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September 1, 2015

17:26

@mathmomike wrote:

Does anyone know references or previous work to the following three questions:

  1. Consider the graph G_NNI of unrooted binary phylogenetic trees on leaf set {1,..,n} where two trees form an edge if they are one NNI apart. Similarly G_SPR (where trees are joined if they are one SPR apart). Both these graphs are regular (each tree has the same number of neighbors) so if you start anywhere then after a while you will be at each tree with (asymptotically) uniform probability - the question is what is the mixing time (time to be near uniform as a function of n) for this random walk? Note I'm not talking about data (or Bayesian methods) here - just a pure mixing time question regarding this discrete graph. Does anyone know a paper that studies this (I think I saw one once, but all my papers/notes got lost in the 2010/2011 earthquakes here!).

  2. There are various notions of the centre of a tree - e.g. the "centroid" (explained very nicely in the recent Tanglegrams paper by Matsen/Billey/Kas/Konvalinka paper on ArXiv). However does anyone know any paper that discusses what we might call a 'leaf-centroid'. Given a tree T call a vertex v of T a leaf-centroid if each of the components of T-v contains at most half of the leaves of T. If T has no vertices of degree 2 then (just like the centroid) a tree either has a unique leaf-centroid or two adjacent leaf centroids. However even for this class ( trees without vertices of degree 2) the leaf-centroid can be different from the centroid! Just wondering if anyone has seen this notion mentioned or studied before?

  3. Anyone know an early (pre-1960s) reference to the simple but fundamental result: A collection C of nonempty subsets of X (including X) forms a hierarchy (nested family) if and only if C is the set of clusters of a rooted X-tree? It may be implicit in Linneaus (or even Aristotle!) but some more explicitly mathematical statement would be good.

Any advice will help for a book ('mathematical phylogeny') that I'm now half-way through writing I might ask a few further questions over the coming month or two.

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06:00
Background: Eurypterids are a diverse group of chelicerates known from ~250 species with a sparse Ordovician record currently comprising 11 species; the oldest fully documented example is from the Sandbian of Avalonia. The Middle Ordovician (Darriwilian) fauna of the Winneshiek Lagerstätte includes a new eurypterid species represented by more than 150 specimens, including some juveniles, preserved as carbonaceous cuticular remains. This taxon represents the oldest described eurypterid, extending the documented range of the group back some 9 million years. Results: The new eurypterid species is described as Pentecopterus decorahensis gen. et sp. nov.. Phylogenetic analysis places Pentecopterus at the base of the Megalograptidae, united with the two genera previously assigned to this family by the shared possession of two or more pairs of spines per podomere on prosomal appendage IV, a reduction of all spines except the pair on the penultimate podomere of appendage V, and an ornamentation of guttalate scales, including angular scales along the posterior margin of the dorsal tergites and in longitudinal rows along the tergites. The morphology of Pentecopterus reveals that the Megalograptidae are representatives of the derived carcinosomatoid clade and not basal eurypterids as previously interpreted. Conclusions: The relatively derived position of megalograptids within the eurypterids indicates that most eurypterid clades were present by the Middle Ordovician. Eurypterids either underwent an explosive radiation soon after their origination, or earlier representatives, perhaps Cambrian in age, remain to be discovered. The available instars of Pentecopterus decorahensis suggest that eurypterids underwent extreme appendage differentiation during development, a potentially unique condition among chelicerates. The high degree of appendage specialization in eurypterids is only matched by arachnids within chelicerates, supporting a sister taxon relationship between them.
04:52

A little over a week ago I was at the 6th International Barcode of Life Conference, held at Guelph, Canada. It was my first barcoding conference, and was quite an experience. Here are a few random thoughts.

AttendeesIt was striking how diverse the conference crowd was. Apart from a few ageing systematists (including veterans of the cladistics wars), most people were young(ish), and from all over the world. There clearly something about the simplicity and low barrier to entry of barcoding that has enabled its widespread adoption. This also helps give barcoding a cohesion, no matter what the taxonomic group or the problem you are tackling, you are doing much the same thing as everybody else (but see below). While ageing systematists (like myself) may hold their noses regarding the use of a single, short DNA sequence and a tree-building method some would dismiss as "phenetic", in many ways the conference was a celebration of global-scale phylogeography.

Awesome drone footage from #DNAbarcodes2015. Thanks to everyone who helped make this conference so fantastic!!! https://t.co/37nYuIxGuz

— Mike Wright (@MIKEisWRIGHT20) August 22, 2015

Standards aren't enoughAnd yet, standards aren't enough. I think what contributes to DNA barcoding's success is that sequences are computable. If you have a barcode, there's already a bunch of barcodes sequences you can compare yours to. As others add barcodes, your sequences will be included in subsequent analyses, analyses which may help resolve the identity of what you sequenced.

To put this another way, we have standard image file formats, such as JPEG. This means you can send me a bunch of files, safe in the knowledge that because JPEG is a standard I will be able to open those files. But this doesn't mean that I can do anything useful with them. In fact, it's pretty hard to do anything with images part from look at them. But if you send me a bunch of DNA sequences for the same region, I can build a tree, BLAST GenBank for similar sequences, etc. Standards aren't enough by themselves, to get the explosive growth that we see in barcodes the thing you standardise on needs to be easy to work with, and have a computational infrastructure in place.

Next generation sequencing and the hacker cultureClassical DNA barcoding for animals uses a single, short mtDNA marker that people were sequencing a couple of decades ago. Technology has moved on, such that we're seeing papers such as An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. As I've argued earlier (Is DNA barcoding dead?) this misses the point about the power of standardisation on a simple, scalable method.

At the same time, it was striking to see the diversity of sequencing methods being used in conference presentations. Barcoding is a broad church, and it seemed like it was a natural home for people interested in environmental DNA. There was excitement about technologies such as the Oxford Nanopore MinION™, with people eager to share tips and techniques. There's something of a hacker culture around sequencing (see also Biohackers gear up for genome editing), just as there is for computer hardware and software.

Community

So this happened #dnabarcodes2015 pic.twitter.com/EQ6OqNSTjn

— Kevin Morey (@moreykev94) August 21, 2015 The final session of the conference started with some community bonding, complete with Paul Hebert versus Quentin Wheeler wielding light sables. If, like me, you weren't a barcode, things started getting a little cult-like. But there's no doubt that Paul's achievement in promoting a simple approach to identifying organisms, and then translating that into a multi-million dollar, international endeavour is quite extraordinary.

