MetMAP: An integrated Matlab TM package for analysis and optimization of metabolic systems. - Julio Vera; Néstor V. Torres (Silico Biol., 2003)

SBML export interface for the systems biology toolbox for MATLAB. - Henning Schmidt; Gunnar Drews; Julio Vera; Olaf Wolkenhauer (Bioinform., 2007)

Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy. - Julio Vera; Raul Curto; Marta Cascante; Néstor V. Torres (Bioinform., 2007)

PLMaddon: a power-law module for the MatlabTM SBToolbox. - Julio Vera; Cheng Sun; Yvonne Oertel; Olaf Wolkenhauer (Bioinform., 2007)

Dynamic properties of a delayed protein cross talk model. - Svetoslav G. Nikolov; Julio Vera; Vladimir Kotev; Olaf Wolkenhauer; Valko Petrov (Biosyst., 2008)

A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. - Julio Vera; Julie Bachmann; Andrea C. Pfeifer; Verena Becker; Jose A. Hormiga; Néstor Torres Darias; Jens Timmer; Ursula Klingmüller; Olaf Wolkenhauer (BMC Syst. Biol., 2008)

Dynamics of receptor and protein transducer homodimerisation. - Julio Vera; Thomas Millat; Walter Kolch; Olaf Wolkenhauer (BMC Syst. Biol., 2008)

Multi-objective steady state optimization of biochemical reaction networks using a constrained genetic algorithm. - Hannes Link; Julio Vera; Dirk Weuster-Botz; Néstor Torres Darias; Ezequiel Franco-Lara (Comput. Chem. Eng., 2008)

A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. - Xin Lai 002; Svetoslav G. Nikolov; Olaf Wolkenhauer; Julio Vera (Comput. Biol. Chem., 2009)

Exploration of homodimer receptor: homodimer protein interactions. - Julio Vera; Taesoo Kwon; Ulf Schmitz; Walter Kolch; Olaf Wolkenhauer (Int. J. Bioinform. Res. Appl., 2009)

Non-coding RNA detection methods combined to improve usability, reproducibility and precision. - Peter Raasch; Ulf Schmitz; Nadja Patenge; Julio Vera; Bernd Kreikemeyer; Olaf Wolkenhauer (BMC Bioinform., 2010)

Optimization of biochemical systems through mathematical programming: Methods and applications. - Julio Vera; Carlos González-Alcón; Alberto Marín-Sanguino; Néstor V. Torres (Comput. Oper. Res., 2010)

Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics. - Svetoslav G. Nikolov; Xin Lai 002; Ulf W. Liebal; Olaf Wolkenhauer; Julio Vera (Int. J. Syst. Sci., 2010)

A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks. - Svetoslav G. Nikolov; Julio Vera; Ulf Schmitz; Olaf Wolkenhauer (Theory Biosci., 2011)

Supervised Cluster Analysis of miRNA Expression Data Using Rough Hypercuboid Partition Matrix. - Sushmita Paul; Julio Vera (PReMI, 2015)

Personalized cancer immunotherapy using Systems Medicine approaches. - Shailendra K. Gupta; Tanushree Jaitly; Ulf Schmitz; Gerold Schuler; Olaf Wolkenhauer; Julio Vera (Briefings Bioinform., 2016)

The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions. - Ulf Schmitz; Hojjat Naderi-Meshkin; Shailendra K. Gupta; Olaf Wolkenhauer; Julio Vera (Briefings Bioinform., 2016)

Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. - Massimiliano Zanin; Ivan Chorbev; Blaz Stres; Egils Stalidzans; Julio Vera; Paolo Tieri; Filippo Castiglione; Derek Groen; Huiru Zheng; Jan Baumbach; Johannes A. Schmid; José Basilio; et al. (Briefings Bioinform., 2019)

Exosomal lncRNAs and cancer: connecting the missing links. - Hojjat Naderi-Meshkin; Xin Lai 002; Raheleh Amirkhah; Julio Vera; John E. J. Rasko; Ulf Schmitz (Bioinform., 2019)

An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. - Nivedita Singh; Martin Eberhardt; Olaf Wolkenhauer; Julio Vera; Shailendra K. Gupta (BMC Bioinform., 2020)

Melanoma Segmentation and Classification Employing Imaging and Graph Encodings. - Luis Carlos Rivera Monroy; Martin Eberhardt; Christian Ostalecki; Andreas Baur; Julio Vera; Andreas K. Maier (CHASE, 2022)

Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. - Julio Vera; Xin Lai 002; Andreas Baur; Michael Erdmann; Shailendra K. Gupta; Cristiano Guttà; Lucie Heinzerling; Markus V. Heppt; Philipp Maximilian Kazmierczak; Manfred Kunz; Christopher Lischer; Brigitte M. Pützer; et al. (Briefings Bioinform., 2022)

Employing Graph Representations for Cell-Level Characterization of Melanoma MELC Samples. - Luis Carlos Rivera Monroy; Leonhard Rist; Martin Eberhardt; Christian Ostalecki; Andreas Baur; Julio Vera; Katharina Breininger; Andreas Maier 001 (ISBI, 2023)

Comparative Analysis of Radiomic Features and Gene Expression Profiles in Histopathology Data using Graph Neural Networks. - Luis Carlos Rivera Monroy; Leonhard Rist; Martin Eberhardt; Christian Ostalecki; Andreas Bauer; Julio Vera; Katharina Breininger; Andreas K. Maier (Bildverarbeitung für die Medizin, 2024)

Abstract: Multi-level Cancer Profiling through Joint Cell-graph Representations. - Luis Carlos Rivera Monroy; Leonhard Rist; Frauke Wilm; Christian Ostalecki; Andreas Baur; Julio Vera; Katharina Breininger; Andreas K. Maier (Bildverarbeitung für die Medizin, 2025)

ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature. - Luca Musella; Alejandro Afonso Castro; Xin Lai 002; Max Widmann; Julio Vera (PLoS Comput. Biol., 2025)

Graph neural networks in multi-stained pathological imaging: extended comparative analysis of Radiomic features. - Luis Carlos Rivera Monroy; Leonhard Rist; Christian Ostalecki; Andreas Bauer; Julio Vera; Katharina Breininger; Andreas K. Maier (Int. J. Comput. Assist. Radiol. Surg., 2025)