UPF Collaborative Projects 2018



Spatial transcriptomics by laser capture microdissection to identify distinct neuronal populations

Berta Alsina

Phasing north African chromosomes

Elena Bosch

Population genomics through the analysis of ancient human remains

David Comas

Methylome of skin microbiome components to determine foreign DNA restriction

Marc Güell

Deconvoluting cellularcomposition of senescence using single celldata

Pura Muñoz



UPF Collaborative Projects 2016-2017



Circular RNA in hepatic cells

Juana Díaz

Methods for genotyping large number of yeast strains

Lucas Carey

Assessing RNA deregulation in synaptopathologies affecting intellectual performance

Andrés Ozaita

Single-cell characterization of a cancer transcriptome

Eduardo Eyras

Transcriptomics of dried blood spot samples

Robert Castelo

Isolation of cell size mutants by flow citometry and ultrasequencing

José Ayté

Publications Publications


• De Valles-Ibañez G, Esteve-Solé A, Piquer M, González-Navarro A, Hernández-Rodríguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez A, Martín-Nalda A, Martínez-Gallo M, García-Prat M, del Pino L, Cuscó I, Codina-Solà M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobrán R, Yagüe J, Alsina L, Juan M,  and Casals F. Evaluating the genetics of common variable immunodeficiency: monogenetic model and beyond. 2018. In press. Frontiers in Immunology.

The BIOMEPOC Project: Personalized Biomarkers and Clinical Profiles in Chronic Obstructive Pulmonary Disease. Arch Bronconeumol. 2018 Oct 18.



• Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. • The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol Ecol Resour. 2017 Oct 23. doi: 10.1111/1755-0998.12728. [Epub ahead of print].

• Casals F, Anglada R, Bonet N, Rasal R, van der Gaag KJ, Hoogenboom J, Solé-Morata N, Comas D, Calafell F. Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations. Forensic Sci Int Genet. 2017 Sep;30:66-70.

• Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C, Bertranpetit J.Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Hum Genet. 2017 May;136(5):499-510. 

• Spataro N, Roca-Umbert A, Cervera-Carles L, Vallès M, Anglada R, Pagonabarraga J, Pascual-Sedano B, Campolongo A, Kulisevsky J, Casals F, Clarimón J, Bosch E. Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients. Mov Disord. 2017 Jan;32(1):165-169. 



• Calafell F, Anglada R, Bonet N, González-Ruiz M, Prats-Muñoz G, Rasal R, Lalueza-Fox C, Bertranpetit J, Malgosa A, Casals F. An assessment of a massively parallel sequencing approach for the identification of individuals from mass graves of the Spanish Civil War (1936-1939).Electrophoresis. 2016 Oct;37(21):2841-2847.

• Mondal M, Casals F, Xu T, Dall'Olio GM, Pybus M, Netea MG, Comas D, Laayouni H, Li Q, Majumder PP, Bertranpetit J. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat Genet. 2016 Sep;48(9):1066-70.

• de Valles-Ibáñez G, Hernandez-Rodriguez J, Prado-Martinez J, Luisi P, Marquès-Bonet T, Casals F. Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes. Genome Biol Evol. 2016 Mar 26;8(3):871-7. 

• E Bosch and F Casals: Next Generation Sequencing for Rare Disease. Book chapter in: Genome-Wide Association Studies: From Polymorphism to Personalized Medicine. Cambridge University Press, 2016.

F Casals and E Bosch. Next Generation Sequencing for Complex Disorders. Book chapter in: Genome-Wide Association Studies: From Polymorphism to Personalized Medicine. Cambridge University Press, 2016.

Courses Courses

RNASeq- How low can you go?

Organized by Werfen & New England Biolabs & Genomics Core Facility UPF. At the UPF, 27-29 May 2019.



Past courses

  • Illumina & Verogen Forensic Genomics Workshop, at the Genomics Core Facility (Universitat Pompeu Fabra, Barcelona). 20-21 March 2018. Organized by the Genomics Core Facility & Illumina&Verogen.


  • Illumina Forensics Workshop, at the Genomics Core Facility (Universitat Pompeu Fabra, Barcelona). 22-23 November 2016. Organized by the Genomics Core Facility & Illumina. Program & Registration



  • Targeted resequencing for cancer studies. The solid tumor gene panel  Barcelona, 21-23 January 2015. Organized by the Genomics Core Facility & Illumina. Program.

Demo day

Demo day