Article
Biochemical Research Methods
Josef Spidlen, Wayne Moore, David Parks, Michael Goldberg, Kim Blenman, James S. Cavenaugh, Ryan Brinkman
Summary: FCS 3.2 is a revised flow cytometry data standard that aims to capture instrument conditions and measurement features more precisely, providing a uniform file format. The new version supports mixed data types to efficiently handle new types of data and use cases, but is incompatible with existing FCS file readers.
Article
Biochemical Research Methods
Alexander Senf, Robert Davies, Frederic Haziza, John Marshall, Juan Troncoso-Pastoriza, Oliver Hofmann, Thomas M. Keane
Summary: To protect sensitive genetic data, a file container specification has been defined to enable direct analysis of encrypted genetic data without the need to create decrypted copies.
Article
Acoustics
Janek T. Groehl, Lina K. Hacker, Ben Cox, Kris Dreher, Stefan Morscher, Avotra C. Rakotondrainibe, Francois E. Varray, Lawrence Yip, William Vogt, Sarah Bohndeik
Summary: Photoacoustic imaging is a promising modality for patient management, but the lack of uniformity in data formats hinders progress and collaboration. The International Photoacoustic Standardisation Consortium has developed a consensus data format and conversion tools to facilitate data exchange and comparison.
Article
Multidisciplinary Sciences
Leho Tedersoo, Rainer Kungas, Ester Oras, Kajar Koster, Helen Eenmaa, Ali Leijen, Margus Pedaste, Marju Raju, Anastasiya Astapova, Heli Lukner, Karin Kogermann, Tuul Sepp
Summary: The study found that while data sharing has improved over the past decade, differences in data availability and willingness to share data still exist among different disciplines. It is recommended to incentivize researchers to share data through benefits such as recognition and rewards, with funding agencies covering data management costs and enforcing data sharing surveillance.
Review
Biochemistry & Molecular Biology
Marine Djaffardjy, George Marchment, Clemence Sebe, Raphael Blanchet, Khalid Bellajhame, Alban Gaignard, Frederic Lemoine, Sarah Cohen-Boulakia
Summary: Data analysis pipelines are established as an effective means for bioinformatics data analysis and experiments. However, scripting languages are not sufficient for building large-scale pipelines capable of handling big data and running on high performance computing clusters. Scientific workflow systems provide modular, reproducible, and reusable solutions for bioinformatics data analysis pipelines.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Jennie Louise, Andrea R. Deussen, Jodie M. Dodd
Summary: This study systematically compared various methods for processing and analyzing DNA methylation data. The results showed that different choices in data processing led to different results, and some choices may generate false significant findings. The study suggests a need for more focus on replication and greater use of sensitivity analyses.
Article
Multidisciplinary Sciences
Dragan Maric, Jahandar Jahanipour, Xiaoyang Rebecca Li, Aditi Singh, Aryan Mobiny, Hien Van Nguyen, Andrea Sedlock, Kedar Grama, Badrinath Roysam
Summary: The study introduces a method that utilizes 10-color epifluorescence immunostaining and deep neural networks for large-scale analysis of multiple biological processes in brain tissues. This approach accelerates pre-clinical drug evaluation and brain histology studies by simultaneously profiling various cell types in their native context.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Lucas Pereira, Nuno Velosa, Manuel Pereira
Summary: This paper proposes a new Energy Monitoring and Disaggregation Data Format (EMD-DF64) for the Non-Intrusive Load Monitoring research field. The lack of widely accepted data models and common interfaces to access public datasets has been a significant issue. The EMD-DF64 provides a unique interface to create, manage, and access high-frequency electric energy consumption datasets, leveraging the Sony WAVE64 format.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Kim R. M. Blenman, Josef Spidlen, David R. Parks, Wayne Moore, Adam Treister, Robert Leif, Chris Bray, Michael Goldberg, Ryan Brinkman
Summary: With the advancement of microscopy imaging and flow cytometry, the number of probes has increased rapidly, leading to the creation of arbitrary synonyms for probe tags in publications and software, causing issues in readability and data analysis. The development of a standardized nomenclature for probe tags is essential for ensuring data quality and facilitating data integration across multiple platforms.
Review
Immunology
Zicheng Hu, Sanchita Bhattacharya, Atul J. Butte
Summary: Modern cytometry technologies allow profiling of the immune system at a single-cell resolution with over 50 protein markers, and the number of publicly available cytometry datasets is increasing. Analyzing cytometry data remains challenging due to its high dimensionality, large cell numbers, and dataset heterogeneity, but machine learning techniques are well suited for addressing these challenges and have been employed in various aspects of cytometry data analysis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Velen Yifei Wu, Binqi Chen, Rebecca Christofferson, Gregory Ebel, Anna C. Fagre, Emily N. Gallichotte, Amy R. Sweeny, Colin J. Carlson, Sadie J. Ryan
Summary: The growing threat of vector-borne diseases has led to increased focus on studying vector-virus interactions. However, inconsistent terminology, scattered records, and insufficient detail in publications have made it difficult to reuse or synthesize the experimental data. To address this issue, the authors propose a minimum data and metadata standard for reporting vector competence experiments, aiming to make these important experimental data more accessible and reusable.
