snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package. - Augustin Luna; Kristin K. Nicodemus (Bioinform., 2007)

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). - Augustin Luna; Margot Sunshine; Martijn P. van Iersel; Mirit I. Aladjem; Kurt W. Kohn (Bioinform., 2011)

A Formal MIM Specification and Tools for the Common Exchange of MIM Diagrams: an XML-Based Format, an API, and a Validation Method. - Augustin Luna; Evrim I. Karac; Margot Sunshine; Lucas Chang; Ruth Nussinov; Mirit I. Aladjem; Kurt W. Kohn (BMC Bioinform., 2011)

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. - Kumar Chandan; Martijn P. van Iersel; Mirit I. Aladjem; Kurt W. Kohn; Augustin Luna (Bioinform., 2012)

Software support for SBGN maps: SBGN-ML and LibSBGN. - Martijn P. van Iersel; Alice Villéger; Tobias Czauderna; Sarah E. Boyd; Frank T. Bergmann; Augustin Luna; Emek Demir; Anatoly A. Sorokin; Ugur Dogrusöz; Yukiko Matsuoka; Akira Funahashi; Mirit I. Aladjem; et al. (Bioinform., 2012)

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. - Jake Y. Fried; Martijn P. van Iersel; Mirit I. Aladjem; Kurt W. Kohn; Augustin Luna (Bioinform., 2013)

Formalization of molecular interaction maps in systems biology; Application to simulations of the relationship between DNA damage response and circadian rhythms - Augustin Luna (2013)

MIMTool: A Tool for Drawing Molecular Interaction Maps. - Mine Edes; Can C. Özturan; Türkan Haliloglu; Augustin Luna; Ruth Nussinov (CoRR, 2014)

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 . - Huaiyu Mi; Falk Schreiber; Stuart L. Moodie; Tobias Czauderna; Emek Demir; Robin Haw; Augustin Luna; Nicolas Le Novère; Anatoly A. Sorokin; Alice Villéger (J. Integr. Bioinform., 2015)

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. - Anatoly A. Sorokin; Nicolas Le Novère; Augustin Luna; Tobias Czauderna; Emek Demir; Robin Haw; Huaiyu Mi; Stuart L. Moodie; Falk Schreiber; Alice Villéger (J. Integr. Bioinform., 2015)

Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. - Augustin Luna; Geoffrey B. McFadden; Mirit I. Aladjem; Kurt W. Kohn (PLoS Comput. Biol., 2015)

The digital revolution in phenotyping. - Anika Oellrich; Nigel Collier; Tudor Groza; Dietrich Rebholz-Schuhmann; Nigam Shah; Olivier Bodenreider; Mary Regina Boland; Ivo I. Georgiev; Hongfang Liu; Kevin M. Livingston; Augustin Luna; Ann-Marie Mallon; et al. (Briefings Bioinform., 2016)

PaxtoolsR: pathway analysis in R using Pathway Commons. - Augustin Luna; Özgün Babur; Bülent Arman Aksoy; Emek Demir; Chris Sander (Bioinform., 2016)

rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. - Augustin Luna; Vinodh N. Rajapakse; Fabricio G. Sousa; Jianjiong Gao; Nikolaus Schultz; Sudhir Varma; William C. Reinhold; Chris Sander; Yves Pommier (Bioinform., 2016)

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Swapnil Bhatia; Mike Bissell; Kevin Clancy; Thomas E. Gorochowski; Raik Grünberg; Augustin Luna; et al. (J. Integr. Bioinform., 2018)

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. - Curtis Madsen; Ángel Goñi-Moreno; Zachary Palchick; Umesh P; Nicholas Roehner; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Mike Bissell; Kevin Clancy; Robert Sidney Cox III; Thomas E. Gorochowski; et al. (J. Integr. Bioinform., 2019)

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. - Adrien Rougny; Vasundra Touré; Stuart L. Moodie; Irina Balaur; Tobias Czauderna; Hanna Borlinghaus; Ugur Dogrusoz; Alexander Mazein; Andreas Dräger; Michael L. Blinov; Alice Villéger; Robin Haw; et al. (J. Integr. Bioinform., 2019)

AlignmentViewer: Sequence Analysis of Large Protein Families. - Roc Reguant; Yevgeniy Antipin; Robert P. Sheridan; Christian Dallago; Drew Diamantoukos; Augustin Luna; Chris Sander; Nicholas Paul Gauthier (F1000Research, 2020)

Synthetic biology open language visual (SBOL visual) version 2.2. - Hasan Baig; Pedro Fontanarrosa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Michael Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2020)

Systems biology graphical notation markup language (SBGNML) version 0.3. - Frank T. Bergmann; Tobias Czauderna; Ugur Dogrusoz; Adrien Rougny; Andreas Dräger; Vasundra Touré; Alexander Mazein; Michael L. Blinov; Augustin Luna (J. Integr. Bioinform., 2020)

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. - Igor V. Rodchenkov; Ozgun Babur; Augustin Luna; Bülent Arman Aksoy; Jeffrey V. Wong; Dylan Fong; Max Franz; Metin Can Siper; Manfred Cheung; Michael Wrana; Harsh Mistry; Logan Mosier; et al. (Nucleic Acids Res., 2020)

Synthetic biology open language visual (SBOL Visual) version 2.3. - Hasan Baig; Pedro Fontanarossa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Shyam Bhakta; Swapnil Bhatia; Mike Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2021)

CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. - Augustin Luna; Fathi Elloumi; Sudhir Varma; Yanghsin Wang; Vinodh N. Rajapakse; Mirit I. Aladjem; Jacques Robert; Chris Sander; Yves Pommier; William C. Reinhold (Nucleic Acids Res., 2021)

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. - Özgün Babur; Augustin Luna; Anil Korkut; Funda Durupinar; Metin Can Siper; Ugur Dogrusoz; Alvaro Sebastian Vaca Jacome; Ryan Peckner; Karen E. Christianson; Jacob D. Jaffe; Paul T. Spellman; Joseph E. Aslan; et al. (Patterns, 2021)

StonPy: a tool to parse and query collections of SBGN maps in a graph database. - Adrien Rougny; Irina Balaur; Augustin Luna; Alexander Mazein (Bioinform., 2023)

drGAT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network. - Yoshitaka Inoue; Hunmin Lee; Tianfan Fu; Augustin Luna (CoRR, 2024)

Strategies to include prior knowledge in omics analysis with deep neural networks. - Kisan Thapa; Meric Kinali; Shichao Pei; Augustin Luna; Özgün Babur (Patterns, 2025)

GraphPINE: Graph Importance Propagation for Interpretable Drug Response Prediction. - Yoshitaka Inoue; Tianfan Fu; Augustin Luna (CoRR, 2025)

User-Guided Force-Directed Graph Layout. - Hasan Balci; Augustin Luna (CoRR, 2025)