The Soneji Lab

Faculty of Medicine | Lund University

Introduction

Our lab is rethinking how big-data can be visualised, and since early 2017 have been exploring virtual reality (VR) as a vehicle to convey as much information to the user as possible. Our focus is single-cell gene expression as it produces higher dimensional data that is often reduced to three components, making it the ideal problem on which to implement VR solutions. Given how much single-cell data is being produced, more intuitive methods are needed to allow all researchers to analyse it, and we believe VR may be the key to achieving this.

News & Updates

Follow the latest lab updates below. CellexalVR feature announcements, news segments as well as events where CellexalVR was featured will be posted here.

The Soneji lab wins a project grant from Cancerfonden

The Soneji lab was awarded a 3 year project grant from Cancerfonden to carry on the development of CellexalVR. We thank them for their support!

Reuters news piece

CellexalVR was covered in a Reuters piece as one of two projects at Lund University that use virtual reality to visualise and analyse data.

DATA Panel and audience discussion

CellexalVR was shown at the DATA Theme Meeting that took place at Lund University on June 20th, 2018. Shamit Soneji took part in the panel discussion that covered topics relating to VR and how it can be used in research and education.

Multi-user feature

CellexalVR now features multi-user support. Several users can connect from different places, be in the same virtual environment and analyze data together. In this session there were three users; Shamit Soneji and Johan Rodhe (BMC Lund, Sweden) and Steve Taylor (CBRG Oxford, Weatherall Inst, UK).

Members

Shamit Soneji, PhD

Group Leader

Shamit is the head of the bioinformatics lab at the Division of Molecular Hematology and Lund Stem Cell Center. He obtained his PhD from the University of London. and went on do to postdocs at the Weatherall institute at the University of Oxford, and the Cancer institute at UCL. He was recruited to Lund University in 2013. His research interests focus on single-cell biology, and in particular exploring new methods to visualise big-data.

Email: shamit.soneji@med.lu.se

Phone: +46 46 222 08 72

Stefan Lang, PhD

Postdoctoral Fellow

Stefan has a background (PhD 2008) in genetics and immunology with a focus on the bioInformatic analysis of the produced data, has work experience in epigenetics and transcriptomics. Company experience from 2012 to 2014 and is working in this group since 2014. His main programming languages are R and Perl with an moderate interest in Julia. He is currently interested in single cell expression mainly from the 10x platform and integration of single cell workflow into our Virtual Reality environment.

Email: stefan.lang@med.lu.se

Phone: +46 46 222 08 72

Oscar Legetth

Software Engineer

Oscar has a background in Computer Science and Engineering. He started working in the Soneji lab in 2017 and since then he has been working on developing data visualisation platforms in virtual reality.

Email: oscar.legetth@med.lu.se

Phone: +46 46 222 08 72

Johan Rodhe

Software Engineer

Johan has a background in Computer Science and Engineering. He also started working in the Soneji lab in 2017 and is working on developing data visualisation tools in virtual reality. Additional to developing the virtual environment he is interested in machine learning and computer vision.

Email: johan.rodhe@med.lu.se

Phone: +46 46 222 08 72

Projects

CellexalVR

CellexalVR is a virtual reality platform for the visualisation and analysis of single-cell gene expression data. Analysing data in virtual reality provides a fully immersive environment where the user can visualise and interact with the data without restriction, with a focus on data visibility and point selection.



Website Preprint at bioRxiv

SCExV

Single cell gene expression assays have become a powerful tool with which to dissect heterogeneous populations. While methods and software exist to interrogate such data, what has been lacking is a unified solution combining analysis and visualisation which is also accessible and intuitive for use by non-bioinformaticians, as well as bioinformaticians.


Website Paper

Selected publications

2016

Cellular Barcoding Links B-1a B Cell Potential to a Fetal Hematopoietic Stem Cell State at the Single-Cell Level.

Kristiansen TA, Jaensson Gyllenbäck E, Zriwil A, Björklund T, Daniel JA, Sitnicka E, Soneji S, Bryder D, Yuan J.

Immunity. 2016 Aug 16;45(2):346-57View abstract

Mitotic History Reveals Distinct Stem Cell Populations and Their Contributions to Hematopoiesis.

Säwén P, Lang S, Mandal P, Rossi DJ, Soneji S, Bryder D.

Cell Rep 2016 Mar 29;14(12):2809-18View abstract

2015

SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data.

Lang S, Ugale A, Erlandsson E, Karlsson G, Bryder D, Soneji S.

BMC Bioinformatics. 2015 Oct 5;16:320View abstract

Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.

Pina C, Teles J, Fugazza C, May G, Wang D, Guo Y, Soneji S, Brown J, Edén P, Ohlsson M, Peterson C, Enver T.

Cell Rep. 2015 Jun 16;11(10):1503-10.View abstract

2014

Hematopoietic stem cells are intrinsically protected against MLL-ENL-mediated transformation.

Ugale A, Norddahl GL, Wahlestedt M, Säwén P, Jaako P, Pronk CJ, Soneji S, Cammenga J, Bryder D.

Cell Rep. 2014 Nov 20;9(4):1246-55.View abstract

2013

Dynamic analysis of gene expression and genome-wide transcription factor binding during lineage specification of multipotent progenitors.

*May G, *Soneji S, Tipping AJ, Teles J, McGowan SJ, Wu M, Guo Y, Fugazza C, Brown J, Karlsson G, Pina C, Olariu V, Taylor S, Tenen DG, Peterson C, Enver T. *Joint first author.

Cell Stem Cell. 2013 Dec 5;13(6):754-68.View abstract

2012

Inferring rules of lineage commitment in haematopoiesis.

Pina C, Fugazza C, Tipping AJ, Brown J, Soneji S, Teles J, Peterson C, Enver T.

Nat Cell Biol. 2012 Feb 19;14(3):287-94.View abstract

2011

Coexistence of LMPP-like and GMP-like leukemia stem cells in acute myeloid leukemia.

Goardon N, Marchi E, Atzberger A, Quek L, Schuh A, Soneji S, Woll P, Mead A, Alford KA, Rout R, Chaudhury S, Gilkes A, Knapper S, Beldjord K, Begum S, Rose S, Geddes N, Griffiths M, Standen G, Sternberg A, Cavenagh J, Hunter H, Bowen D, Killick S, Robinson L, Price A, Macintyre E, Virgo P, Burnett A, Craddock C, Enver T, Jacobsen SE, Porcher C, Vyas P.

Cancer Cell. 2011 Jan 18;19(1):138-52.View abstract

Complete list of publications

Our funders