After the community bonding, came a wonderful talk by Dan Janzen. The room was transfixed as Dan made the case for conservation, based on his own life experiences, including Area de Conservación Guanacaste where he and Winnie Hallwachs have been involved since the 1970s. I sat next to Dan at a dinner after the conference, and showed him iNaturalist, a great tool for documenting biodiversity with your phone. He was intrigued, and once we found pictures taken near his house in Costa Rica, he was able to identify the individual animals in the photos, such as a bird that has since been eaten by a snake.

Dark taxaMy own contribution to the conference was a riff on the notion of dark taxa, and mostly consisted of me trying think through how to respond to DNA barcoding. Two graphs, three responses from Roderic Page The three responses to barcoding that I came up with are:
  1. By comparison to barcoding, classical taxonomy is digitally almost invisible, with great chunks of the literature still not scanned or accessible. So, one response is to try and get the core data of taxonomy digitised and linked as fast as possible. This is why I built BioStor and BioNames, and why I continually rant about the state of efforts to digitise taxonomy.
  2. This is essentially President Obama's "bucket" approach, maybe the sane thing to do is see barcoding as the future and envisage what we could do in a sequence only world. This is not to argue that we should ignore the taxonomic literature as such, but rather lets start with sequences first and see what we can do. This is the motivation for my Displaying a million DNA barcodes on Google Maps using CouchDB, and my experiments with Visualising Geophylogenies in Web Maps Using GeoJSON. These barely scratch the surface of what can be done.
  3. The third approach is to explore how we integrate taxonomy and barcoding at global scale, in which case linking at specimen level (rather, than, say using taxonomic names) seems promising, albeit requiring a massive effort to reconcile multiple specimen identifiers.

Summary

@rdmpage Thanks for spreading the word! Looks like an interesting conference, which is a rare thing indeed.

— Nakensnegl (@kueda) August 23, 2015 Yes, the barcoding conference was that rare thing, a well organised (including well-fed), interesting, indeed eye-opening, conference.

Source: iPhylo
03:26
PhD position in theory/analysis of gene regulation A PhD position is available in the group of Prof. Erik van Nimwegen at the Biozentrum of the University of Basel and Swiss Institute of Bioinformatics (http://bit.ly/1FfckPo). We are looking for highly motivated individuals with strong mathematical and computational skills that are interested to perform theoretical and computational research in the area of gene regulation. Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A list of our group’s publications can be found http://bit.ly/1MZBckp . Our lab also takes part in a number of collaborative projects within Switzerland including StoNets, which studies the ways in which cells control and exploit stochasticity in gene regulatory networks, and BrainStemX, which studies the gene regulatory networks underlying mammalian forebrain development. The precise topic of the PhD research project will be determined jointly with the candidate and candidates that display initiative and independence will be given priority. Candidates should have strong mathematical and computational skills, and experience in such areas as stochastic processes, dynamical systems theory, and Bayesian statistics is a plus. Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biological data and collaborate with experimental biologists. The candidates should have a good knowledge of English. German is helpful but not necessary. The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The start date will by mutual arrangement. Basel is a very international city and a center of life science research, with over 900 life science research companies in the area, including Novartis and Roche. Several other academic institutions are also in the city, including the Friedrich Miescher Institute, the ETH Zurich Biosystems Science and Engineering Department, and the Swiss Tropical Institute. The city is less than 5km from both France and Germany and an hour and a half from the Swiss Alps. To apply, please send a single pdf containing your application letter, CV, and the names of two references to erik.vannimwegen-at-unibas.ch Review of applications will begin immediately. Thomas Julou via Gmail
Source: EVOLDIR
03:26
Post-doc position in computational genomics/gene regulatory networks A post-doctoral position is available in the group of Prof. Erik van Nimwegen (http://bit.ly/1FfckPo) at the Biozentrum of the University of Basel and Swiss Institute of Bioinformatics. We are looking for highly motivated individuals with strong mathematical and computational skills that are interested to perform theoretical research in computational genomics, genome-wide regulatory networks, and stochastic gene regulation in single cells. Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A list of our groups publications can be found at http://bit.ly/1MZBckp . Our lab also takes part in a number of collaborative projects within Switzerland including StoNets, which studies the ways in which cells control and exploit stochasticity in gene regulatory networks, and BrainStemX, which studies the gene regulatory networks underlying mammalian forebrain development. For this position we are in particular looking for candidates that are interested in developing methods for the analysis of next-generation sequencing data, including RNA-seq, single-cell RNA-seq, and ChIP-seq data. The precise topic of the research project will be determined jointly with the candidate and candidates that display initiative and independence will be given priority. Candidates should have strong mathematical and computational skills, and experience in such areas as stochastic processes, dynamical systems theory, and Bayesian statistics is a plus. Experience with next-generation sequencing data is desirable but not strictly required. Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biologists. The candidates should have a good knowledge of English. German is helpful but not necessary. The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The start date will be by mutual arrangement. Basel is a very international city and a center of life science research, with over 900 life science research companies in the area, including Novartis and Roche. Several other academic institutions are also in the city, including the Friedrich Miescher Institute, the ETH Zurich Biosystems Science and Engineering Department, and the Swiss Tropical Institute. The city is less than 5km from both France and Germany and an hour and a half from the Swiss Alps. To apply, please send a single pdf containing your application letter, CV, and the names of two references to erik.vannimwegen-at-unibas.ch Review of applications will begin immediately. Thomas Julou via Gmail
Source: EVOLDIR
03:26
Free summer school (July 3rd-9th 2016): Introduction to the concepts and methods of networks in evolutionary studies (sequence similarity networks, genome networks and bipartite graphs) This summer school will be held in Roscoff, France, between July 3rd 2016 (date of arrival) and July 9th (date of departure) (http://bit.ly/1FfckPh). This school is designed in priority for biologists and bio-informaticians (completing a PhD degree or currently post-doctoral fellows), who wish to learn the bases of network analyses. The main notions (regarding various types of networks, the relevance of their analyses, and some bases in graph theory) will be introduced by short theoretical classes, followed by practical case-studies, introducing the basics in programming required to run such network analyses as well as to use the existing software/tools. Our goal is that, by the end of this summer school, all applicants will be qualified to perform network analyses of their own datasets. More precisely, we will focus on the following concepts and methods: - Introgressive evolution and large-scale diversity studies. - Construction and analysis of sequence similarity networks (construction and sorting of connected components, definition of gene families, search for composite genes, implementation of centrality measures) - Construction and analysis of genome networks (construction of weighted genome networks, implementation of their diameter, shortest paths, analyses of labeled nodes, etc.) - Construction and analysis of gene-genome bipartite graphs (detection of connected components, and their articulation points, and twins) In addition, conferences on networks and evolution will be delivered by leading scientists during this school. Expected speakers feature : Fernando Baquero, Robert Beiko, Marco Fondi, Michel Habib, Philippe Huneman, Mattis List, Philippe Lopez, and Marc-Andr Slosse. This summer school is funded by ERC grant (FP7/2007-2013 Grant Agreement # 615274). Hence, registration is free, housing and food (breakfast, lunch and dinner) are also fully covered. Applicants will only need to fund their travel to Roscoff. 10 places only are available, with a mandatory requirement: applicants must show basic computer skills (i.e. to be familiar with Linux environment and with at least one programming language, preferably R or Python). Applications are to be submitted asap, and no later than January 15th 2016, by email to : eric.bapteste@upmc.fr , and contain a brief letter describing why this class will be of significant interest for the applicant and his/her future studies. Applicants will be selected based on their motivation, and their resume, including the names of two scientific referees. We are excited to meet you soon in Roscoff. Eric Bapteste + Philippe Lopez Bapteste Eric via Gmail
Source: EVOLDIR

