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David Hoksza
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2020 – today
- 2024
- [j27]Tomás Skopal
, Ladislav Peska, David Hoksza, Ivaná Sixtova
, David Bernhauer:
Visualizations for universal deep-feature representations: survey and taxonomy. Knowl. Inf. Syst. 66(2): 811-840 (2024) - 2023
- [j26]Piotr Gawron, David Hoksza, Janet Piñero, María Peña-Chilet, Marina Esteban-Medina, Jose Luis Fernandez-Rueda, Vincenza Colonna, Ewa Smula, Laurent Heirendt, François Ancien, Valentin Grouès, Venkata P. Satagopam, Reinhard Schneider, Joaquín Dopazo, Laura I. Furlong, Marek Ostaszewski:
Visualization of automatically combined disease maps and pathway diagrams for rare diseases. Frontiers Bioinform. 3 (2023) - [c44]Vít Skrhak, Kamila Riedlova, Marian Novotny, David Hoksza:
Cryptic binding site prediction with protein language models. BIBM 2023: 2883-2888 - [c43]Vít Skrhak, David Hoksza:
Framework for Protein Structures Conformation Analysis. BIBM 2023: 4942-4944 - [c42]Ladislav Peska
, Ivaná Sixtova
, David Hoksza
, David Bernhauer
, Tomás Skopal
:
Visual Representations for Data Analytics: User Study. CHIRA (2) 2023: 231-243 - 2022
- [j25]Christos P. Feidakis, Radoslav Krivák, David Hoksza, Marian Novotny
:
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands. Bioinform. 38(24): 5452-5453 (2022) - [j24]Mihaly Varadi
, Stephen Anyango
, David R. Armstrong
, John M. Berrisford, Preeti Choudhary
, Mandar S. Deshpande
, Nurul Nadzirin, Sreenath Nair
, Lukás Pravda, Ahsan Tanweer
, Bissan Al-Lazikani
, Claudia Andreini
, Geoffrey J. Barton, David Bednar, Karel Berka
, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský
, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali
, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec
, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías
, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra
, Gerardo Pepe
, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy
, Atilio O. Rausch
, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato
, Pawel Rubach
, Luis Serrano, Gulzar Singh, Petr Skoda
, Carlos Oscar Sánchez Sorzano
, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton
, Michael J. E. Sternberg
, Christine A. Orengo, Sameer Velankar
:
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50(D1): 534-542 (2022) - [j23]David Jakubec, Petr Skoda
, Radoslav Krivák, Marian Novotny
, David Hoksza
:
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. Nucleic Acids Res. 50(W1): 593-597 (2022) - [c41]David Hoksza, Hamza Gamouh
:
Exploration of protein sequence embeddings for protein-ligand binding site detection. BIBM 2022: 3356-3361 - [c40]Ivaná Sixtova
, Tomás Skopal
, David Hoksza, Jakub Matejík, Tomás Uher:
Machine and human interpretable patient visualizations. BIBM 2022: 3879-3881 - 2021
- [j22]David Hoksza
, Piotr Gawron, Marek Ostaszewski
, Jan Hasenauer, Reinhard Schneider
:
Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. 22(1): 608 (2021) - [j21]Blake A. Sweeney
, Anton I. Petrov, Carlos Eduardo Ribas, Robert D. Finn, Alex Bateman
, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin Ray Gutell
, Simon Kay, Steven J. Marygold, Gilberto dos Santos, Adam Frankish
, Jonathan M. Mudge
, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford
, Simona Panni, Pablo Porras
, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg:
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49(Database-Issue): D212-D220 (2021) - [j20]Sune S. Nielsen
, Marek Ostaszewski
, Fintan McGee
, David Hoksza
, Simone Zorzan:
Machine Learning to Support the Presentation of Complex Pathway Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 18(3): 1130-1141 (2021) - 2020
- [j19]David Hoksza
, Piotr Gawron, Marek Ostaszewski
, Jan Hasenauer
, Reinhard Schneider
:
Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. 21(4): 1249-1260 (2020) - [j18]Mihaly Varadi
, John M. Berrisford, Mandar S. Deshpande
, Sreenath Nair
, Aleksandras Gutmanas
, David R. Armstrong
, Lukás Pravda
, Bissan Al-Lazikani
, Stephen Anyango
, Geoffrey J. Barton, Karel Berka
, Tom L. Blundell, Neera Borkakoti
, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali
, Toby J. Gibson
, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas
, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar
, Emmanuel D. Levy, Fábio Madeira
