Project: Precision medicine in inherited blindness using integrated omics in human and animal models

2020-01-01 – 2026-10-31

Abstract: This multidisciplinary project aims (1) to decipher cis-regulation in human retina by chromatin conformation profiling, and by the study of regulatory elements in a human and animal model;; (2) to design an integrative framework for omics data analysis to explain missing heritability in inherited
blindness;; (3) to design and test antisense oligonucleotide-based treatments of novel targets, ultimately resulting in precision medicine for inherited blindness.

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- Journal Article
- A1
- open access
saseR : juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval

Alexandre Segers (UGent) , Jeroen Gilis, Mattias Van Heetvelde (UGent) , Davide Risso, Elfride De Baere (UGent) and Lieven Clement (UGent)

(2026) GENOME BIOLOGY. 27(1).
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- Journal Article
- A1
- open access
Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data

Cristian Castiglione, Alexandre Segers (UGent) , Lieven Clement (UGent) and Davide Risso

(2026) BIOSTATISTICS. 27(1).
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- Journal Article
- A1
- open access
De novo and inherited dominant variants in U4 and U6 snRNA genes cause retinitis pigmentosa

Mathieu Quinodoz, Kim Rodenburg, Zuzana Cvackova, Karolina Kaminska, Suzanne E. de Bruijn, Ana Belen Iglesias-Romero, Erica G. M. Boonen, Mukhtar Ullah, Nick Zomer, Marc Folcher, et al.

(2026) NATURE GENETICS. 58(1). p.169-179
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- Journal Article
- A1
- open access
Advancing DIA-based limited proteolysis workflows : introducing DIA-LiPA

Chloé Van Leene (UGent) , Emin Araftpoor (UGent) , An Staes (UGent) , Andrea Argentini (UGent) , Marcel Bühler (UGent) , Lieven Clement (UGent) and Kris Gevaert (UGent)

(2026) ANALYTICAL CHEMISTRY. 98(7). p.5499-5512
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- Journal Article
- A1
- open access
Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates

Thomas Naert (UGent) , Taiyo Yamamoto, Shuting Han, Ruth Röck, Melanie Horn, Philipp Bethge, Nikita Vladimirov, Fabian F. Voigt, Joana Figueiro-Silva, Ruxandra Bachmann-Gagescu, et al.

(2026) NATURE BIOTECHNOLOGY. 44(6). p.1023-1036
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- Journal Article
- A1
- open access
msqrob2TMT : robust linear mixed models for inferring differential abundant proteins in labeled experiments with arbitrarily complex

Stijn Vandenbulcke (UGent) , Christophe Vanderaa (UGent) , Oliver Crook, Lennart Martens (UGent) and Lieven Clement (UGent)

(2025) MOLECULAR & CELLULAR PROTEOMICS. 24(7).
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- PhD Thesis
Dimensionality reduction and outlier detection for transcriptomics and proteomics data

Alexandre Segers (UGent)

(2025)
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- Journal Article
- A1
- open access
Generation and characterization of three human induced pluripotent stem cell lines (UGENTi005, UGENTi006 and UGENTi007) from patients with autosomal dominant adult-onset maculopathy due to RPE65 variant c.1555G>A, p.(E519K)

Eline Van Vooren (UGent) , Filip Van Den Broeck (UGent) , Esperanza Daal (UGent) , Mehrnaz Ghazvini, Julie De Zaeytijd (UGent) , Bart Leroy (UGent) , Miriam Bauwens (UGent) and Elfride De Baere (UGent)

(2025) STEM CELL RESEARCH. 89.
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- Journal Article
- A1
- open access
RPE65 variant p.(E519K) causes a novel dominant adult-onset maculopathy in 83 affected individuals

Eline Van Vooren (UGent) , Filip Van Den Broeck (UGent) , Quinten Mahieu (UGent) , Eline Geens (UGent) , Mattias Van Heetvelde (UGent) , Marieke De Bruyne (UGent) , Stijn Van de Sompele (UGent) , Sheetal Uppal, Eugenia Poliakov, Claire-Marie Dhaenens, et al.

(2025) INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE. 66(12).
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- Journal Article
- A1
- open access
Cracking rare disorders : a new minimally invasive RNA-seq protocol

Laurenz De Cock, Erika D'haenens (UGent) , Lies Vantomme (UGent) , Lynn Backers, Aude Beyens (UGent) , Kathleen Claes (UGent) , Griet De Clercq (UGent) , Robin de Putter (UGent) , Candy Kumps (UGent) , Nika Schuermans (UGent) , et al.

(2025) NPJ GENOMIC MEDICINE. 10(1).

Academic Bibliography

Project: Precision medicine in inherited blindness using integrated omics in human and animal models

saseR : juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval

Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data

De novo and inherited dominant variants in U4 and U6 snRNA genes cause retinitis pigmentosa

Advancing DIA-based limited proteolysis workflows : introducing DIA-LiPA

Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates

msqrob2TMT : robust linear mixed models for inferring differential abundant proteins in labeled experiments with arbitrarily complex

Dimensionality reduction and outlier detection for transcriptomics and proteomics data

Generation and characterization of three human induced pluripotent stem cell lines (UGENTi005, UGENTi006 and UGENTi007) from patients with autosomal dominant adult-onset maculopathy due to RPE65 variant c.1555G>A, p.(E519K)

RPE65 variant p.(E519K) causes a novel dominant adult-onset maculopathy in 83 affected individuals

Cracking rare disorders : a new minimally invasive RNA-seq protocol

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saseR : juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval

Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data

De novo and inherited dominant variants in U4 and U6 snRNA genes cause retinitis pigmentosa

Advancing DIA-based limited proteolysis workflows : introducing DIA-LiPA

Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates

msqrob2TMT : robust linear mixed models for inferring differential abundant proteins in labeled experiments with arbitrarily complex

Dimensionality reduction and outlier detection for transcriptomics and proteomics data

Generation and characterization of three human induced pluripotent stem cell lines (UGENTi005, UGENTi006 and UGENTi007) from patients with autosomal dominant adult-onset maculopathy due to RPE65 variant c.1555G&gt;A, p.(E519K)

RPE65 variant p.(E519K) causes a novel dominant adult-onset maculopathy in 83 affected individuals

Cracking rare disorders : a new minimally invasive RNA-seq protocol

Generation and characterization of three human induced pluripotent stem cell lines (UGENTi005, UGENTi006 and UGENTi007) from patients with autosomal dominant adult-onset maculopathy due to RPE65 variant c.1555G>A, p.(E519K)