Thomas Moerman1,2, Sara Aibar Santos3,4, Carmen Bravo González-Blas3,4, Jaak Simm2,5, Yves Moreau2,5, Jan Aerts1,2, Stein Aerts3,4. 1. KU Leuven ESAT/STADIUS, VDA-lab. 2. IMEC Smart Applications and Innovation Services. 3. Laboratory of Computational Biology, VIB Center for Brain & Disease Research. 4. Department of Human Genetics, KU Leuven, Leuven, Belgium. 5. KU Leuven ESAT/STADIUS, Bioinformatics Lab.
Abstract
SUMMARY: Inferring a Gene Regulatory Network (GRN) from gene expression data is a computationally expensive task, exacerbated by increasing data sizes due to advances in high-throughput gene profiling technology, such as single-cell RNA-seq. To equip researchers with a toolset to infer GRNs from large expression datasets, we propose GRNBoost2 and the Arboreto framework. GRNBoost2 is an efficient algorithm for regulatory network inference using gradient boosting, based on the GENIE3 architecture. Arboreto is a computational framework that scales up GRN inference algorithms complying with this architecture. Arboreto includes both GRNBoost2 and an improved implementation of GENIE3, as a user-friendly open source Python package. AVAILABILITY AND IMPLEMENTATION: Arboreto is available under the 3-Clause BSD license at http://arboreto.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Inferring a Gene Regulatory Network (GRN) from gene expression data is a computationally expensive task, exacerbated by increasing data sizes due to advances in high-throughput gene profiling technology, such as single-cell RNA-seq. To equip researchers with a toolset to infer GRNs from large expression datasets, we propose GRNBoost2 and the Arboreto framework. GRNBoost2 is an efficient algorithm for regulatory network inference using gradient boosting, based on the GENIE3 architecture. Arboreto is a computational framework that scales up GRN inference algorithms complying with this architecture. Arboreto includes both GRNBoost2 and an improved implementation of GENIE3, as a user-friendly open source Python package. AVAILABILITY AND IMPLEMENTATION: Arboreto is available under the 3-Clause BSD license at http://arboreto.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Saskia Trump; Soeren Lukassen; Markus S Anker; Robert Lorenz Chua; Johannes Liebig; Loreen Thürmann; Victor Max Corman; Marco Binder; Jennifer Loske; Christina Klasa; Teresa Krieger; Bianca P Hennig; Marey Messingschlager; Fabian Pott; Julia Kazmierski; Sven Twardziok; Jan Philipp Albrecht; Jürgen Eils; Sara Hadzibegovic; Alessia Lena; Bettina Heidecker; Thore Bürgel; Jakob Steinfeldt; Christine Goffinet; Florian Kurth; Martin Witzenrath; Maria Theresa Völker; Sarah Dorothea Müller; Uwe Gerd Liebert; Naveed Ishaque; Lars Kaderali; Leif-Erik Sander; Christian Drosten; Sven Laudi; Roland Eils; Christian Conrad; Ulf Landmesser; Irina Lehmann Journal: Nat Biotechnol Date: 2020-12-24 Impact factor: 54.908
Authors: Eszter Posfai; John Paul Schell; Adrian Janiszewski; Isidora Rovic; Alexander Murray; Brian Bradshaw; Tatsuya Yamakawa; Tine Pardon; Mouna El Bakkali; Irene Talon; Natalie De Geest; Pankaj Kumar; San Kit To; Sophie Petropoulos; Andrea Jurisicova; Vincent Pasque; Fredrik Lanner; Janet Rossant Journal: Nat Cell Biol Date: 2021-01-08 Impact factor: 28.824
Authors: Sunny Z Wu; Daniel L Roden; Chenfei Wang; Holly Holliday; Kate Harvey; Aurélie S Cazet; Kendelle J Murphy; Brooke Pereira; Ghamdan Al-Eryani; Nenad Bartonicek; Rui Hou; James R Torpy; Simon Junankar; Chia-Ling Chan; Chuan En Lam; Mun N Hui; Laurence Gluch; Jane Beith; Andrew Parker; Elizabeth Robbins; Davendra Segara; Cindy Mak; Caroline Cooper; Sanjay Warrier; Alistair Forrest; Joseph Powell; Sandra O'Toole; Thomas R Cox; Paul Timpson; Elgene Lim; X Shirley Liu; Alexander Swarbrick Journal: EMBO J Date: 2020-08-13 Impact factor: 11.598
Authors: Florian Wünnemann; Asaf Ta-Shma; Gregor Andelfinger; Christoph Preuss; Severine Leclerc; Patrick Piet van Vliet; Andrea Oneglia; Maryse Thibeault; Emily Nordquist; Joy Lincoln; Franka Scharfenberg; Christoph Becker-Pauly; Philipp Hofmann; Kirstin Hoff; Enrique Audain; Hans-Heiner Kramer; Wojciech Makalowski; Amiram Nir; Sebastian S Gerety; Matthew Hurles; Johanna Comes; Anne Fournier; Hanna Osinska; Jeffrey Robins; Michel Pucéat; Orly Elpeleg; Marc-Phillip Hitz Journal: Nat Genet Date: 2019-12-16 Impact factor: 38.330
Authors: Robert Lorenz Chua; Soeren Lukassen; Saskia Trump; Bianca P Hennig; Daniel Wendisch; Fabian Pott; Olivia Debnath; Loreen Thürmann; Florian Kurth; Maria Theresa Völker; Julia Kazmierski; Bernd Timmermann; Sven Twardziok; Stefan Schneider; Felix Machleidt; Holger Müller-Redetzky; Melanie Maier; Alexander Krannich; Sein Schmidt; Felix Balzer; Johannes Liebig; Jennifer Loske; Norbert Suttorp; Jürgen Eils; Naveed Ishaque; Uwe Gerd Liebert; Christof von Kalle; Andreas Hocke; Martin Witzenrath; Christine Goffinet; Christian Drosten; Sven Laudi; Irina Lehmann; Christian Conrad; Leif-Erik Sander; Roland Eils Journal: Nat Biotechnol Date: 2020-06-26 Impact factor: 54.908