are available in the Institute for Genomics and Evolutionary Medicine (iGEM) at Temple University in Philadelphia, USA. We are interested in early and mid-career scientists who integrate concepts, methods, and tools from evolutionary biology to address significant questions in biomedicine and phylogenomics. Successful candidates will have a primary focus on one or more of the following: large scale analytics of sequence and expression data, and development of methods and computational tools. They will be core faculty of iGEM @ Temple and one of the academic departments (e.g., Biology or Computer Science). They will work closely with and benefit from our expertise in molecular evolution, population genetics, phylogenomics, phylomedicine, and computational biology. Applicants should submit their detailed curriculum vitae and a summary of current and future research interests by e-mail to firstname.lastname@example.org (send a single PDF file). Successful candidates will be provided for salary support for an initial period and they will work closely with one or more of the current or future tenured faculty in iGEM (http://bit.ly/1EEr1MB). They will be expected to develop a strong, extramurally funded, and collaborative research program. For all questions, please contact Sudhir Kumar by email (email@example.com). Temple University located is in the heart of historic Philadelphia, and is the sixth largest provider of graduate school education in the USA. Situated in close proximity to New York City and Washington DC, Philadelphia is home to a large biotech industry and has many outstanding academic and research institutions. Sudhir Kumar Director, iGEM@Temple firstname.lastname@example.org via Gmail
Evolutionary Informatics Faculty Positions (Assistant/Associate Professors) The Institute for Genomics and Evolutionary Medicine (iGEM) at Temple University invites applications for tenured and tenure-track faculty positions. We are interested in early and mid-career scientists who are developing theories, methods, algorithms, software, and resources for addressing significant problems in the domain of genome sequences and variation data. As core faculty of iGEM (http://bit.ly/YVV0zL), successful candidates will be part of an interdisciplinary team of world-class faculty in biology, genomics and computer and information sciences. The successful faculty will have their tenure home in the Department of Computer and Information Sciences. Applicants for the assistant professor position should have the potential to develop a significant, extramurally funded research program Applicants for the senior position are expected to have an outstanding and continuing track record of research and funding. Applicants should submit email@example.com single pdf containing a cover letter, a detailed curriculum vitae, a summary of current and future research interests, and a statement of teaching philosophy. Please include in the cover letter a link to a Google Scholar profile. Through their research and teaching statements applicants should inform the search committee about the transformative and cross-disciplinary aspects of their work. Review of applications will begin on March 21, 2015 and continue until the positions are filled. Temple University is located in the heart of historic Philadelphia, and is the sixth largest provider of graduate school education in the USA. Situated between New York City and Washington DC, Philadelphia is home to a large biotech industry and has many outstanding academic, research, and cultural institutions. Temple University is an equal opportunity, equal access, affirmative action employer committed to achieving a diverse community (AA, EOE, m/f/d/v). ==============Sudhir Kumar, Ph.D. Director, iGEM@Temple (http://bit.ly/YVV0zL) Institute for Genomics and Evolutionary Medicine Carnell Professor of Biology Temple University (SERC 710) Philadelphia, PA 19122, USA http://bit.ly/1EEr3UF http://bit.ly/1yOyFnd via Gmail
Want to give a talk or a poster at the Systematics Association Biennial meeting (Oxford, UK 26-28 August 2015)? There is an exciting programme that includes both plenaries and thematic symposia, as well as contributed sessions. Scheduled symposia include: - The value of long term monitoring plots for plant systematics and ecology in the tropics - Comparative approaches to the origin of biodiversity - Accelerating the pace of taxonomy - Rooted in deep time: Palaeontological contributions to systematics Abstract submission now open: http://bit.ly/1Jy9MNF Registration for attendees is open too. The website for registration & accommodation bookings is here: http://bit.ly/1Jy9O8i *Registration Rates* 220 Full 3 day rate SA member 250 Full 3 day rate non-member 130 Student 3 day rate SA member 160 Student 3 day rate non-member 85 Full 1 day rate 60 Student 1 day rate The 3 day rate includes sandwich lunch (meat, fish and vegetarian) and 2 drinks receptions. The day rate includes sandwich lunch. *Accommodation* All accommodation, if desired must be booked for three nights. The accommodation is at Christchurch for 25th, 26th and 27th August with breakfast included. Prices shown are for all 3 nights. 186 Single standard room 261 Single ensuite room 384 Twin ensuite room 306 Twin set room (would suit two students sharing) 40 Conference dinner (menu choice available at conference) For further contact / queries, email: firstname.lastname@example.org email@example.com via Gmail
