Jorge Ruiz Orera receives one of the Doctoral School PhD Special Awards from the PhD Programme in Biomedicine of the Pompeu Fabra University

During the 2016-2017 academic year, 106 PhD theses were read and eight of them have been awarded

Congratulations to Jorge Ruiz Orera, doctoral student at the Evolutionary Genomics group of GRIB  (IMIM-UPF) for his thesis "Understanding the mechanisms of de novo gene evolution using transcriptomics data", supervised by Dr. Mar Albà. In his research, he investigated the mechanisms for de novo gene origination and evolution using highthroughput sequencing of complete transcripts and ribosome-protected fragments. The thesis identifies thousands of new de novo genes in human, chimpanzee, and mouse and presents evidence that these genes are mostly expressed from recently arisen promoters. It also shows that a large number of poorly conserved genes, including genes previously believed to be non-coding, are translated and finds a link between the capacity of a sequence to be translated and its nucleotide sequence composition. This doctoral research shows that there is abundant raw material for de novo birth of new functional proteins, and hence, its results contribute to a better understanding of the mechanisms of gene evolution. This thesis has been awarded with the International PhD Mention.

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"We found a way to share the unsharable", an interview with the eTOX project coordinators F. Pognan and F. Sanz

The eTOX project partners developed innovative strategies and novel software tools to better predict the safety and side effects of new candidate medicines for patients. In an interview with the Innovative Medicine Iniciative (IMI) Programme Office, project coordinator Francois Pognan of Novartis, and academic coordinator Ferran Sanz, Director of GRIB (IMIM-UPF), explain how the tools developed by the project are already helping pharmaceutical companies make better-informed decisions in their pursuit of developing safer drugs for patients.

"For the academic world", Ferran Sanz says, "the way in which we have learned how to collaborate with the pharmaceutical industry is potentiating our capabilities to create spin offs and to establish research contracts with the pharmaceutical industry, beyond this particular project".

Read the interview at 'We found a way to share the unsharable' - an interview with the eTOX...

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Jordi Mestres, head of the Systems Pharmacology group of GRIB. Photo of Josep Cano.


Jordi Mestres elected Fellow of the Royal Society of Chemistry

Congratulations to Jordi Mestres, head of the Systems Pharmacology group of GRIB (IMIM-UPF), elected Fellow of the Royal Society of Chemistry of the United Kingdom. Achieving this status is an important milestone in a researcher's career as it indicates scientific quality and is one of the most important recognitions a chemist can receive.

The Royal Society of Chemistry is a non-profit organisation that is more than 175 years old and has more than 54,000 members across the world. Its aim is to advance excellence in the chemical sciences, investing in the education of future generations, creating and maintaining standards, encouraging innovation, and advising governments.

To become a member, you must have at least 5 years professional experience and your work must have made a significant impact in the field of chemistry, contributing notably to the advancement of the chemical sciences. "I am absolutely delighted and honoured to be elected Fellow of the Royal Society of Chemistry and become part of the select group of scientists who have made important contributions in the field of chemistry", said Mestres. "I am deeply grateful to the Royal Society of Chemistry for this recognition. It is immensely satisfying and encourages me to push towards more ambitious goals and reach new heights", the researcher added.

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FAIRPlus grant awarded

The FAIRPlus proposal, coordinated by ELIXIR, has just passed stage two review and invited into contract negotiations. The project proposal was submitted to the Innovative Medicines Initiative (IMI), and will see ELIXIR Nodes and other academic partners supporting EFPIA companies and specific IMI projects in making their data FAIR: Findable, Accessible, Interoperable and Re-usable. The following ELIXIR Nodes are involved as partners: ELIXIR Spain, ELIXIR Netherlands, ELIXIR UK, ELIXIR Luxembourg, ELIXIR Switzerland and EBI. IMIM takes part in the project through the the Integrative Biomedical Informatics Group of the GRIB led by Laura I. Furlong and Ferran Sanz.

ELIXIR unites Europe's leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. It coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access services that are vital for their research. More information about ELIXIR

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The researchers Quim Aguirre, Baldo Oliva, Laura Furlong, Emre Guney, Janet Piñero and Ferran Sanz

A new computational method for exploring the reuse of drugs

The Proximal pathway Enrichment Analysis method can be applied to reuse drugs targeting mechanisms shared by different diseases, such as Alzheimer’s and type 2 diabetes.

Researchers led by Emre Guney of the Research Programme on Biomedical Informatics (GRIB, UPF-IMIM), have developed a new computational method to reuse drugs that target biological pathways common to more than one disease. The results have been presented in the journal Pharmaceuticals.

Reference article: Aguirre-Plans J, Piñero J, Menche J, Sanz F, Furlong LI, Schmidt HHHW, Oliva B, Guney E. Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. Pharmaceuticals. June, 2018. DOI:

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EU-wide network explores sudden cardiac arrest causes to help prevention and treatment

Scientists across Europe are creating a large database of sudden cardiac arrest cases to improve direct patient care.