August 30, 2015

16:30

Last week I blogged about Spinach and the iron fallacy. I analysed an early set of data by Thomas Richardson (1848), who calculated the amount of iron in combusted ash for various vegetables and fruits, and showed that spinach is not at all unusual in its constituents. The idea that spinach is rich in iron is untrue, and the story about a mis-placed decimal point seems to be nothing more than an urban myth.

In the meantime, Joachim Dagg, at the Natural History Apostilles blog, has reanalysed Richardson's data and revealed that The first source for the spinach-iron myth is likely to have been a somewhat inappropriate attempt to combine his data for the percent iron values in relation to the ash with the percent values of the ashes in in relation to the fresh matter.

So, I have recalculated the phylogenetic network using these "adjusted" values. I used the percent values of the chemical constituents in relation to the pure ash (raw ash minus carbonic acid, charcoal and sand), and combined them with the percent values of the ashes. The issue here is that radish roots and leaves have the largest ash values, followed by cherry stems and spinach. This leads to an over-statement of the chemical contents. In particular, the iron content moves spinach from being ranked sixth to second (behind radish foliage, which is not usually eaten).


August 29, 2015

23:36
The Hughes Lab is seeking a Postdoctoral Scholar to work on PlantVillage. This position is in collaboration with the lab of Dr Marcel Salathe at EPFL, Switzerland who together with Hughes is the co-founder of PlantVillage. The position is available in the Centre for Infectious Disease Dynamics (www.cidd.psu.edu), The Pennsylvania State University, University Park Campus. PlantVillage (www.plantvillage.com) wants to impact global food production by making the knowledge needed to increase crop yields immediately available to all growers around the world. Agriculture was humanitys first and arguably most important knowledge society. It was knowledge that led to crop domestication and the many improvements in the subsequent 10,000 years, providing the foundation for modern civilization. But the knowledge is not available everywhere. The move towards universal access to broadband via mobile devices offers the promise of democratizing access. The smartphone platform PlantVillage is already doing that. PlantVillage makes available thousands of pages and images of high quality, science-based knowledge on plant health. This is free to anyone with a smartphone or Internet connection. We provide any grower, anywhere, the essential knowledge they need. In addition, we provide the world`s largest social network within a community platform of global experts. Post a question and the global community answers it. Using our platform, growers are not limited by their lack of access to knowledge and so can get the latest advice on nutrient delivery, pest management and cultivation, as well as where to source seeds and sell produce. The Postdoctoral Scholar position at Penn State involves the development of approaches that facilitate the automatic identification of plant diseases via smartphones. This involves codifying both the diseases and the decisions plant pathologists make. This is important for the development of eventual algorithms that automate disease diagnosis. The ideal candidate will have a range of applicable skills including plant pathology, image recognition of diseases, biostatistics and modeling disease in plants. The position also requires contributing to the PlantVillage database by collecting images of healthy and diseased plants as well as adding content to the PlantVillage library. The candidate should also engage in the community Q&A portion of PlantVillage as well as liaising with a diverse group of stakeholders interested in disease detection in crops. This position will involve travel to field sites both nationally and internationally to source images. Candidates should demonstrate a track record of publication; have extremely strong organizational, written, and oral communication skills; and be able to work both independently and as part of a collaborative team. This position is initially funded for one year, with the possibility of a second year. For further information, please feel free to contact Dr Hughes (dph14@psu.edu; +1 814- 863-6073). Interested applicants should upload a curriculum vitae, a 1-2 page statement of research interests that explicitly describes professional qualifications for this position, and contact information for three referees. Review of applicants is ongoing and the position will begin when a suitable candidate is selected. The Pennsylvania State University requires all applicants to register and complete the application form at the Penn State employment website at http://bit.ly/1KuA1ZTwww.cidd.psu.edu), The Pennsylvania State University, University Park Campus. PlantVillage (www.plantvillage.com) wants to impact global food production by making the knowledge needed to increase crop yields immediately available to all growers around the world. Agriculture was humanitys first and arguably most important knowledge society. It was knowledge that led to crop domestication and the many improvements in the subsequent 10,000 years, providing the foundation for modern civilization. But the knowledge is not available everywhere. The move towards universal access to broadband via mobile devices offers the promise of democratizing access. The smartphone platform PlantVillage is already doing that. PlantVillage makes available thousands of pages and images of high quality, science-based knowledge on plant health. This is free to anyone with a smartphone or Internet connection. We provide any grower, anywhere, the essential knowledge they need. In addition, we provide the world`s largest social network within a community platform of global experts. Post a question and the global community answers it. Using our platform, growers are not limited by their lack of access to knowledge and so can get the latest advice on nutrient delivery, pest management and cultivation, as well as where to source seeds and sell produce. The Postdoctoral Scholar position at Penn State involves the development of approaches that facilitate the automatic identification of plant diseases via smartphones. This involves codifying both the diseases and the decisions plant pathologists make. This is important for the development of eventual algorithms that automate disease diagnosis. The ideal candidate will have a range of applicable skills including plant pathology, image recognition of diseases, biostatistics and modeling disease in plants. The position also requires contributing to the PlantVillage database by collecting images of healthy and diseased plants as well as adding content to the PlantVillage library. The candidate should also engage in the community Q&A portion of PlantVillage as well as liaising with a diverse group of stakeholders interested in disease detection in crops. This position will involve travel to field sites both nationally and internationally to source images. Candidates should demonstrate a track record of publication; have extremely strong organizational, written, and oral communication skills; and be able to work both independently and as part of a collaborative team. This position is initially funded for one year, with the possibility of a second year. For further information, please feel free to contact Dr Hughes (dph14@psu.edu; +1 814- 863-6073). Interested applicants should upload a curriculum vitae, a 1-2 page statement of research interests that explicitly describes professional qualifications for this position, and contact information for three referees. Review of applicants is ongoing and the position will begin when a suitable candidate is selected. The Pennsylvania State University requires all applicants to register and complete the application form at the Penn State employment website at http://bit.ly/1KuA1ZT David Hughes: Hughes, is a behavioral ecologist who has studied social insects and their diseases in 11 countries on 5 continents. He has worked with diverse diseases as well as the behavior of healthy and infected ants under field (rain- and temperate forests) and laboratory conditions. In recent years he has become interested in plant diseases. www.hugheslab.com Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. David Hughes CIDD, Dept Entomology & Biology, Penn State www.hugheslab.com www.plantvillage.com dhughes@psu.edu twitter: @zombieantguy, @plantvillage 814 863 6073 (Office) 814 777 7366 (Cell) David Hughes via Gmail
Source: EVOLDIR
14:39

