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Journal Articles
- 2024
[j15]Maria A Rujano, Jan-Willem Boiten
, Christian Ohmann, Steve Canham, Sergio Contrino, Romain David, Jonathan Ewbank, Claudia Filippone, Claire Connellan, Ilse Custers, Rick van Nuland, Michaela Theresia Mayrhofer, Petr Holub, Eva García Álvarez, Emmanuel Bacry, Nigel Hughes, Mallory Ann Freeberg, Birgit Schaffhauser, Harald Wagener, Alex Sánchez-Pla, Guido Bertolini, Maria Panagiotopoulou:
Sharing sensitive data in life sciences: an overview of centralized and federated approaches. Briefings Bioinform. 25(4) (2024)- 2023
- [j14]Jirí Horák, Katarína Furmanová, Barbora Kozlíková, Tomás Brázdil, Petr Holub, M. Kacenga, Matej Gallo, R. Nenutil, Jan Byska, Vít Rusnák:
xOpat: eXplainable Open Pathology Analysis Tool. Comput. Graph. Forum 42(3): 63-73 (2023) - [j13]Romain David, Audrey S. Richard, Claire Connellan, Katharina B. Lauer, Maria Luisa Chiusano, Carole A. Goble, Martin Houde, Isabel Kemmer, Antje Keppler, Philippe Lieutaud, Christian Ohmann, Maria Panagiotopoulou, Sara Raza Khan, Arina Rybina, Stian Soiland-Reyes, Charlotte Wit, Rudolf Wittner, Rafael Andrade Buono, Sarah Arnaud Marsh, Pauline Audergon, Dylan Bonfils, José María Carazo, Remi Charrel, Frederik Coppens, Wolfgang Fecke, Claudia Filippone, Eva G. Alvarez, Sheraz Gul, Henning Hermjakob, Katja Herzog, Petr Holub, Lukasz Kozera, Allyson L. Lister, José López-Coronado, Bénédicte Madon, Kurt Majcen, William Martin, Wolfgang Müller, Elli Papadopoulou, Christine M. A. Prat, Paolo Romano, Susanna-Assunta Sansone, Gary Saunders, Niklas Blomberg, Jonathan Ewbank:
Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness. Data Sci. J. 22: 35 (2023) - [j12]Christian Ohmann, Maria Panagiotopoulou, Steve Canham, Petr Holub, Kurt Majcen, Gary Saunders, Maddalena Fratelli, Jing Tang, Philip Gribbon, Reagon Karki, Mari Kleemola, Katja Moilanen, Daan Broeder, Walter Daelemans, Pieter Fivez:
Proposal for a framework of contextual metadata in selected research infrastructures of the life sciences and the social sciences & humanities. Int. J. Metadata Semant. Ontologies 16(4): 261-277 (2023) - 2021
- [j11]Athos Antoniades, Maria Papaioannou, Apostolos Malatras, Gregory Papagregoriou, Heimo Müller, Petr Holub, Constantinos Deltas, Christos N. Schizas:
Integration of Biobanks in National eHealth Ecosystems Facilitating Long-Term Longitudinal Clinical-Omics Studies and Citizens' Engagement in Research Through eHealthBioR. Frontiers Digit. Health 3: 628646 (2021) - 2020
- [j10]Peter Wittenburg, Franciska de Jong, Dieter Van Uytvanck, Massimo Cocco, Keith G. Jeffery, Michael Lautenschlager, Hannes Thiemann, Margareta Hellström, Ari Asmi, Petr Holub:
State of FAIRness in ESFRI Projects. Data Intell. 2(1-2): 230-237 (2020) - 2019
- [j9]Sebastian Mate, Marvin O. Kampf, Wolfgang Rödle, Stefan Kraus, Rumyana Proynova, Kaisa Silander, Lars Ebert, Martin Lablans, Christina Schüttler, Christian Knell, Niina Eklund, Michael Hummel, Petr Holub, Hans-Ulrich Prokosch:
Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC. Appl. Clin. Inform. 10(04): 679-692 (2019) - 2018
- [j8]Pavel Troubil, Hana Rudová, Petr Holub:
Dynamic reconfiguration in multigroup multicast routing under uncertainty. J. Heuristics 24(3): 395-423 (2018) - 2017
- [j7]Chao Pang, Fleur D. L. Kelpin, David van Enckevort, Niina Eklund, Kaisa Silander, Dennis Hendriksen, Mark de Haan, Jonathan Jetten, Tommy de Boer, Bart Charbon, Petr Holub, Hans L. Hillege, Morris A. Swertz:
BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. Bioinform. 33(22): 3627-3634 (2017) - 2016
- [j6]Vít Rusnák, Lukás Rucka, Petr Holub:
Toward natural multi-user interaction in advanced collaborative display environments. Future Gener. Comput. Syst. 54: 313-325 (2016) - [j5]Milan Kabát, Vojtech David, Petr Holub, Martin Pulec:
High-performance forward error correction: Enabling multi-gigabit flows and beyond on commodity GPU and CPU hardware in presence of packet loss. Future Gener. Comput. Syst. 54: 326-335 (2016) - 2013
