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General Information



Sonia.jpg Name: Sònia Casillas
Title: PhD
Category: Research Technician
Institution:

Universitat Autònoma de Barcelona
Faculty of Life Sciences
Department of Genetics and Microbiology


I am a research technician at the Genomics, Bioinformatics and Evolution Group of the Department of Genetics and Microbiology of the Universitat Autònoma de Barcelona, with the role to manage the UAB-Bioinformatics Service.

I obtained my degree in Biology (BSc) in 2001 at the Universitat Autònoma de Barcelona. In 2003 I obtained my Master in Genetics (MSc) for the same university after finishing the doctorate courses and presenting the research project "Bioinformatics platform for the representation and analysis of the nucleotide diversity in Drosophila". Later, in 2008 I obtained my PhD in Bioinformatics and Population Genetics with the thesis work entitled "Development and application of bioinformatic tools for the representation and analysis of genetic diversity", receiving also the "European Doctorate Mention".

My teaching experience is in bioinformatics and genetics for the BSc in Biology at the Universitat Autònoma de Barcelona and introductory courses of bioinformatics for the e-Biointel company and the UAB-Bioinformatics Service.

My research fields are Population Genetics, Genomics and Bioinformatics. At present, I am developing bioinformatic tools for the evolutionary analysis and interpretation of DNA diversity.

 

Research Lines
  • Data mining in population genetics
  • Bioinformatic tools for the analysis of nucleotide diversity
  • Development of databases on DNA polymorphism
  • Evolution of non-coding DNA
  • Comparative genomics
  • Genome assembling and annotation

Publications

Egea et al. 2008 NAR


Egea, R., Casillas, S. and Barbadilla, A. (2008). Standard and Generalized McDonald-Kreitman Test: a website to detect selection by comparing different classes of DNA sites. Nucleic Acids Research, 36 (Web Server issue): W157-W162. [PubMed] [Journal] [PDF] [Web Site]

 
Casillas 2008 PhD Thesis


Casillas, S. (2008). Development and application of bioinformatic tools for the representation and analysis of genetic diversity. PhD Thesis, Universitat Autònoma de Barcelona. [PDF] [Presentation] [UAB-Divulg@]

 
Casillas et al. 2007 Fly



Casillas, S., Egea, R., Petit, N., Bergman, C.M. and Barbadilla, A. (2007). Drosophila Polymorphism Database (DPDB): a portal for nucleotide polymorphism in Drosophila. Fly 1 (4): 205-211. [Journal] [PDF] [Suppl. Files: 1]

Casillas et al. 2007 MBE


Casillas, S., Barbadilla, A. and Bergman, C.M. (2007). Purifying selection maintains highly conserved noncoding sequences in Drosophila. Molecular Biology and Evolution 24 (10): 2222-2234. [PubMed] [Journal] [PDF] [Suppl. Files: 1,2,3,4,5]


Petit et al. 2007 Journal of Molecular Evolution


Petit, N., Casillas, S., Ruiz, A. and Barbadilla, A. (2007). Protein polymorphism is negatively correlated with conservation of intronic sequences and complexity of expression patterns in Drosophila melanogaster. Journal of Molecular Evolution, 64 (5): 511-518. [PubMed] [Journal] [PDF] [Suppl. Files: 1] [UAB-Divulg@]


Egea et al. 2007 NAR


Egea, R., Casillas, S. Fernández, E., Senar, M.A. and Barbadilla, A. (2007). MamPol: a database of nucleotide polymorphism in the Mammalia class. Nucleic Acids Research, 35 (Database issue): D624-D629. [PubMed] [Journal] [PDF] [Suppl. Files: 1,2] [Web Site]


Casillas et al. 2006 BMC Evolutionary Biology


Casillas, S., Negre, B., Barbadilla, A. and Ruiz, A. (2006). Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila. BMC Evolutionary Biology, 6: 106. [PubMed] [Journal] [PDF] [Suppl. Files: 1,2,3,4,5


Casillas and Barbadilla 2006 NAR


Casillas, S. and Barbadilla, A. (2006). PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. Nucleic Acids Research, 34 (Web Server issue): W632-634. [PubMed] [Journal] [PDF] [Web Site]


Casillas et al. 2005 Bioinformatics


Casillas, S., Petit, N. and Barbadilla, A. (2005). DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus. Bioinformatics, 21 (Suppl.2): ii26-ii30. [PubMed] [Journal] [PDF] [Web Site]


Negre et al. 2005 Genome Research


Negre, B., Casillas, S., Suzanne, M., Sánchez-Herrero, E., Akam, M., Nefedov, M., Barbadilla, A., de Jong, P. and Ruiz, A. (2005). Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Research, 15: 692-700. [PubMed] [Journal] [PDF] [Suppl. Files: 1,2] [Evaluated for Faculty of 1000 Biology]


