Publications

Publications by HumanISE

2024

Proceedings of the 19th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, VISIGRAPP 2024, Volume 4: VISAPP, Rome, Italy, February 27-29, 2024

Authors
Radeva, P; Furnari, A; Bouatouch, K; de Sousa, AA;

Publication
VISIGRAPP (4): VISAPP

Abstract

2024

Proceedings of the 19th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, VISIGRAPP 2024, Volume 3: VISAPP, Rome, Italy, February 27-29, 2024

Authors
Radeva, P; Furnari, A; Bouatouch, K; de Sousa, AA;

Publication
VISIGRAPP (3): VISAPP

Abstract

2024

Proceedings of the 19th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, VISIGRAPP 2024, Volume 2: VISAPP, Rome, Italy, February 27-29, 2024

Authors
Radeva, P; Furnari, A; Bouatouch, K; de Sousa, AA;

Publication
VISIGRAPP (2): VISAPP

Abstract

2024

Proceedings of the 19th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, VISIGRAPP 2024, Volume 1: GRAPP, HUCAPP and IVAPP, Rome, Italy, February 27-29, 2024

Authors
Rogers, TB; Méneveaux, D; Ziat, M; Ammi, M; Jänicke, S; Purchase, HC; Bouatouch, K; de Sousa, AA;

Publication
VISIGRAPP (1): GRAPP, HUCAPP, IVAPP

Abstract

2024

Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data

Authors
Peres, A; Klein, V; Frankel, B; Lees, W; Polak, P; Meehan, M; Rocha, A; Lopes, JC; Yaari, G;

Publication
BRIEFINGS IN BIOINFORMATICS

Abstract
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.

CloseRead Abstract

2024

Report from the 14th International Workshop on Automating Test Case Design, Selection, and Evaluation (A-TEST 2023)

Authors
Faria, JP; Verbeek, F; Fasolino, AR;

Publication
ACM SIGSOFT Softw. Eng. Notes

Abstract