SINGEK: ESRs participate in the 2017 WORKSHOP on GENOMICS

Workshop on Genomics 2017

8th-21th January, Český Krumlov (Czech Republic)


All SINGEK ESRs will start the New Year by attending to this workshop as their first scientific training activity. This workshop has in the organizing committee Karin Rengefors (Lund University), supervisor of “ESR 13 – Next-Generation microbial population genetics using single-cell genomics”.

You can follow news from this workshop in its website or via Twitter at @evomics.

SINGEK: Opening Meeting including all 15 recruited ESRs

More than 30 researchers, including the 15 recruited Early Stage Researchers (ESRs), have met for the SINGEK Opening Meeting at the Institute of Marine Sciences, Barcelona (7-9 November, 2016).

SINGEK project (Promoting SINgle cell GEnomics to explore the ecology and evolution of hidden microeuKaryotes) will  focus on the study of microeukaryotes in natural systems, among which we can find protozoa, algae and microscopic fungi. The study of microeukaryotes is essential to comprehend eukaryotic diversity and evolution, including the origin of plants and animals, and also to better understand their role  in all ecosystems. In order to address this challenging task, however, the use of new and more accurate molecular techniques is required.

“The SINGEK project has a double objective. On the one hand, study the genomes of novel and uncultured microeukaryotes with the novel Single Cell Genomics (SCG) tool, applied until now in other fields as cancer research. And on the other hand, provide a unique and structured PhD training programme to train a new generation of scientists with the highest expertise in SCG, including also transferable skills essential for successful career development” explains Ramon Massana, ICM researcher in the Marine Biology and Oceanography department, and SINGEK Coordinator.

SINGEK will train 15 ESR from 9 different countries such as EEUU, Germany, Iran, Spain, Greece or Brazil, that will develop their research in fields related to bioinformatics, genomics, ecology and microbial evolution, under the supervision of 15 expert researchers from 12 science institutions from 5 different countries (Spain, France, Belgium, Sweden and UK). The project also counts with 8 Partner Organisations that will be involved in several tasks, as hosting students during their secondments, providing complementary training in complementary skills as scientific writing, or developing the project’s communication and outreach plan at different levels.

“All the research individual projects will cover the world of microorganisms from different perspectives, such as organisms’ interactions, marine microbial community composition and their involvement in climate change mitigation, development and improvement of SCG techniques and DNA sequencing, and other issues like multicellular organism emergence and a more complex view of the tree of life” states Iñaki Ruiz-Trillo, ICREA researcher from the Institute of Evolutionary Biology (CSIC-UPF) and also member of the SINGEK Coordinating Team.

SINGEK has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie program. The project has a duration of 4 years and a budget of 3,9M€.

Tara Oceans PhD offer / SYMBIOME

PhD POSITION AVAILABLE at Station Biologique de Roscoff – CNRS / UPMC

The project “SYMBIOME: an eco ‐systemic approach to eukaryotic symbioses in global photic plankton” offers a PhD position to a highly-motivated student with taste for ecology and biostatistics (and no fear for bioinformatics and plankton) to “unravel the main eukaryotic (protist) holobionts in the world plankton using the power of Tara Oceans size-fractionated combined datasets (metaB, T, G, microscopy)”.

This PhD thesis will be co-­supervised by Colomban de Vargas and Stéphane Audic (bioinformatics and statistics) at CNRS-­Roscoff, and Eric Pelletier (bio/systems ‐ informatics) at Genoscope.

– basic training in biology and ecology.
– skills in biostatistics (programming language Perl or Python, and R, in Unix/Linux)
– interest in ecology and evolution of marine eukaryotes and symbioses
– techniques of molecular biology and ecology

Send an email to Colomban de Vargas (vargas@sb-­ and Eric Pelletier ( including:
– your detailed CV, including your academic record and research experience
– a motivation statement (why you are interested in this project, max. 500 words)
– a short essay commenting a paper you have recently read and that changed your vision of science (max.300 words).

2nd edition of the EukRef Workshop in Barcelona

2nd edition of the EukRef Workshop

28th November – 2nd December 2016, Barcelona

This second workshop that will take place at the Institute of Marine Sciences in Barcelona from November 28th to December 2nd, 2016. It will bring together taxonomists with expertise in individual lineages that span the eukaryotic tree of life to curate reference 18S rDNA sequences of these lineages by incorporating knowledge of phylogenetic, morphological, and/or environmental contextual data. This second edition will be particularly (but not exclusively) focused on Amoebozoa and Rhizaria. During the workshop, the working group will integrate the curation efforts on individual eukaryotic groups into a biological data warehouse consisting of curated sequences, flexible taxonomy, and phylogenetic trees and their underlying sequence alignments. We will further use this 18S rDNA reference database to investigate the environmental distribution of eukaryotic microbes from large-scale HTES datasets. Each curator is encouraged to use their curated data to address research questions of interest. It will be discussed how to tackle such projects and encourage participants to publish their results.

Thanks to the generous contribution of the Moore Foundation, the cost of housing, breakfast and lunch, and reimburse for the cost of flights up to $400 will be covered for participants within Europe and $1500 for those from the rest of the world.

Application deadline: September 16th 2016

Follow EUKREF updates in Twitter: @EukRef

SINGEK: ESRs already appointed!

The SINGEK Coordination Team is happy to announce that the 15 Early Stage Research (ESR) positions have already been filled.