- [j4]Petr Holub, Martin Srom, Martin Pulec, Jiri Matela, Martin Jirman:
GPU-accelerated DXT and JPEG compression schemes for low-latency network transmissions of HD, 2K, and 4K video. Future Gener. Comput. Syst. 29(8): 1991-2006 (2013) - 2011
- [j3]Petr Holub, Hana Rudová, Milos Liska:
Data transfer planning with tree placement for collaborative environments. Constraints An Int. J. 16(3): 283-316 (2011) - 2006
- [j2]Petr Holub, Ludek Matyska, Milos Liska, Lukás Hejtmánek, Jirí Denemark, Tomás Rebok, Andrei Hutanu, Ravi Paruchuri, Jan Radil, Eva Hladká:
High-definition multimedia for multiparty low-latency interactive communication. Future Gener. Comput. Syst. 22(8): 856-861 (2006) - [j1]Andrei Hutanu, Gabrielle Allen, Stephen David Beck, Petr Holub, Hartmut Kaiser, Archit Kulshrestha, Milos Liska, Jon MacLaren, Ludek Matyska, Ravi Paruchuri, Steffen Prohaska, Edward Seidel, Brygg Ullmer, Shalini Venkataraman:
Distributed and collaborative visualization of large data sets using high-speed networks. Future Gener. Comput. Syst. 22(8): 1004-1010 (2006)
Conference and Workshop Papers
- 2022
- [c31]Francesca Frexia, Cecilia Mascia, Rudolf Wittner, Markus Plass, Heimo Müller, Jörg Geiger, Petr Holub:
The Common Provenance Model: Capturing Distributed Provenance in Life Sciences Processes. MIE 2022: 415-416 - 2021
- [c30]Elliot Fairweather, Rudolf Wittner, Martin Chapman, Petr Holub, Vasa Curcin:
Non-repudiable Provenance for Clinical Decision Support Systems. IPAW 2021: 165-182 - [c29]Rudolf Wittner, Petr Holub, Heimo Müller, Jörg Geiger, Carole A. Goble, Stian Soiland-Reyes, Luca Pireddu, Francesca Frexia, Cecilia Mascia, Elliot Fairweather, Jason R. Swedlow, Josh Moore, Caterina Strambio-De-Castillia, David Grunwald, Hiroki Nakae:
ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen And Data. IPAW 2021: 222-225 - 2017
- [c28]Rumyana Proynova, Diogo Alexandre, Martin Lablans, David van Enckevort, Sebastian Mate, Niina Eklund, Kaisa Silander, Michael Hummel, Petr Holub, Frank Ückert:
A Decentralized IT Architecture for Locating and Negotiating Access to Biobank Samples. GMDS 2017: 75-79 - 2014
- [c27]Jiri Marek, Hana Rudová, Petr Holub:
Local Search Heuristics for Media Streams Planning with Transcoding. NCA 2014: 167-170 - [c26]Pavel Troubil, Hana Rudová, Petr Holub:
Media Streams Planning with Uncertain Link Capacities. NCA 2014: 197-204 - 2013
- [c25]Jiri Marek, Petr Holub, Hana Rudová:
Local Search Heuristics for Media Streams Planning Problem. AINA 2013: 945-953 - [c24]Pavel Troubil, Hana Rudová, Petr Holub:
Media Streams Planning with Transcoding. NCA 2013: 41-48 - 2012
- [c23]Petr Slovák, Peter Novák, Pavel Troubil, Vít Rusnák, Petr Holub, Erik C. Hofer:
Exploring Collaboration in Group-to-Group Videoconferencing. COOP 2012: 229-244 - [c22]Vít Rusnák, Lukás Rucka, Petr Holub:
Towards User-Aware Multi-touch Interaction Layer for Group Collaborative Systems. MEMICS 2012: 200-212 - [c21]Petr Holub, Jiri Matela, Martin Pulec, Martin Srom:
UltraGrid: low-latency high-quality video transmissions on commodity hardware. ACM Multimedia 2012: 1457-1460 - 2011
- [c20]Petr Slovák, Peter Novák, Pavel Troubil, Petr Holub, Erik C. Hofer:
Exploring trust in group-to-group video-conferencing. CHI Extended Abstracts 2011: 1459-1464 - [c19]Jiri Matela, Vít Rusnák, Petr Holub:
Efficient JPEG2000 EBCOT Context Modeling for Massively Parallel Architectures. DCC 2011: 423-432 - [c18]Jiri Matela, Martin Srom, Petr Holub:
Low GPU Occupancy Approach to Fast Arithmetic Coding in JPEG2000. MEMICS 2011: 136-145 - 2010
- [c17]Petr Slovák, Pavel Troubil, Petr Holub:
GColl: enhancing trust in flexible group-to-group videoconferencing. CHI Extended Abstracts 2010: 3607-3612 - [c16]Jiri Matela, Vít Rusnák, Petr Holub:
GPU-Based Sample-Parallel Context Modeling for EBCOT in JPEG2000. MEMICS 2010: 77-84 - [c15]Kenny Welshons, Patrick Dorn, Andrei Hutanu, Petr Holub, John Vollbrecht, Gabrielle Allen:
Design and implementation of a production dynamically configurable testbed. TG 2010: 21:1-21:8 - 2009
