RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq

Valentine Svensson, Lior Pachter

Molecular Cell 2018 | doi:10.1016/j.molcel.2018.09.026

In Journal

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

In Journal

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

In Journal

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

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

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)

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