Author

Colin J. Birkenbihl

University of BonnORCID 0000-0002-7212-7700Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 4 Approach:statistical model· 4 Organism:human· 3 Assay:bulk RNA-seq· 2 Research Focus:clustering· 2 Research Focus:database / resource· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2

Frequent Co-Authors

Daniel Domingo‐FernándéziD· 4 shared Martin Hofmann‐ApitiusiD· 4 shared Charles Tapley HoytiD· 3 shared Mehdi AliiD· 2 shared Sarah MubeeniD· 2 shared Alpha Tom KodamulliliD· 1 shared Andrej KonotopeziD· 1 shared Benjamin M. GyoriiD· 1 shared

Activity by Year

2019-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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4 shared papersBioinformatics

Daniel Domingo‐FernándézORCID

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Author profile →

5 papers

Recent·Most cited

Blood-based Transcriptomics Reveal Sex- and Amyloid-Modulated Biology of Plasma pTau217 in Preclinical Alzheimer's Disease

Mabel Seto, Hannah M Klinger, Michelle J. Clifton, Vaibhav A. Janve, Jane A. Brown, Colin J. Birkenbihl, Gillian Coughlan, Diana L Townsend, Ting‐Chen Wang, Michael J Properzi, Bernard Jimmy Hanseeuw, Jasmeer P. Chhatwal, Hyun‐Sik Yang, Yanling Wang, Philip L. De Jager, , Rachel F. Buckley

The paper identifies gene associations with plasma pTau217 in preclinical Alzheimer's disease, showing modulation by APOEε4, Aβ-PET, and sex, with X-linked genes playing a role.

bioRxiv · Nov 21, 2025 · PreprintNeuroscience

Exploring the intricacies and pitfalls of the ATN framework: An assessment across cohorts and thresholding methodologies

Yasamin Salimi, Daniel Domingo‐Fernándéz, Martin Hofmann‐Apitius, Colin J. Birkenbihl, the Alzheimer’s Disease Neuroimaging Initiative, the Japanese Alzheimer’s Disease Neuroimaging Initiative, the Alzheimer’s Disease Repository Without Borders Investigators

This paper evaluates how different thresholding methods affect ATN profiles across AD cohorts, finding high variability and limited generalizability of results.

bioRxiv · Dec 6, 2022 · PreprintBioinformatics

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

Helena Balabin, Charles Tapley Hoyt, Colin J. Birkenbihl, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Paul G. Plöger, Martin Hofmann‐Apitius, Daniel Domingo‐Fernándéz

The paper introduces STonKGs, a Transformer model trained on biomedical text and knowledge graphs, which outperforms single-modality models in classification tasks.

Bioinformatics · Jan 3, 2022Peer-reviewedBioinformatics

CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations

Vinay Srinivas Bharadhwaj, Mehdi Ali, Colin J. Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann‐Apitius, Charles Tapley Hoyt, Daniel Domingo‐Fernándéz

CLEP generates patient representations by integrating prior biological knowledge with patient data, improving classification performance compared to using raw transcriptomics data.

Bioinformatics · May 3, 2021Peer-reviewedBioinformatics

Integration of Structured Biological Data Sources using Biological Expression Language

Charles Tapley Hoyt, Daniel Domingo‐Fernándéz, Sarah Mubeen, Josep Marín-Llaó, Andrej Konotopez, Christian Ebeling, Colin J. Birkenbihl, Özlem Muslu, Bradley W. English, Simon Müller, Mauricio Lacerda, Mehdi Ali, Scott Colby, Dénes Türei, Nicolàs Palacio‐Escat, Martin Hofmann‐Apitius

The paper introduces Bio2BEL, a set of Python packages that convert multi-modal biological data into Biological Expression Language for integration and analysis.

bioRxiv · May 8, 2019 · PreprintBioinformatics