- [c14]David Antos, Ludek Matyska, Petr Holub, Jirí Sitera:
VirtCloud: Virtualising Network for Grid Environments. AINA 2009: 876-883 - [c13]Petr Slovák, Pavel Troubil, Petr Holub:
GColl group-to-group videoconferencing system: design and first experiences. CollaborateCom 2009: 1-9 - [c12]Michal Procházka, Petr Holub, Eva Hladká:
jSon: Network of Active Elements with Peer-to-Peer Control Plane. ICN 2009: 208-213 - [c11]Milos Liska, Petr Holub:
CoUniverse: Framework for Building Self-Organizing Collaborative Environments Using Extreme-Bandwidth Media Applications. ICN 2009: 259-265 - [c10]Petr Slovák, Pavel Troubil, Petr Holub:
GColl: A Flexible Videoconferencing Environment for Group-to-Group Interaction. INTERACT (2) 2009: 165-168 - 2008
- [c9]Milos Liska, Petr Holub:
CoUniverse: Framework for Building Self-organizing Collaborative Environments Using Extreme-Bandwidth Media Applications. Euro-Par Workshops 2008: 339-351 - 2007
- [c8]Eva Hladká, Daniel Kouril, Michal Procházka, Ludek Matyska, Petr Holub:
Transparent security for collaborative environments. CollaborateCom 2007: 79-84 - [c7]Andrei Hutanu, Ravi Paruchuri, Daniel Eiland, Milos Liska, Petr Holub, Steven R. Thorpe, Yufeng Xin:
Uncompressed HD video for collaborative teaching - an experiment. CollaborateCom 2007: 253-261 - [c6]Petr Holub, Eva Hladká, Michal Procházka, Milos Liska:
Secure and Pervasive Collaborative Platform for Medical Applications. HealthGrid 2007: 229-238 - 2006
- [c5]Michal Procházka, Petr Holub, Eva Hladká:
Active Element Network with P2P Control Plane. IWSOS/EuroNGI 2006: 257 - 2005
- [c4]Petr Holub, Eva Hladká, Ludek Matyska:
Scalability and Robustness of Virtual Multicast for Synchronous Multimedia Distribution. ICN (2) 2005: 876-883 - 2004
- [c3]Petr Holub, Martin Kuba, Ludek Matyska, Miroslav Ruda:
Grid Infrastructure Monitoring as Reliable Information Service. European Across Grids Conference 2004: 220-229 - [c2]Eva Hladká, Petr Holub, Jirí Denemark:
User-Empowered Programmable Network Support for Collaborative Environment. ECUMN 2004: 367-376 - [c1]Petr Holub, Lukás Hejtmánek:
Distributed Encoding Environment based on Grids and IBP Infrastructure. TERENA Networking Conference 2004
Informal and Other Publications
- 2022
- [i4]Jan-Willem Boiten, Christian Ohmann, Ayodeji Adeniran, Steve Canham, Mónica Cano Abadia, Gauthier Chassang, Maria Luisa Chiusano, Romain David, Maddalena Fratelli, Philip Gribbon, Petr Holub, Rebecca Ludwig, Michaela Theresia Mayrhofer, Mihaela Matei, Arshiya Merchant, Maria Panagiotopoulou, Luca Pireddu, Alex Sánchez-Pla, Irene Schlünder, George Tsamis, Harald Wagener:
EOSC-LIFE WP4 TOOLBOX: Toolbox for sharing of sensitive data - a concept description. CoRR abs/2207.14296 (2022) - 2020
- [i3]Elliot Fairweather, Rudolf Wittner, Martin Chapman, Petr Holub, Vasa Curcin:
Non-repudiable provenance for clinical decision support systems. CoRR abs/2006.11233 (2020) - 2019
- [i2]Isabelle Perseil, Petr Holub:
Towards a reconstructive methodology for building a provenance metamodel that fits the complex bioinformatics pipelines. RO 2019 - 2017
- [i1]Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutiérrez, Neil P. Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla J. García, Josep Lluis Gelpí, Simon L. Gladman, Carole A. Goble, Montserrat González Ferreiro, Alejandra N. González-Beltrán, Philippa C. Griffin, Björn A. Grüning, Jonas Hagberg, Petr Holub, Rob W. W. Hooft, Jon C. Ison, Daniel S. Katz, Brane Leskosek, Federico López-Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola J. Mulder, Yasset Pérez-Riverol, Robert Pergl, Horst Pichler, Bernard J. Pope, Ferran Sanz, Maria Victoria Schneider, Victoria Stodden, Radoslaw Suchecki, Radka Svobodová Vareková, Harry-Anton Talvik, Ilian T. Todorov, Andrew E. Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch:
Four simple recommendations to encourage best practices in research software. F1000Research 6: 876- (2017)
Coauthor Index
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