Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Berglund, Emelie, Maaskola, Jonas, Schultz, Niklas, Friedrich, Stefanie, Marklund, Maja, Bergenstråhle, Joseph, Tarish, Firas, Tanoglidi, Anna, Vickovic, Sanja, Larsson, Ludvig, Salmén, Fredrik, Ogris, Christoph, Wallenborg, Karolina, Lagergren, Jens, Ståhl, Patrik, Sonnhammer, Erik, Helleday, Thomas, Lundeberg, Joakim
Published in Nature communications (20.06.2018)
Published in Nature communications (20.06.2018)
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Journal Article
ToMExO: A probabilistic tree-structured model for cancer progression
Mohaghegh Neyshabouri, Mohammadreza, Lagergren, Jens
Published in PLoS computational biology (01.12.2022)
Published in PLoS computational biology (01.12.2022)
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Journal Article
Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes
Ullah, Ikram, Karthik, Govindasamy-Muralidharan, Alkodsi, Amjad, Kjällquist, Una, Stålhammar, Gustav, Lövrot, John, Martinez, Nelson-Fuentes, Lagergren, Jens, Hautaniemi, Sampsa, Hartman, Johan, Bergh, Jonas
Published in The Journal of clinical investigation (01.04.2018)
Published in The Journal of clinical investigation (01.04.2018)
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Journal Article
Computational Cancer Biology: An Evolutionary Perspective
Beerenwinkel, Niko, Greenman, Chris D, Lagergren, Jens
Published in PLoS computational biology (04.02.2016)
Published in PLoS computational biology (04.02.2016)
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Journal Article
Scuphr: A probabilistic framework for cell lineage tree reconstruction
Koptagel, Hazal, Jun, Seong-Hwan, Hård, Joanna, Lagergren, Jens
Published in PLoS computational biology (01.05.2024)
Published in PLoS computational biology (01.05.2024)
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Journal Article
Inferring tumor progression in large datasets
Mohaghegh Neyshabouri, Mohammadreza, Jun, Seong-Hwan, Lagergren, Jens
Published in PLoS computational biology (09.10.2020)
Published in PLoS computational biology (09.10.2020)
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Journal Article
Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
Geras, Agnieszka, Darvish Shafighi, Shadi, Domżał, Kacper, Filipiuk, Igor, Rączkowski, Łukasz, Szymczak, Paulina, Toosi, Hosein, Kaczmarek, Leszek, Koperski, Łukasz, Lagergren, Jens, Nowis, Dominika, Szczurek, Ewa
Published in Genome Biology (17.05.2023)
Published in Genome Biology (17.05.2023)
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Journal Article
A-to-I editing of microRNAs in the mammalian brain increases during development
Ekdahl, Ylva, Farahani, Hossein Shahrabi, Behm, Mikaela, Lagergren, Jens, Öhman, Marie
Published in Genome research (01.08.2012)
Published in Genome research (01.08.2012)
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Journal Article
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
Åkerborg, Örjan, Sennblad, Bengt, Arvestad, Lars, Lagergren, Jens
Published in Proceedings of the National Academy of Sciences - PNAS (07.04.2009)
Published in Proceedings of the National Academy of Sciences - PNAS (07.04.2009)
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Journal Article
SUMOylation mediates the nuclear translocation and signaling of the IGF-1 receptor
Sehat, Bita, Tofigh, Ali, Lin, Yingbo, Trocmé, Eric, Liljedahl, Ulrika, Lagergren, Jens, Larsson, Olle
Published in Science signaling (09.02.2010)
Published in Science signaling (09.02.2010)
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Journal Article
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics
Jun, Seong-Hwan, Toosi, Hosein, Mold, Jeff, Engblom, Camilla, Chen, Xinsong, O'Flanagan, Ciara, Hagemann-Jensen, Michael, Sandberg, Rickard, Aparicio, Samuel, Hartman, Johan, Roth, Andrew, Lagergren, Jens
Published in Nature communications (22.02.2023)
Published in Nature communications (22.02.2023)
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Journal Article
Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests
Frånberg, Mattias, Gertow, Karl, Hamsten, Anders, Lagergren, Jens, Sennblad, Bengt
Published in PLoS genetics (01.09.2015)
Published in PLoS genetics (01.09.2015)
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Journal Article
Genome-wide survey for biologically functional pseudogenes
Svensson, Orjan, Arvestad, Lars, Lagergren, Jens
Published in PLoS computational biology (01.05.2006)
Published in PLoS computational biology (01.05.2006)
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Journal Article
Fast and general tests of genetic interaction for genome-wide association studies
Frånberg, Mattias, Strawbridge, Rona J, Hamsten, Anders, de Faire, Ulf, Lagergren, Jens, Sennblad, Bengt
Published in PLoS computational biology (01.06.2017)
Published in PLoS computational biology (01.06.2017)
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Journal Article
Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response
Iglesias, Maria Jesus, Jesus Iglesias, Maria, Reilly, Sarah-Jayne, Emanuelsson, Olof, Sennblad, Bengt, Pirmoradian Najafabadi, Mohammad, Folkersen, Lasse, Mälarstig, Anders, Lagergren, Jens, Eriksson, Per, Hamsten, Anders, Odeberg, Jacob
Published in PloS one (27.02.2012)
Published in PloS one (27.02.2012)
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Journal Article
Birth-death prior on phylogeny and speed dating
Akerborg, Orjan, Sennblad, Bengt, Lagergren, Jens
Published in BMC evolutionary biology (04.03.2008)
Published in BMC evolutionary biology (04.03.2008)
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Journal Article
Correction: Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response
Jesus Iglesias, Maria, Reilly, Sarah-Jayne, Emanuelsson, Olof, Sennblad, Bengt, Pirmoradian Najafabadi, Mohammad, Folkersen, Lasse, Mälarstig, Anders, Lagergren, Jens, Eriksson, Per, Hamsten, Anders, Odeberg, Jacob
Published in PloS one (13.04.2012)
Published in PloS one (13.04.2012)
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