Nine doctoral students from the PhD Programme in Biomedicine will receive the Doctoral School PhD Extraordinary Award

Nine doctoral students from the PhD Programme in Biomedicine will receive the Doctoral School PhD Extraordinary Award

During the 2017-2018 academic year, a total of 86 PhD theses were read and their corresponding examination committees put 21 of them forward to compete for the PhD Special Awards. 



The PhD Programme in Biomedicine run by the DCEXS currently enrols 456 doctoral students. During the 2017-2018 academic year, a total of 86 PhD theses were read and their corresponding examination committees put 21 of them forward to compete for the PhD Special Awards. The awards ceremony will take place during the 2020 UPF Graduation Ceremony for master's and doctoral degree students.  

The Special Award Comittee that awarded the nine candidates was formed by Dr. Berta Alsina, Dr. Elena Bosch, Dr. Juana Díez, Dr. Fernando G. Benavides, Dr. Joaquim Gea,  Dr. Cristina López-Rodriguez, Dr. Mariano Sentí, Dr. Ruben Vicente, Dr. Núria Centeno and Dr. Alfonso Martínez-Arias. The granted candidates are:

Berta Canal de Torres, for her thesis “Control of S-phase progression in response to stress”, directed by Dr. Eulàlia de Nadal and Dr. Francesc Posas from the UPF, and currently at the Institute for Research in Biomedicine. She identified a novel safeguard mechanism dedicated to coordinate replication and transcription machineries in response to stress to prevent collisions and genomic instability. More concretely, using the budding yeast Saccharomyces cerevisiae, this doctoral research describes how osmotic, heat, oxidative and low glucose stresses promote the activation of specific protein enzymes called kinases, which are able to induce a transient replication delay that prevents transcription-associated recombination, DNA damage and genomic instability.

Selected publications from the thesis:

1.Canal B*, Duch B*, de Nadal E, Posas F. A novel mechanism for the prevention of transcription replication conflicts. Molecular & Cellular Oncology, 28(3):e1451233, 2018.

2.Duch A*, Canal B*, Barroso SI, García-Rubio M, Seisenbacher G, Aguilera A, de Nadal E and Posas F. Mrc1 integrates inputs from multiple signaling kinases to prevent genomic instability triggered by transcription-replication conflicts. Nature Communications,9(1):379, 2018 .


Maria Gomis González, for her thesis “Neurobiological mechanisms involved in memory function and dysfunction: focus on the endocannabinoid system and associated signaling pathways”, directed by Dr. Rafael Maldonado and Dr. Andrés Ozaita from the UPF. She used specific murine mouse models combined with behavioral, biochemical, cell biology and pharmacological approaches to reveal the cellular and molecular mechanisms involved in different physiopathological conditions that course with memory impairment. This experimental setup was conducted paying special attention to the endocannabinoid system (ECS) and its associated signaling pathways, as endogenous neuromodulators with a pivotal role in the regulation of memory. 

Selected publications from the thesis:

1. Busquets-Garcia A*, Gomis-González M*, Srivastava RK*, Cutando L, Ortega-Álvaro A, Ruehle S, Remmers F, Bindila L, Bellocchio L, Marsicano G, Lutz B, Maldonado R, Ozaita A. Peripheral and central CB1 cannabinoid receptors control stress-induced impairment of memory consolidation. Proceedings of the National Academy of Sciences of the USA, 113(35):9904-9909, 2016.

2. Gomis-González M, Busquets-Garcia A, Matute C, Maldonado R., Mato S., Ozaita A. Possible therapeutic doses of cannabinoid type 1 receptor antagonist reverses key alterations in fragile X syndrome mouse model. Genes, 7(9), 56, 2016.


Alba Gutiérrez Sacristán, for her thesis “A bioinformatics approach to the study of comorbidity. Insight into mental disorders”, directed by Dr. Laura Inés Furlong from the Hospital del Mar Medical Research Institute.  She developed a new bioinformatics approach for the exploitation of information contained in clinical health records as well as the identification of comorbidity patterns. Furthermore, by using automatic text mining tools, this thesis also presented PsyGeNET, a database of psychiatric disorders and their genes developed in collaboration with experts in the field of psychiatry and neurosciences. Psychiatric patients frequently present other comorbid diseases, which affect both treatment options and clinical evolution. In this regard, a tool such as PsyGeNET supports the study of the molecular and cellular mechanisms that underpin psychiatric disease comorbidities, providing new insights into new disease biomarkers and drug targets.

