The Solana lab is looking for a postdoctoral computational researcher to work on single-cell transcriptomic and genomics of planarian stem cell differentiation. Our lab just started in Oxford Brookes University. We are currently three lab members but we will expand soon. We recently obtained funding from the MRC to expand our single-cell analysis of planarian stem cells.

Background

Single-cell analysis methods are revolutionizing the study of stem cells and development. The planarian Schmidtea mediterranea is a very promising model for stem cell biology thanks to its large number of stem cells. They continuously differentiate to all adult cell types and that enable its amazing regenerative capacities. We have previously used single-cell transcriptomics to study stem cell differentiation in planarians (see Plass, Solana et al. Science 2018). Combining clustering algorithms with graph mathematics and RNA metabolism information, we were able to reconstruct the differentiation lineage tree of planarian stem cells. Our methods, together with those of other groups analysing the developmental biology of Zebrafish, Xenopus and other models at the single-cell level, have been the Breakthrough of the Year 2018 by the Science Magazine.

Research

Future projects in the lab will use these methods and develop them further to study stem cells in planarians and other organisms. Planarians offer the advantage that the whole lineage tree of differentiation is present in just one stage, their adult. Therefore, we can study all differentiated cells, their progenitors and the stem cells all at once. We will use single-cell genomic methods to investigate the regulation of stem cell differentiation at the genomic and transcriptomic level. We will also use the same tools to study other planarian species to get insights into cell type evolution and the regulation of their differentiation. Finally, we will examine other regenerative species to establish the fundamental cellular mechanisms that underlie animal regeneration.

Application

For details about funding possibilities contact Dr. Jordi Solana jsolana[at]brookes.ac.uk

For suitability enquiries please include a CV and a brief motivation email.

To apply, please follow the link:

https://www.jobs.ac.uk/job/BPG192/postdoctoral-research-fellow-biological-and-medical-sciences

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The Turing Centre for Living Systems (CENTURI) wishes to attract talented PhD students to the Luminy campus (Marseille, France) and will fund up to 12 PhD fellowships to start in 2019, for three years. PhD students will work in an interdisciplinary life science environment, and have backgrounds in any of the following fields: cell or developmental biology, immunology, neurobiology, biophysics, theoretical physics, computer science, bioinformatics, applied mathematics, engineering. PhD projects must involve at least two research groups from different disciplines, to foster collaborations and interdisciplinarity.

Candidates can either apply to one of the advertised CENTURI projects or submit their own project, providing that they meet the application criteria and that their application is supported by at least one host lab.

Expected profile – selection criteria

Candidates must have, or expect to obtain a Master’s degree in biology, computer science, computational biology, mathematics, physics or engineering. Candidates will be evaluated on the following criteria:

• Academic achievements
• Past research experience (internships)
• Ability to work on a collaborative research project
• Ability to work in a multidisciplinary research environment
• Enthusiasm and communication skills

To see the list of PHD projects and to apply, please visit: http://centuri-livingsystems.org/recruitment

PhD duration: 3 years

Deadline for application: February 15, 2019

Interviews in Marseille (pre-selected candidates only): April 23 – 26, 2019

How to apply:

Students are required to apply on CENTURI’s website. Applications must include the following documents (compiled into a single PDF file):

• CV
• cover letter
• transcript of your MSc’s grades (M1 and M2 if available)

2 letters of recommendation must also be sent by your references at info@centuri-livingsystems.org.

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Identity and Diversity: Developmental Biology from Molecules to Cells to Organisms

Mt. Holyoke College, MA, USA

June 16th-20th, 2019 (GRS June 15th-16th)

https://www.grc.org/developmental-biology-conference/2019/

The 2019 Gordon Conference on Developmental Biology will present the most recent, cutting-edge research in the field. In keeping with this year’s theme of Identity and Diversity: Developmental Biology from Molecules to Cells to Organisms, we will have nine sessions of oral presentations covering cell identity and robustness in the era of single-cell ‘omics, developmental time, chromatin and epigenetic influences on cell identity, dynamic imaging (and imaging dynamics), new concepts of pattern, metabolism and growth control, developmental robustness in noisy systems and will feature a number of investigators working towards in vitro precision in vivo. This year we will also pay tribute to 50 years of “Positional Information”, recognizing the 1969 landmark paper and the work by Lewis Wolpert and others that led to this conceptual synthesis.