Post Doctoral position in epigenetics and genome stability We are welcoming applications from enthusiastic and independent post-doctoral candidates to participate in our FRM grant-funded project related to epigenetics and genome stability. The fellowship is for 2 years and should start before June 2015. Background Genomic stability can be disturbed by the activity of repeated sequences such as transposable elements (TEs). Epigenetic mechanisms allow the silencing of these sequences. As a consequence, the presence of TEs in a genome may affect the chromatin structure of the regions in which they are inserted. Environmental factors have also been described as affecting genome stability, namely by affecting the rate of transposition„ and could be associated with environment related diseases such as cancer. Project The purpose of the project is to establish the link between TEs, environment and epigenetics. Drosophila is one of the best-fitted model for this project since we have an easy access to Drosophila natural variability, the species genome is small and harbors low amounts of TEs, and it is easily manipulated in the lab. The project consists in the analysis of Drosophila responses to stress by analyzing chromatin structure, piRNA abundances and mRNA levels, with an emphasis on TEs. Candidates The applicants are expected to have a strong background in epigenetics with a confirmed interest in genomics and evolutionary biology. Skills in data analysis and/or bioinformatics are necessary, but the candidate will benefit from the LBBE bioinformatics and statistical environment. The ideal candidate should be highly motivated, curious and enthusiastic to work in a collaborative team. Proven ability to identify research objectives and meet agreed deadlines, self-motivation and flexibility are essential. Excellent written and oral skills in English are required. Environment The host laboratory (LBBE) is a stimulating, cosmopolitan and pleasant place to work, where one can meet biologists, computer scientists, mathematicians and statisticians working on problems that range from ecology to medicine, through genomics and evolution. Lyon is the second largest city in France, is famous for its food, is a UNESCO World Heritage site and enjoys a very convenient central location in Europe. Please send one PDF file to Cristina Vieira firstname.lastname@example.org including: - a cover letter - a concise summary of previous research activities (2 pages max) - a curriculum vitae including publication list - contact details for 2-3 referees applications will be selected by the end of March via Gmail
A laboratory technician (Research Assistant III) position is available with Dr. Matthew Herron. This position is based at the University of Montana in Missoula, MT (but may also involve work in collaborating labs. The Herron Lab Group uses experimental evolution of the unicellular green alga Chlamydomonas reinhardtii to understand the evolution of multicellularity. The person in this position will contribute to this project through collaboration with postdocs and graduate students; take on a specific line of investigation assigned by the principal investigator; and train and supervise undergraduate work-study students. The Research Assistant III will maintain orderly, up-to-date written and electronic notebooks consistent with standard NIH guidelines; actively participate in weekly group meetings; and significantly contribute to research communications and grants by analyzing and interpreting data, preparing publication-quality figures and tables, and composing the methods and results sections of manuscript narratives in a quality that would merit manuscript co-authorship. The person in this position will demonstrate expertise in molecular microbiology, microbial cell culture, and have a working knowledge of all aspects of nucleic acid preparation and analysis, PCR, and standard genetic analyses. Required skills include demonstrated ability to work independently,to recognize and creatively solve technical problems, to effectively transmit protocol knowledge to new students and postdocs, to assist lab personnel as needed, and to follow through on assigned tasks in a timely manner. Strong demonstrated ability in oral and written communication skills, demonstrated experience and expertise in molecular microbiology and microbial cell culture, and working knowledge of nucleic acid preparation and analysis, PCR, and standard genetic analyses are also required. Required Experience: bachelors degree in Biology, Chemistry or a related discipline and two (2) years of research experience or an equivalent combination of education and experience Preferred Qualifications: masters degree About the University of Montana University of Montana is located in Missoula, a vibrant community of 67,000, surrounded by mountain grandeur. The city has been singled out in national publications for its high quality of life and abundant recreational opportunities in surrounding state and national forests and nearby Glacier National Park and Yellowstone National Park complement a thriving intellectual atmosphere. HOW TO APPLY: Submit a Letter of Interest, detailed resume, and names and contact information for three professional references at http://bit.ly/1ybEPbr . via Gmail
Dear all the information concerning the Evolutionary biology meeting at Marseilles can be found at the AEEB web site: www.aeeb.fr best regards Pierre Pierre PONTAROTTI via Gmail
Postdoc position: Why do animals have personality? It’s a pleasure to announce a postdoctoral position in the research group of Dr Hanne Løvlie at Linköping University, Sweden, on the topic of animal personality. The project will focus on mechanisms underlying variation in personality, the link to variation in cognition and learning, and the role of underlying variation in the monoamine systems (i.e. serotonin, dopamine), and is in collaboration with Prof. Svante Winberg (Uppsala University). Despite intense recent research interest, we still do not know why animals have personality. This is partly because the architecture of animal personality is poorly understood. The aim of the announced position is to improve our overall understanding of the causes and consequences of variation in animal personality. More specifically the aim is to investigate the relationship between variation in personality and learning (together with other aspects of cognition), and their underlying genetic and physiological bases, with particular focus on the brain monoamines serotonin and dopamine. In other words, an exciting interdisciplinary project is offered that aims to improve our understanding of the relationships between personality and cognition, and their underlying mechanisms. We use the charismatic red junglefowl and domestic chickens as our main models, which together with excellent molecular tools enables a strong experimental approach. The post includes responsibility for conducting lab/fieldwork, carrying out behavioural and/or physiological