, M. S. Madhusudhan, Henry J. Martell
, Stuart A. MacGowan
, Jake E. McGreig
, Saqib Mir, Abhik Mukhopadhyay, Luca Parca
, Typhaine Paysan-Lafosse
, Leandro G. Radusky, António J. M. Ribeiro
, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda
, Radka Svobodová Vareková
, Jonathan D. Tyzack
, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton
, Michael J. E. Sternberg
, Christine A. Orengo, Sameer Velankar
:
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48(Database-Issue): D344-D353 (2020) - [j17]Sumaiya Iqbal
, David Hoksza, Eduardo Pérez-Palma
, Patrick May
, Jakob B. Jespersen
, Shehab S. Ahmed, Zaara T. Rifat, Henrike O. Heyne, Mohammad Sohel Rahman, Jeffrey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J. Campbell, Dennis Lal:
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. Nucleic Acids Res. 48(Webserver-Issue): W132-W139 (2020)
2010 – 2019
- 2019
- [j16]Jan Jelínek
, David Hoksza, Jan Hajic
, Jan Pesek, Jan Drozen, Tomás Hladík, Michal Klimpera, Jirí Vohradský, Josef Pánek:
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. Database J. Biol. Databases Curation 2019: baz047 (2019) - [j15]David Hoksza
, Piotr Gawron, Marek Ostaszewski
, Ewa Smula, Reinhard Schneider
:
MINERVA API and plugins: opening molecular network analysis and visualization to the community. Bioinform. 35(21): 4496-4498 (2019) - [j14]Lukás Jendele, Radoslav Krivák, Petr Skoda
, Marian Novotny
, David Hoksza
:
PrankWeb: a web server for ligand binding site prediction and visualization. Nucleic Acids Res. 47(Webserver-Issue): W345-W349 (2019) - 2018
- [j13]David Hoksza
, Piotr Gawron, Marek Ostaszewski
, Reinhard Schneider
:
MolArt: a molecular structure annotation and visualization tool. Bioinform. 34(23): 4127-4128 (2018) - [j12]Radoslav Krivák
, David Hoksza
:
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. J. Cheminformatics 10(1): 39:1-39:12 (2018) - [c39]Radoslav Krivák, Lukás Jendele, David Hoksza:
Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface. BCB 2018: 645-650 - [c38]Jan Jelínek
, Petr Skoda
, David Hoksza:
Software framework for similarity-based prediction of protein interfaces. BIBM 2018: 2759-2761 - 2017
- [j11]Richard Elias, David Hoksza
:
TRAVeLer: a tool for template-based RNA secondary structure visualization. BMC Bioinform. 18(1): 487 (2017) - [j10]Jan Jelínek
, Petr Skoda
, David Hoksza:
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. BMC Bioinform. 18(15): 63-72 (2017) - [c37]Rastislav Galvanek, David Hoksza:
Template-based prediction of RNA tertiary structure using its predicted secondary structure. BIBM 2017: 2238-2240 - [c36]Petr Skoda
, David Hoksza, Jan Jelínek
:
Platform for ligand-based virtual screening integration. BIBM 2017: 2256-2259 - [c35]Radoslav Krivák, David Hoksza, Petr Skoda
:
Improving quality of ligand-binding site prediction with Bayesian optimization. BIBM 2017: 2278-2279 - 2016
- [j9]Jakub Velkoborsky, David Hoksza
:
Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization. J. Cheminformatics 8(1): 74:1-74:14 (2016) - [c34]Petr Skoda
, David Hoksza:
Benchmarking platform for ligand-based virtual screening. BIBM 2016: 1220-1227 - [c33]Rastislav Galvanek
, David Hoksza, Josef Pánek:
Template-based prediction of RNA tertiary structure. BIBM 2016: 1897-1900 - [c32]David Hoksza, Petr Skoda
:
Using Bayesian modeling on molecular fragments features for virtual screening. CIBCB 2016: 1-6 - [c31]Jan Jelínek, Petr Skoda, David Hoksza:
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. ICCABS 2016: 1 - 2015
- [j8]Petr Cech
, David Hoksza
, Daniel Svozil
:
MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinform. 16: 253:1-253:8 (2015) - [j7]Radoslav Krivák
, David Hoksza
:
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. J. Cheminformatics 7: 12 (2015) - [j6]David Hoksza
, Daniel Svozil
:
Multiple 3D RNA Structure Superposition Using Neighbor Joining. IEEE ACM Trans. Comput. Biol. Bioinform. 12(3): 520-530 (2015) - [c30]Radoslav Krivák
, David Hoksza
:
P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features. AlCoB 2015: 41-52 - [c29]Petr Skoda, David Hoksza:
Exploration of topological torsion fingerprints. BIBM 2015: 822-828 - [c28]Martin Sícho
, Daniel Svozil
, David Hoksza
:
Activity-driven exploration of chemical space with morphing. BIBM 2015: 1024-1031 - [c27]David Hoksza
, Jan Jelínek
:
