Ghent University Academic Bibliography

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instaGRAAL : chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck (UGent) , J. Mark Cock, et al.

(2020) GENOME BIOLOGY. 21(1).
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DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance

Flora D'Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, V Berrens, Rebecca, Junbin Qian, Pawel Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, et al.

(2020) GENOME BIOLOGY. 21(1).
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Essential guidelines for computational method benchmarking

Lukas M Weber, Wouter Saelens (UGent) , Robrecht Cannoodt (UGent) , Charlotte Soneson, Alexander Hapfelmeier, Paul P Gardner, Anne-Laure Boulesteix, Yvan Saeys (UGent) and Mark D Robinson

(2019) GENOME BIOLOGY. 20.
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Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles : a multi-center evaluation

Channabasavaiah B. Gurumurthy, Aidan R O'Brien, Rolen M Quadros, John Adams, Pilar Alcaide, Shinya Ayabe, Johnathan Ballard, Surinder K Batra, Marie-Claude Beauchamp, Kathleen A Becker, et al.

(2019) GENOME BIOLOGY. 20(1).
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Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Koen Van den Berge (UGent) , Fanny Perraudeau, Charlotte Soneson, Michael I Love, Davide Risso, Jean-Philippe Vert, Mark D Robinson, Sandrine Dudoit and Lieven Clement (UGent)

(2018) GENOME BIOLOGY. 19.
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Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

Alemu Takele Assefa (UGent) , Katrijn De Paepe, Celine Everaert (UGent) , Pieter Mestdagh (UGent) , Olivier Thas (UGent) and Jo Vandesompele (UGent)

(2018) GENOME BIOLOGY. 19.
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The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data

Gerben Menschaert (UGent) , Xiaojing Wang, Andrew R Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk (UGent) , Bing Zhang, Eric W Deutsch, Tobias Ternent and Juan Antonio Vizcaíno

(2018) GENOME BIOLOGY. 19.
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stageR : a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Koen Van den Berge (UGent) , Charlotte Soneson, Mark D Robinson and Lieven Clement (UGent)

(2017) GENOME BIOLOGY. 18.
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Disorders of sex development : insights from targeted gene sequencing of a large international patient cohort

Stefanie Eggers, Simon Sadedin, Jocelyn A. van den Bergen, Gorjana Robevska, Thomas Ohnesorg, Jacqueline Hewitt, Luke Lambeth, Aurore Bouty, Ingrid M. Knarston, Tiong Yang Tan, et al.

(2016) GENOME BIOLOGY. 17.
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Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes

Dmitry E. Andreev, Patrick B. F. O'Connor, Alexander V. Zhdanov, Ruslan Dmitriev (UGent) , Ivan N. Shatsky, Dmitri B. Papkovsky and Pavel V. Baranov

(2015) GENOME BIOLOGY. 16.

Academic Bibliography

instaGRAAL : chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance

Essential guidelines for computational method benchmarking

Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles : a multi-center evaluation

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

The proBAM and proBed standard formats : enabling a seamless integration of genomics and proteomics data

stageR : a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Disorders of sex development : insights from targeted gene sequencing of a large international patient cohort

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes

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