Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. - Adriano Barbosa-Silva; Venkata P. Satagopam; Reinhard Schneider 002; José Miguel Ortega (BMC Bioinform., 2008)

Arena3D: visualization of biological networks in 3D. - Georgios A. Pavlopoulos; Seán I. O'Donoghue; Venkata P. Satagopam; Theodoros G. Soldatos; Evangelos Pafilis; Reinhard Schneider 002 (BMC Syst. Biol., 2008)

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. - Venkata P. Satagopam; Margarita C. Theodoropoulou; Christos K. Stampolakis; Georgios A. Pavlopoulos; Nikolaos Papandreou; Pantelis G. Bagos; Reinhard Schneider 002; Stavros J. Hamodrakas (Database J. Biol. Databases Curation, 2010)

Reflect: A practical approach to web semantics. - Seán I. O'Donoghue; Heiko Horn; Evangelos Pafilis; Sven Haag; Michael Kuhn 004; Venkata P. Satagopam; Reinhard Schneider 002; Lars Juhl Jensen (J. Web Semant., 2010)

Caipirini: using gene sets to rank literature. - Theodoros G. Soldatos; Seán I. O'Donoghue; Venkata P. Satagopam; Adriano Barbosa-Silva; Georgios A. Pavlopoulos; Ana Carolina Wanderley-Nogueira; Nina da Mota Soares-Cavalcanti; Reinhard Schneider 002 (BioData Min., 2012)

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction. - Evangelos Pafilis; Georgios A. Pavlopoulos; Venkata P. Satagopam; Nikolas Papanikolaou; Heiko Horn; Christos Arvanitidis; Lars Juhl Jensen; Reinhard Schneider 002; Ioannis Iliopoulos (BIBE, 2013)

Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator. - Jeroen de Ridder; Thomas Abeel; Magali Michaut; Venkata P. Satagopam; Nils Gehlenborg (PLoS Comput. Biol., 2013)

The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013. - Jeroen de Ridder; Yana Bromberg; Magali Michaut; Venkata P. Satagopam; Manuel Corpas; Geoff MacIntyre; Theodore Alexandrov (PLoS Comput. Biol., 2013)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Nikolas Papanikolaou; Georgios A. Pavlopoulos; Evangelos Pafilis; Theodosios Theodosiou; Reinhard Schneider 002; Venkata P. Satagopam; Christos A. Ouzounis; Aristides G. Eliopoulos; Vasilis J. Promponas; Ioannis Iliopoulos (Bioinform., 2014)

The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data. - Norman E. Davey; Venkata P. Satagopam; Salvador Santiago-Mozos; Carlos Villacorta-Martin; Tanmay A. M. Bharat; Reinhard Schneider 002; John A. G. Briggs (PLoS Comput. Biol., 2014)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Nikolas Papanikolaou; Georgios A. Pavlopoulos; Evangelos Pafilis; Theodosios Theodosiou; Reinhard Schneider 002; Venkata P. Satagopam; Christos A. Ouzounis; Aristides G. Eliopoulos; Vasilis J. Promponas; Ioannis Iliopoulos (Bioinform., 2015)

Semantic Web Technologies for a Knowledge Base of Biomedical Facts Extracted from Scientific Literature. - Valentin Grouès; Maria Biryukov; Christophe Trefois; Venkata P. Satagopam (SWAT4LS, 2016)

Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. - Venkata P. Satagopam; Wei Gu; Serge Eifes; Piotr Gawron; Marek Ostaszewski; Stephan Gebel; Adriano Barbosa-Silva; Rudi Balling; Reinhard Schneider 002 (Big Data, 2016)

BioKB - Text mining and semantic technologies for the biomedical content discovery. - Maria Biryukov; Valentin Grouès; Venkata P. Satagopam (SWAT4LS, 2017)

nala: text mining natural language mutation mentions. - Juan Miguel Cejuela; Aleksandar Bojchevski; Carsten Uhlig; Rustem Bekmukhametov; Sanjeev Kumar Karn; Shpend Mahmuti; Ashish Baghudana; Ankit Dubey; Venkata P. Satagopam; Burkhard Rost (Bioinform., 2017)

SmartR: an open-source platform for interactive visual analytics for translational research data. - Sascha Herzinger; Wei Gu; Venkata P. Satagopam; Serge Eifes; Kavita Rege; Adriano Barbosa-Silva; Reinhard Schneider 002 (Bioinform., 2017)

ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software. - Laurent Heirendt; Sylvain Arreckx; Christophe Trefois; Yohan Yarosz; Maharshi Vyas; Venkata P. Satagopam; Reinhard Schneider 002; Ines Thiele; Ronan M. T. Fleming (CoRR, 2017)