experiments, analysing data and writing up results for publication. The postdoc will have access to previously collected behavioural, physiological and genetic data. To some extent is the topic of the project is flexible and can be tailored to fit the skills and interests of the successful candidate. Funding is available for two years, but is contingent on satisfactory progress in year one. The post doc is a stipend (i.e. no tax will be deducted) of 20,000SEK/month. The stipend does not give entitlement to sickness benefit, parental allowance, holiday pay or pension. Funding is awarded from Carl Trygger’s Foundation. Requirements The successful candidate should be enthusiastic and dedicated to science, with a PhD and possibly some postdoctoral experience in a field of relevance to the project (e.g. animal behaviour, evolutionary biology, molecular biology, quantitative genetics and/or neurobiology). The candidate should have demonstrated excellent quantitative and analytic skills, and excellent communication abilities, particularly in written English. The latter should be demonstrated by a proven track record of publication. The candidate should also demonstrate their ability to work as part of a team. Previous experience of working with vertebrates, especially birds, is advantageous, but not necessary. If you are interested in this position, please send: (1) a letter of motivation (including a brief description of research experience and why you are suitable for the announced position), (2) a CV including a list of publications and contact details of two referees to: email@example.com. Please merge all documents into a single pdf-file and include your name in the file name. Deadline for submitting an application is 9th of March 2015. The position has a negotiable start, but a start date before summer 2015 is preferred. Please feel free to contact me if you have any questions about the position! Linköping University is a modern university with a consistently growing biology division. A major research focus at the Biology division is on animal behaviour, including behavioural genetics and animal welfare. Linköping is located central in Sweden, only a couple of hours away from other university cities, like Stockholm, Uppsala and Lund. Hanne Løvlie, Assistant professor IFM Biology, AVIAN Behavioural Genomics and Physiology Group Linköping University 58183 Linköping, Sweden firstname.lastname@example.org Home page and more information: http://bit.ly/1ybEOV7 Hanne Lovlie via Gmail
Postdoc: WHERE : Institute of Computational Biology (IBC), Montpellier (France), http://bit.ly/1xBTByk WHAT : Methodological developments in evolutionary genomics Three-year post-doctoral position at the Institute of Computational Biology (IBC), Montpellier (France) : Methodological developments in evolutionary genomics. One young investigator position opens immediately at the Institute for Computational Biology (IBC, http://bit.ly/1xBTByk) of Montpellier (France) to work on the development of innovative inference methods and software in population genomics or phylogenetics to analyze large-scale genomic data in the fields of health, agronomy and environment (Work Package 2 evolutionary genomics of the IBC). The candidate will develop its own research on some of the following topics : selective processes, demographic history, spatial genetic processes, very large phylogenies reconstruction, gene/species tree reconciliation, using maximum likelihood, bayesian and simulation-based inference. We are seeking a candidate with a strong background in mathematical and computational evolutionary biology, with interest in applications and software development. The successfull candidate will work on his own project, build in collaboration with any researchers* involved in the WP2 project and working at the IBC labs (AGAP, CBGP, ISEM, I3M, LIRMM, MIVEGEC). IBC hires young investigators, typically with a PhD plus some post-doc experience, a high level of publishing, strong communication abilities, and a taste for multidisciplinary research. Working full-time at IBC, these young researchers will play a key role in Institute life. Most of their time will be devoted to scientific projects. In addition, they are expected to actively participate in the coordination of workpackages, in the hosting of foreign researchers and in the organization of seminars and events (summer schools, conferences…). In exchange, these young researchers will benefit from an exceptional environment thanks to the presence of numerous leading international researchers, not to mention significant autonomy for their work. Montpellier hosts one of the most vibrant communities of biodiversity research in Europe with several research centers of excellence in the field. This positions is open for up to 3 years with a salary above the French post-doc standard. Living at Montpellier: http://bit.ly/1rsnOrN Contacts WP2 Evolutionary Genetics : Jean-Michel Marin : http://bit.ly/1ATaNjw Franois Rousset : http://bit.ly/1rsnOrR Vincent Ranwez : http://bit.ly/1ATaNjy Olivier Gascuel : http://bit.ly/1rsnOrT Submit my application : http://bit.ly/1ATaMfp * WP2 researchers : Vincent Berry, Franois Chevenet, Jean-Franois Dufayard, Olivier Gascuel, Mathieu Gautier, Raphal Leblois, Jean-Michel Marin, Miguel Navascus, Fabio Pardi, Martine Peeters, Pierre Pudlo, Vincent Ranwez, Franois Rousset, Cline Scornavacca, Renaud Vitalis. via Gmail
