Nicolas Alcaraz
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KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape
N Alcaraz, J Pauling, R Batra, E Barbosa, A Junge, AGL Christensen, ...
BMC systems biology 8 (1), 1-6, 2014
KeyPathwayMiner: detecting case-specific biological pathways using expression data
N Alcaraz, H Kücük, J Weile, A Wipat, J Baumbach
Internet Mathematics 7 (4), 299-313, 2011
Efficient key pathway mining: combining networks and OMICS data
N Alcaraz, T Friedrich, T Kötzing, A Krohmer, J Müller, J Pauling, ...
Integrative Biology 4 (7), 756-764, 2012
De novo pathway-based biomarker identification
N Alcaraz, M List, R Batra, F Vandin, HJ Ditzel, J Baumbach
Nucleic acids research 45 (16), e151-e151, 2017
KeyPathwayMinerWeb: online multi-omics network enrichment
M List, N Alcaraz, M Dissing-Hansen, HJ Ditzel, J Mollenhauer, ...
Nucleic Acids Research 44 (W1), W98-W104, 2016
On the performance of de novo pathway enrichment
R Batra, N Alcaraz, K Gitzhofer, J Pauling, HJ Ditzel, M Hellmuth, ...
NPJ systems biology and applications 3 (1), 1-8, 2017
Robust de novo pathway enrichment with KeyPathwayMiner 5
N Alcaraz, M List, M Dissing-Hansen, M Rehmsmeier, Q Tan, ...
F1000Research 5, 2016
Orthologous proteins of experimental de-and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes
NA Martin, A Nawrocki, V Molnar, ML Elkjaer, EK Thygesen, M Palkovits, ...
PloS one 13 (8), e0202530, 2018
Elucidation of epithelial–mesenchymal transition-related pathways in a triple-negative breast cancer cell line model by multi-omics interactome analysis
JK Pauling, AG Christensen, R Batra, N Alcaraz, E Barbosa, MR Larsen, ...
Integrative biology 6 (11), 1058-1068, 2014
Change in autoantibody and cytokine responses during the evolution of neuromyelitis optica in patients with systemic lupus erythematosus: a preliminary study
KT Kovacs, SR Kalluri, A Boza-Serrano, T Deierborg, T Csepany, M Simo, ...
Multiple Sclerosis Journal 22 (9), 1192-1201, 2016
Elucidation of altered pathways in tumor‐initiating cells of triple‐negative breast cancer: A useful cell model system for drug screening
AG Christensen, S Ehmsen, MG Terp, R Batra, N Alcaraz, J Baumbach, ...
Stem Cells 35 (8), 1898-1912, 2017
A simulated annealing algorithm for maximum common edge subgraph detection in biological networks
SJ Larsen, FG Alkćrsig, HJ Ditzel, I Jurisica, N Alcaraz, J Baumbach
Proceedings of the Genetic and Evolutionary Computation Conference 2016, 341-348, 2016
The epigenetic factor BORIS (CTCFL) controls the androgen receptor regulatory network in ovarian cancer
M Salgado-Albarrán, R González-Barrios, L Guerra-Calderas, N Alcaraz, ...
Oncogenesis 8 (8), 1-12, 2019
CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines
L Guerra-Calderas, R González-Barrios, CC Patińo, N Alcaraz, ...
Oncotarget 9 (24), 17028, 2018
De Novo Pathway-Based Classification of Breast Cancer Subtypes
M List, N Alcaraz, R Batra
Protein-Protein Interaction Networks, 201-213, 2020
The GBAF chromatin remodeling complex binds H3K27ac and mediates enhancer transcription
K Jefimov, N Alcaraz, SL Kloet, S Värv, SA Sakya, CD Vaagenso, ...
bioRxiv, 445148, 2018
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection
M Salgado-Albarran, EI Navarro-Delgado, D Moral-Morales, N Alcaraz, ...
arXiv preprint arXiv:2011.08902, 2020
De Novo Pathway Enrichment with KeyPathwayMiner
N Alcaraz, A Hartebrodt, M List
Protein-Protein Interaction Networks, 181-199, 2020
A functional genetic screen identifies the Mediator complex as essential for SSX2-induced senescence
NH Brückmann, SN Bennedsen, PHG Duijf, MG Terp, M Thomassen, ...
Cell death & disease 10 (11), 1-12, 2019
2 Epigenetic Data and
R Gonzalez-Barrios, M Salgado-Albarran, N Alcaraz, C Arriaga-Canon, ...
Analyzing Network Data in Biology and Medicine: An Interdisciplinary …, 2019
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