Abstracts due March 15th for talk consideration

2019 dev bio GRS_GRC poster

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Genetics Unzipped – a new fortnightly podcast from the UK Genetics Society – has launched ahead of the society’s centenary celebrations throughout 2019.

Presented by award-winning science writer and former Naked Genetics/Naked Scientists podcast host Kat Arney and produced by First Create The Media, Genetics Unzipped will bring you a wide range of stories from the world of genetics, genomics and DNA.

Listeners can expect to hear interviews with experts from around the world, all the latest science news, and a special centenary series celebrating 100 ideas in genetics.

The first full episode is a behind-the-scenes peek at the iconic 2018 Royal Institution Christmas Lectures on the theme ‘Who am I?’, presented by Professors Alice Roberts and Aoife McLysaght, alongside professional pyromaniac and demonstration expert Fran Scott.

The second episode weaves together stories and sounds to explore the deadly DNA that causes Huntington’s disease, find out how a chicken virus managed to win three Nobel prizes, and discovers the silky science of spidergoats.

Founded in 1919, the Genetics Society is one of the oldest learned societies in the world dedicated to supporting and promoting the research, teaching and application of genetics. The Society is a registered charity whose membership includes over 1900 of the UK’s active professional geneticists, including teachers, researchers and students, and is open to anyone with an interest in genetic research or teaching, or in the practical breeding of plants and animals.

Kat Arney is an award-winning science writer, public speaker and broadcaster, and author of the popular genetics books Herding Hemingway’s Cats and How to Code a Human. She co-presented the ground-breaking Naked Scientists BBC radio show and podcast for 15 years, produced and presented the Naked Genetics podcast for 6 years, and has fronted numerous BBC radio 4 science programmes including the comedy factual series Did the Victorians Ruin the World?

Kat founded the communications and media consultancy company First Create the Media in 2018 to enable organisations and companies to find and tell compelling stories about science.

Email podcast@geneticsunzipped.com to get in touch with questions and suggestions for future topics and guests.

Genetics Unzipped is online at Geneticsunzipped.com. Subscribe for free from Apple Podcasts, Google Play, Stitcher, Blubrry, TuneIn, Spotify, Spreaker and all good podcast apps.

(2 votes)

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The Center for Craniofacial Molecular Biology is looking for a talented Public Communications Coordinator to join the team!

Job Description
The Herman Ostrow School of Dentistry of USC’s Center for Craniofacial Molecular Biology is a unique facility that unites world-class researchers in a variety of disciplines centered around structures of the craniofacial region. Since its inception in 1991, CCMB has been home to several major discoveries and has attracted top researchers from around the world.

Position specific job summary:
This position will be responsible for editing scientific manuscripts in developmental biology and related biomedical fields. In addition, this position will manage the Center’s public communications programs to promote the Center and its research projects and programs.

Position specific job accountabilities:
Edits scientific manuscripts and presentations for content and style in preparation for submission and publication. Produces newsletters and other educational and promotional materials in printed and digital formats. Develops content for social media; develops and maintains website and database; coordinates and manages press and communication tasks such as contents, interviews, website news, etc.

Position specific job qualifications:
Must have a deep understanding of biomedical research and help to prepare research manuscripts and grant applications. Must have Master’s degree in biology or a related field; PhD preferred. Must be a confident communicator and presenter, excellent in verbal and written communication skills. Must possess excellent organizational and planning skills. Must be proactive, reliable, responsible and accurate with an attention to detail. Must possess the ability to keep information confidential. Must have a tactical understanding of social media platforms. Must be self-motivated with a positive and professional approach to management.

