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Method

Partial alignment of multislice spatially resolved transcriptomics data

Xinhao Liu
Ron Zeira
Benjamin J. Raphael

First Published August 8, 2023

Method

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

Zeynep Kalender Atak
Ibrahim Ihsan Taskiran
Jonas Demeulemeester
Christopher Flerin
David Mauduit
Liesbeth Minnoye Gert Hulselmans
... [+2 authors] ...,
Valerie Christiaens
Ghanem-Elias Ghanem
Jasper Wouters
Stein Aerts

First Published April 8, 2021

Method

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

Sergey Aganezov
Benjamin J. Raphael

First Published September 4, 2020

Method

Cross-species analysis of enhancer logic using deep learning

Liesbeth Minnoye
Ibrahim Ihsan Taskiran
David Mauduit
Maurizio Fazio
Linde Van Aerschot
Gert Hulselmans Valerie Christiaens Samira Makhzami Monika Seltenhammer Panagiotis Karras Aline Primot Edouard Cadieu Ellen van Rooijen Jean-Christophe Marine Giorgia Egidy
... [+10 authors] ...,
Ghanem-Elias Ghanem
Leonard Zon
Jasper Wouters
Stein Aerts

First Published July 30, 2020

Method

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

Jack Kuipers
Katharina Jahn
Benjamin J. Raphael
Niko Beerenwinkel

First Published October 13, 2017

Method

De novo discovery of mutated driver pathways in cancer

Fabio Vandin
Eli Upfal
Benjamin J. Raphael

First Published June 7, 2011