Author

Jindřich Soukup

MSD (Czech Republic)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 2 Neuroscience· 2

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:cell type annotation· 2 Approach:deep learning· 2 Organism:human· 2 Assay:proteomics· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Danny A. BittoniD· 3 shared Martin Vagenknecht· 2 shared Rebecca S. MathewiD· 2 shared Vanessa M. Peterson· 2 shared Alejandro Vázquez-Otero· 1 shared Alex M. Tamburino· 1 shared Andrej Palička· 1 shared Anna C. StolliD· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Danny A. BittonORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Plaque-associated oligodendrocyte proteostatic failure underlies myelin loss in Alzheimers disease

Jong Shin, Nandita Joshi, B Miller, Shams Vellarikkal, Jianhua Huang, Fan Wu, Yi Cui, Aparna Murali, Joshua Chason, Christopher Scott Campbell, Khoi Chu, Reza Roozafzoon, Mark Dostalík, Jindřich Soukup, Gina Savastano, , Bilal Çakır

This study shows that amyloid plaques disrupt oligodendrocyte proteostasis, leading to myelin loss in Alzheimer's disease.

bioRxiv · Aug 6, 2026 · PreprintNeuroscience

InCytokine, an open-source software, reveals a TREM2 variant specific cytokine signature

Deepak Kumar Jha, Marco Ancona, Filip Oplt, Sonia L. Farmer, Martin Vagenknecht, Alejandro Vázquez-Otero, Illia Prazdnyk, Jindřich Soukup, Rebecca S. Mathew, Vanessa M. Peterson, Danny A. Bitton

InCytokine is an open-source tool for analyzing cytokine and chemokine data from protein arrays, revealing genotype-specific signatures in TREM2 variants.

International Journal of Molecular Sciences · Jan 23, 2026Peer-reviewedBioinformatics

AnNoBrainer, an Automated Annotation of Mouse Brain Images using Deep Learning

Roman Peter, Petr Hrobař, Josef Navratil, Martin Vagenknecht, Jindřich Soukup, Keiko Tsuji, Nestor X. Barrezueta, Anna C. Stoll, Renee C. Gentzel, Jonathan A. Sugam, Jacob Marcus, Danny A. Bitton

AnNoBrainer automates mouse brain image annotation using deep learning, improving accuracy, reproducibility, and efficiency compared to manual methods.

Neuroinformatics · Aug 6, 2024Peer-reviewedNeuroscience

A Deep Learning Genome-Mining Strategy Improves Biosynthetic Gene Cluster Prediction

Geoffrey D. Hannigan, David Příhoda, Andrej Palička, Jindřich Soukup, Ondřej Klempíř, Lena Rampula, Jindrich Durcak, Michael Wurst, Jakub Kotowski, Dan Chang, Rurun Wang, Grazia Piizzi, Gergely Temesi, Daria J. Hazuda, Christopher H. Woelk, Danny A. Bitton

This paper introduces DeepBGC, a deep learning method for improved biosynthetic gene cluster prediction, uncovering previously undetectable clusters with potential novel biological activities.

Nucleic Acids Research · Aug 8, 2019Peer-reviewedBioinformatics