Apply here: https://usccareers.usc.edu/job/los-angeles/public-communications-coordinator/1209/9457185

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Post-doc in wing pattern formation and morphogenesis:

1.Job/ project description:

The research will involve using and refining an existing mathematical model of wing morphogenesis to explore whether it can be used to predict how wing morphology changes over generations in an artificial selection experiment. These predictions would be contrasted with predictions stemming from a quantitative genetics analysis of fly populations.

The research will take place in the Center of Excellence in Experimental and computational developmental biology of the Biotechnology Institute of the University of Helsinki, Finland.

For a full description of the project check the modeling in part of this funded project: http://www.biocenter.helsinki.fi/salazar/SalazarCiudad_research_plan.pdf

The job is for 1,5 years.

2. Background:

Why organisms are the way they are?

Can we understand the processes by which complex organisms are build in each generation and how these evolved?

The process of embryonic development is now widely acknowledged to be crucial to understand evolution since any change in the phenotype in evolution (e.g. morphology) is first a change in the developmental process by which this phenotype is produced. Over the years we have come to learn that there is a set of developmental rules that determine which phenotypic variation can possibly arise in populations due to genetic mutation (the so called genotype-phenotype map). Since natural selection can act only on existing phenotypic variation, these rules of development have an effect on the direction of evolutionary change.

Our group is devoted to understand these developmental rules and how these can help to better understand the direction of evolutionary change. The ultimate goal is to modify evolutionary theory by considering not only natural selection in populations but also developmental biology in populations. For that aim we combine mathematical models of embryonic development that relate genetic variation to morphological variation with population models. The former models are based on what is currently known in developmental biology.

There are two traditional approaches to study phenotypic evolution. One is quantitative genetics and one is developmental evolutionary biology. The former is based in the statistics of the association between genetic relatedness and phenotypic variation between individuals in populations, the latter in the genetic and bio-mechanical manipulation of the development of lab individuals. While the former models trait variation with an statistical linear approach the latter models it by deterministic non-linear models of gene networks and tissue bio-mechanics. For the most, these two approaches are largely isolated from each other.

The current project aims to contrast and put together these two approaches in a specific easy to study system: the fly wing. In brief, we are growing fly populations and, in each generation, we select the founders of the next generation based on how close they resemble an arbitrary optimal morphology in their wings (based on the proportions between several of their traits). In each generation also, we estimate the G matrix and the selection gradient to see how well one can predict evolution in the next generation. The quantitative genetics predictions will be contrasted with the predictions stemming from a wing morphogenesis model that we built based on our current understanding of wing developmental biology (see Dev Cell. 2015 Aug 10;34(3):310-22 for the model and for slightly similar approaches: Nature. 2013 May 16;497(7449):361-4. and Nature. 2010 Mar 25;464(7288):583-6).

Our center of excellence includes groups working in tooth, wing, hair and mammary glands development. In addition to evolutionary and developmental biologists the center of excellence includes bioinformaticians, populational and quantitative geneticists, systems biologists and paleontologists. The group leaders of the center involved in this project are Jukka Jernvall, Salazar-Ciudad and Shimmi.

“The Academy of Finland’s Centres of Excellence are the flagships of Finnish research. They are close to or at the very cutting edge of science in their fields, carving out new avenues for research, developing creative research environments and training new talented researchers for the Finnish research system.”

3. Requirements:

The applicant must hold a PhD in either evolutionary biology, developmental biology or, preferably, in evolutionary developmental biology (evo-devo). Applicants with a PhD in theoretical or mathematical biology are also welcome.

Programming skills or a willingness to acquire them is required.

The most important requirement is a strong interest and motivation on science and evolution. A capacity for creative and critical thinking is also required.

4. Description of the position:

The fellowship will be for a period of up to 1,5 years (100% research work: no teaching involved).

Salary according to Finnish postdoc salaries.

5. The application must include:

-Motivation letter including a statement of interests

-CV (summarizing degrees obtained, subjects included in degree and grades, average grade).

-Summary of PhD project, its main conclusions and its underlying motivation.

-Application should be sent to: isaac.salazar@helsinki.fi

No official documents are required for the application first stage but these may be required latter on.

