SINGEK: Training workshop for ESRs on Genome Annotation

Workshop on Genome Annotation: Challenges in Eukaryotes and Consequences Evolutionary Genomics

13th-16th February 2018, Observatoire Oceanologique de Banyuls sur mer

This week, SINGEK ESRs have attended to this workshop on genomic annotation organized by Gwenaël PiganeauI (OBS Banyuls-CNRS) and Klaas VANDEPOELE (Ghent University, VIB), supervisors of the SINGEK individual research projects: “ESR9 – Genomic insights into interactions in green microalgae” and “ESR10 – New tools for genome annotation in unknown microeukaryote lineages“, respectively.

Among the lecturers and experts, François BUCCHINI (ESR10 at Ghent University, VIB) contributed to this training activity as a trainer during the hands-on sessions on the TRAPID tool for comparative and functional annotations.

Everybody made a great job!

SciLifeLab course on Single Cell Genomics (Uppsala, March 2018)

SINGEK: New paper about comparative genomic analysis of the “pseudofungus” H. Catenoides

We are happy to announce that a new SINGEK paper is out in Open Biology:

“Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

G. Leonard, A. Labarre, D. S. Milner, A. Monier, D. Soanes, J. G. Wideman, F. Maguire, S. Stevens, D. Sain, X. Grau-Bové, A. Sebé-Pedrós, J. E. Stajich, K. Paszkiewicz, M. W. Brown, N. Hall, B. Wickstead and T. A. Richards


Schematic phylogenetic tree summarizing the evolution of cell and genomic characters relevant to the evolution of the Pseudofungi.

Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium
catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.

SINGEK: Imer’s Video at 2nd BCN Science Slam

2nd BCN Science Slam 2017 (October, 2017)

Congratulations IMER!!

Imer Muhovic, SINGEK ESR15 based at aScidea (Barcelona), won the 2nd BCN Science Slam organized by the ITN DivIDE (Centre for Genomic Regulation, Barcelona).

His talk was entitled “Software for Humans” and here is his great performance at Black Lab bar:

Imer has been invited by the Marie Curie Alumni Association to present again at the Science Slam during their annual meeting on 2nd of February 2018 in Leuven, Belgium.
Good luck and thanks for spreading SINGEK to different audiences!!

SINGEK: Mid-Term Meeting & two training workshops

Mid-Term Meeting and two training workshops for ESRs in October 2017

Three relevant events were conducted within the SINGEK Consortium during this month:

– A Workshop on Genome Assembly was organized by the CNAG – CRG‘s Team: Ivo Gut, Holger Heyn (supervisors of ESR 6) and Tyler Alioto. This 3-day workshop, part of the training program for SINGEK ESRs, aimed to provide them an overview of bioinformatic assembly tools and hands-on experience through some examples.

– The SINGEK Mid-Term Meeting took place on October 24th at the Institute of Marine Sciences, Barcelona. During this meeting, the Coordinator of the Network, Ramon Massana, provided an update about the project progress and implementation. In addition, all 15 ESRs presented his/her individual research project and the results obtained so far. Several sessions were also devoted to discuss different aspects of the project with our Project Officer, Mrs. Giuliana Donini (Research Executive Agency), an external expert, Mr. Jean-Louis Marchal and an innovation expert, Mrs. Marusela Oliveras Salva.

– A Worshop on Scientific Writing was offered by the Partner Organisation ThePaperMill, in which all ESRs drew on experiences from well-written papers, learned to recognize common errors, and gained practical tools for writing in clear, simple language.

SINGEK: New Blog release


We are glad to announce that our SINGEK Blog has been released!

Do not miss our posts!

CRG Symposium: 7th International Workshop on Genomic Epidemiology

7th International Workshop on Genomic Epidemiology

16th CRG Symposium, 20th-22nd September, PRBB, Barcelona

The 16th CRG Symposium: Seventh International Workshop on Genomic Epidemiology will take place at the PRBB Auditorium from 20 to 22 September 2017 will gather speakers to discuss about the progress in sequencing and with other technologies for biomolecular analysis, and their applications in research and clinical settings.