Casillas and Barbadilla 2004 NAR


Sònia Casillas and Antonio Barbadilla (2004). PDA: a pipeline to explore and estimate polymorphism in large DNA databases. Nucleic Acids Research, 32 (Web Server issue): W166-169. [PubMed] [Journal] [PDF] [Web Site]

 

Grants

Tècnic de Suport a la Recerca (UAB)


Type: Research Technician, UAB-Bioinformatics Platform
Funding agency: Universitat Autònoma de Barcelona
Dates: 01/10/2006 - 30/09/2007
See a Group picture

 
Marie Curie European fellowship for short stays abroad (PHD20)



Type: Marie Curie European fellowship for short stays abroad (PHD20)
Funding agency: European Comission
Reference: HPMT-GH-01-00285-13
Dates: 16/01/2006 - 15/04/2006
See Group picture

 
PhD fellowship



Type: Beca Predoctoral de Formación de Personal Investigador (FPI)
Project: BMC2002-01708
Funding agency: Ministerio de Ciencia y Tecnología (MCyT)
Dates: 01/05/2003 - 30/09/2006

 
e-Biointel grant for the development of bioinformatic platforms and course materials



Funding agency: e-Biointel
Dates: 01/02/2002 - 31/10/2002

Teaching

Una invitació a la Bioinformàtica


Exposició "Una invitació a la Bioinformàtica", englobada dins l'Any de la Computació de la UAB.

- Facultat de Biociències: del 15 al 18 d'abril del 2008 [pdf díptic]
- ETSE: del 19 al 22 de maig del 2008 [pdf díptic]

Web de l'exposició: http://bioinf3.uab.cat/expobi/

 

Genomics and Perl - Universitat de Girona (Master degree)

Bioinformatics course (Master degree)
Place: Universitat de Girona
Duration: december 2007
Materials (in catalan): [
ppt Genòmica ] [ppt Perl ] [Perl, Exercicis guiats] [Perl, Exercici integrador ]

 

Bioinformatics - Plataforma Bioinformàtica UAB


Bioinformatics courses of the UAB Bioinformatics Platform
Place: Universitat Autònoma de Barcelona
Duration: since 2006

 
Biocomputation - Practicum



Practicum Biocomputation (4th course Biology degree).
Place: Universitat Autònoma de Barcelona
Duration: year 2006-2007

 
Genetics - Practicum



Practicum Genetics (2nd course Biology degree).
Place: Universitat Autònoma de Barcelona
Duration: year 2005-2006

 
Bioinformatics - e-Biointel



Description: Bioinformatics courses of the e-Biointel company
Place: Universitat Autònoma de Barcelona
Duration: since 2003

Projects

Association studies assisted by Inference and Semantic Technologies (ASSIST)

Project coordinator: P. Mitkas (CERTH/ITI)
Duration: 2006-2008
Funding Agency: Sixth Framework Programme. STRP: Integrated biomedical information for better health.
Code: FP6-IST-2004-027510 


Patterns of nucleotide diversity in different functional regions of Drosophila and Chordates



Researchers: Antonio Barbadilla (IP), S. Casillas, N. Petit, R. Egea, E. Betrán
Duration: 2007-2010
Funding Agency: Ministerio de Ciencia y Tecnología (MCyT)
Code: BFU2006-08640/BMC

 
Comparative and functional genomics in Drosophila



Complete Title: Comparative and functional genomics in Drosophila: causes and consequences of the natural chromosomic rearrangements
Researchers: Alfredo Ruiz (IP), A. Barbadilla, J. González, F. Casals, B. Negre, M. Puig, C. Santa, S. Casillas
Duration: 2002-2005
Funding Agency: Ministerio de Ciencia y Tecnología (MCyT)
Code: BMC2002-01708

 
Creation of a techology-based company



Researchers: Antonio Barbadilla (IP)
Duration:  2001-2002
Funding agency: Centre d'Innovació i Desenvolupament Empresarial (CIDEM)
Code: 

 
The role of recombination in the generation of the natural chromosomic and nucleotidic diversity


a/e

IP: Alfredo Ruiz
Duration:  1999 - 2002
Funding agency: Ministerio de Ciencia y Tecnología (MCyT)
Code: PB98-0900-C02

Subproject 2: Distribution of local recombination rates caused by gene conversion and crossing-over along the genome. A. Barbadilla (IP), A. Navarro, C. Santa and S. Casillas. DGICYT - PB98-0900-C02-02. 1999-2002.