6. Deadline:

There is no specific deadline but the position will start in July 2019.

7. Interested candidates should check the centres page:

http://www.biocenter.helsinki.fi/bi/evodevo/ECDev.html

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Postdoctoral position in the Saunders laboratory, Mechanobiology Institute, Singapore

A postdoctoral research position in quantitative biology is available from March 2019 in Asst. Prof. Timothy Saunders’ group at the Mechanobiology Institute, Singapore. The Saunders lab has been active since 2013 and studies the fundamental processes shaping organs and tissues during development.

The Saunders lab extensively uses live imaging of developing Drosophila and zebrafish embryos to understand how complex tissue shape emerges. The position will involve developing image analysis tools to quantitatively analyse such datasets. We are particularly interested in utilising machine learning to improve data analysis. Further, there is the opportunity to develop theoretical tools for understanding tissue mechanics and signalling.

This position is partially funded by an HFSP Young Investigator Award and there are opportunities to work with collaborators in Austria, Spain and Portugal. In particular, the researcher will analyse ex vivo data from Drosophila embryonic extracts and develop biophysical models of this system.

The Saunders lab works at the interface between developmental biology and biophysics. As such, this position offers researchers with expertise in either image analysis or biophysics to work directly with developmental biologists. This offers an exciting opportunity for a dedicated researcher to be part of a genuinely interdisciplinary lab tackling fundamental problems in developmental biology.

Candidates should have strong experience in at least one of the following, and display a willingness to learn the other: (1) experience with image analysis and handling large datasets; (2) biophysical modelling of developing systems. Knowledge of microscopy methods is desired.

The Saunders’ lab is a young group at the Mechanobiology Institute. This provides an exciting prospect for a motivated post-doc to be involved in developing research directions. The post-doc will also be expected to guide and help the graduate students in the laboratory.  More information can be found at: https://mbi.nus.edu.sg/timothy-saunders/saunders-lab/

Qualifications:

1) A Ph.D in Biophysics, Computational Biology, or related subject. Applicants with a background in biology but who can show proficiency in computational analysis are also encouraged to apply.

2) At least one first-author paper in English submitted to an international peer-reviewed journal

3) Experience in at least one of: (i) Image analysis and handling large datasets; and (ii) Biophysical modelling

Salary and benefits are commensurable to educational qualifications and working experience of the candidates. Benefits include annual leave, medical and flexi-benefits, etc.

If interested, please contact Asst. Prof. Saunders with curriculum vitae and a letter of research interest.

Asst. Prof. Timothy Saunders

Principal Investigator, Mechanobiology Institute, National University of Singapore, Singapore
Email: dbsste@nus.edu.sg

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Embryology 2019 application is due February 1, 2019. Go apply!! (http://www.mbl.edu/education/courses/embryology/).

If that is not enough, check out my evaluation of my course experience.

Embryology 2018:

I evaluate experiences by this basic philosophy: Some things are a good experience, some are a good story. When I’m lucky, sometimes they are both.

My summer at #Embryo2018 had all three scenarios.

The story:

I applied to Embryology in January 2018 because I was eager to fall deeper in love with developmental biology. Unfortunately, I was waitlisted in March and bummed to not join the 2018 cohort. Fast-forward to the week before the course started in June, I received an email of an open spot. I accepted, booked flights, got over a hump of imposter syndrome, and in a whirlwind of a week ended up in Woods Hole, MA for a six-week experience that I will never forget.

The experience:

As a whole experience, this course changed how I approach science in three main ways:

I acknowledged that failure is evident, but less likely if you actually try the experiment. Thinking up imaginative experiments and trying them is not something to be scared of, but something to be celebrated. Yes, science is 95% failure, but the ride might as well be interesting and without fear.

Creativity and use of whatever tools are at hand can yield clever and important results.  Scientists performed some of the most delicate, and important embryological experiments by simply attaching an eyelash to a glass pipet or wooden stick to use as a knife. Creativity is celebrated, and most embryologists could give MacGyver a run for his money.