Postdoctoral scientist in bacteria genomics Department of Biomedical Sciences - Unit of Diagnostic Bacteriology The Institute of Tropical Medicine (ITM) is internationally recognized as a center of excellence for education, research and service delivery in the field of tropical medicine. The Unit of Diagnostic Bacteriology at the Department of Biomedical Sciences is developing and validating innovative diagnostic tests for tropical bacterial infections. We recently launched several new projects in which we use metagenomics and genomics to identify and study pathogens in clinical samples. To support these activities and to develop new projects, we are looking for a postdoctoral scientist in genomics data analysis. Assignment: * Coordinate the bioinformatics activities at the Diagnostic Bacteriology Unit. * Develop and validate a metagenomics approach to identify bacteria in clinical samples. * Develop the data analysis for a study on whole genome sequencing of Salmonella isolates. * Assist in the data analysis of genomics, transcriptomics and proteomics projects in the unit. * Develop your own research lines and apply for competitive grants. * Coach MSc and PhD students. Profile: * You have a Master degree in biology, bioengineering or bioinformatics (or equivalent) and a PhD degree in sciences, preferably in the field of genomics or metagenomics. * You have strong skills in bioinformatic analysis of whole genome sequence data. * Additional skills in the analysis of transcriptomics and proteomics data are an asset. * Additional skills in bacteriology and molecular biology are an asset. * You have excellent knowledge of English. * You have proven that you can work in a multi-disciplinary context and lead research lines. Offer: * An intellectually stimulating, international and socially committed environment, with room for personal initiative. * A full time contract as postdoctoral scientist for one year, extendable. Starting date is as soon as possible. * A salary set according to the pay scales of the ITM and the Flemish universities. * Reimbursement of public transport costs, bicycle compensation and luncheon vouchers. * You will work at the ITM headquarter in the bustling city of Antwerp. Interested? For more information about this position, please contact Prof. Stijn Deborggraeve, Head of the Diagnostic Bacteriology Unit (email@example.com). Applications with motivation letter, application form and contact details of at least 3 references should be received by email at firstname.lastname@example.org by February 16, 2015. Please use the application form available as a download on www.itg.be/vacatures. * Please consider the environment before printing this e-mail Disclaimer: http://bit.ly/1efLUUJ Directions to our location(s): http://bit.ly/19GixVwwww.itg.be/vacatures. * Please consider the environment before printing this e-mail Disclaimer: http://bit.ly/1efLUUJ Directions to our location(s): http://bit.ly/19GixVw Stijn Deborggraeve via Gmail
Dear Colleagues, We are pleased to announce the 2nd Ecology and Evolutionary Biology Symposium - 2015, Turkey (EEBST 2015, http://bit.ly/1z208DA). The symposium will be convening on August 6-7 2015 at the Middle East Technical University, Ankara. This will be the second international ecology-evolution symposium organized in Turkey, after EEBST 2014 ( http://bit.ly/I8szWP) held last year at Bogazici University, Istanbul. These symposia series started out as a project by the Ecology & Evolution Network of Turkey (“evoeko”). Our goal is to promote cutting edge research in ecology, evolutionary biology, and related interdisciplinary areas in Turkey and in the region. This year’s keynote speakers will be: - Resit Akcakaya (Stony Brook University), - Sergey Gavrilets (University of Tennessee), - Rasmus Nielsen (University of California, Berkeley), and - Daniel Simberloff (University of Tennessee). We invite talks and poster presentations in all areas of ecology and evolutionary biology. All presentations will be in English and we welcome international participation. Important Dates for registration and abstract submission are: - Registration open: March 1 - Abstract submission for oral and poster presentations: March 1 - May 15 - Symposium program announced: June 1 - Registration closes: July 15 This will be a unique opportunity for meeting Turkey’s evolutionary biologist and ecologist research community and setting up collaborations. For any questions, contact email@example.com or visit the website at: http://bit.ly/1z208DA We look forward to seeing you in Ankara! On behalf of the Organizing Committee Aysegul Birand (firstname.lastname@example.org) and Mehmet Somel (email@example.com) firstname.lastname@example.org via Gmail
January 23, 2015
Computational Biologist - Research & Development 23andMe Mountain View, CA, United States Do you wish that your work had a more direct impact on people? Are you excited about the potential of human genetics to make a real difference in the world? At 23andMe, we believe that genetics is on the cusp of huge advances, and that our unique database of hundreds of thousands of genotypes and almost two hundred million phenotype data points gives us an incredible opportunity to advance not only biomedical research, but our understanding of ourselves. We are looking for a colleague with extensive training and experience in computational biology to join our highly productive, world-class research team. This person will be involved in the analysis of human genetic data and the development of product features that depend on a mix of computational skills, statistical knowledge, creativity, and biological insight. The scope and breadth of our vision means that most of the necessary techniques have yet to be developed anywhere in the world. We are looking for someone excited to work with our Product Managers in a cross-functional collaboration to define and design features that help 23andMe deliver a quality experience to our customers. This includes improving existing ancestry features and tools, as well as developing and expanding in novel directions. This person is also expected to participate in the communication and public relations efforts of the company, including giving scientific talks, presenting at genealogy conferences, and disseminating research findings to a non-scientific audience. QUALIFICATIONS: - PhD in Computational Biology or related field (eg, Genetics, Computer Science, Engineering, Physics, Math, Bioinformatics) - Strong bioinformatics and biostatistics background - Background in algorithm development - Proficiency with scripting languages (eg, Python, R, bash) - Enthusiasm for working in a highly collaborative environment ALSO VALUABLE: - Evolutionary or population genetics research experience - Demonstrated record of developing and distributing tools for the analysis and visualization of genomics data - Experience with C/C++ Experience mentoring other scientists and familiarity with epidemiological principles are highly desirable. Apply online: http://bit.ly/1szeN0H ABOUT US 23andMe is the leading personal genetics company. We are dedicated to helping individuals understand their own genetic information through DNA analysis technologies and web-based interactive tools. Our mission is to personalize health care by making and supporting meaningful discoveries through genetic research. Combining web development, computer science, genetics, social media, and informatics, 23andMe is at the forefront of a new era in personal genetics. email@example.com via Gmail
