Handling Cycles in Conformational Behaviour Visualization. - Ales Krenek (WSCG, 2000)

Early Experiences with the EGrid Testbed. - Gabrielle Allen; Thomas Dramlitsch; Tom Goodale; Gerd Lanfermann; Thomas Radke; Edward Seidel; Thilo Kielmann; Kees Verstoep; Zoltán Balaton; Péter Kacsuk; Ferenc Szalai; Jörn Gehring; et al. (CCGRID, 2001)

Haptic Rendering of Complex Force Fields. - Ales Krenek (IPT/EGVE, 2003)

Building 3D State Spaces of Virtual Environments with a TDS-Based Algorithm. - Ales Krenek; Igor Peterlík; Ludek Matyska (PVM/MPI, 2003)

The first deployment of workload management services on the EU DataGrid Testbed: feedback on design and implementation - Giuseppe Avellino; Stefano Beco; Barbara Cantalupo; Fabrizio Pacini; Annalisa Terracina; Alessandro Maraschini; D. Colling; Salvatore Monforte; Marco Pappalardo; Livio Salconi; Francesco Giacomini; Elisabetta Ronchieri; et al. (CoRR, 2003)

The EU DataGrid Workload Management System: towards the second major release - Giuseppe Avellino; S. Barale; Stefano Beco; Barbara Cantalupo; D. Colling; Francesco Giacomini; Alessio Gianelle; Andrea Guarise; Ales Krenek; Daniel Kouril; Alessandro Maraschini; Ludek Matyska; et al. (CoRR, 2003)

The DataGrid Workload Management System: Challenges and Results. - Giuseppe Avellino; Stefano Beco; Barbara Cantalupo; Alessandro Maraschini; Fabrizio Pacini; Massimo Sottilaro; Annalisa Terracina; D. Colling; Francesco Giacomini; Elisabetta Ronchieri; Alessio Gianelle; Mirco Mazzucato; et al. (J. Grid Comput., 2004)

Haptically Driven Travelling through Conformational Space. - Igor Peterlík; Ales Krenek (WHC, 2005)

Best Practices of User Account Management with Virtual Organization Based Access to Grid. - Jirí Denemark; Michal Jankowski; Ales Krenek; Ludek Matyska; Norbert Meyer; Miroslav Ruda; Pawel Wolniewicz (PPAM, 2005)

gLite Job Provenance. - Frantisek Dvorák; Daniel Kouril; Ales Krenek; Ludek Matyska; Milos Mulac; Jan Pospisil 001; Miroslav Ruda; Zdenek Salvet; Jirí Sitera; Michal Vocu (IPAW, 2006)

A uniform job monitoring service in multiple job universes. - Miroslav Ruda; Ales Krenek; Milos Mulac; Jan Pospisil 001; Zdenek Sustr (GMW@HPDC, 2007)

Job Provenance - Insight into Very Large Provenance Datasets. - Ales Krenek; Ludek Matyska; Jirí Sitera; Miroslav Ruda; Frantisek Dvorák; Jiri Filipovic; Zdenek Sustr; Zdenek Salvet (IPAW, 2008)

Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services. - Ales Krenek; Martin Petrek; Jan Kmunícek; Jiri Filipovic; Zdenek Sustr; Frantisek Dvorák; Jirí Sitera; Jiri Wiesner; Ludek Matyska (PDP, 2008)

gLite Job Provenance - a job-centric view. - Ales Krenek; Jirí Sitera; Ludek Matyska; Frantisek Dvorák; Milos Mulac; Miroslav Ruda; Zdenek Salvet (Concurr. Comput. Pract. Exp., 2008)

Special Issue: The First Provenance Challenge. - Luc Moreau 001; Bertram Ludäscher; Ilkay Altintas; Roger S. Barga; Shawn Bowers; Steven P. Callahan; George Chin Jr.; Ben Clifford; Shirley Cohen; Sarah Cohen Boulakia; Susan B. Davidson; Ewa Deelman; et al. (Concurr. Comput. Pract. Exp., 2008)

