| 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, 1-6, 2014 | 71 | 2014 |
| 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 | 59 | 2016 |
| 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 | 58 | 2011 |
| 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 | 57 | 2017 |
| 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 | 55 | 2012 |
| 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), 6, 2017 | 45 | 2017 |
| The AIMe registry for artificial intelligence in biomedical research J Matschinske, N Alcaraz, A Benis, M Golebiewski, DG Grimm, L Heumos, ... Nature methods 18 (10), 1128-1131, 2021 | 44 | 2021 |
| The evolutionary landscape of SARS-CoV-2 variant B. 1.1. 519 and its clinical impact in Mexico City A Cedro-Tanda, L Gómez-Romero, N Alcaraz, G de Anda-Jauregui, ... Viruses 13 (11), 2182, 2021 | 42 | 2021 |
| Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection M Salgado-Albarrán, EI Navarro-Delgado, A Del Moral-Morales, ... NPJ systems biology and applications 7 (1), 21, 2021 | 40 | 2021 |
| Emergence and spread of the potential variant of interest (VOI) B. 1.1. 519 of SARS-CoV-2 predominantly present in Mexico AP Rodríguez-Maldonado, JA Vázquez-Pérez, A Cedro-Tanda, ... Archives of virology 166 (11), 3173-3177, 2021 | 39* | 2021 |
| 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 | 29 | 2018 |
| Robust de novo pathway enrichment with KeyPathwayMiner 5 N Alcaraz, M List, M Dissing-Hansen, M Rehmsmeier, Q Tan, ... F1000Research 5, 2016 | 29 | 2016 |
| Recycling of modified H2A-H2B provides short-term memory of chromatin states V Flury, N Reverón-Gómez, N Alcaraz, KR Stewart-Morgan, A Wenger, ... Cell 186 (5), 1050-1065. e19, 2023 | 28 | 2023 |
| 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), 41, 2019 | 20 | 2019 |
| 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 | 20 | 2016 |
| Promoter sequence and architecture determine expression variability and confer robustness to genetic variants H Einarsson, M Salvatore, C Vaagensø, N Alcaraz, J Bornholdt, S Rennie, ... Elife 11, e80943, 2022 | 16 | 2022 |
| 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 | 15 | 2014 |
| Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells S Bakoulis, R Krautz, N Alcaraz, M Salvatore, R Andersson Nucleic acids research 50 (4), 2111-2127, 2022 | 13 | 2022 |
| 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 | 13 | 2017 |
| Transcriptome analysis identifies GATA3-AS1 as a long noncoding RNA associated with resistance to neoadjuvant chemotherapy in locally advanced breast cancer patients L Contreras-Espinosa, N Alcaraz, A Inti, J Díaz-Chávez, ... The Journal of Molecular Diagnostics 23 (10), 1306-1323, 2021 | 12 | 2021 |
