Ghent University Academic Bibliography

Journal Article
A1
open access

Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment.

Máté Kiss, Laszlo Halasz, Eva Hadadi, Wilhelm K. Berger, Petros Tzerpos, Szilard Poliska, Daliya Kancheva, Aurélie Gabriel, Romina Mora Barthelmess, Ayla Debraekeleer, et al.

(2025) GENOME MEDICINE. 17(1).

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Journal Article
A1
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CD4+ T cells license Kupffer cells to reverse CD8+ T cell dysfunction induced by hepatocellular priming

Valentina Venzin, Cristian G. Beccaria, Chiara Perucchini, Pietro Delfino, Elisa B. Bono, Leonardo Giustini, Federica Moalli, Marta Grillo, Valeria Fumagalli, Chiara Laura, et al.

(2025) NATURE IMMUNOLOGY. 16(1).

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Journal Article
A1
open access

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Wouter Saelens (UGent) , Olga Pushkarev and Bart Deplancke

(2025) NATURE COMMUNICATIONS. 16(1).

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A1
open access

Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress

Koen Deserranno (UGent) , Elise Callens (UGent) , Danique Berrevoet (UGent) , Aaron Verplancke (UGent) , Tamara De Vos (UGent) , Tom Taghon (UGent) , Dieter Deforce (UGent) and Filip Van Nieuwerburgh (UGent)

(2025) BMC GENOMICS. 27(1).

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Journal Article
A1
open access

Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

Chananchida Sang-aram (UGent) , Robin Browaeys (UGent) , Ruth Seurinck (UGent) and Yvan Saeys (UGent)

(2024) ELIFE. 12.

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Journal Article
A1
open access

NBAtlas : a harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors

Noah Bonine (UGent) , Vittorio Zanzani (UGent) , Annelies Van Hemelryk (UGent) , Bavo Vanneste (UGent) , Christian Zwicker (UGent) , Tinne THONE (UGent) , Sofie Roelandt (UGent) , Sarah-Lee Bekaert (UGent) , Jan Koster, Isabelle Janoueix-Lerosey, et al.

(2024) CELL REPORTS. 43(10).

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Transcriptomic profiling of human dental pulp cells treated with tricalcium silicate-based cements by RNA sequencing

Elanagai Rathinam (UGent) , Srinath Govindarajan (UGent) , Sivaprakash Rajasekharan (UGent) , Heidi Declercq (UGent) , Dirk Elewaut (UGent) , Peter De Coster (UGent) and Luc Martens (UGent)

(2021) CLINICAL ORAL INVESTIGATIONS. 25(5). p.3181-3195

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Journal Article
A1
open access

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

Alemu Takele Assefa, Jo Vandesompele (UGent) and Olivier Thas (UGent)

(2020) BMC GENOMICS. 21(1).

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Journal Article
A1
open access

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Wei-Jun Li, Yu-Jia Song, Hong-Liang Han, Hui-Qian Xu, Dong Wei, Guy Smagghe (UGent) and Jin-Jun Wang

(2020) BMC GENOMICS. 21(1).

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Journal Article
A1
open access

SMARTer single cell total RNA-sequencing

Karen Verboom, Celine Everaert (UGent) , Nathalie Bolduc, Kenneth Livak, Nurten Yigit (UGent) , Dries Rombaut, Jasper Anckaert (UGent) , Simon Lee, Morten Venø, Jørgen Kjems, et al.

(2019) NUCLEIC ACIDS RESEARCH. 47(16).

Academic Bibliography

Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment.

CD4+ T cells license Kupffer cells to reverse CD8+ T cell dysfunction induced by hepatocellular priming

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress

Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

NBAtlas : a harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors

Transcriptomic profiling of human dental pulp cells treated with tricalcium silicate-based cements by RNA sequencing

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

SMARTer single cell total RNA-sequencing

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