Buj R, Mallona I, Díez-Villanueva A, Zafon C, Mate JL, Roca M, Puig-Domingo M, Reverter JL, Mauricio D, Peinado MA, Jordà M
Author: maplab.cat
The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data.
Mallona I, Sierco A, Peinado MA. The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data. Methods Mol Biol. 2018;1766:123-135. doi: 10.1007/978-1-4939-7768-0_7.
CpG Islands. Methods and Protocols
CpG islands constitute key genomic elements playing a fundamental role in essential biological processes such as development and cell differentiation. CpG islands are short stretches of DNA enriched in CpG dinucleotides, firstly identified by Adrian Bird in the 80’s. The human genome contains about 28,000 of these elements that are tightly associated to the regulation of 40% of the genes. Epigenetic alterations of specific CpG islands constitute molecular landmarks of multiple diseases including cancer, cardiovascular and neurological diseases, becoming principal targets as biomarkers and advanced therapeutic strategies.
The authoritative series Methods in Molecular Biology published by Springer Nature has released a new volume devoted to cover different aspects related with the study of these genomic elements. The book covers bioinformatic and molecular biology methods useful to identify and to explore the functions of CpG islands, as well as reviews on key applications of its study. Tanya Vavouri and Miguel A. Peinado, from the IJC and the IGTP, are the editors and have counted with the contribution of internationally renowned scientists in the fields of genomics and epigenomics.
The book contents and the online version may be found at: https://link.springer.com/book/10.1007/978-1-4939-7768-0.
Reference: Vavouri T, Peinado MA (ed.) CpG Islands: Methods and Protocols. Methods Mol Biol. 2018;1766. https://doi.org/10.1007/978-1-4939-7768-0
Increased global DNA hypomethylation in distant metastatic and dedifferentiated thyroid cancer.
Survivin, a key player in cancer progression, increases in obesity and protects adipose tissue stem cells from apoptosis.
Ejarque M, Ceperuelo-Mallafré V, Serena C, Pachón G, Núñez-Álvarez Y, Terrón-Puig M, Calvo E, Núñez-Roa C, Oliva-Olivera W, Tinahones FJ, Peinado MA, Vendrell J, Fernández-Veledo S. Survivin, a key player in cancer progression, increases in obesity and protects adipose tissue stem cells from apoptosis. Cell Death Dis. 2017 May 18;8(5):e2802. doi: 10.1038/cddis.2017.209.
Truke, a web tool to check for and handle excel misidentified gene symbols
Izaskun Mallona and Miguel A. Peinado. Truke, a web tool to check for and handle excel misidentified gene symbols. BMC Genomics (2017) 18:242
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JOB POSITION: EPIGENOMICS BIOINFORMATICIAN (ref. 2017/05) [CLOSED]
We are assembling an interdisciplinary group to develop a collaborative project between academia and private entrepreneurship and welcome creative people from diverse backgrounds. Our project aims to bring the advances of Genomics and Epigenomics technologies to routine applications in health and biomedical research. Please visit our web sites for more information about our work.
- Our tools: http://maplab.cat
- Our Institute: http://igtp.cat
- Our group at IMPPC: https://goo.gl/DMK2Xt and at the BIB: https://goo.gl/Hy0RgJ
DOWNLOAD ADVERTISEMENT: Job Offer
Requirements:
We are looking for a bionformatician to be responsible of the computational analysis of epigenetic changes in genome-scale projects using in-house developed next generation sequencing technology. The ultimate goal of the project is the improvement of genomic tools to analyze genetic and epigenetic variations in cancer and other diseases.
A good background on the analysis of epigenetic modifications, especially methylation, using NGS technologies is highly desirable, as well as experience in job scheduling in grid/cloud computing. Proven proficiency in the management of Biological Databases, programming languages (R, Perl, C++, Python, etc.) and statistical methods is required.
Conditions: Salary will be internationally competitive.
How to apply: Please send your application to rrhh@igtp.cat and copy to: mpeinado@igtp.cat
Applications should include:
- A CV including your contact details
- Names, email and telephone number of at least two referees
- A short statement of motivation
PLEASE QUOTE THE REFERENCE CODE ON ALL APPLICATIONS
Position posted: January 2017
Last date for Applications: 15th February 2017
The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.
Jordà M, Díez-Villanueva A, Mallona I, Martín B, Lois S, Barrera V, Esteller M, Vavouri T, Peinado MA. The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells. Genome Res. 2017; 27:118-132.
Chainy, an universal tool for standardized relative quantification in real-time PCR.
Mallona I, Díez-Villanueva A, Martín B, Peinado MA. Chainy, an universal tool for standardized relative quantification in real-time PCR. Bioinformatics. 2017 May 1;33(9):1411-1413. doi: 10.1093/bioinformatics/btw839.
DNA methylation profiling identifies PTRF/Cavin-1 as a novel tumor suppressor in Ewing sarcoma when co-expressed with caveolin-1.
Huertas-Martínez J, Court F, Rello-Varona S, Herrero-Martín D, Almacellas-Rabaiget O, Sáinz-Jaspeado M, Garcia-Monclús S, Lagares-Tena L, Buj R, Hontecillas-Prieto L, Sastre A, Azorin D, Sanjuan X, López-Alemany R, Moran S, Roma J, Gallego S, Mora J, García Del Muro X, Giangrande PH, Peinado MA, Alonso J, de Alava E, Monk D, Esteller M, Tirado OM. DNA methylation profiling identifies PTRF/Cavin-1 as a novel tumor suppressor in Ewing sarcoma when co-expressed with caveolin-1. Cancer Lett. 2017 Feb 1;386:196-207. doi: 10.1016/j.canlet.2016.11.020. Epub 2016 Nov 25.
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