CoDeNios: a function level co-design tool. - Yann Thoma; Eduardo Sanchez (WCAE, 2002)

Hardware spiking neural network with run-time reconfigurable connectivity in. - Daniel Roggen; Stephane Hofmann; Yann Thoma; Dario Floreano (Evolvable Hardware, 2003)

Developmental Processes in Silicon: An Engineering Perspective. - Gianluca Tempesti; Daniel Mange; Enrico Petraglio; André Stauffer; Yann Thoma (Evolvable Hardware, 2003)

A Dynamic Routing Algorithm for a Bio-inspired Reconfigurable Circuit. - Yann Thoma; Eduardo Sanchez; Juan-Manuel Moreno Aróstegui; Gianluca Tempesti (FPL, 2003)

Ontogenetic Development and Fault Tolerance in the POEtic Tissue. - Gianluca Tempesti; Daniel Roggen; Eduardo Sanchez; Yann Thoma; Richard Canham; Andrew M. Tyrrell (ICES, 2003)

Hardware Realization of a Bio-inspired POEtic Tissue. - Juan Manuel Moreno; Yann Thoma; Eduardo Sanchez; Oriol Torres; Gianluca Tempesti (Evolvable Hardware, 2004)

A Reconfigurable Chip for Evolvable Hardware. - Yann Thoma; Eduardo Sanchez (GECCO (1), 2004)

Prototyping with a Bio-Inspired Reconfigurable Chip. - Yann Thoma; Eduardo Sanchez; Daniel Roggen; Carl Hetherington; Juan Manuel Moreno (IEEE International Workshop on Rapid System Prototyping, 2004)

POEtic: A Prototyping Platform for Bio-inspired Hardware. - Juan Manuel Moreno; Yann Thoma; Eduardo Sanchez (ICES, 2005)

An adaptive FPGA and its distributed routing. - Yann Thoma; Eduardo Sanchez (ReCoSoC, 2005)

MOVE Processors That Self-replicate and Differentiate. - Joël Rossier; Yann Thoma; Pierre-André Mudry; Gianluca Tempesti (BioADIT, 2006)

PERPLEXUS: Pervasive Computing Framework for Modeling Complex Virtually-Unbounded Systems. - Eduardo Sanchez; Andrés Pérez-Uribe; Andres Upegui; Yann Thoma; Juan Manuel Moreno; Alessandro E. P. Villa; Henri Volken; Andrzej Napieralski; Gilles Sassatelli; Erwan Lavarec (AHS, 2007)

The Perplexus bio-inspired reconfigurable circuit. - Andres Upegui; Yann Thoma; Eduardo Sanchez; Andrés Pérez-Uribe; Juan Manuel Moreno; Jordi Madrenas (AHS, 2007)

Fault Tolerance Using Dynamic Reconfiguration on the POEtic Tissue. - Will Barker; David M. Halliday; Yann Thoma; Eduardo Sanchez; Gianluca Tempesti; Andrew M. Tyrrell (IEEE Trans. Evol. Comput., 2007)

UbiManager: A Software Tool for Managing Ubichips. - Yann Thoma; Andres Upegui (AHS, 2008)

Dynamic Routing on the Ubichip: Toward Synaptogenetic Neural Networks. - Andres Upegui; Yann Thoma; Andrés Pérez-Uribe; Eduardo Sanchez (AHS, 2008)

BAF: A Bio-Inspired Agent Framework for Distributed Pervasive Applications. - Olivier Brousse; Gilles Sassatelli; Thierry Gil; Yoann Guillemenet; Michel Robert; François Grize; Eduardo Sanchez; Yann Thoma; Andres Upegui; Juan Manuel Moreno; Jordi Madrenas (GEM, 2008)

The Perplexus Programming Framework: Combining Bio-inspiration and Agent-Oriented Programming for the Simulation of Large Scale Complex Systems. - Olivier Brousse; Gilles Sassatelli; Thierry Gil; Michel Robert; François Grize; Eduardo Sanchez; Andres Upegui; Yann Thoma (ICES, 2008)