Science is fun, it’s social, and the people at the top still genuinely enjoy it. This course was a good reminder that the popular “loner, anti-social scientist” stereotype is a work of fiction. I met incredible peers taking the course, enthusiastic TAs who worked tirelessly to give us embryos at all hours, and faculty who were willing to share their experiences with us and demonstrate their love for science. Experiments can be hard, but sharing the experience with other scientists going through the same paces make the long road in academia much more inviting.

99 % of the time, #Embryo18 was both a good story & a good experience:

When I describe my time at the MBL this summer, the version I give varies depending on the audience. To my colleagues, I explain how every day we listened and interacted with phenomenal seminars. TAs and faculty supplied embryos and all of the reagents to work with them. We had the rest of the day to try any experiment we could think of. I mention how we used several cutting-edge microscopes and had access to staff to help us use them. I talk about the privilege and freedom of having only to think about experiments, free of grants, meetings and other obligations. I end with a couple of my favorite stories about my scientific heroes I had the pleasure of meeting (https://www.youtube.com/watch?v=QZrrDDabEuo&feature=youtu.be).

When I tell my non-science friends about the course, I describe it as science summer camp where you make incredible new friends and stay up all night exploring organisms you would never think to study. I explain how in this course we learned history, we networked, and we grooved our way through town on the Fourth of July. We also swam at the beach, went whale watching, won the annual softball game, and even met the Prince of Monaco! For everyone, I end my#Embryo18 story the same by concluding the course was a magical six weeks I could have never imagined.

I can’t guarantee all of the same stories and experiences to the 2019 cohort, but I can guarantee both a good experience and a good story. Go apply now!

(5 votes)

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The Thompson lab, based at University College London, is currently seeking a Research Fellow working on understanding gene network heterogeneity in development.

Recently, we found that cell-cell variation in cell cycle position facilitates symmetry breaking during development, as it primes cells to respond to different differentiation cues (Gruenheit et al, Developmental Cell, 2018).

You will perform single cell gene expression analysis to understand the molecular mechanisms underlying this cell cycle control of cell fate choice you. For this, you will utilise our recently generated single cell RNA-seq dataset in which gene expression in 1000s of single cells was generated at different times after receiving differentiation cues.

Your aim will be to reconstruct gene network dynamics to follow their temporal changes in gene activity in individual cells from different cell cycle positions as they differentiate along different linages. You will develop novel computational and statistical methods (e.g. gene network identification, pseudotime, machine learning) to characterize the dynamics of gene network activity, and capture temporal changes in gene network activity in individual cells from different cell cycle stages as they differentiate. Live imaging of transcription and molecular genetic approaches to modify network activity in genetically modified cells will be used to validate your findings. You will also develop predictive models to understand the mechanism controlling cell fate choice. This will include computer simulation of the molecular basis of cell cycle control of differentiation.  High throughput live cell imaging to quantify the differentiation behaviour of cells at different cell cycle phases will be used to test these models. This framework will be fundamental in generating new hypothesis guiding future experiments.

You will join a multidisciplinary team led by Professor Chris Thompson. The approaches used in the lab include transcriptomics, functional genomics, molecular genetics, live cell imaging and mathematical modelling.

Candidates with extensive experience of using either computational genomic approaches or wet lab approaches to understand the molecular basis of gene networks will be considered. You should currently hold or be about to obtain a PhD in Computational, Cell, Molecular or Developmental Biology.

The post is funded by Wellcome and is available for 24 months in the first instance (with a possibility of extension).

Appointment at Grade 7 is dependent upon having been awarded a PhD, if this is not the case, initially appointment will be at research assistant Grade 6B (Salary £30,922 – £32,607 per annum) with payment at Grade 7 being backdated to the date of final submission of the PhD thesis.

https://www.jobs.ac.uk/job/BPE898/research-fellow-single-cell-transcriptomics-of-cell-cycle-heterogeneity-and-cell-fate-choice

Informal enquiries are welcome to Chris Thompson (christopher.thompson@ucl.ac.uk)

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