@ss107 wrote:

The rate matrix (Q) for Jukes-Cantor generally is expressed as described here: https://en.wikipedia.org/wiki/Models_of_DNA_evolution#Most_common_models_of_DNA_evolution

The factor (1/4) comes because the base frequency is 0.25 in Jukes-Cantor analysis and μ is the rate of substitution.

The transition/probability matrix [P(t)] for any branch length (t) is the exponentiation of Q multiplied by t.

What I understand is: The matrix P will be entirely different if the substitution rate μ have two different values (say 0.25 and 1).

The question I have: Is there any restriction on the value of μ?

Related software packages like SeqGen/MrBayes expresses the rate matrix in terms of six rates {AC, AG, AT, CG, CT, GT} which all equals μ in this discussion.

From the examples from the related manuals, I think they normalize the rates such that their sum would be 1. That means, for JC, 6 μ = 1 always!

Generally, the substitution rates are taken as input either as percentages of the rate sum or they are scaled to the GT rate. I believe this information is not enough to decide the actual rate.

In simple terms, for JC, saying,

AC = AG = AT = CG = CT = GT

is not enough. You have to explicitly tell what the value is. Based on that value, the transition/probability matrix can change drastically.

If I always normalize the values then rate matrix for JC reduces to a matrix with static values.

I know some of my understanding is wrong. Where am I wrong?

