Explanipedia

Establishment of an imaging-based screening pipeline for the identification of human ribosome biogenesis inhibitors Open

Claudia Gafko, Réka Hollandi, Kerstin Dörner, Matteo Rosellini, Ivo Zemp , et al. · 2025

Background Ribosomes are huge ribonucleoprotein particles that mediate protein synthesis in all organisms. The synthesis of ribosomes is a complex process that involves hundreds of supporting factors in mammalian cells, including proto-onc…

A Morpho-Proteomic Atlas of Mitosis at Sub-Minute Resolution Open

Ede Migh, Vivien Miczán, Frederik Post, Krisztián Koós, Attila Beleon , et al. · 2025

Summary Precise spatiotemporal protein organization is critical for fundamental biological processes including cell division 1,2 . Indeed, aberrant mitosis and mitotic factors are involved in diverse diseases, including various cancers 3,4…

When the pen is mightier than the sword: semi-automatic 2 and 3D image labelling Open

Réka Hollandi, David Bauer, Ákos Diósdi, Bálint Schrettner, Tímea Tóth , et al. · 2024

Data is the driving engine of learning-based algorithms, the creation of which fundamentally determines the performance, accuracy, generalizability and quality of any model or method trained on it. When only skilled or trained personnel ca…

Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2 Open

Vilja Pietiäinen, Minttu Polso, Ede Migh, Christian Guckelsberger, Mária Harmati , et al. · 2023

Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2 Open

Vilja Pietiäinen, Minttu Polso, Ede Migh, Christian Guckelsberger, Mária Harmati , et al. · 2022

Here, we describe a scalable and automated, high-content microscopy -based mini-immunofluorescence assay (mini-IFA) for serological testing i.e., detection of antibodies. Unlike conventional IFA, which often relies on the use of cells infe…

Deep Visual Proteomics defines single-cell identity and heterogeneity Open

Andreas Mund, Fabian Coscia, András Kriston, Réka Hollandi, Ferenc Kovács , et al. · 2022

Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Prote…

Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2 Open

Vilja Pietiäinen, Minttu Polso, Ede Migh, Christian Guckelsberger, Mária Harmati , et al. · 2022

Single-cell extracted imaging features created in project "Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2". The dataset includes train (with annotations) and test features used in the manuscript. Four SARS-C…

Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2 Open

Vilja Pietiäinen, Minttu Polso, Ede Migh, Christian Guckelsberger, Mária Harmati , et al. · 2022

Single-cell extracted imaging features created in project "Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2". The dataset includes train (with annotations) and test features used in the manuscript. Four SARS-C…

α/β-Peptides as Nanomolar Triggers of Lipid Raft-Mediated Endocytosis through GM1 Ganglioside Recognition Open

Anasztázia Hetényi, Enikő Szabó, Norbert Imre, Kaushik Nath Bhaumik, Attila Tököli , et al. · 2022

Cell delivery of therapeutic macromolecules and nanoparticles is a critical drug development challenge. Translocation through lipid raft-mediated endocytic mechanisms is being sought, as it can avoid rapid lysosomal degradation. Here, we p…

Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism Open

Kerstin Dörner, Lukas Badertscher, Bianka Horváth, Réka Hollandi, Csaba Molnár , et al. · 2022

Ribosome assembly is an essential process that is linked to human congenital diseases and tumorigenesis. While great progress has been made in deciphering mechanisms governing ribosome biogenesis in eukaryotes, an inventory of factors that…

Nucleus segmentation: towards automated solutions Open

Réka Hollandi, Nikita Moshkov, Lassi Paavolainen, Ervin Tasnádi, Filippo Piccinini , et al. · 2022

Applications of deep learning in single-cell analysis Open

Réka Hollandi · 2021

Egy mélytanulás alapú, annotálásra, tanításra és egysejt elemzésre alkalmas teljes munkafolyamatot mutatunk be ebben a disszertációban. Leírjuk, hogyan lehet megfelelően nagy méretű és megbízható minőségű annotált adathalmazokat könnyedén …

Author Correction: Test-time augmentation for deep learning-based cell segmentation on microscopy images Open

Nikita Moshkov, Botond Mathe, Attila Kertész‐Farkas, Réka Hollandi, Péter Horváth · 2021

AI-driven Deep Visual Proteomics defines cell identity and heterogeneity Open

Andreas Mund, Fabian Coscia, Réka Hollandi, Ferenc Kovács, András Kriston , et al. · 2021

The systems-wide analysis of biomolecules in time and space is key to our understanding of cellular function and heterogeneity in health and disease 1 . Remarkable technological progress in microscopy and multi-omics technologies enable in…

Erratum to “Maternal Smoking Highly Affects the Function, Membrane Integrity, and Rheological Properties in Fetal Red Blood Cells” Open

