Publications
RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq
Valentine Svensson, Lior Pachter
Molecular Cell 2018 | doi:10.1016/j.molcel.2018.09.026
SpatialDE: identification of spatially variable genes
Valentine Svensson, Sarah A. Teichmann, Oliver Stegle
Nature Methods 2018 | doi:10.1038/nmeth.4636
In Journal | SpatialDE Software
Exponential scaling of single-cell RNA-seq in the past decade
Valentine Svensson, Roser Vento-Tormo, Sarah A. Teichmann
Nature Protocols (2018) | doi:10.1038/nprot.2017.149
Computational approaches for interpreting scRNA-seq data
Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gözde Kar
FEBS Letters (2017) | doi:10.1002/1873-3468.12684
Power Analysis of Single Cell RNA-Sequencing Experiments
Valentine Svensson, Kedar Nath Natarajan, Lam-Ha Ly, Ricardo Miragaia, Charlotte Labalette, Iain M. Macaulay, Ana Cvejic & Sarah A. Teichmann,
Nature Methods (2017) | doi:10.1038/nmeth.4220
Public Fulltext | In Journal | umis
Software
Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria
Tapio Lönnberg, Valentine Svensson, Kylie R. James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S. F. Soon, Lily G. Fogg, Arya Sheela Nair, Urijah N. Liligeto, Michael J. T. Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D. Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T. Bunn, Christian R. Engwerda, William R. Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A. Teichmann
Science Immunology (2017) | doi:10.1126/sciimmunol.aal2192
Link to Public Fulltext | Companion data site
Single-cell analysis at the threshold
Xi Chen, J Christopher Love, Nicholas E Navin, Lior Pachter, Michael J T Stubbington, Valentine Svensson, Jonathan V Sweedler & Sarah A Teichmann
Nature Biotechnology (2016)
MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs
Mélanie A. Eckersley-Maslin, Valentine Svensson, Christel Krueger, Thomas M. Stubbs, Pascal Giehr, Felix Krueger, Ricardo J. Miragaia, Charalampos Kyriakopoulos, Rebecca V. Berrens, Inês Milagre, Jörn Walter, Sarah A. Teichmann, Wolf Reik
Cell Reports (2016)
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew NJ McKenzie, Ruddy Montandon, Oliver Billker, Steven Woodhouse, Pietro Cicuta, Mario Nicodemi, Sarah A Teichmann,
Genome Biology (2016)
Single cell RNA-sequencing reveals a continuous spectrum of differentiation in haematopoietic cells
Iain C. Macaulay, Valentine Svensson, Charlotte Labalette, Lauren Ferreira, Fiona Hamey, Thierry Voet, Sarah A. Teichmann, Ana Cvejic
Cell Reports (2016) | doi:10.1016/j.celrep.2015.12.082
In Journal | Analysis Notebooks
The Technology and Biology of Single-Cell RNA Sequencing
Aleksandra A Kolodziejczyk, Jong Kyoung Kim, Valentine Svensson, John C. Marioni, Sarah A. Teichmann,
Molecular Cell (2015)
An atlas of mouse CD4+ T cell transcriptomes
Michael J. T. Stubbington, Bidesh Mahata, Valentine Svensson, Andrew Deonarine, Jesper K. Nissen, Alexander G. Betz, Sarah A. Teichmann
Biology direct (2015)
Posters
Mapping scRNA-seq data onto cell type taxonomies
Valentine Svensson, Lior Pachter
Single Cell Genomics 2018
doi: 10.7490/f1000research.1116276.1
SpatialDE – Identification of spatially variable genes
Valentine Svensson, Sarah A Teichmann, Oliver Stegle
EBI Research Retreat 2017
doi: 10.7490/f1000research.1114480.1
Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation
Valentine Svensson, Tapio Lönnberg, Kylie R James, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
Single Cell Genomics Conference 2016, Cambridge
Mathematical and Statistical Aspects of Molecular Biology (MASAMB) 2016, Cambridge
Cell Symposia: Technology. Biology. Data Science. Conference 2016, Berkeley
NIPS Workshop on Machine Learning in Computational Biology (MLCB) 2016, Barcelona
doi: 10.7490/f1000research.1113890.1
Computationally resolving the bifurcation of Th1 and Tfh cell fates with single-cell RNA-sequencing
Valentine Svensson, Tapio Lönnberg, Kylie James, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
EBI-Sanger-Cambridge PhD Symposium (eSCAMPS) 2016, Cambridge
Next Gen Immunology Conference 2016, Tel Aviv
Single Cell Biology Conference 2016, Cambridge
Quantitative Genomics Student Conference 2016, London
EBI Research Retreat 2016
EMBL Lab Day 2016, Heidelberg
doi: 10.7490/f1000research.1113887.1
Using computational topology to study cell cycle in single-cell RNA-seq data
Valentine Svensson, Sarah A Teichmann
EBI Research Retreat 2015
Quantitative Methods in Gene Regulation III 2015, Cambridge
Single Cell Genomics Conference 2015, Utrecht
doi: 10.7490/f1000research.1113889.1
Resolving the cellular hierarchy of thrombocyte lineage development using single cell RNA-Seq
Iain Macauley, Charlotte Labalette, Valentine Svensson, Lauren Ferreira, Fiona K Hamey, Sarah A Teichmann, Ana Cvejic
Single Cell Genomics 2015, Utrecht
2nd Bioinformatics Student Symposium 2015, Norwich
doi: 10.7490/f1000research.1113888.1
Power analysis of single cell RNA-seq experiments using ERCC spike-ins
Valentine Svensson, Sarah A Teichmann
EMBL Predoc Retreat 2014, Plzeň
Single Cell Genomics 2014, Stochkolm
Genome Informatics 2014, Cambridge
doi: 10.7490/f1000research.1113885.1
Single cell RNA sequencing - Teichmann Group
Valentine Svensson
EMBL Lab Day 2014, Heidelberg
doi: 10.7490/f1000research.1113886.1