Title: Postdoctoral Researcher available in the Evans Lab at Michigan State University’s Kellogg Biological Station (Hickory Corners, MI). A postdoctoral position is available in microbial ecology and soil biogeochemistry at Kellogg Biological Station, Michigan State University. The Evans Lab (http://bit.ly/1y7hrjO) is interested in how microbes respond to climate change and how these responses influence ecosystem processes. To investigate these questions, we use molecular techniques, physiological assays, modeling, and terrestrial climate manipulations. The postdoctoral candidate will have the opportunity to conduct work at the KBS Long Term Ecological Research Site (kbs.lter.edu) or Great Lakes Bioenergy Research Center (glbrc.msu.edu), where long-term data on natural and agro-ecosystems and inter-disciplinary research teams provide an excellent context for scientific questions in the time period of a postdoctoral position. Research questions could focus on, but are not limited to, interactions among changes in rainfall patterns, nitrogen dynamics, and microbial community function. Responsibilities include: data collection in existing climate manipulation or crop management experiments, microbial community or physiological analysis, participation in lab and KBS community, data management, and manuscript preparation. The successful candidate will have the opportunity to interact with the many researchers working on KBS long-term projects, distinguished faculty at KBS, as well as faculty on campus in Departments of Microbiology and Molecular Genetics and Integrative Biology. The candidate will also have the ease and efficiency that comes with access to much available data and state-of-the-art field sites outside their door. KBS and the Evans Lab prioritize postdoctoral research career development, and it is a fun place to spend two years. The ideal candidate will have a strong background in microbial ecology, including experience with metagenomic/metatranscriptomic protocols and data and statistical analyses. However, other specific and well-refined skillsets that can be applied to these types of questions will be equally considered. Demonstration of strong written and oral communication skills is a must, and a PhD and research experience in appropriate disciplines is required. The postdoctoral appointment will be for 2 years. Start date is May 2015, but requests for other start dates near this time will be considered (indicate in cover letter). To apply, please send a cover letter (including research interests and an indication of field, lab, and data analysis skills), CV, and contact information (name, position, phone, email) for 3 references to firstname.lastname@example.org. We will begin reviewing applications in mid-February, 2015. email@example.com via Gmail
The Biodesign Institute at Arizona State University and the Center for Evolution and Cancer is searching for a Staff Scientist or Postdoctoral Research Associate to perform analysis of high throughput sequencing data on multi-region samples to measure genetic diversity within breast cancers, AML, and potentially other types of cancer. They will be responsible for setting up and maintaining a state-of-the art pipeline for high throughput sequencing data, as well as the development of new algorithms to mine that data. The Center for Evolution and Cancer was the first of its kind to apply evolutionary biology to cancer biology both at the cell level, studying the evolutionary dynamics of carcinogenesis and therapeutic resistance, and at the organismal level, studying the evolution of cancer suppression in whales, elephants and other species. Scholars will be part of a highly interdisciplinary research team led by Dr. Carlo Maley and also be part of a larger community of interdisciplinary researchers at Arizona State University in the Center for Evolution and Medicine and the Centre for Evolution and Cancer at the Institute for Cancer Research in London, bringing together evolutionary biologists, ecologists, computational biologists, mathematical modelers, cancer biologists and oncologists to make fundamental discoveries in understanding cancer and improving cancer prevention and management. Interactions among faculty, Postdocs and students across the Institute and the University are central to a variety of ongoing research and educational programs. These interactions allow our Postdoctoral Research Associates to develop their expertise in research and build towards an independent research program. Alternatively, this position could develop into a longterm collaboration as a staff scientist in the Maley lab. Faculty, Postdocs and students are actively involved with a number of other centers, institutes, and research groups on campus that promote transdisciplinary approaches to issues of local and national significance, affording outstanding research and training experiences that extend beyond traditional disciplinary boundaries. The Biodesign Institute is a research hub that makes an important contribution to the advancement of ASU as a leader of knowledge generation and utilization. Qualifications: Ph.D. or extensive expertise in computational biology, bioinformatics, systems biology, biostatistics, or related field. The ideal candidate would have expertise in both evolutionary biology and high throughput sequence analysis of neoplasms. Background in single cell sequencing and/or the human microbiota would be favored. Relevant publications in high quality peer review journals is desired. To apply, please submit to firstname.lastname@example.org as a single pdf document the following materials: 1) a cover letter specifying relevant qualifications and training, 2) curriculum vitae, 3) statement of current research