Solutions will be presented for the accumulation, handling and interpretation of huge data sets, including the identification of rare and common genetic variants associated with disease, functional evaluation of genetic variation, understanding of gene networks and epigenomic phenomena in health and disease, pharmacogenomics, gene-gene and gene-environment interactions. Examples of the application of these technologies for epidemiological scale studies in different disease areas will be presented.

Participants in the meeting are welcomed to present their research results with a short abstract of 300 words. A limited number of slots will be available in the programme for selected participants for short talks.


Registration deadline: August 31

Follow updates from this CRG Symposium in its website.

Open position at aScidea (TecnioSpring+ program)

OPEN POSITION AVAILABLE at aScidea: Bioinformatics R&D Scientist

aScidea Genomics & Bioinformatics CRO, a SINGEK hosting institution and Supervisor of the individual research project ESR15, offers a new position:

We are looking for a highly motivated and proactive person with a strong interest in learning and participating in an innovative and growing environment. This person will work as Bioinformatics R&D Scientist at our R&D Department and will develop its own research project in the framework of TecnioSpring+ program, and will be involved in current active projects in the company, such as SINGEK, aimed to develop single cell bioinformatics pipelines to advance the precision of the omics discoveries.

Tasks / responsibilities
– Develop Scientific Software and data analysis under the TecnioSpring+ program.

– PhD in Computational Biology/Bioinformatics or similar.
– Prior experience of at least 2 years in Bioinformatics software and data analysis.
– Strong background in algorithms, statistics and data management and mining.
– Excellent programming skills. Experience in python.
– Familiar with Machine Learning techniques is a plus.
– Knowledge on SQL and noSQL databases.
– Knowledge on big data analytics.
– Fluent English (Catalan/Spanish is a plus).
– Working permit in the EU.

– Full time contract, starting at mid-January 2018.
– Flexible working
– Salary according to both candidate’s experience and company pay scales.
– An exciting and growing environment.

If you are interested in this position, please send a CV, a cover letter and 2-3 recommendation letters to: before August 15th.
Please write the tag [TECNIOSPRING] in the e-mail header.

SINGEK: New introductory VIDEO

A new introductory video about our SINGEK Innovative Training Network is out:

We are really grateful to SINGEK fellows (including some Early Stage Researchers) who contributed to informally present our ambitions and drive!

Enjoy it!

EMBO Workshop on Comparative genomics of eukaryotic microbes

Comparative genomics of eukaryotic microbes: Dissecting sources of evolutionary diversity

EMBO Workshop, 14th-19th October, Sant Feliu (Girona)

EMBO – excellence in life sciences organizes a workshop in St Feliu de Guíxols (Girona, Spain) from 14th to 19th October 2017, which will be focused on comparative genomics of eukaryotic microorganisms.

Unicellular eukaryotes comprise the overwhelming majority of eukaryotic cellular and genomic diversity, pervading all branches of the eukaryotic tree of life. Recent sequencing efforts have significantly increased the number of unicellular eukaryotes for which genomic/cellular/proteomic data are available. Metagenomics, transcriptomics,single-cell genomics, and other approaches are being applied to unravel the ecology, physiology, diversity and evolution of microbial eukaryotes and are shedding light on fundamental questions such as the origin of the eukaryotic cell, endosymbiosis, the origin of multicellularity and the evolution of major cellular systems in eukaryotes.

Although there are conferences devoted to genomics of prokaryotes and that of plants and animals, this EMBO Workshop will be the only forum bringing together this diverse community with a range of expertise and which concentrates on microbial eukaryotes.


There is a need, particularly in organisms without large communities, to have a forum where approaches, new methodologies and datasets can be shared to the advancement of this field. In particular, three of the SINGEK project supervisors will be involved in this  EMBO conference: Thomas Richards (as organizer, University of Exeter, supervisor of ESR11), Ramiro Logares (as speaker. CSIC Institut De Ciències Del Mar, supervisor of ESR2) and Iñaki Ruiz-Trillo (also as speaker, IBE: Institute of Evolutionary Biology CSIC – UPF, supervisor of ESR3).


You can follow updates from this EMBO Workshop in its Website or via Facebook.

Abstract Submission is open until 15th August!!