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Mikaela Koutrouli
Mikaela Koutrouli
Post-doctoral fellow at Genentech
Verified email at gene.com
Title
Cited by
Cited by
Year
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
D Szklarczyk, R Kirsch, M Koutrouli, K Nastou, F Mehryary, R Hachilif, ...
Nucleic Acids Research 51 (D1), D638-D646, 2023
33572023
A guide to conquer the biological network era using graph theory
M Koutrouli, E Karatzas, D Paez-Espino, GA Pavlopoulos
Frontiers in bioengineering and biotechnology 8, 34, 2020
2802020
The scverse project provides a computational ecosystem for single-cell omics data analysis
I Virshup, D Bredikhin, L Heumos, G Palla, G Sturm, A Gayoso, I Kats, ...
Nature biotechnology 41 (5), 604-606, 2023
1452023
The STRING database in 2023: Protein-protein association networks and functional enrichment analyses for any sequenced genome of interest., 2023, 51, pp
D Szklarczyk, R Kirsch, M Koutrouli, K Nastou, F Mehryary, R Hachilif, ...
D638-D646. DOI: https://doi. org/10.1093/nar/gkac1000, 0
40
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review
FA Baltoumas, S Zafeiropoulou, E Karatzas, M Koutrouli, F Thanati, ...
Biomolecules 11 (8), 1245, 2021
202021
NORMA: the network makeup artist—a web tool for network annotation visualization
M Koutrouli, E Karatzas, K Papanikolopoulou, GA Pavlopoulos
Genomics, Proteomics and Bioinformatics 20 (3), 578-586, 2022
122022
FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data
M Koutrouli, K Nastou, P Piera Líndez, R Bouwmeester, S Rasmussen, ...
Bioinformatics 40 (2), btae010, 2024
102024
Exploring Networks in the STRING and Reactome Database
M Koutrouli, P Hatzis, GA Pavlopoulos
Academic Press, 2021
102021
A Guide to Conquer the Biological Network Era Using Graph Theory. Front Bioeng Biotechnol 2020; 8: 34
M Koutrouli, E Karatzas, D Paez-Espino, GA Pavlopoulos
72020
The STRING database in 2025: protein networks with directionality of regulation
D Szklarczyk, K Nastou, M Koutrouli, R Kirsch, F Mehryary, R Hachilif, ...
Nucleic Acids Research, gkae1113, 2024
52024
The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
E Karatzas, M Koutrouli, FA Baltoumas, K Papanikolopoulou, ...
Bioinformatics Advances 2 (1), vbac036, 2022
52022
Systems Medicine
M Koutrouli, P Hatzis, GA Pavlopoulos
52021
Single-cell atlas of transcriptomic vulnerability across multiple neurodegenerative and neuropsychiatric diseases
D Lee, M Koutrouli, NY Masse, GE Hoffman, S Kinrot, X Wang, P NM, ...
medRxiv, 2024.10. 31.24316513, 2024
42024
The Network Analysis Profiler (NAP v2. 0): A web tool for visual topological comparison between multiple networks
M Koutrouli, T Theodosiou, I Iliopoulos, G Pavlopoulos
EMBnet.journal 26, e943, 2021
42021
U-CIE [/juː'siː/]: Color encoding of high-dimensional data
M Koutrouli, JH Morris, LJ Jensen
32021
Lifestyle factors in the biomedical literature: An ontology and comprehensive resources for named entity recognition
E Nourani, M Koutrouli, Y Xie, D Vagiaki, S Pyysalo, K Nastou, S Brunak, ...
Bioinformatics, btae613, 2024
2*2024
Improving dictionary-based named entity recognition with deep learning
K Nastou, M Koutrouli, S Pyysalo, LJ Jensen
Bioinformatics 40 (Supplement_2), ii45-ii52, 2024
12024
Spatial Transcriptomics Sequencing of Mouse Liver at 2µm Resolution Using a Novel Spatial DNA Chip
X Ding, K Hoff, R Swaminathan, M Koutrouli, S Pollom, T Huang, X Li, ...
bioRxiv, 2024.01. 08.574734, 2024
2024
Spatial Transcriptomics Sequencing of Mouse Liver at 2 Micron Resolution Using a Novel Spatial DNA Chip
X Ding, K Hoff, R Swaminathan, S Pollom, T Huang, X Li, G Zhou, Z Bai, ...
2024
Targeted disruption of linkage-specific ubiquitylation reveals a key role of K29-linked ubiquitylation in epigenome integrity
J Arroyo-Gomez, J Wang, C Guerillon, E Isaakova, N Reveron-Gomez, ...
bioRxiv, 2024.10. 29.620783, 2024
2024
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