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02:24
Post-doctoral position in molecular evolution Three two-year post-doctoral positions are available in the Ellegren lab at the Evolutionary Biology Centre, Uppsala University, Sweden (http://bit.ly/1IsgBil). Two positions are broadly defined as population genomics and one as molecular evolution (presented below), although there is some extent of overlap both in terms of concepts and data used among the positions. We are interested in how sequence evolution and evolution of base-composition are related to factors such as epigenetic modifications, life history and recombination. Avian genomes are in focus for our research (allowing analyses of highly heterogeneous recombination landscapes) and we perform whole-genome re-sequencing of population samples to obtain detailed estimates of the site-frequency spectrum. Examples of on-going work are studies of methylation in avian genomes based on whole-genome bisulfite sequencing and how methylation affects substitution patterns and gene expression, how GC-biased gene conversion give genomic signals mimicking those of selection (and how signals of gBGC and selection can be separated), and the link between life history and rates of diversity/divergence. The specific questions to be addressed will be decided in dialogue with the successful candidate and will depend on her/his interests and background. Recent publications from the group relating to the project include Weber et al 2014 Genome Biology 15:542 and 15:549; Mugal et al 2015 G3 5:441-447; Smeds et al 2015 Nature Communications 6:7330; Uebbing et al 2015 Mol Biol Evol, in press. Suitable background to this position is a PhD geared toward molecular evolution, population genetics, or bioinformatics. Experience from bioinformatic analyses of next-generation sequencing data is of merit. Start date is flexible, ideally before January 1, 2016. The position can be extended for up to two more years. For full consideration, please send application materials by September 18, 2015. Interested candidates should submit the following to Hans.Ellegren@ebc.uu.se - a cover letter stating research interests, - CV, including publication record - a short (1-2 page) description of research accomplishments, - email addresses and phone numbers of three references Please feel free to contact me at the above email address with questions. The venue for the position, the Evolutionary Biology Centre, is situated in central Uppsala. The working atmosphere is international with the great majority of PhD students and post-docs recruited from abroad. The Centre constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, housing some 300 scientists and graduate students. The scientific environment with numerous seminars, journal clubs and social activities offer excellent possibilities for contacts and collaborations. Local platforms for high-performance computational analyses (http://bit.ly/SetGti), NGS, SNP genotyping and proteomic analyses (http://bit.ly/17a7QLt) ensure immediate access to state-of-the-art technology. Uppsala University is the oldest university in Scandinavia and the city of Uppsala is a vibrant student town with beautiful and easy accessible surroundings conveniently situated close to Stockholm. The Ellegren group is part of the Department of Evolutionary Biology (http://bit.ly/1DLY70Z), which is a branch of the larger Department of Ecology and Genetics (http://bit.ly/1L4KtWv). The Department of Evolutionary Biology houses 8 independent research groups and about 25 PhD students, 25 postdocs, and several bioinformaticians. A common theme is that we address key questions in evolutionary biology, like speciation, local adaptation, life history evolution, genome and molecular evolution, using genomic approaches. We have tight connections with several other research groups in the Department of Ecology and Genetics within the Evolutionary Biology Centre. Professor Hans Ellegren Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE-752 36 Uppsala Sweden Email: Hans.Ellegren@ebc.uu.se LAB WEB PAGE: http://bit.ly/1IsgBil Hans Ellegren via Gmail
Source: EVOLDIR
02:09
ASSISTANT PROFESSOR IN COMPUTATIONAL BIOLOGY/GENOMICS The Department of Biology at Washington University in St. Louis (http://bit.ly/17dDCTv ) invites applications for a tenuretrack faculty position at the Assistant Professor level from candidates whose research employs computational and/or genomicscale approaches to answer important biological and/or evolutionary questions. We seek an innovative and accomplished scientist whose research program will complement and diversify existing departmental areas including epigenetics in plant/animal/microbial systems, developmental biology. The successful candidate will have an appointment at the rank of Assistant Professor in the Department of Biology and is expected to establish an externally funded research program. Contributions to both undergraduate and graduate teaching and research mentoring are required. Duties will also include writing research publications, serving as a formal advisor to undergraduate students, and participating in departmental committees and university service. Qualifications include a PhD degree and strong research, mentoring and teaching credentials. Competitive start-up funding, laboratory development resources and ancillary support commensurate with the candidate’s qualifications and needs are available with this position. Consideration of applicants will begin on October 1, 2015 and will continue until the position is filled. Applicants should submit the following materials in a single pdf file format: cover letter; current curriculum vitae; separate statements of research and teaching interests; and the names and contact information of three individuals who can serve as references upon request. Application materials must be submitted electronically to: computationalsearch@wustl.edu Questions regarding the search process should be directed to Douglas Chalker (dchalker@wustl.edu), Chair of the Search Committee. Washington University is committed to excellence through diversity, and we particularly encourage applications from persons from underrepresented groups. Washington University is an Affirmative Action Employer “Musick, Judy” via Gmail
Source: EVOLDIR
01:54
Two post-doctoral positions in population genomics Three two-year post-doctoral positions are available in the Ellegren lab at the Evolutionary Biology Centre, Uppsala University, Sweden (http://bit.ly/1IsgBil). Two positions are broadly defined as population genomics (presented below) and one as molecular evolution, although there is some extent of overlap both in terms of concepts and data used among the positions. 1. Population genomics We use flycatchers of the genus Ficedula to study evolutionary processes related to the evolution of heterogeneous genomic landscapes of species differentiation (e.g. Ellegren et al 2012 Nature 491:756-760). There is increasing evidence that genomic regions with elevated differentiation (‘differentiation islands’) can evolve by processes unrelated to speciation. For example, the concept of linked selection, which is particularly pronounced in low-recombining regions, will locally reduce the effective population size and thereby enhance genetic drift of segregating variants. Pursuing these studies using haplotype-based statistics and NGS-data from sequencing platforms generating long reads is one possible direction of research for the post-doc. Other directions include, for example, demographic analyses and studies of the recombination landscape. The specific questions to be addressed will be decided in dialogue with the successful candidate and will depend on her/his interests and background. Recent publications from the group relating to the project include Nadachowska-Brzyska et al 2015 Current Biology 25:1375-1380; Nater et al 2015 Systematic Biology, in press; Smeds et al. 2015 Nature Communications 6:7330; Suh et al 2015 PLoS Biology 13:1002224. 2. Population genomics The wolf was once widespread in Scandinavia, as well as in other parts of Europe, but long-term persecution led to its extinction by the 1960s. Two animals founded a new population in Sweden in the 1970s and a limited number of immigrants have subsequently become integrated with the population and it has grown to several hundreds of individuals. The population is highly inbred (inbreeding coefficient of newborns is currently 0.25 on average) and there are signs of inbreeding depression. We are now conducting whole-genome re-sequecning of 100 animals sampled from throughout the time period since the new population was founded. The post-doc will be responsible for analysing these data with the aims of investigating the rate of allelic loss, the extent and distribution of genomic regions identical-by-descent, the genomic contribution of each founder to the extant population, and to compare genetic relationships derived from the pedigree and genome sequence data. Several other research questions can apply as well. The project is a collaboration with Grimso Wildlife Research Station of the Swedish University of Agricultural Sciences. Suitable background to these position is a PhD geared toward evolutionary biology, population genetics, or bioinformatics. Experience from bioinformatic analyses of next-generation sequencing data is of merit. Depending on the direction of research to be taken, experience of demographic modeling, molecular evolutionary analyses or conservation biology could also be of merit. Start date is flexible, ideally before January 1, 2016. The positions can be extended for up to two more years. For full consideration, please send application materials by September 18, 2015. Interested candidates should submit the following to Hans.Ellegren@ebc.uu.se - a cover letter stating research interests, - CV, including publication record - a short (1-2 page) description of research accomplishments, - email addresses and phone numbers of three references Please feel free to contact me at the above email address with questions. The venue for the positions, the Evolutionary Biology Centre, is situated in central Uppsala. The working atmosphere is international with the great majority of PhD students and post-docs recruited from abroad. The Centre constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, housing some 300 scientists and graduate students. The scientific environment with numerous seminars, journal clubs and social activities offer excellent possibilities for contacts and collaborations. Local platforms for high-performance computational analyses (http://bit.ly/SetGti), NGS, SNP genotyping and proteomic analyses (http://bit.ly/17a7QLt) ensure immediate access to state-of-the-art technology. Uppsala University is the oldest university in Scandinavia and the city of Uppsala is a vibrant student town with beautiful and easy accessible surroundings conveniently situated close to Stockholm. The Ellegren group is part of the Department of Evolutionary Biology (http://bit.ly/1DLY70Z), which is a branch of the larger Department of Ecology and Genetics (http://bit.ly/1L4KtWv). The Department of Evolutionary Biology houses 8 independent research groups and about 25 PhD students, 25 postdocs, and several bioinformaticians. A common theme is that we address key questions in evolutionary biology, like speciation, local adaptation, life history evolution, genome and molecular evolution, using genomic approaches. We have tight connections with several other research groups in the Department of Ecology and Genetics within the Evolutionary Biology Centre. Professor Hans Ellegren Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE-752 36 Uppsala Sweden Email: Hans.Ellegren@ebc.uu.se LAB WEB PAGE: http://bit.ly/1IsgBil Hans Ellegren via Gmail