The following ESRs will start their work in October 2016:

ESR 1 – Aurélie Labarre, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain

ESR 2 – Ina Deutschmann, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain

ESR 3 – Konstantina Mitsi, Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain

ESR 4 – Javier Florenza, Uppsala University (UU), Uppsala, Sweden

ESR 5 – Max Emil Schön, Uppsala University (UU), Uppsala, Sweden

ESR 6 – Atefeh Lafzi, National Centre for Genomic Analysis (CNAG-CRG), Barcelona, Spain

ESR 7 – Luis Javier Galindo, Unité Ecologie Systematique Evolution (Univ. Paris-Sud-CNRS-AgroParisTech), Paris, France

ESR 8 – Laura Rubinat, Station Biologique de Roscoff (SBR-CNRS), Roscoff, France

ESR 9 – Luiz Felipe de Almeida, Observatoire Oceanologique de Banyuls sur mer (OBS Banyuls-CNRS), Banyuls, France

ESR 10 – François Bucchini, Ghent University (VIB), Ghent, Belgium

ESR 11– Vanessa Smilansky, University of Exeter (UNEXE), Exeter, UK

ESR 12– Jari Iannucci, University of Exeter (UNEXE), Exeter, UK

ESR 13– Raphael Gollnisch, Lund University (LU), Lund, Sweden

ESR 14– Alexandra Beliavskaia, University of Liverpool (UOL), Liverpool, UK

ESR 15– Imer Muhovic, aScidea, Barcelona, Spain


Details of each ESR will be available soon in our website.

SINGEK: Application period is closed

Thank you very much to all candidates who applied for our 15 ESR positions within the ITN SINGEK.

Candidates will be evaluated from the 3th May on, and pre-selected candidates will be invited to have a personal teleconference interview with the relevant project supervisor(s), in such case you will receive an email during May.

Good luck!

SINGEK: Extended application deadline

Extended application deadline: 17:00 GMT on the 29th April 2016

The deadline for applying to the PhD positions within the SINGEK Training Network has been extended until 29th April.

Don’t miss this great opportunity to be part of this top-level PhDs network!!

Please, read carefully all instructions provided at SINGEK website before applying. If you have any question regarding the application process or required documents, please do not hesitate to contact us ( For specific questions related with ESR projects, contact the supervisors to get more details.


ISME16: 16th International Symposium on Microbial Ecology

16th International Symposium on Microbial Ecology

21th-26th August 2016 – Montreal (Canada)

This biannual appointment for microbial lovers organized by the International Society for Microbial Ecology (ISME) & The ISME Journal will be in Montréal, Canada, from 21 to 26 August 2016. Luckily Registration and Submissions are now Open until 1st April!

MEEG Summer Course: Marine Ecological & Environmental Genomics

12th Summer Course on Marine Ecological & Evolutionary Genomics

June 13th – 24th 2016 – Roscoff (France)

Marine genomics knowledge is crucial for understanding the marine environment and for an efficient use of its resources. State of the art NGS methods have revolutionized the field, spawning applications in basic research and environmental management. The course will give insight into population, environmental, biodiversity, comparative, evolutionary and functional genomics through lectures, case studies and computer labs. (Summer Course Website).




IV Edition Ramon Margalef Summer Colloquia

4th Edition: “Microbes in a changing world: diversity and biogeochemistry

10th July to 15th July -2016 – Barcelona (Spain)



The Colloquium is inspired by the figure of Ramon Margalef (Barcelona, 1919-2004), who worked for many years in the Institut de Ciències del Mar and the University of Barcelona. He was one of the founders of modern ecology, broke old paradigms and contributed to science with innovative theories about the spatiotemporal structure of the ecosystems, the relations between diversity, biodiversity, stability and connectivity, the fundamental paper of energy in the biological productivity and the interrelations between ecological succession and evolution. He wrote ca. 400 papers and books including, “On certain unifying principles in ecology”, “Perspectives in Ecological Theory”, “Information Theory in Ecology”, and “Our Biosphere”. Margalef was also an encouraging teacher and mentor. He recognized the importance of the physical environment to understand the behaviour of species and ecosystems.

We believe this 4th Colloquium will be, again, an excellent opportunity to foster learning and discussions on the relevance of an interdisciplinary perspective in Ecology. We expect to attain this important aim through a very dynamic colloquium, with an important component of discussion, exchange of ideas and research.

Microbes in a changing world: diversity and biogeochemistry

Microbes dominate all types of ecosystems and are the main responsible for biogeochemical cycling. Recent methodological developments have put them at the forefront of research in soil, freshwater and marine research, and even in the human body considered as an ecosystem. To what extend ecological theories developed for macroorganisms apply to microbial ecology? What are the main drivers of microbial diversity? What is the true extend of microbial diversity? Are there typical properties of microbial succession? How microbe-microbe and microbe-macroorganism relationships affect biogeochemical cycling? To what extend the technological developments that generate lists of organisms and their genes are related to whole ecosystem biogeochemical cycling? How the physical dynamics of the environment affect microbial diversity and biogeochemical function? How will global change affect microbes and the functions that they perform? We will address all these issues with contributions of well-known microbial ecology, oceanography, biogeochemistry and ecology researchers; and discussions between the participants. Although all these questions will be examined in a cross-system scenario, our target ecosystems will be marine.

The aim of this Colloquium is to enhance the exchange of ideas and to promote imaginative thinking by bringing together ecological knowledge from experts on different scientific areas.

More information at the website of the Colloquia: