J
Jens Lagergren
Researcher at Royal Institute of Technology
Publications - 102
Citations - 5049
Jens Lagergren is an academic researcher from Royal Institute of Technology. The author has contributed to research in topics: Tree (data structure) & Phylogenetic tree. The author has an hindex of 37, co-authored 88 publications receiving 4552 citations. Previous affiliations of Jens Lagergren include Science for Life Laboratory & SERC Reliability Corporation.
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DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data
Jose Bonet,Mandi Chen,Mandi Chen,Marc Dabad,Simon Heath,Abel Gonzalez-Perez,Nuria Lopez-Bigas,Nuria Lopez-Bigas,Jens Lagergren,Jens Lagergren +9 more
TL;DR: DeepMP as mentioned in this paper is a CNN-based model that takes information from Nanopore signals and base-calling errors to detect whether a given motif in a read is methylated or not, and it introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells.
Journal ArticleDOI
Motif Yggdrasil: sampling sequence motifs from a tree mixture model.
TL;DR: The Motif Yggdrasil sampler is described; the first Gibbs sampler based on a general tree that uses unaligned sequences and it is shown that the MY model improves the modeling of difficult motif instances and that the use of the tree achieves a substantial increase in nucleotide level correlation coefficient.
Posted ContentDOI
Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue
Camilla Engblom,Kim Thrane,Qirong Lin,Alma Andersson,Hosein Toosi,Xinsong Chen,Embla Steiner,Giulia Mantovani,Michael Hagemann-Jensen,Sami Saarenpää,Mattias Jangard,Jakob Michaëlsson,Johan Hartman,Jens Lagergren,Jeff E. Mold,Joakim Lundeberg,Jonas Frisén +16 more
TL;DR: Spatial transcriptomics of VDJ sequences (Spatial VDJ) as mentioned in this paper was developed to map immunoglobulin and TR antigen receptors in human tissue sections, which can capture lymphocyte spatial clonal architecture across tissues, which could have important therapeutic implications.
Journal ArticleDOI
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.
Jose Bonet,Mandi Chen,Mandi Chen,Marc Dabad,Simon Heath,Abel Gonzalez-Perez,Nuria Lopez-Bigas,Nuria Lopez-Bigas,Jens Lagergren,Jens Lagergren +9 more
TL;DR: DeepMP as discussed by the authors is a CNN-based model that takes information from Nanopore signals and base-calling errors to detect whether a given motif in a read is methylated or not, and it introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells.
Journal ArticleDOI
Fast and general tests of genetic interaction for genome-wide association studies
Mattias Frånberg,Mattias Frånberg,Mattias Frånberg,Rona J. Strawbridge,Anders Hamsten,Ulf de Faire,Ulf de Faire,Jens Lagergren,Jens Lagergren,Jens Lagergren,Bengt Sennblad,Bengt Sennblad +11 more
TL;DR: Computationally efficient tests of interaction for the complete family of generalized linear models (GLMs) are presented and it is shown that jointly testing the full set of interaction parameters yields superior power and control of false positive rate.