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!!


SINGEK: Iñaki Ruiz-Trillo elected as new EMBO member

Iñaki Ruiz-Trillo, supervisor of “ESR3 – Uncultured opisthokonts and the origin of metazoan multicellularity“, has been elected as new EMBO – excellence in life sciences member as recognition of research excellence. He is one of the 65 outstanding life scientists in the list published by this institution this week. Congratulations Iñaki!!


Iñaki is an ICREA research professor at IBE: Institute of Evolutionary Biology (CSIC – UPF) and is currently the Principal Investigator of the Multicell Genome Lab. His group focuses on how animal multicellularity emerged from our common unicellular ancestor.


Check more details about Iñaki’s profile and his role in SINGEK here.

SINGEK: ESR3 attends to the 2017 MCAA Conference

2017 MCAA Conference and General Assembly

Our SINGEK ESR3 Konstantina Mitsi has participated in the 2017 MARIE CURIE ALUMNI ASSOCIATION (MCAA) Conference and General Assembly, which was held on Friday 24th and Saturday 25th March 2017 in Salamanca, Spain.

The program covered the main areas of interests of the MCAA members in terms of career, networking and societal challenges. The event included a poster session and a ‘science lab’ event at which delegates stepped up to the challenge of presenting their project in three minutes maximum.

More info about this event is available here.

SINGEK: ESRs participate in the ITN Science Slam Barcelona

ITN BCN Science Slam 2017

3rd of March, 21:00h, Bar mau mau (Barcelona)

Some SINGEK ESRs will participate in the ITN BCN Science Slam together with other PhD students from 6 different European Training Networks.

The ITN BCN Science Slam is a science communication event organized by the ITN Opathy (Centre for Genomic Regulation, Barcelona) where young scientists will explain their research projects in short 5/10-minute-talks that are easy to follow and afterwards the audience will get to vote.

During the short talks, the important thing will not be primarily the scientific outcome of their work, but to explain it in an understandable, entertaining and concise way. In this edition, the winner of the ITN BCN Science Slam will be invited to present his/her talk in the Science Slam of the Marie Curie Alumni Association in Salamanca, Spain on 24th of March.

The ITN BCN Science Slam will take place from 21:00 to 22:30 in the bar “mau mau”.


bar mau mau

Fontrodona 35

08004 Barcelona


You can follow news from this event via Twitter at @SINGEK_ITN., @OpathyITN


SINGEK: New paper about SCG of oceanic unculturable picoeukaryotes

We are glad to announce that a new SINGEK paper is out in Scientific Reports/ NatureJournal:

“Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells”

J-F. Mangot, R. Logares, P. Sánchez, F. Latorre, Y. Seeleuthner, S. Mondy, M. E. Sieracki, O. Jaillon, P. Wincker, C. de Vargas and R. Massana

Comparison of tetranucleotide frequencies of SAGs in an ESOM map.

Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating coassembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.