Article
Biochemistry & Molecular Biology
Jaco Botha, Haley R. Pugsley, Aase Handberg
Summary: This study compared the performance of traditional flow cytometry with high-resolution imaging flow cytometry, finding the latter to have higher sensitivity and repeatability in detecting and quantifying extracellular vesicles. By selecting the appropriate flow cytometry platform, researchers can better conduct EV studies, improving the reliability and reproducibility of research results.
Article
Biochemical Research Methods
Caio Santos Bonilha
Summary: BCyto is an open-source R package/shiny app that allows cell biologists without coding skills to reliably analyze FCM data in R. It provides various useful tools and an intuitive interface for data visualization and analysis.
MOLECULAR AND CELLULAR PROBES
(2022)
Article
Biophysics
Philip Laird, Anthony Wertz, Gus Welter, David Maslove, Alexander Hamilton, Joo Heung Yoon, Douglas E. Lake, Amanda E. Zimmet, Ryan Bobko, J. Randall Moorman, Michael R. Pinsky, Artur Dubrawski, Gilles Clermont
Summary: The study aimed to develop a standardized format for exchanging clinical and physiologic data from different sites without the need for specific schemas or tools. A collaborative process was used to establish a standard that allows for interoperability and data sharing with common analysis tools.
PHYSIOLOGICAL MEASUREMENT
(2021)
Article
Multidisciplinary Sciences
Kaiwen Wang, Yuqiu Yang, Fangjiang Wu, Bing Song, Xinlei Wang, Tao Wang
Summary: While scRNA-seq data analysis techniques are advanced, research on CyTOF data analysis has lagged behind. Dimension reduction methods were benchmarked on real and synthetic CyTOF samples, highlighting the high level of complementarity between the methods. The study provides useful guidelines for choosing the appropriate method based on data structure and analytical needs.
NATURE COMMUNICATIONS
(2023)
Article
Hematology
Marketa Zaliova, Eliska Potuckova, Lenka Hovorkova, Alena Musilova, Lucie Winkowska, Karel Fiser, Jan Stuchly, Ester Mejstrikova, Julia Starkova, Jan Zuna, Jan Stary, Jan Trka
Article
Hematology
Marketa Zaliova, Jan Stuchly, Lucie Winkowska, Alena Musilova, Karel Fiser, Martina Slamova, Julia Starkova, Martina Vaskova, Ondrej Hrusak, Lucie Sramkova, Jan Stary, Jan Zuna, Jan Trka
Article
Toxicology
Pavel Rossner, Kristyna Vrbova, Simona Strapacova, Andrea Rossnerova, Antonin Ambroz, Tana Brzicova, Helena Libalova, Eliska Javorkova, Pavel Kulich, Zbynek Vecera, Pavel Mikuska, Pavel Coufalik, Kamil Krumal, Lukas Capka, Bohumil Docekal, Pavel Moravec, Omar Sery, Ivan Misek, Petr Fictum, Karel Fiser, Miroslav Machala, Jan Topinka
TOXICOLOGICAL SCIENCES
(2019)
Article
Oncology
Violeta Bakardjieva-Mihaylova, Karolina Skvarova Kramarzova, Martina Slamova, Michael Svaton, Katerina Rejlova, Marketa Zaliova, Alena Dobiasova, Karel Fiser, Jan Stuchly, Marek Grega, Blanka Rosova, Roman Zachoval, Petr Klezl, Vaclav Eis, Eva Kindlova, Tomas Buchler, Jan Trka, Ludmila Boublikova
Article
Multidisciplinary Sciences
Jana Balounova, Iva Splichalova, Martina Dobesova, Michal Kolar, Karel Fiser, Jan Prochazka, Radislav Sedlacek, Andrea Jurisicova, Hoon-ki Sung, Vladimir Korinek, Meritxell Alberich-Jorda, Isabelle Godin, Dominik Filipp
NATURE COMMUNICATIONS
(2019)
Article
Immunology
Tomas Kalina, Karel Fiser, Martin Perez-Andres, Daniela Kuzilkova, Marta Cuenca, Sophinus J. W. Bartol, Elena Blanco, Pablo Engel, Menno C. van Zelm
FRONTIERS IN IMMUNOLOGY
(2019)
Article
Biochemical Research Methods
Miroslav Kratochvil, David Bednarek, Tomas Sieger, Karel Fiser, Jiri Vondrasek
Article
Hematology