Source: EVOLDIR
01:54
Bioinformatician We seek a dedicated and talented person to join Hans Ellegren’s research group at the Evolutionary Biology Centre, Uppsala University, Sweden (http://bit.ly/1IsgBil) as bioinformatician. We work with large-scale genomic approaches to general evolutionary questions such as speciation, DNA sequence evolution and sex chromosome evolution. Our main study system is birds and we have sequenced and assembled the flycatcher genome in house (Ellegren et al 2012 Nature 491:756-760), and were part of the large avian phylogenomics consortium (Jarvis et al 2014 Science 346:1320-1331). By whole-genome re-sequencing of large population samples of different flycatcher species we gather extensive amounts of SNP data and use these for population genomic analyses. The bioinformatician, who will be fully integrated with the research group, will work with genome assembly and detection of structural variation using data from NGS-technologies that provide long (>10 kb) reads. She/he will also be responsible for curation of flycatcher genome sequence data and participate in research projects. The position is initially for one year but can be extended. It can also be combined with PhD studies. Suitable background is a BSc or MSc in, for example, bioinformatics or computer science. Experience from working with NGS-data in UNIX environment is of merit, as is familiarity with relevant programming languages (e.g. Perl, Pyton). To apply for the position, please visit the Uppsala University web site for Open Positions and log in and register your application at http://bit.ly/1NNhnO5 Closing date for the application is Sep 20. Please feel free to contact me at Hans.Ellegren@ebc.uu.se with any questions. Our research group consists of some 15 scientists, including PhD students, post-docs and bioinformaticians. The research is funded by the European Research Council (ERC), Knut and Alice Wallenbergs Foundation and the Swedish Research Council. The venue for the position, the Evolutionary Biology Centre, is situated in central Uppsala. The working atmosphere is international with the great majority of PhD students and post-docs recruited from abroad. The Centre constitutes an exciting arena for multidisciplinary research in evolutionary biology in a broad sense, housing some 300 scientists and graduate students. The scientific environment with numerous seminars, journal clubs and social activities offer excellent possibilities for contacts and collaborations. Local platforms for high-performance computational analyses (http://bit.ly/SetGti), NGS, SNP genotyping and proteomic analyses (http://bit.ly/17a7QLt) ensure immediate access to state-of-the-art technology. Uppsala University is the oldest university in Scandinavia and the city of Uppsala is a vibrant student town with beautiful and easy accessible surroundings conveniently situated close to Stockholm. The Ellegren group is part of the Department of Evolutionary Biology (http://bit.ly/1DLY70Z), which is a branch of the larger Department of Ecology and Genetics (http://bit.ly/1L4KtWv). The Department of Evolutionary Biology houses 8 independent research groups and about 25 PhD students, 25 postdocs, and several bioinformaticians. A common theme is that we address key questions in evolutionary biology, like speciation, local adaptation, life history evolution, genome and molecular evolution, using genomic approaches. We have tight connections with several other research groups in the Department of Ecology and Genetics within the Evolutionary Biology Centre. Professor Hans Ellegren Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvgen 18D SE-752 36 Uppsala Sweden Email: Hans.Ellegren@ebc.uu.se LAB WEB PAGE: http://bit.ly/1IsgBil Hans Ellegren via Gmail
Source: EVOLDIR
00:54
Post-doctoral position: Pinniped population genomicsWith Dr Joe Hoffman (Bielefeld University, Germany), Prof Oliver Kruger (Bielefeld University, Germany), and Dr Jochen Wolf (Evolutionary Biology Centre, Uppsala, Sweden) A two-year postdoctoral researcher position is available to work in the groups of Joe Hoffman at Bielefeld University in Germany and Jochen Wolf at the Evolutionary Biology Centre in Uppsala, Sweden. This postdoc position is broadly embedded in a research project on Galapagos sea lions (Zalophus wollebaeki) that Prof Fritz Trillmich and Dr Jochen Wolf started 12 years ago (http://bit.ly/YgunGe). Using whole genome re-sequencing data from more than 100 individuals across the entire species range, the postdoc will explore key evolutionary processes such as the genetic basis of speciation, adaptation and fitness. An important feature of this system is the presence of different ecotypes in an essentially sympatric setup (Wolf et al. 2008, Shafer & Wolf 2013). There will also be the opportunity to work on Antarctic fur seals (Arctocephalus gazella), opening a comparative axis to the project. Funding: This postdoc is funded by the German Science Foundation (DFG) for up to two years and includes health insurance. The pay scale is TVL E13 (100%). The postdoc will be based in Bielefeld, but will have considerable flexibility over how much time they spend in Bielefeld and in Uppsala. A joint postdoc will provide you with an excellent opportunity for international travel and collaboration, and experience of working in diverse environments. The environment: The postdoc will join the Department of Animal Behaviour at Bielefeld University, Germany (http://bit.ly/1eK4Lnp) and the Evolutionary Biology Centre, Uppsala University, Sweden (http://www.ebc.uu.se). The department of Animal Behaviour in Bielefeld is the oldest of its kind in Germany and currently hosts six principal investigators, seven postdocs and twenty PhD students. It offers a stimulating international environment and an excellent research infrastructure. The working language of the Department is English. Bielefeld is a small city with an attractive historical centre and easy access to the Teutoburger Wald for hiking and other outdoor pursuits. It offers a very high standard of living and is well connected to most major European cities. The Evolutionary Biology Centre is one of the worlds leading research institutions in evolutionary biology. It is part of Uppsala University which has been ranked first place among all European Universities in the subject of biology (CHE European ranking) and bridges a broad variety of disciplines. The scientific environment with numerous seminars, journal clubs and social activities offers excellent possibilities for contacts and collaborations. Dr Wolf’s lab is part of the Department of Evolutionary Biology (http://bit.ly/1MTPN0Q) and addresses fundamental evolutionary questions using a wide range of different approaches. As a member of the Science for Life Laboratory (http://bit.ly/17a7QLt) we have access to high performance computing resources (http://bit.ly/SetGti), excellent lab facilities and extended bioinformatic infrastructure (http://bit.ly/SOCSVQ). The lab is situated in the student town of Uppsala, which offers rich opportunities for cultural and outdoor activities. Sweden’s capital Stockholm is less than an hour’s train ride away. Qualifications: The successful applicant will hold a PhD degree, have a thorough background in population genetics and/or comparative genomics and be experienced in handling large genome-wide data sets. Population geneticists with a more theoretical background are also encouraged to apply. A high standard of spoken and written English is required. How to apply: Please provide: (i) a letter of motivation including a maximum 2-page statement of your research interests, relevant skills and experience; (ii) a CV including publication list; and (iii) names and contact details of three referees willing to write confidential letters of recommendation. All materials should be emailed as a single PDF file to: joseph.hoffman@uni-bielefeld.de with ‘Postdoc application’ in the subject line. The application deadline is October 5th 2015 and interviews will take place in the following few weeks. The start date is flexible and will depend on the timeframe of the most qualified applicant, but would ideally be before the end of this year. For further information, please see http://bit.ly/1B0eNNc and http://bit.ly/1fMkoQU or contact Joe Hoffman (joseph.hoffman@uni-bielefeld.de) or Jochen Wolf (jochen.wolf@ebc.uu.se) with any informal inquiries. The University of Bielefeld is an equal opportunity employer and particularly welcomes applications from women. Given equal suitability, qualifications and professional achievement, women will be given preference, unless particular circumstances pertaining to a male applicant apply. For representative publications, please see: Poelstra JW, Vijay N, Bossu CM et al. Wolf JBW (2014) The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344: 1410-1414. Forcada, J. & Hoffman, J.I. (2014). Climate change selects for heterozygosity in a declining fur seal population. Nature, 511: 462V465. Hoffman JI, Simpson F, David P et al. (2014) High-throughput sequencing reveals inbreeding depression in a natural population. PNAS, 111: 3775V3780. Shafer ABA, Wolf JBW (2013) Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology. Ecol Lett, 16: 940V950. Ellegren H, Smeds L, Burri R et al. Wolf JBW (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491: 756V760. Wolf JBW, Harrod C, Brunner S et al. (2008) Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galapagos sea lion populations. BMC Evol Biol, 8: 150. Joe Hoffman Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany +49 (0)521 1062711 http://bit.ly/1B0eNNc Joe Hoffman via Gmail
Source: EVOLDIR
00:24
PhD studies available at Adam Mickiewicz University in Poznan, Poland A PhD position is available within a grant from National Science Centre entitled “The regulatory roles of long non-coding RNAs in the context of RNA:RNA interactions” (2014/15/D/NZ2/00525). The project is centered around long non-coding RNAs (lncRNAs), including prediction of novel lncRNAs, deciphering their functions, expression estimation using next-generation sequencing data, evolutionary analyses and developing biological databases. Moreover, laboratory tests will be performed to provide experimental evidence for selected predictions. As a result, it is required that the candidate possesses basic knowledge in the area o molecular biology, while experience in bioinformatics and/or programming skills will enhance the application greatly. A short description of the project is available at: http://bit.ly/1MTis4e Requirements: * Masters degree in biological sciences * Knowledge of basics of molecular biology * Fluency in English * Writing and editing scientific texts * Optionally: programming skills, experience in bioinformatics Conditions: * A scholarship from National Science Centre of 3000 PLN/month * Term of scholarship: 36 months Candidates are asked to submit their applications at miszcz@amu.edu.pl, including: * Motivation letter * Curriculum Vitae * At least one reference letter * Any additional documents that might enhance candidate’s application Deadline: September 10th, 2015. Best regards, Micha Szczeniak, PhD Adam Mickiewicz University in Poznan, Poland Michal Szczesniak via Gmail
Source: EVOLDIR