interests and expertise (2 page maximum), 4) two letters of reference, and 5) one peer-reviewed publication. Please include ‘Application for Postdoc- Sequencing’ in the email subject line. Initial review of applications will begin on February 1, 2015; if not filled, review will continue every week thereafter until the search is closed. A background check is required for employment. Arizona State University is a new model for American higher education, an unprecedented combination of academic excellence, energy and broad access. This New American University is a single, unified institution comprising four differentiated campuses positively impacting the economic, social, cultural and environmental health of the communities it serves. Its research is inspired by real world application blurring the boundaries that traditionally separate academic disciplines. ASU serves more than 80,000 students in metropolitan Phoenix, Arizona, the nation’s fifth largest city. ASU champions intellectual and cultural diversity, and welcomes students from all fifty states and more than one hundred nations across the globe. Arizona State University is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will be considered without regard to race, color, sex, religion, national origin, disability, protected veteran status, or any other basis protected by law. via Gmail
*The Nouragues Travel Grant 2015* The Nouragues annual call for proposals is aimed at facilitating access to the Nouragues station for scientists of all research fields. Graduate students, post-doctoral researchers, and established scientists may apply. Submitted proposals will be evaluated by a Science Advisory Board and selected based on their excellence, the quality of expected publications, and the feasibility of the project. The grants will not exceed 9,000€ in total, and will be for a duration of one year. Reapplications will be evaluated based on the achievements of the previous years. Grant recipients will be expected to contribute to the dissemination of knowledge in French Guiana, via participation in outreach programs of the collaborating Nouragues Natural Reserve. In 2015, experimental projects and projects related to the new COPAS instrument (Canopy Operational Permanent Access System) will be especially considered. Deadline for application: March 6th, 2015. For more information : http://bit.ly/1y6JdIU Amaia IRIBAR-PELOZUELO Chargée de coordination scientifique CEBA Laboratoire Evolution et Diversité Biologique UMR 5174 Université Paul Sabatier, bât 4R1, bureau 124 118 route de Narbonne, 31062 Toulouse Cedex 9 - France tél : + 33 (0)5 61 55 64 95 fax : + 33 (0)5 61 55 73 27 link: www.labex-ceba.fr Amaia Iribar-Pelozuelo via Gmail
—001a11c269868d4829050d433a40 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable *Title: *Postdoctoral Position “Evolutionary Physiology- Integrative Biology *Description: *The Department of Integrative Biology at the University of California, Berkeley invites applications for a Postdoctoral Employee starting in the summer of 2015. The successful candidate will have the opportunity to study the evolution of metabolic physiology of insects using a range of model systems including montane willow leaf beetles (*Chrysomela aeneicollis*), wing-polymorphic Florida sand crickets (*Gryllus firmus*) or related cricket species, and *Drosophila *species. Understanding the potential for evolution of metabolic physiology in response to changing environments is an essential component of predicting organismal responses to climate change. The details of the project are flexible depending on the interests of the successful candidate, but will involve some combination of field work, biochemistry and physiology, molecular biology, and modelling. Please see cmwilliamslab.com for more information. The Integrative Biology program is ranked in the top 10 biology programs nationwide (National Research Council, 2010). The department and wider campus provide a thriving and exciting intellectual culture with extensive opportunities for collaboration. *Responsibilities: *(1) Perform field work; (2) Insect husbandry; (3) Design and carry out experiments on insects using biochemistry, physiology, and molecular biology; (4) Data analysis and statistical modelling; (5) Preparing and submitting papers for publication; (6) Supervising and mentoring undergraduate students *Minimum/Basic Qualifications Required: *Applicants must complete all degree requirements except the dissertation by the time of application. *Additional Required Qualifications: *The successful candidate will have a strong publication record in peer-reviewed journals and a background in biochemistry, physiology or molecular biology. Applicants must have PhD or equivalent by the expected start date. *Appointment: *This position reports to Dr. Caroline Williams. The initial appointment will be at 100% time for 1 year with the expectation of extension based on satisfactory performance and availability of funding. The approximate start date of this position will be July 1, 2015. *Salary*: $42,000-$49,128/annually, depending prior postdoctoral experience and qualifications. Generous benefits are included( http://bit.ly/1gm3hSu). *To Apply*: http://bit.ly/1AXjk0f Interested individuals should submit (via the website above) application documents as PDFs, which includes (i) an updated curriculum vitae (required), (ii) a cover letter (required), (iii) names with contact information for 3-5 individuals who have agreed to provide a reference (required) for this specific position (contact information includes title, institution, email, basis for this individual’s recommendation of the applicant). Letters of reference may be requested of the finalists. Department Contact: CarolineWilliams, Supervisor, email@example.com The initial review date for this recruitment is February 17, 2015; please apply by this date to be fully considered for the position. The position will be open until filled. All letters will be treated as confidential per University of California policy and California state law. Please refer potential referees, including when letters are provided via a third party (i.e., dossier service or career center), to the UCBerkeley statement of confidentiality ( http://bit.ly/1wTEkon) prior to submitting their letters. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see: http://bit.ly/1tbbcKE via Gmail