Compression of Vector Field Changing in Time. - Tomas Golembiovsky; Ales Krenek (MEMICS, 2010)

Nemesis - a molecular modeling package. - Jakub Stepán; Petr Kulhánek; Milan Lenco; Zora Strelcová; Ales Krenek; Jaroslav Koca (J. Cheminformatics, 2013)

Empirical charges for chemoinformatics applications. - Tomás Bouchal; Radka Svobodová Vareková; Tomás Racek; Crina-Maria Ionescu; Stanislav Geidl; Ales Krenek; Jaroslav Koca (J. Cheminformatics, 2014)

High-quality and universal empirical atomic charges for chemoinformatics applications. - Stanislav Geidl; Tomás Bouchal; Tomás Racek; Radka Svobodová Vareková; Václav Hejret; Ales Krenek; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2015)

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. - Tomás Racek; Jana Pazúriková; Radka Svobodová Vareková; Stanislav Geidl; Ales Krenek; Francesco L. Falginella; Vladimír Horský; Václav Hejret; Jaroslav Koca (J. Cheminformatics, 2016)

Acceleration of Mean Square Distance Calculations with Floating Close Structure in Metadynamics Simulations. - Jana Pazúriková; Jaroslav Olha; Ales Krenek; Vojtech Spiwok (CoRR, 2018)

Similarity Search for an Extreme Application: Experience and Implementation. - Vladimir Mic; Tomás Racek; Ales Krenek; Pavel Zezula (SISAP, 2021)

Property Map Collective Variable as a Useful Tool for a Force Field Correction. - Dalibor Trapl; Martin Krupicka; Vladimír Visnovský; Jana Hozzová; Jaroslav Olha; Ales Krenek; Vojtech Spiwok (J. Chem. Inf. Model., 2022)

De-novo Identification of Small Molecules from Their GC-EI-MS Spectra. - Adam Hájek; Michal Starý; Filip Jozefov; Helge Hecht; Elliott James Price; Ales Krenek (CoRR, 2023)

Onedata4Sci: Life science data management solution based on Onedata. - Tomás Svoboda; Tomás Racek; Josef Handl; Jozef Sabo; Adrián Rosinec; Lukasz Opiola; Wojciech Jesionek; Milan Esner; Markéta Pernisová; Natallia Madzia Valasevich; Ales Krenek; Radka Svobodová Vareková (CoRR, 2023)

αCharges: partial atomic charges for AlphaFold structures in high quality. - Ondrej Schindler; Karel Berka; Alessio Cantara; Ales Krenek; Dominik Tichý; Tomás Racek; Radka Svobodová Vareková (Nucleic Acids Res., 2023)

A survey of the European Open Science Cloud services for expanding the capacity and capabilities of multidisciplinary scientific applications. - Amanda Calatrava; Hernán Asorey; Ján Astalos; Alberto Azevedo; Francesco Benincasa; Ignacio Blanquer; Martin Bobák 001; Francisco Vilar Brasileiro; Laia Codó; Laura del Cano; Borja Esteban; Meritxell Ferret; et al. (Comput. Sci. Rev., 2023)

GenomeCruzer, a 3D Interactive Environment for Genomic Data Visualization and Analysis. - Cassisa Anna; Jamal Elhasnaoui; Uliveto Chiara; Riccardo Corsi; Elena Grassi; Dalibor Stuchlík; Livio Trusolino; Ales Krenek; Luca Vezzadini; Andrea Bertotti; Claudio Isella; Enzo Medico (BIOSTEC (1), 2025)

SpecTUS: Spectral Translator for Unknown Structures annotation from EI-MS spectra. - Adam Hájek; Helge Hecht; Elliott James Price; Ales Krenek (CoRR, 2025)