August 28, 2015

23:54

Advanced Bioinformatics Workshop for Early Career Researchers 9 - 13 November, 2015 The University of Adelaide, North Terrace Campus Hosted by the Australian Centre for Ancient DNA (ACAD), this workshop is back for 2015, and early bird registration is currently open. The workshop is based on the successful 2012 to 2014 workshops encompassing an intensive 5 day hands-on training course tutored by international experts utilising the latest techniques and available software for the analysis of Next Generation Sequencing (NGS), Genomics and Metagenomics data. This years line-up is Paul Stothard (variant discovery, RNA-seq), Rob Knight (metagenomics, QIIME), Martin Kircher (NGS and data pre-processing) and Remco Bouckaert (BEAST, SNAPP). Pre-requisites: Delegates must be familiar with UNIX environments and basic command lines, and will have a basic knowledge of the technology and analytical tools of NGS. Early bird registration is now open with 40 seats available, so be quick to reserve your place. Further information can be found at the official website: http://bit.ly/1LIaQF0 via Gmail

Source: EVOLDIR
23:54

3 Postdoc and 2 PhD positions in theoretical biology, systems biology & experimental evolution At the Theoretical Research in Evolutionary Life Sciences group (TRÊS, formerly known as Theoretical Biology) at the University of Groningen in the Netherlands, we have the following 5 positions immediately available: (1) Postdoc (2.5-3yr): Towards a quantitative evolutionary theory of caste-specific senescence in social insects. The reproductive casts of eusocial insect species typically far outlive their genetically nearly identical worker casts. This makes them uniquely suitable for developing and testing evolutionary theories of ageing. In this project, quantitative evolutionary models will be developed to predict cast-specific senescence profiles and how they vary with species-specific social structure, ecology and life history characteristics of social insects. Both relatively simple analytical life history models and more complex systems biological simulation models will be developed. In close collaboration with several experimental social insect groups in Germany, models will be parameterized with life history data and experimental data from other projects in order to test predictions and guide further experimental research. Contact: Ido Pen (i.r.pen@rug.nl) (2) Postdoc (2yr): The evolution of self-organized division of labour in social insects. Division of labour (DOL) is characterized by the coordinated interaction of individuals that collectively achieve a common goal with high efficiency by specializing on certain tasks. DOL plays a crucial role for life on this planet; yet its evolution is not well-understood. Natural selection on DOL is indirect, since DOL is not a heritable property in itself but the result of self- organisation. The challenge is to understand how selection acting on individual behaviour results in the evolution of well-organized collective behaviour. To meet this challenge, we will develop and analyse models for the evolution of self-organized division of labour in social insects. In the project we will study how evolved division of labour is shaped by the interplay of internal factors (such as genetic system, mating structure, behavioural architecture) and external conditions (such as the spatial and temporal distribution of resources or between-colony conflicts). Contact: Franjo Weissing (f.j.weissing@rug.nl) (3) Postdoc (1yr): The evolution of dispersal syndromes. The study of ‘behavioural syndromes’ or ‘animal personalities’ is currently a hot topic in the behavioural sciences. In organisms ranging from squids to chimpanzees it has been shown that individuals differ systematically in their behavioural tendencies, that this differences are stable in time, and that behavioural differences in quite different domains (like dispersal and parental behaviour) are correlated with each other. Over the years, our group has developed many models for explaining the evolutionary emergence and stability of such syndromes. In this project, we will develop evolutionary models for dispersal syndromes. In hundreds of species it has been shown that genetically similar individuals differ strongly in their dispersal and migration tendencies, and that these differences are correlated with other behavioural and physiological differences. A general explanation for the emergence and structure of these syndromes is, however, still lacking. This is a joint project with empirical behavioural ecologists (Prof. Dr. Jan Komdeur, Dr. Hannah Dugdale). It is an ideal stepping-stone for writing a grant proposal for a longer stay at the University of Groningen. Contact: Franjo Weissing (f.j.weissing@rug.nl) (4) PhD (4yr): Molecular evolution of the bacterial chemotaxis network. The molecular network underlying chemotaxis in bacteria has emerged as a prototype for studying the molecular basis of behavior and evolutionary adaptation. This small signal- transduction network has been extensively studied in Escherichia coli, but has also been characterized in other bacteria, such as Bacillus subtilis. Surprisingly, many components of the chemotaxis network are shared across species, while striking interspecific differences exist in the topology and complexity of the network. In this project, we will combine systems-biology modelling, evolutionary analyses and bio-informatic approaches to explain these patterns, and also aim to develop broader insights into the evolution of molecular networks. Contact: Sander van Doorn (g.s.van.doorn@rug.nl) (5) PhD (4yr): Genome architecture and adaptation Evolutionary models typically assume that traits have a simple genetic basis, but in reality genes occur in a complex genomic context. In this project, we focus on the architecture of the genome, and how it affects mutation, recombination and, eventually, phenotypic adaptation. Also, we will investigate how selection and non-adaptive processes shape the genomic architecture and evolvability of traits. The project will integrate proximate and ultimate research approaches, using a combination of microbial evolution experiments, computational modelling and bio- informatics. Contact: Sander van Doorn (g.s.van.doorn@rug.nl) To apply for a specific position, please send a letter of motivation and an extensive CV (including the names and email addresses of three referees) to the contact person indicated for the position. via Gmail

Source: EVOLDIR
23:54
Post-Doctoral Fellowship in Bacterial Pathogen Evolutionary Genomics A post-doctoral researcher position is available in the Laboratory for Bacterial Evolution and Pathogenesis at The Roslin Institute, University of Edinburgh with Professor J. Ross Fitzgerald, in collaboration with colleagues at National Health Service (NHS) Scotland and Dr Nick Loman at the University of Birmingham. The 2 year Scottish executive-funded project will investigate the evolutionary genomics of the human pathogen Legionella pneumophila, responsible for major outbreaks of Legionnaires disease in human populations, using a comparative next generation sequencing approach. Building on recent and ongoing work from the group, the post-doc will investigate the evolutionary origin, dissemination, and pathogenicity of the common strains of Legionella associated with outbreaks in Scotland, and the rest of the world. In addition, high throughput sequencing including Illumina and Nanopore sequencing technologies will be applied to develop a culture-free approach for identifying Legionella strain variation in environmental and clinical samples, in order to enhance outbreak investigations. The candidate will have a PhD in bacterial genomics/computational biology and have broad experience of handling large numbers of bacterial genome sequences for comparative and evolutionary analyses. The Roslin Institute is a world-class centre for biomedical research of relevance to both animal and human health with a strong focus on infectious diseases. The Institute has access to state of the art research facilities for imaging, proteomics, and genomics, including high-throughput sequencing. The project will involve close collaboration with clinical and public health colleagues in the NHS, Scotland and other research groups within Edinburgh Infectious Diseases in the University of Edinburgh. Informal enquiries: Ross.Fitzgerald@ed.ac.uk Relevant selected references: McAdam PR, Vander Broek CW, Lindsay DS, Ward MJ, Hanson MF, Gillies M, Watson M, Stevens JM, Edwards GF, Fitzgerald JR. Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak. Genome Biol. 2014 Nov 3;15(11):504. McAdam PR, Richardson EJ, Fitzgerald JR. High-throughput sequencing for the study of bacterial pathogen biology. Curr Opin Microbiol. 2014 Jun;19:106-13. – The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. FITZGERALD Ross via Gmail
Source: EVOLDIR
18:08

@ematsen wrote:

I'm going to keep on advertising this position with @trvrb until I'm hoarse, because I think that B cell receptor analysis is just about the coolest thing right now.

If you need a practical reason to check this out, this is a way for you to get in on the ground level of a new subfield of molecular evolution / phylogenetics which is rich in data and very weak in methods, and to get biomedical funding for phylogenetic work (which is a good thing in the current funding environment).

Here is the text of the ad:

A new postdoctoral position is available in the groups of Trevor Bedford and Erick Matsen at the Fred Hutchinson Cancer Research Center located in Seattle, WA. This position will focus on analyzing immune repertoire sequence data from an evolutionary perspective.

Deep sequencing of B cell repertoires has opened up the possibility of understanding the immune response at a molecular level. This project will analyze repertoire data to compare processes of clonal expansion and affinity maturation in primary and secondary immune responses. These studies will allow, for the first time, a detailed mechanistic understanding of original antigenic sin in viral infection; results from these studies may allow construction of vaccines that better deal with a diversity of pathogen exposures. This work represents a collaboration with experimental colleagues at the Fred Hutch, Emory University and Adaptive Biotechnologies. There will be no want of fresh data.

The ideal candidate will have experience with working with sequence data and a strong interest in model-based statistical analysis of real data sets. Data sets will comprise millions of B cell repertoire sequences and so strong coding abilities are essential. Candidates should have experience in at least one programming language and a proven track-record of peer reviewed publications. Candidates with PhDs from diverse backgrounds are encouraged to apply, including biology, mathematics, statistics, physics and computer science. However, experience in phylogenetics or immunological bioinformatics is especially opportune. The Fred Hutch is an equal opportunity employer, committed to workforce diversity. Women and minorities are particularly encouraged to apply.

The position is available immediately with flexible starting dates for a 2-year appointment with possibility of extension. Informal inquires are welcome. Applications will be accepted until the position is filled. The Fred Hutchinson Cancer Research Center offers competitive salaries commensurate with experience and skills, complete with benefits.

To apply please send (1) cover letter that includes the names and contacts for three references and a short statement of research interests, (2) a current CV and (3) code samples or links to published/distributed code to trevor@bedford.io.

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17:21

@ematsen wrote:

News to me: p4 phylogenetics toolkit, which does inference and manipulation.

P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences. Its specialty is that it can use heterogeneous models, where the characteristics of the model can differ over the data or over the tree.

  • P4 can be used as a phylogenetic toolkit, the elements of which you can string together in different ways depending on the job at hand. It is useful for programmatic manipulation of phylogenetic data and trees. If you want to do something interesting with your trees or data, p4 might have at least some of what you want to do already in place.
  • P4 will read data in a few of the common phylogenetic formats (eg Nexus, Phylip, clustalw, fasta, pir/nbrf), but does not read other formats in bioinformatics (eg EMBL, genbank). P4 will read in trees in Nexus or Phylip format.
  • P4 will do some elementary data manipulation, eg extracting a Nexus-defined charset from an alignment, or converting data from one format to another. P4 will also do tree manipulation, and tree drawing. It has a big tree viewer, to be able to view big trees (eg up to 5000 taxa) on the screen.
  • P4 is meant to be easily extensible, so if you want to do something that it cannot do, it is often easy to add that functionality.

As far as I can tell, there isn't an overlap with @jeetsukumaran's DendroPy or Paul Lewis' Phycas.

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