POSTDOCTORAL POSITION IN PLANT EVOLUTIONARY BIOLOGY Research Group of Dr. Susana Magallón (http://bit.ly/1AXjkxk) Instituto de Biología, Universidad Nacional Autónoma de México (UNAM) Mexico City, Mexico RESEARCH TOPICS: • Effect of fossil calibrations in molecular clock analyses of flowering plants. • Stochastic local clocks applied to dating seed plants. DATES: • Application deadline: February 23, 2015. • Start of the postdoctoral position: September, 2015. REQUIRED OF CANDIDATES: PhD degree obtained in the 3 years previous to date of hire; 36 years old or younger at the date of hire; research productivity demonstrated through scientific publication record. APPLICATION MATERIALS: CV; statement of academic interests and goals (1 page max.); PDFs of publications; one academic reference. FUNDING: The candidate will enter a competitive selection to obtain one of the Postdoctoral Fellowships granted by the Coordination for Scientific Research, UNAM (http://bit.ly/1yWkoGu). The position is available for one year, with the possibility to extend to a second year. PLEASE SUBMIT REQUESTS OF INFORMATION AND APPLICATIONS TO: firstname.lastname@example.org * * * * * Susana Magallón PhD Instituto de Biología Universidad Nacional Autónoma de México 3er Circuito de Ciudad Universitaria Del. Coyoacán México D.F. 04510 Mexico Phone: (52-55) 5622-9087 Fax: (55-52) 5550-1760 Email: email@example.com Email: firstname.lastname@example.org http://bit.ly/MbSPl7 http://bit.ly/1AXjkxk Susana Magallon via Gmail
January 22, 2015
The Biodesign Institute at Arizona State University and the Center for Evolution and Cancer is searching for a Postdoctoral Research Associate to help develop methods to reconstruct the phylogenies of cell lineages from within neoplasms. This will require the development of new likelihood models and the integration of multi-modal data (e.g., point mutations and chromosomal alterations). Initial data will derive from SNP arrays and exome sequencing of Barrett’s esophagus tissue samples. We will also work on developing methods to extract regularities across forests of phylogenetic trees from tumors. The Center for Evolution and Cancer was the first of its kind to apply evolutionary biology to cancer biology both at the cell level, studying the evolutionary dynamics of carcinogenesis and therapeutic resistance, and at the organismal level, studying the evolution of cancer suppression in whales, elephants and other species. Scholars will be part of a highly interdisciplinary research team led by Dr. Carlo Maley, will collaborate with Mary Kuhner in Joe Felsenstein’s lab, and also be part of a larger community of interdisciplinary researchers at Arizona State University in the Center for Evolution and Medicine and the Centre for Evolution and Cancer at the Institute for Cancer Research in London, bringing together evolutionary biologists, ecologists, computational biologists, mathematical modelers, cancer biologists and oncologists to make fundamental discoveries in understanding cancer and improving cancer prevention and management. Interactions among faculty, Postdocs and students across the Institute and the University are central to a variety of ongoing research and educational programs. These interactions allow our Postdoctoral Research Associates to develop their expertise in research and build towards an independent research program. Faculty, Postdocs and students are actively involved with a number of other centers, institutes, and research groups on campus that promote transdisciplinary approaches to issues of local and national significance, affording outstanding research and training experiences that extend beyond traditional disciplinary boundaries. The Biodesign Institute is a research hub that makes an important contribution to the advancement of ASU as a leader of knowledge generation and utilization. Qualifications: Ph.D. in evolutionary biology, computational biology, bioinformatics, biostatistics, or related field. Experience in developing phylogenetic methods is required. Experience with the BEAST software package is preferable but not required. Relevant publications in high quality peer review journals is desired. To apply, please submit to email@example.com as a single pdf document the following materials: 1) a cover letter specifying relevant qualifications and training, 2) curriculum vitae, 3) statement of current research interests and expertise (2 page maximum), 4) two letters of reference, and 5) one peer-reviewed publication. Please include ‘Application for Postdoc- Phylogeneticist’ in the email subject line. Initial review of applications will begin on February 1, 2015; if not filled, review will continue every week thereafter until the search is closed. A background check is required for employment. Arizona State University is a new model for American higher education, an unprecedented combination of academic excellence, energy and broad access. This New American University is a single, unified institution comprising four differentiated campuses positively impacting the economic, social, cultural and environmental health of the communities it serves. Its research is inspired by real world application blurring the boundaries that traditionally separate academic disciplines. ASU serves more than 80,000 students in metropolitan Phoenix, Arizona, the nation’s fifth largest city. ASU champions intellectual and cultural diversity, and welcomes students from all fifty states and more than one hundred nations across the globe. Arizona State University is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will be considered without regard to race, color, sex, religion, national origin, disability, protected veteran status, or any other basis protected by law. via Gmail
For the last few weeks I've been working on a little project to display phylogenies on web-based maps such as OpenStreetMap and Google Maps. Below I'll sketch out the rationale, but if you're in a hurry you can see a live demo here: http://iphylo.org/~rpage/geojson-phylogeny-demo/, and some examples below.
The second example shows DNA barcodes similar to ABFG379-10 for Proechimys guyannensis and its relatives.Background
People have been putting phylogenies on computer-based maps for a while, but in most cases these have required stand-alone software, such as Google Earth, or GeoJSON for encoding geographic information. Despite the obvious appeal of placing trees in maps, and calls for large-scale geophylogeny databases (e.g., do:10.1093/sysbio/syq043), computerised drawing trees on maps has remained a bit of a niche activity. I think there are several reasons for this:
So there are a number of obstacles to making this easy. The increasing availability of geotagged sequences in GenBank (see Guest post: response to "Putting GenBank Data on the Map"), especially DNA barcodes, helps. For the demo I created a simple pipeline to take a DNA barcode, query BOLD for similar sequences, retrieve those, align them, build a neighbour joining tree, annotate the tree with latitude and longitudes, and encode that information in a NEXUS file.
To layout the tree on a map (say OpenStreetMap using Leaflet or Google Maps) I convert the NEXUS file to GeoJSON. There are a couple of problems to solve when doing this.Typically when drawing a phylogeny we compute x and y coordinates for a device such as a computer screen or printer where these coordinates have equal units and are linear in both horizontal and vertical dimensions. In web maps coordinates are expressed in terms of latitude and longitude, and in the widely-used Web Mercator projection the vertical axis (latitude) is non-linear. Furthermore, on a web map the user can zoom in and out, so pixel-based coordinates only make sense with respect to a given zoom level.
To tackle this I compute the layout of the tree in pixels at zoom level 0, when the web map comprises a single "tile".
The tile coordinates are then converted to latitude and longitude, so that they can be placed on the map. The map applications take care of zooming in and out, so the tree scales appropriately. The actual sampling localities are simply markers on the map. Another problem is to reduce the visual clutter that results from criss-crossing lines connecting connecting the tips of the tree and the associated sampling localities. To make the diagram more comprehensible, I adopt the approach used by GenGIS to reorder the nodes in the tree to minimise the crossings (see algorithm in doi:10.7155/jgaa.00088). The tree and the lines connecting it to the localities are encoded as "LineString" objects in the GeoJSON file.
There are a couple of things which could be done with this kind of tool. The first is to add it as a visualisation to a set of phylogenies or occurrence data. For example, imagine my "million barcode map" having the ability to display a geophylogeny for any barcode you click on.
Another use would be to create a geographically indexed database of phylogenies. There are databases such as CouchDB that store JSON as a native format, and it would be fairly straightforward to consume GeoJSON for a geophylogeny, ignore the bits that draw the tree on the map, and index the localities. We could then search for trees in a given region, and render them on a map.
There's still some work to do (I need to make the orientation of the tree optional and there are some edges case that need to be handled), but it's starting to reach the point when it's fun just to explore some examples, such as these microendemic Agnotecous crickets in New Caledonia (data from doi:10.1371/journal.pone.0048047 and GBIF).
Roderic D M Page wrote:
I've been experimenting with drawing "geophylogenies" on web maps and have created a live demo at http://iphylo.org/~rpage/geojson-phylogeny-demo/ All a bit crude, but the idea is to take either a NEXUS tree file with added geographical coordinates, or query the BOLD database of DNA barcodes (most of which are geotagged) and create an interactive phylogeny on a map. The demo uses OpenStreeMap, I've code for Google Maps as well (hope to add this to the demo shortly). The layout borrows from GenGIS (see http://dx.doi.org/10.1101/gr.095612.109 and http://kiwi.cs.dal.ca/GenGIS/Main_Page ) but doesn't need a standalone program. There are some other advantages to using GeoJSON, such as storage in document databases like CouchDB, but I'll blog about these.
To give you a sense of the visualisation, below is the classic Banza example that I used in 2007 when I started playing with trees on Google Earth http://iphylo.blogspot.co.uk/2007/06/google-earth-phylogenies.html, inspired by Bill Piel's pioneering experiments.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology