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IJC Bioinformatics Unit

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SciProfiles: 1917403

Keywords

Bioinformatics, Data science, Software, Machine learning

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Spain

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Employment (4)

Fundación Josep Carreras Contra la Leucemia: Badalona, Barcelona, ES

2021-06-14 to present | Head of Bioinformatic Unit
Employment
Source: Self-asserted source
Angelika Merkel

Centro Nacional de Análisis Genómico (CNAG-CRG): Barcelona, ES

2013-05-27 to 2019-03-31 | PostDoc (Statistical Genomics and Bioinformatic Development)
Employment
Source: Self-asserted source
Angelika Merkel

RIKEN Yokohama Institute: Yokohoma, JP

2012-12-01 to 2013-03-30 | Short-term PostDoc (Genome Technologies)
Employment
Source: Self-asserted source
Angelika Merkel

Centre de Regulació Genòmica: Barcelona, Catalunya, ES

2009-10-15 to 2012-06-31 | PostDoc (Bioinformatics and Genomics)
Employment
Source: Self-asserted source
Angelika Merkel

Works (32)

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard

2024-09-19 | Preprint | Author
DOI: 10.1101/2024.09.16.609142
Contributors: Yu-Yu Lin; Kersten Breuer; Dieter Weichenhan; Pascal Lafrenz; Agata Wilk; Maryna Chepeleva; Oliver Mücke; Maximilian Schönung; Franziska Petermann; Philipp Kensche et al.
Source: Self-asserted source
Angelika Merkel

Endothelial TDP-43 controls sprouting angiogenesis and vascular barrier integrity, and its deletion triggers neuroinflammation

JCI Insight
2024-02-01 | Journal article
DOI: 10.1172/jci.insight.177819
Part of ISSN: 2379-3708
Contributors: Víctor Arribas; Yara Onetti; Marina Ramiro-Pareta; Pilar Villacampa; Heike Beck; Mariona Alberola; Anna Esteve-Codina; Angelika Merkel; Markus Sperandio; Ofelia M. Martínez-Estrada et al.
Source: Self-asserted source
Angelika Merkel

METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer

Molecular Cancer
2023-07-29 | Journal article
DOI: 10.1186/s12943-023-01809-8
Part of ISSN: 1476-4598
Contributors: Raquel García-Vílchez; Ana M. Añazco-Guenkova; Sabine Dietmann; Judith López; Virginia Morón-Calvente; Silvia D’Ambrosi; Paz Nombela; Kepa Zamacola; Isabel Mendizabal; Saioa García-Longarte et al.
Source: Self-asserted source
Angelika Merkel

Global Impairment of Immediate-Early Genes Expression in Rett Syndrome Models and Patients Linked to Myelination Defects

International Journal of Molecular Sciences
2023-01-11 | Journal article | Author
DOI: 10.3390/ijms24021453
Part of ISSN: 1422-0067
Contributors: Paolo Petazzi; Olga Caridad Jorge-Torres; Antonio Gomez; Iolanda Scognamiglio; Jordi Serra-Musach; Angelika Merkel; Daniela Grases; Clara Xiol Viñas; MARIA DEL MAR O'CALLAGHAN; Judith Armstrong et al.
Source: Self-asserted source
Angelika Merkel
grade
Preferred source (of 2)‎

Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary

Briefings in Bioinformatics
2022-09-20 | Journal article
DOI: 10.1093/bib/bbac161
Part of ISSN: 1467-5463
Part of ISSN: 1477-4054
Contributors: Pedro Blecua; Veronica Davalos; Izar de Villasante; Angelika Merkel; Eva Musulen; Laia Coll-SanMartin; Esteller M.
Source: Self-asserted source
Angelika Merkel

Novel Targeting of DNA Methyltransferase Activity Inhibits Ewing Sarcoma Cell Proliferation and Enhances Tumor Cell Sensitivity to DNA Damaging Drugs by Activating the DNA Damage Response

Frontiers in Endocrinology
2022-05-31 | Journal article
DOI: 10.3389/fendo.2022.876602
Part of ISSN: 1664-2392
Contributors: Camilla Cristalli; Maria Cristina Manara; Sergio Valente; Evelin Pellegrini; Alberto Bavelloni; Alessandra De Feo; William Blalock; Elisabetta Di Bello; David Piñeyro; Angelika Merkel et al.
Source: Self-asserted source
Angelika Merkel

Experimental and Bioinformatic Approaches to Studying DNA Methylation in Cancer

Cancers
2022-01-11 | Journal article
DOI: 10.3390/cancers14020349
Part of ISSN: 2072-6694
Contributors: Angelika Merkel; Esteller M.
Source: Self-asserted source
Angelika Merkel

Systemic Inflammation in Preclinical Ulcerative Colitis

Gastroenterology
2021-11 | Journal article
DOI: 10.1053/j.gastro.2021.07.026
Part of ISSN: 0016-5085
Contributors: Daniel Bergemalm; Erik Andersson; Johan Hultdin; Carl Eriksson; Stephen T. Rush; Rahul Kalla; Alex T. Adams; Åsa V. Keita; Mauro D’Amato; Fernando Gomollon et al.
Source: Self-asserted source
Angelika Merkel

Whole-genome DNA hyper-methylation in iPSC-derived dopaminergic neurons from Parkinson’s disease patients

Clinical Epigenetics
2019-12 | Journal article
DOI: 10.1186/s13148-019-0701-6
Part of ISSN: 1868-7075
Part of ISSN: 1868-7083
Source: Self-asserted source
Angelika Merkel
grade
Preferred source (of 2)‎

Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture

Biotechnology and Bioengineering
2019-03 | Journal article
DOI: 10.1002/bit.26891
Part of ISSN: 0006-3592
Part of ISSN: 1097-0290
Source: Self-asserted source
Angelika Merkel

gemBS: high throughput processing for DNA methylation data from bisulfite sequencing

Bioinformatics
2019-03-01 | Journal article
DOI: 10.1093/bioinformatics/bty690
Contributors: Angelika Merkel; Marcos Fernández-Callejo; Eloi Casals; Santiago Marco-Sola; Ronald Schuyler; Ivo G Gut; Simon C Heath; John Hancock
Source: check_circle
Crossref

Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes

Cell Reports
2019-01 | Journal article
DOI: 10.1016/j.celrep.2018.12.098
Part of ISSN: 2211-1247
Source: Self-asserted source
Angelika Merkel

Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils

Cell Reports
2018-09 | Journal article | Author
DOI: 10.1016/j.celrep.2018.08.018
Part of ISSN: 2211-1247
Contributors: Luigi Grassi; Farzin Pourfarzad; Sebastian Ullrich; Angelika Merkel; Felipe Were; Enrique Carrillo-de-Santa-Pau; Guoqiang Yi; Ida H. Hiemstra; Anton T.J. Tool; Erik Mul et al.
Source: Self-asserted source
Angelika Merkel
grade
Preferred source (of 2)‎

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

Nature Medicine
2018-06 | Journal article
DOI: 10.1038/s41591-018-0028-4
Part of ISSN: 1078-8956
Part of ISSN: 1546-170X
Source: Self-asserted source
Angelika Merkel

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

Genome Biology
2017 | Journal article
DOI: 10.1186/s13059-017-1156-8
PMID: 28126036
Part of ISBN: 1305901711
Source: Self-asserted source
Angelika Merkel

Comparative analysis of neutrophil and monocyte epigenomes

2017-12-22 | Preprint
DOI: 10.1101/237784
Contributors: Daniel Rico; Joost HA Martens; Kate Downes; Enrique Carrillo-de-Santa-Pau; Vera Pancaldi; Alessandra Breschi; David Richardson; Simon Heath; Sadia Saeed; Mattia Frontini et al.
Source: Self-asserted source
Angelika Merkel

GEMBS – high through-put processing for DNA methylation data from Whole Genome Bisulfite Sequencing (WGBS)

2017-10-11 | Preprint
DOI: 10.1101/201988
Contributors: Angelika Merkel; Marcos Fernández-Callejo; Eloi Casals; Santiago Marco-Sola; Ronald Schuyler; Ivo G. Gut; Simon Heath
Source: check_circle
Crossref

Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time

Biotechnology and Bioengineering
2016 | Journal article
DOI: 10.1002/bit.25990
PMID: 27072894
Source: Self-asserted source
Angelika Merkel

Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage

Cancer Cell
2016 | Journal article
DOI: 10.1016/j.ccell.2016.09.014
Source: Self-asserted source
Angelika Merkel

Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems

Cell Reports
2016 | Journal article
DOI: 10.1016/j.celrep.2016.10.054
PMID: 27851971
Source: Self-asserted source
Angelika Merkel

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers

Genome biology
2015 | Journal article
PMID: 25644835
Source: Self-asserted source
Angelika Merkel

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.

Nature genetics
2015-06 | Journal article
DOI: 10.1038/ng.3291
PMID: 26053498
Source: Self-asserted source
Angelika Merkel

Grape RNA-Seq analysis pipeline environment

Bioinformatics
2013 | Journal article
DOI: 10.1093/bioinformatics/btt016
Source: Self-asserted source
Angelika Merkel

An integrated encyclopedia of DNA elements in the human genome

Nature
2012 | Journal article
DOI: 10.1038/nature11247
PMID: 22955616
ISBN:

1476-4687
Source: Self-asserted source
Angelika Merkel

Landscape of transcription in human cells

Nature
2012 | Journal article
DOI: 10.1038/nature11233
ISBN:

0028083614764687
Source: Self-asserted source
Angelika Merkel

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Genome research
2012-09 | Journal article
DOI: 10.1101/gr.132159.111
PMID: 22955988
Source: Self-asserted source
Angelika Merkel

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

PLoS Biology
2011 | Journal article
DOI: 10.1371/journal.pbio.1001046
Source: Self-asserted source
Angelika Merkel

Review of ‘Cap-analysis gene expression’

BioEssays
2011 | Journal article
DOI: 10.1002/bies.201000144
Source: Self-asserted source
Angelika Merkel

Detecting Microsatellites in Genome Data: Variance in Definitions and Bioinformatic Approaches Cause Systematic Bias

Evolutionary bioinformatics online
2008 | Journal article
Source: Self-asserted source
Angelika Merkel

Detecting short tandem repeats from genome data: opening the software black box.

Briefings in Bioinformatics
2008 | Journal article
PMID: 18621747
Source: Self-asserted source
Angelika Merkel

Evolution of microsatellite DNA

Life Sciences
2008 | Journal article
DOI: 10.1002/9780470015902.a0020847
ISBN: 9780470015902
Source: Self-asserted source
Angelika Merkel

Genome analysis of the platypus reveals unique signatures of evolution.

Nature
2008 | Journal article
DOI: 10.1038/nature07253
PMID: 18464734
ISBN:

1476-4687 (Electronic)$\backslash$n0028-0836 (Linking)
Source: Self-asserted source
Angelika Merkel

Peer review (1 review for 1 publication/grant)

Review activity for npj genomic medicine. (1)
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