Neural Development on the Ubichip by Means of Dynamic Routing Mechanisms. - Andres Upegui; Andrés Pérez-Uribe; Yann Thoma; Eduardo Sanchez (ICES, 2008)

The PERPLEXUS bio-inspired hardware platform: A flexible and modular approach. - Andres Upegui; Yann Thoma; Eduardo Sanchez; Andrés Pérez-Uribe; Juan Manuel Moreno; Jordi Madrenas; Gilles Sassatelli (Int. J. Knowl. Based Intell. Eng. Syst., 2008)

Ubichip, Ubidule, and MarXbot: A Hardware Platform for the Simulation of Complex Systems. - Andres Upegui; Yann Thoma; Héctor F. Satizábal; Francesco Mondada; Philippe Rétornaz; Yoan Graf; Andrés Pérez-Uribe; Eduardo Sanchez (ICES, 2010)

Math2Mat: From Octave/Matlab to VHDL. - Yann Thoma; Etienne Messerli; Michel Starkier; Daniel Molla; Sebastien Masle; Christophe Bianchi; Oliver Gubler; Claude Magliocco; Philippe Crausaz; Samuel Tache; Denis Prêtre; Gregory Trolliet (AHS, 2012)

FPGA2: An open source framework for FPGA-GPU PCIe communication. - Yann Thoma; Alberto Dassatti; Daniel Molla (ReConFig, 2013)

Safe Implementation of Embedded Software for a Portable Device Supporting Drug Administration. - Alena Simalatsar; Romain Bornet; Wenqi You; Yann Thoma; Giovanni De Micheli (BIBE, 2014)

FPGA-GPU communicating through PCIe. - Yann Thoma; Alberto Dassatti; Daniel Molla; Enrico Petraglio (Microprocess. Microsystems, 2015)

Genomic Data Clustering on FPGAs for Compression. - Enrico Petraglio; Rick Wertenbroek; Flavio Capitao; Nicolas Guex; Christian Iseli; Yann Thoma (ARC, 2017)

TUCUXI: An Intelligent System for Personalized Medicine from Individualization of Treatments to Research Databases and Back. - Alevtina Dubovitskaya; Thierry Buclin; Michael Ignaz Schumacher; Karl Aberer; Yann Thoma (BCB, 2017)

Pipelined Multi-FPGA Genomic Data Clustering. - Rick Wertenbroek; Enrico Petraglio; Yann Thoma (ICA3PP, 2017)

k-mer Counting with FPGAs and HMC In-Memory Operations. - Rick Wertenbroek; Yann Thoma (AHS, 2018)

Acceleration of the Pair-HMM forward algorithm on FPGA with cloud integration for GATK. - Rick Wertenbroek; Yann Thoma (BIBM, 2019)

A low fluctuation control strategy for PMSM direct drive system targeting Particle Beam Instrumentation Application. - Jonathan Emery; Patrik Andersson; Federico Roncarolo; Yann Thoma (CCTA, 2019)

SpikeOnChip : A Custom Embedded Platform for Neuronal Activity Recording and Analysis. - Rick Wertenbroek; Yann Thoma; Flavio Maurizio Mor; Sara Grassi; Marc Olivier Heuschkel; Adrien Roux; Luc Stoppini (IEEE Trans. Biomed. Circuits Syst., 2021)

XSI - a genotype compression tool for compressive genomics in large biobanks. - Rick Wertenbroek; Simone Rubinacci; Ioannis Xenarios; Yann Thoma; Olivier Delaneau (Bioinform., 2022)

Simultaneous Quantification of Multiple Drugs by Machine Learning on Electrochemical Sensors. - Tatsunori Matsumoto; Lin Du; Yann Thoma; Sandro Carrara (ISCAS, 2024)

A Portable Linux-based Firmware for NVMe Computational Storage Devices. - Rick Wertenbroek; Yann Thoma; Alberto Dassatti (ACM Trans. Storage, 2025)