Ghent University Academic Bibliography

Journal Article
A1
open access

Benchmarking digital PCR partition classification methods with empirical and simulated duplex data

Yao Chen (UGent) , Ward De Spiegelaere (UGent) , Wim Trypsteen (UGent) , David Gleerup (UGent) , Jo Vandesompele (UGent) , Antoon Lievens (UGent) , Matthijs Vynck (UGent) and Olivier Thas (UGent)

(2024) BRIEFINGS IN BIOINFORMATICS. 25(3).

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Journal Article
A1
open access

Computational deconvolution of DNA methylation data from mixed DNA samples

Maísa Renata Ferro Dos Santos (UGent) , Edoardo Giuili (UGent) , Andries De Koker (UGent) , Celine Everaert (UGent) and Katleen De Preter (UGent)

(2024) BRIEFINGS IN INFORMATICS. 25(3).

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Journal Article
A1
open access

Digital PCR threshold robustness analysis and optimization using dipcensR

Matthijs Vynck (UGent) , Wim Trypsteen (UGent) , Olivier Thas (UGent) , Jo Vandesompele (UGent) and Ward De Spiegelaere (UGent)

(2024) BRIEFINGS IN BIOINFORMATICS. 25(6).

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Journal Article
A1
open access

Breaking free from references : a consensus-based approach for community profiling with long amplicon nanopore data

Willem Stock (UGent) , Coralie Rousseau, Glen Dierickx (UGent) , Sofie D'hondt (UGent) , Luz Amadei Martínez (UGent) , Simon M. Dittami, Luna van der Loos (UGent) and Olivier De Clerck (UGent)

(2024) BRIEFINGS IN BIOINFORMATICS. 26(1).

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Journal Article
A1
open access

Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison

Dries Heylen, Murih Pusparum, Jurgis Kuliesius, Jim Wilson, Young-Chan Park, Jacek Jamiołkowski, Valentino D'Onofrio (UGent) , Dirk Valkenborg, Jan Aerts, Gökhan Ertaylan, et al.

(2024) BRIEFINGS IN BIOINFORMATICS. 26(1).

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Journal Article
A1
open access

A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data

Jens Uwe Loers (UGent) and Vanessa Vermeirssen (UGent)

(2024) BRIEFINGS IN BIOINFORMATICS. 25(5).

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Journal Article
A1
open access

Closing the circle : current state and perspectives of circular RNA databases

Marieke Vromman (UGent) , Jo Vandesompele (UGent) and Pieter-Jan Volders (UGent)

(2021) BRIEFINGS IN BIOINFORMATICS. 22(1). p.288-297

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Journal Article
A1
open access

Explainability in transformer models for functional genomics

Jim Clauwaert (UGent) , Gerben Menschaert (UGent) and Willem Waegeman (UGent)

(2021) BRIEFINGS IN BIOINFORMATICS. 22(5).

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Algebraic shortcuts for leave-one-out cross-validation in supervised network inference

Michiel Stock (UGent) , Tapio Pahikkala, Antti Airola, Willem Waegeman (UGent) and Bernard De Baets (UGent)

(2020) BRIEFINGS IN BIOINFORMATICS. 21(1). p.262-271

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A broken promise : microbiome differential abundance methods do not control the false discovery rate

Stijn Hawinkel (UGent) , Federico Mattiello (UGent) , Luc Bijnens and Olivier Thas (UGent)

(2019) BRIEFINGS IN BIOINFORMATICS. 20(1). p.210-221

Academic Bibliography

Benchmarking digital PCR partition classification methods with empirical and simulated duplex data

Computational deconvolution of DNA methylation data from mixed DNA samples

Digital PCR threshold robustness analysis and optimization using dipcensR

Breaking free from references : a consensus-based approach for community profiling with long amplicon nanopore data

Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison

A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data

Closing the circle : current state and perspectives of circular RNA databases

Explainability in transformer models for functional genomics

Algebraic shortcuts for leave-one-out cross-validation in supervised network inference

A broken promise : microbiome differential abundance methods do not control the false discovery rate

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