This thesis has been awarded the International PhD Mention.

Selected publications from the thesis:

1. Gutiérrez-Sacristán A, Grosdidier S, Valverde O, Torrens M, Bravo À, Piñero J, Sanz F, and Furlong LI, PsyGeNET: a knowledge platform on psychiatric disorders and their genes, Bioinformatics, 31(18):3075–3077, 2015.

2. Gutiérrez-Sacristán A, Bravo À, Giannoula A, Mayer MA, Sanz F, and Furlong LI, comoRbidity: an R package to analyze disease comorbidities, Bioinformatics, 34(18):3228-3230, 2017.


Cyntia Beatriz Manzano Salgado, for her thesis “Prenatal exposure to perfluoroalkyl substances and child health”, directed by Dr. Maribel Casas Sanahuja and Martine Vrijheid, from the Barcelona Institute for Global Health. She evaluated the transfer of Perfluoroalkyl substances (PFAS) from mother to fetus and the determinants of maternal PFAS exposure during pregnancy. More concretely, this doctoral research evaluated the association between prenatal exposure to PFAS and child health, specifically: fetal growth and preterm birth, obesity and cardio-metabolic risk, and immune and respiratory health in early and mid-childhood, using data from the “Infancia y Medioambiente” (INMA) Spanish birth cohort. The results from this thesis indicate that PFOA can cross the placental barrier more efficiently than other PFAS and, that mothers were ubiquitously exposed to perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) during the years 2003-2008. Overall, the thesis finds little and inconsistent evidence for an association between prenatal PFAS exposure and child health outcomes, and therefore, prospective studies with follow-ups beyond mid-childhood will be necessary to fully address this question.

This thesis has been awarded the International PhD Mention.

Selected publications from the thesis:

1. Manzano-Salgado CB, Casas M, Lopez-Espinosa MJ, Ballester F, Ibarluzea J, Santa-Marina L, Schettgen T, Vioque J, Sunyer J, Vrijheid M. Variability of perfluoroalkyl substance concentrations in pregnant women by socio-demographic and dietary factors in a Spanish birth cohort. Environment International. 92-93:357-365, 2016.

2. Manzano-Salgado CB, Casas M, Lopez-Espinosa M-J, Ballester F, Iñiguez C, Martínez D, Costa O, Santa-Marina L, Pereda-Pereda E, Schettgen T, Sunyer J, Vrijheid M. Prenatal exposure to perfluoroalkyl substances and birth outcomes in a Spanish birth cohort. Environment International, 108:278-284, 2017.


Carlos Pardo Pastor, for his thesis “PIEZO ion channels in cancer cell mechanotransduction”, directed by Dr. Miguel Angel Valverde from the UPF. He investigated the roles played by the mechanosensitive ion channels Piezo1 and Piezo2 in the transduction of mechanical stimuli (confinement, adhesion, substrate rigidity, adhesive ligand concentration) by cancer cells. In summary, this thesis unveils important roles for Piezo channels as a first line of mechanical input detectors in distinct cells. These discoveries are relevant for several fields such as cancer research, and highlight the importance of ion channels as transducers of environmental stimuli. 

Selected publications from the thesis:

1. Hung WC, Yang JR, Yankaskas CL, Wong BS, Wu PH, Pardo-Pastor C, Serra SA, Chiang MJ, Gu Z, Wirtz D, Valverde MA. Confinement Sensing and Signal Optimization via Piezo1/PKA and Myosin II Pathways. Cell Reports, 15:1430-1441, 2016.

2. Pardo-Pastor C, Rubio-Moscardo F, Vogel-González M, Serra SA, Afthinos A, Mrkonjic S, Destaing O, Abenza JF, Fernández-Fernández JM, Trepat X, Albiges-Rizo C, Konstantopoulos K, Valverde MA. Piezo2 channel regulates RhoA and actin cytoskeleton to promote cell mechanobiological responses. Proceedings of the National Academy of Sciences of the USA, 115:1925-1930, 2018.


Marcos Francisco Perez, for his thesis “Inter-individual physiological variation in the nematode Caenorhabditis elegans”, directed by Dr. Ben Lehner from the Center for Genomic Regulation. He has contributed to the identification of causes of inter-individual physiological variation in genetically identical C. elegans worms. More concretely, in the framework of this doctoral research it was discovered that a major driver of variation was the age of an individual’s mother. Surprisingly, it was the progeny of the youngest mothers who displayed phenotypic impairments. Early progeny were smaller at hatching, slow to grow and develop, more sensitive to starvation and produced fewer progeny themselves as an adult. The mechanism for many of these phenotypic differences was identified as the maternal supply of a specific yolk lipoprotein complex, vitellogenin, to the worm’s embryos. Maternal yolk supply increased substantially with maternal age over the reproductive period. The production of sub-optimal early progeny by young mothers may be a result of an ecologically important trade-off between progeny quality and a short generation time.