Jedrzej Hoffmann, Karel Fiser, Christoph Liebetrau, Nora Staubach, David Kost, Sandra Voss, Annkathrin zur Heiden, Oliver Doerr, Christoph Lipps, Holger M. Nef, Helge Moellmann, Christian W. Hamm, Till Keller, Christian Troidl
THROMBOSIS AND HAEMOSTASIS
(2020)
Letter
Cardiac & Cardiovascular Systems
Jedrzej Hoffmann, Valentina O. Puntmann, Karel Fiser, Tina Rasper, Alexander Berkowitsch, Maria Ludovica Carerj, Eike Nagel, Stefanie Dimmeler, Andreas M. Zeiher
CIRCULATION RESEARCH
(2020)
Article
Hematology
Michaela Novakova, Marketa Zaliova, Karel Fiser, Barbora Vakrmanova, Lucie Slamova, Alena Musilova, Monika Bruggemann, Matthias Ritgen, Eva Fronkova, Tomas Kalina, Jan Stary, Lucie Winkowska, Peter Svec, Alexandra Kolenova, Jan Stuchly, Jan Zuna, Jan Trka, Ondrej Hrusak, Ester Mejstrikova
Summary: The study documented a BCP-ALL subtype with early switch to monocytic lineage and loss of B-cell immunophenotype, correlated with three genetic subtypes. The monocytic switch had significant impact on residual disease assessment and treatment outcomes.
Article
Cell Biology
Jana Uhlirova, Lenka Sebestova, Karel Fiser, Tomas Sieger, Jindriska Fiserova, Pavel Hozak
Summary: The nucleoporin TPR plays a crucial role in the regulation of genes related to muscle formation and function and has been shown to affect the morphology of myoblasts and myotubes. However, more evidence is needed to fully understand how TPR specifically influences the expression of myogenic genes.
Article
Hematology
Marketa Zaliova, Lucie Winkowska, Jan Stuchly, Karel Fiser, Petr Triska, Martina Zwyrtkova, Ondrej Hrusak, Julia Starkova, Lucie Sramkova, Jan Stary, Jan Trka, Jan Zuna
Summary: A novel class of genetic aberration affecting the ZNF384 gene has been identified in leukemia cases, mimicking the phenotype of those with canonical ZNF384 fusions. This finding suggests that some ZNF384r-like cases represent the same genetic subtype as leukemia with canonical ZNF384 fusions.
Article
Multidisciplinary Sciences
Martin Modrak, Paul-Christian Buerkner, Tomas Sieger, Tomas Slisz, Martina Vasakova, Grigorij Meseznikov, Luis Fernando Casas-Mendez, Jaromir Vajter, Jan Taborsky, Viktor Kubricht, Daniel Suk, Jan Horejsek, Martin Jedlicka, Adriana Mifkova, Adam Jaros, Miroslav Kubiska, Jana Vachalova, Robin Sin, Marketa Veverkova, Zbysek Pospisil, Julie Vohryzkova, Rebeka Pokrievkova, Kristian Hrusak, Kristina Christozova, Vianey Leos-Barajas, Karel Fiser, Tomas Hyanek
Summary: This study collected data from 213 COVID-19 patients admitted to ten hospitals in Czech Republic, revealing weak evidence for the potential efficacy of azithromycin and favipiravir treatment. Additionally, the external validation of several proposed prognostic models for Covid-19 severity showed unsatisfactory performance on the dataset.
Article
Immunology
Daniela Kuzilkova, Joan Punet-Ortiz, Pei M. Aui, Javier Fernandez, Karel Fiser, Pablo Engel, Menno C. van Zelm, Tomas Kalina
Summary: This study developed a flow cytometric procedure for standardized quantitative expression profiling of surface antigens on blood leukocyte subsets across multiple research laboratories. The designed tubes can discriminate 27 leukocyte subsets and detect the expression of PE-conjugated CD markers.
FRONTIERS IN IMMUNOLOGY
(2022)
Letter
Hematology
Dagmar Schinnerl, Ester Mejstrikova, Angela Schumich, Marketa Zaliova, Klaus Fortschegger, Karin Nebral, Andishe Attarbaschi, Karel Fiser, Maximilian O. Kauer, Niko Popitsch, Sabrina Haslinger, Andrea Inthal, Barbara Buldini, Giuseppe Basso, Jean-Pierre Bourquin, Giuseppe Gaipa, Monika Brueggemann, Tamar Feuerstein, Margarita Maurer-Granofszky, Renate Panzer-Gruemayer, Jan Trka, Georg Mann, Oskar A. Haas, Ondrej Hrusak, Michael N. Dworzak, Sabine Strehl
