Ghent University Academic Bibliography

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Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Viacheslav Mylka (UGent) , Irina Matetovici, Suresh Poovathingal, Jeroen Aerts, Niels Vandamme (UGent) , Ruth Seurinck (UGent) , Kevin Verstaen (UGent) , Gert Hulselmans, Silvie van den Hoecke, Isabelle Scheyltjens, et al.

(2022) GENOME BIOLOGY. 23(1).
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Response to correspondence on '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, Jr. Adams, John, Pilar Alcaide, Shinya Ayabe, Johnathan Ballard, Surinder K. Batra, Marie-Claude Beauchamp, Kathleen A. Becker, et al.

(2021) GENOME BIOLOGY. 22(1).
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PCIP-seq : simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

Maria Artesi, Vincent Hahaut, Basiel Cole (UGent) , Laurens Lambrechts (UGent) , Fereshteh Ashrafi, Ambroise Marçais, Olivier Hermine, Philip Griebel, Natasa Arsic, Frank van der Meer, et al.

(2021) GENOME BIOLOGY. 22(1).
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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, 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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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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Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

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

(2018) GENOME BIOLOGY. 19.

Academic Bibliography

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Response to correspondence on 'Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles : a multi-center evaluation'

PCIP-seq : simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

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

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

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

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