Sudden cardiac arrest (SCA) continues to be a major public health challenge, accounting for about 20 % of all natural deaths in industrialised countries. Although there has been a substantial decline in overall coronary heart disease mortality rates in the past 30 years, SCA rates have fallen to a lesser extent. Some 50 % of all cardiovascular deaths are caused by SCA, a condition in which the heart suddenly and unexpectedly stops beating. With survival rates ranging between 5 % and 20 % there's a need to improve SCA prevention and treatment.

To address this issue, a European public-private consortium is now working on the creation of a joint, harmonised database by analysing SCA victims and DNA samples, along with detailed clinical and medication use information. Funded by H2020 Programme of the European Union, the team of scientists contributing to the ESCAPE-NET project, including the System Pharmacology group of GRIB (IMIM-UPF) led by Jordi Mestres, summarised the objectives of their research in the 'European Heart Journal'.

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Foto de Chus Donlo


The 6th iPiE Forum Meeting was held in Barcelona during the 24th and 25th of April 2018

The 6th iPiE Forum Meeting was held in Barcelona during the 24th and 25th of April 2018, and counted with the presence of the participants of the iPiE Consortium. The Integrative Biomedical Informatics group and the PharmacoInformatics group of GRIB (IMIM-UPF) take part of this european project. The meeting was focused on progress to the development of guidance on how the established approaches and expert system from iPiE can be used in the intelligent testing of APIs at early stages in drug development, and to prioritise legacy APIs for further testing or assessment.

On the first day, an integration workshop was organised to define next steps towards the preparation of prioritisation guidelines. The workshop started with two parallel sessions, one attended by academia and other by industry representatives, including regulatory experts in both. The two groups were allowed for an internal debate that led to concrete conclusions on necessities from both sides. The meeting also included the updates of Work Packages and the progress done in the past months.

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The 3rd European Conference on Translational Bioinformatics brings together more than 130 experts

Attendees discussed the recent advances in information technologies that are facilitating translational research and precision medicine.

The 3rd European Conference on Translational Bioinformatics (ECTB2018) was held on April 16th-17th at the premises of the Barcelona Biomedical Research Park (PRBB) with the attendance of more than 130 European scientists, developers and entrepreneurs, interested in translating genomics and bioinformatics research into healthcare tools and services. The conference aimed to give the participants a unique experience and a forum for discussing fresh scientific results in the translational domain.

The conference brought together world-leading scientists in the area which highlighted on their presentations the recent advances in information technologies that are facilitating translational research and precision medicine. Some of the topics addressed were Big Data integration and analysis, Personalized Medicine, Genome Sequencing initiatives, etc, delivered by scientists from Europe, Canada and the USA.

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Caption: Location of some of the tumours analysed in The Cancer Genome Atlas


Major milestone reached in effort to identify cancers’ genetic roots

The project Cancer Genome Atlas details genetic mutations driving cancer in 27 papers published on 5 April in Cell Press journals. One of the studies is led by Washington University and has the participation of the head of the  Computational RNA Biology group of GRIB,  Eduardo Eyras

An international team coordinated by the National Institutes of Health (NIH) have reached a major milestone in describing the genetic landscape of cancer. The researchers have completed the genetic sequencing and analyses of more than 11,000 tumours from patients, spanning 33 types of cancer. These are part of The Cancer Genome Atlas (TCGA) project, launched in 2005 to pursue the genetic basis of cancer.

Eduardo Eyras  has participated in the study of the splicing alterations in tumours. "These analyses reveal that a significant number of mutations studied previously were poorly classified, and it could be more relevant than was thought to understand cancer and for the identification of therapeutic strategies", describes Eyras.

Article Ref.: Jayasinghe RG, Cao S, Gao O, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ. The Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep, 2018; 23(1): 270-281.e3. DOI: 10.1016/j.celrep.2018.03.052.

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Estructura proteica d'una petita proteïna (stannin)


Nou pas per entendre l’origen dels gens

Han identificat centenars de fragments del genoma sense funció aparent, que tenen capacitat per generar noves proteïnes i, potencialment, convertir-se en nous gens

Com es van crear els blocs bàsics que serveixen per construir qualsevol ésser viu, els gens? És la pregunta que un recent estudi liderat per investigadors del Grup de Genómica Evolutiva del GRIB led by Mar Albà ha intentat resoldre.

El treball, que acaba de publicar la revista Nature Ecology and Evolution, ha permès identificar, mitjançant tècniques de seqüenciació massiva, una gran quantitat de proteïnes noves en el genoma del ratolí. "Aquest treball mostra que un procés anàleg a la formació de gens nous que va tenir lloc al principi de la vida continua actiu avui en dia", explica la Dra. Mar Albà, "queda molta feina per fer per entendre completament l'impacte dels gens de novo en l'evolució recent, però cada vegada tenim més evidència del fet que tenen un pes important". 

Article de referència

Jorge Ruiz-Orera, Pol Grau-Verdaguer, José Luis Villanueva-Cañas, Xavier Messeguer, M.Mar Albà. Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nature Ecology and Evolution, 19 Jan 2018.

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