Using Neo4j for Mining Protein Graphs: A Case Study. DEXA Workshops 2015: 230-234 - 2014
- [j5]David Hoksza
, Petr Skoda
, Milan Vorsilák
, Daniel Svozil
:
Molpher: a software framework for systematic chemical space exploration. J. Cheminformatics 6(1): 7 (2014) - [c26]David Hoksza
, Petr Skoda
:
Scaffold-based chemical space exploration. BIBM 2014: 1-3 - [c25]Josef Pánek, Jan Hajic
, David Hoksza
:
Template-based prediction of ribosomal RNA secondary structure. BIBM 2014: 18-20 - [c24]David Hoksza
, Petr Skoda
:
2D Pharmacophore Query Generation. ISBRA 2014: 289-300 - 2013
- [j4]Jirí Novák
, Timo Sachsenberg, David Hoksza
, Tomás Skopal, Oliver Kohlbacher:
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications. J. Integr. Bioinform. 10(3) (2013) - [c23]Petr Skoda
, David Hoksza
:
Chemical space visualization using ViFrame. ICIS 2013: 541-546 - [c22]Jirí Novák
, Timo Sachsenberg, David Hoksza
, Tomás Skopal
, Oliver Kohlbacher:
A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. PACBB 2013: 101-109 - [c21]David Hoksza
, Peter Szépe, Daniel Svozil
:
MultiSETTER - Multiple RNA Structure Similarity Algorithm. BSB 2013: 59-70 - 2012
- [j3]David Hoksza
, Daniel Svozil
:
Efficient RNA pairwise structure comparison by SETTER method. Bioinform. 28(14): 1858-1864 (2012) - [j2]Jirí Novák
, Tomás Skopal
, David Hoksza
, Jakub Lokoc
:
Non-metric similarity search of tandem mass spectra including posttranslational modifications. J. Discrete Algorithms 13: 19-31 (2012) - [j1]Petr Cech
, Daniel Svozil
, David Hoksza
:
SETTER: web server for RNA structure comparison. Nucleic Acids Res. 40(Web-Server-Issue): 42-48 (2012) - [c20]Jakub Galgonek
, Tomás Skopal
, David Hoksza
:
P3S: Protein Structure Similarity Search. Euro-Par Workshops 2012: 228-237 - [c19]Jakub Galgonek
, Martin Krulis
, David Hoksza
:
On the Parallelization of the SProt Measure and the TM-Score Algorithm. Euro-Par Workshops 2012: 238-247 - [c18]Jirí Novák
, David Hoksza
, Jakub Lokoc
, Tomás Skopal
:
On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering. ISBRA 2012: 189-200 - [c17]Jirí Novák
, Jakub Galgonek
, David Hoksza
, Tomás Skopal
:
SimTandem: Similarity Search in Tandem Mass Spectra. SISAP 2012: 242-243 - 2011
- [c16]David Hoksza
, Daniel Svozil
:
Exploration of Chemical Space by Molecular Morphing. BIBE 2011: 201-208 - [c15]David Hoksza
, Daniel Svozil
:
SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. ISBRA 2011: 37-48 - [c14]Jakub Galgonek, David Hoksza:
On metric approximations of the SProt measure. SISAP 2011: 119-120 - [c13]Jirí Novák
, Tomás Skopal
, David Hoksza
, Jakub Lokoc
, Jakub Galgonek
:
Protein sequences identification using NM-tree. SISAP 2011: 125-126 - 2010
- [c12]Jakub Galgonek
, David Hoksza
:
SProt - from local to global protein structure similarity. BIBM Workshops 2010: 124-129 - [c11]Jirí Novák
, David Hoksza
:
Similarity search and posttranslational modifications in tandem mass spectra. BIBM Workshops 2010: 845-846 - [c10]Jirí Novák, David Hoksza:
Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry. DATESO 2010: 1-12 - [c9]Jirí Novák
, Tomás Skopal
, David Hoksza
, Jakub Lokoc
:
Improving the similarity search of tandem mass spectra using metric access methods. SISAP 2010: 85-92
2000 – 2009
- 2009
- [c8]Jirí Novák
, David Hoksza
:
An application of the metric access methods to the mass spectrometry data. CIBCB 2009: 220-227 - [c7]David Hoksza
:
DDPIn - Distance and density based protein indexing. CIBCB 2009: 263-270 - [c6]Jakub Galgonek
, David Hoksza:
On the Effectiveness of Distances Measuring Protein Structure Similarity. SISAP 2009: 165-166 - 2008
- [c5]David Hoksza, Tomás Skopal:
Native Multidimensional Indexing in Relational Databases. COMAD 2008: 251-260 - [c4]David Hoksza
:
Improved Alignment of Protein Sequences Based on Common Parts. ISBRA 2008: 87-99 - 2007
- [c3]Tomás Skopal, David Hoksza:
Improving the Performance of M-Tree Family by Nearest-Neighbor Graphs. ADBIS 2007: 172-188 - [c2]Tomás Skopal, David Hoksza, Jaroslav Pokorný:
Construction of Tree-Based Indexes for Level-Contiguous Buffering Support. DASFAA 2007: 361-373 - [c1]David Hoksza, Tomás Skopal:
Index-Based Approach to Similarity Search in Protein and Nucleotide Databases. DATESO 2007
Coauthor Index
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last updated on 2024-08-05 21:15 CEST by the dblp team
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