The future of metabolomics in ELIXIR. - Merlijn N. van Rijswijk; Charlie Beirnaert; Christophe Caron; Marta Cascante; Victoria Dominguez Del Angel; Warwick B. Dunn; Timothy M. D. Ebbels; Franck Giacomoni; Alejandra N. González-Beltrán; Thomas Hankemeier; Kenneth Haug; Jose L. Izquierdo-García; et al. (F1000Research, 2017)

Provenance-Enabled Stewardship of Human Data in the GDPR Era. - Pinar Alper; Regina Becker; Venkata P. Satagopam; Christophe Trefois; Valentin Grouès; Jacek Lebioda; Yohan Jarosz (IPAW, 2018)

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide. - Anupama Jigisha; Margherita Francescatto; Farzana Rahman; Nazeefa Fatima; Dan F. DeBlasio; Avinash Kumar Shanmugam; Venkata P. Satagopam; Alberto Santos; Pandurang Kolekar; Magali Michaut; Emre Guney (PLoS Comput. Biol., 2018)

Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART. - Adriano Barbosa-Silva; Dorina Bratfalean; Wei Gu; Venkata P. Satagopam; Paul Houston; Lauren B. Becnel; Serge Eifes; Fabien Richard; Andreas Tielmann; Sascha Herzinger; Kavita Rege; Rudi Balling; et al. (Bioinform., 2019)

Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium. - Wei Gu; Reha Yildirimman; Emmanuel Van der Stuyft; Denny Verbeeck; Sascha Herzinger; Venkata P. Satagopam; Adriano Barbosa-Silva; Reinhard Schneider 002; Bodo M. H. Lange; Hans Lehrach; Yike Guo; David Henderson; et al. (BMC Bioinform., 2019)

PredictProtein - Predicting Protein Structure and Function for 29 Years. - Michael Bernhofer; Christian Dallago; Timothy Karl; Venkata P. Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; et al. (Nucleic Acids Res., 2021)

Translational Challenges of Biomedical Machine Learning Solutions in Clinical and Laboratory Settings. - Carlos Vega; Miroslav Kratochvíl; Venkata P. Satagopam; Reinhard Schneider 002 (IWBBIO (2), 2022)

COBREXA.jl: constraint-based reconstruction and exascale analysis. - Miroslav Kratochvíl; Laurent Heirendt; St. Elmo Wilken; Taneli Pusa; Sylvain Arreckx; Alberto Noronha; Marvin van Aalst; Venkata P. Satagopam; Oliver Ebenhöh; Reinhard Schneider 002; Christophe Trefois; Wei Gu (Bioinform., 2022)

A formalization of one of the main claims of "Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes" by Schubert et al. 20141. - Valentin Grouès; Carlos Vega; Venkata P. Satagopam (Data Sci., 2022)

RDM Services at the Luxembourg National Data Service. - Wei Gu; Christophe Trefois; Pinar Alper; Danielle Welter; Yohan Jarosz; Jacek Lebioda; Linda Ebermann; Regina Becker; Venkata P. Satagopam; Reinhard Schneider 002; Bert Verdonck (CoRDI, 2023)

Experiences From FAIRifying Community Data and FAIR Infrastructure in Biomedical Research Domains. - Dagmar Waltemath; Esther Thea Inau; Lea Michaelis; Venkata P. Satagopam; Irina Balaur (CoRDI, 2023)

Visualization of automatically combined disease maps and pathway diagrams for rare diseases. - 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; et al. (Frontiers Bioinform., 2023)

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. - Alexander Mazein; Marcio Luis Acencio; Irina Balaur; Adrien Rougny; Danielle Welter; Anna Niarakis; Diana Ramirez Ardila; Ugur Dogrusoz; Piotr Gawron; Venkata P. Satagopam; Wei Gu; Andreas Kremer; et al. (Frontiers Bioinform., 2023)

Analysis: Flawed Datasets of Monkeypox Skin Images. - Carlos Vega; Reinhard Schneider 002; Venkata P. Satagopam (J. Medical Syst., 2023)

Graph databases in systems biology: a systematic review. - Ilya Mazein; Adrien Rougny; Alexander Mazein; Ron Henkel; Lea Gütebier; Lea Michaelis; Marek Ostaszewski; Reinhard Schneider 002; Venkata P. Satagopam; Lars Juhl Jensen; Dagmar Waltemath; Judith A. H. Wodke; et al. (Briefings Bioinform., 2024)

BioKC: a collaborative platform for curation and annotation of molecular interactions. - Carlos Vega; Marek Ostaszewski; Valentin Grouès; Reinhard Schneider 002; Venkata P. Satagopam (Database J. Biol. Databases Curation, 2024)

Generation of Synthetic Clinical Text: A Systematic Review. - Basel Alshaikhdeeb; Ahmed Abdelmonem Hemedan; Soumyabrata Ghosh; Irina Balaur; Venkata P. Satagopam (CoRR, 2025)