Krisztina N. Dugmonits, Payal Chakraborty, Réka Hollandi, Szabolcs Zahorán, Gabriella Pankotai-Bodó , et al. · 2021

Neuropilin-1 is a host factor for SARS-CoV-2 infection Open

James L. Daly, Boris Simonetti, Katja Klein, Kai‐En Chen, Maia Kavanagh Williamson , et al. · 2020

Another host factor for SARS-CoV-2 Virus-host interactions determine cellular entry and spreading in tissues. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the earlier SARS-CoV use angiotensin-converting enzyme 2 (ACE2) …

OpSeF: Open Source Python Framework for Collaborative Instance Segmentation of Bioimages Open

Tobias M. Rasse, Réka Hollandi, Péter Horváth · 2020

Various pre-trained deep learning models for the segmentation of bioimages have been made available as developer-to-end-user solutions. They are optimized for ease of use and usually require neither knowledge of machine learning nor coding…

AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments Open

Réka Hollandi, Ákos Diósdi, Gábor Hollandi, Nikita Moshkov, Péter Horváth · 2020

To find objects on images automatically, first we must teach the computer how to recognize them by showing examples. The most robust of such methods use deep learning, needing a large annotated dataset to be efficient. We propose an ImageJ…

Neuropilin-1 is a host factor for SARS-CoV-2 infection Open

James L. Daly, Boris Simonetti, Carlos Antón-Plágaro, Maia Kavanagh Williamson, Deborah K. Shoemark , et al. · 2020

SARS-CoV-2 is the causative agent of COVID-19, a coronavirus disease that has infected more than 6.6 million people and caused over 390,000 deaths worldwide 1,2 . The Spike (S) protein of the virus forms projections on the virion surface r…

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer Open

Réka Hollandi, Ábel Szkalisity, Tímea Tóth, Ervin Tasnádi, Csaba Molnár , et al. · 2020

Single-cell segmentation is typically a crucial task of image-based cellular analysis. We present nucleAIzer, a deep-learning approach aiming toward a truly general method for localizing 2D cell nuclei across a diverse range of assays and …

OpSeF: Open source Python framework for collaborative instance segmentation of bioimages Open

Tobias M. Rasse, Réka Hollandi, Péter Horváth · 2020

Various pre-trained deep learning models for the segmentation of bioimages have been made available as ‘developer-to-end-user’ solutions. They usually require neither knowledge of machine learning nor coding skills, are optimized for ease …

Test-time augmentation for deep learning-based cell segmentation on microscopy images Open

Nikita Moshkov, Botond Mathe, Attila Kertész‐Farkas, Réka Hollandi, Péter Horváth · 2020

Recent advancements in deep learning have revolutionized the way microscopy images of cells are processed. Deep learning network architectures have a large number of parameters, thus, in order to reach high accuracy, they require a massive…

AnnotatorJ: an ImageJ plugin to ease hand-annotation of cellular compartments Open

Réka Hollandi, Ákos Diósdi, Gábor Hollandi, Nikita Moshkov, Péter Horváth · 2020

AnnotatorJ combines single-cell identification with deep learning and manual annotation. Cellular analysis quality depends on accurate and reliable detection and segmentation of cells so that the subsequent steps of analyses e.g. expressio…

Maternal Smoking Highly Affects the Function, Membrane Integrity, and Rheological Properties in Fetal Red Blood Cells Open

Krisztina N. Dugmonits, Payal Chakraborty, Réka Hollandi, Szabolcs Zahorán, Gabriella Pankotai-Bodó , et al. · 2019

An understanding of the basic pathophysiological mechanisms of neonatal diseases necessitates detailed knowledge about the wide range of complications in the circulating fetal RBCs. Recent publications on adult red blood cells (RBCs) provi…

Test-time augmentation for deep learning-based cell segmentation on microscopy images Open

Nikita Moshkov, Botond Mathe, Attila Kertész‐Farkas, Réka Hollandi, Péter Horváth · 2019

Recent advancements in deep learning have revolutionized the way microscopy images of cells are processed. Deep learning network architectures have a large number of parameters, thus, in order to reach high accuracy, they require massive a…

Failure in the compensatory mechanism in red blood cells due to sustained smoking during pregnancy Open

Payal Chakraborty, Krisztina N. Dugmonits, Attila G. Végh, Réka Hollandi, Pavel Horváth , et al. · 2019

A deep learning framework for nucleus segmentation using image style transfer Open

Réka Hollandi, Ábel Szkalisity, Tímea Tóth, Ervin Tasnádi, Csaba Molnár , et al. · 2019

Single cell segmentation is typically one of the first and most crucial tasks of image-based cellular analysis. We present a deep learning approach aiming towards a truly general method for localizing nuclei across a diverse range of assay…

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