Selected publications from the thesis:

1. Perez MF*, Francesconi M*, Hidalgo-Carcedo C, Lehner B. Maternal age generates phenotypic variation in Caenorhabditis elegans. Nature, 552:106-109, 2017.

2. Perez MF, Lehner B. Intergenerational and transgenerational epigenetic inheritance in animals. Nature Cell Biology, 21:143-151, 2019.


Łucasz Roguski, for his thesis “High-throughput sequencing data compression”,  directed by Dr. Sebastian Deorowicz and Dr. Paolo Ribeca from the National Center for Genomic Analysis – Center for Genomic Regulation. He investigated in methods to efficiently store and compress the data generated from sequencing experiments. More concretely, this thesis proposed a novel general purpose FASTQ files compressor, which compared to the standard compression software gzip, leads to a significant reduction in the size of the resulting archive, while also offering high data processing speed. Next, the thesis presented compression methods that exploit the high sequence redundancy present in sequencing data. These methods achieve the best compression ratio among current state-of-the-art FASTQ compressors, without using any external reference sequence. In summary, the algorithms and software introduced in this thesis facilitate the development of integrated approaches towards efficient storage and management of such sequencing data.

Selected publications from the thesis:

1. Roguski Ł, Deorowicz S. DSRC2 – Industry-oriented compression of FASTQ files. Bioinformatics, 30:2213-2215, 2014.

2. Roguski Ł, Ribeca P. CARGO: effective format-free compressed storage of genomic information. Nucleic Acids Research, 44:e114, 2016.


Carlota Rubio Pérez, for her thesis “Understanding the genomic makeup of tumors to guide personalized medicine”, directed by Dr. Abel González Pérez and Dr. Nuria López Bigas from the Institute for Research in Biomedicine.  She describes one of the first pan-cancer driver integrative landscapes, expanding it with the first landscape of genomic-guided therapeutic opportunities. This first result of the thesis became the seed for two other further contributions. First, a software tool called OncoPaD, aimed to aid the design of next generation sequencing mutational cancer gene panels in a rational way. Second, another software tool called the Cancer Genome Interpreter, aimed to support the identification of biologically and therapeutically relevant variants in a patient’s tumor upon sequencing.

This thesis has been awarded the International PhD Mention.

Selected publications from the thesis:

1. Rubio-Perez C*, Tamborero D*, Schroeder MP, Antolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas, N. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell, 27:382-396, 2015.

2. Rubio-Perez C, Deu-Pons J, Tamborero D, Lopez-Bigas N, Gonzalez-Perez A. Rational design of cancer gene panels with OncoPaD. Genome Medicine, 8:98, 2016.


Arturo Urrios Garcia, for his thesis “Distributed computation in multicellular synthetic networks”, directed by Dr. Eulàlia de Nadal and Dr. Francesc Posas from the Universitat Pompeu Fabra and currently at the Institute for Research in Biomedicine.

Currently synthetic biology is focused mainly on implementing gene expression-based devices in single cells. However, inside of a cell there is a lack of spatial distribution between the different elements that perform the computation, and this can be a problem in terms of scalability, causing a metabolic burden to the cell or giving raise to undesired crosstalk events when wiring many elements within a genetic network. He proposed to overcome these limitations by building biological circuits in a multicellular consortium rather than in a single cell and explore how they perform in different scenarios. More concretely, the thesis developed a LEGO-like strategy for multicellular circuits to integrate many different external signals while reducing the number of connections (wiring), building transparent and biocompatible fluidic devices using stereolithography.

Selected publications from the thesis:

1. Urrios A, Macia J, Manzoni R, Conde N, Bonforti A, de Nadal E, Posas F, Solé R. A Synthetic Multicellular Memory Device. ACS Synthetic Biology, 5:862-873, 2016.

2. Urrios A, Gonzalez-Flo E, Canadell D, de Nadal E, Macia J, Posas F. Plug-and-Play Multicellular Circuits with Time-Dependent Dynamic Responses. ACS Synthetic Biology, 7:1095-1104, 2018.





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