OSCBC Publications

2017

Karamitros D, Stoilova B, Aboukhalil Z, Hamey F, Reinisch A, Samitsch M, Quek L, Otoo G, Repapi E, Donndeea J, Usukhbayar B, Calvo J, Taylor S, Goardon N, Six E, Pflumio F, Porcher C, Majet R, Gottgens B, Vyas P. Functional and transcriptional heterogeneity of human hemopoietic lympho-myeloid progenitors at the single cell level. Nature Immunology. In Press. (2017).

Giustacchini A, Thongjuea S, Barkas N, Woll PS, Povinelli BJ, Booth CAG, Sopp P, Norfo R, Rodriguez-Meira A, Ashley N, Jamieson L, Vyas P, Anderson K, Segerstolpe Å, Qian H, Olsson-Strömberg U, Mustjoki S, Sandberg R, Jacobsen SEW, Mead AJ.  Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nat Med. 2017 Jun;23(6):692-702. doi: 10.1038/nm.4336

Campbell KR, Yau C. switchde: inference of switch-like differential expression along single-cell trajectories. Bioinformatics. 2017 Apr 15;33(8):1241-1242. doi: 10.1093/bioinformatics/btw798.

Campbell KR, Yau C.  Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. Wellcome Open Res. 2017 Mar 15;2:19. doi: 10.12688/wellcomeopenres.11087.1.

Wills QF, Mellado-Gomez E, Nolan R, Warner D, Sharma E, Broxholme J, Wright B, Lockstone H, James W, Lynch M, Gonzales M, West J, Leyrat A, Padilla-Parra S, Filippi S, Holmes C, Moore MD, Bowden R. The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq. BMC Genomics. 2017 Jan 7;18(1):53. doi: 10.1186/s12864-016-3445-0.

McCarthy DJ, Campbell KR, Lun AT, Wills QF.  Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics. 2017 Apr 15;33(8):1179-1186. doi: 10.1093/bioinformatics/btw777.

Mead AJ, Neo WH, Barkas N, Matsuoka S, Giustacchini A, Facchini R, Thongjuea S, Jamieson L, Booth CAG, Fordham N, Di Genua C, Atkinson D, Chowdhury O, Repapi E, Gray N, Kharazi S, Clark SA, Bouriez T, Woll P, Suda T, Nerlov C, Jacobsen SEW.  Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation. J Exp Med. 2017 Jul 3;214(7):2005-2021. doi: 10.1084/jem.20161418

2016

Campbell, K. C. and Yau, C. (2016) Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference. PLOS Computational Biology. DOI: 10.1371/journal.pcbi.1005212

Zurauskiene, J. and Yau, C. (2016) pcaReduce: hierarchical clustering of single cell transcriptional profiles. BMC Bioinformatics. DOI: 10.1186/s12859-016-0984-y

Tiago C. Lui1, Sidinh Luc,Takuo Mizukami, Hanane Boukarabila, Supat Thongjuea, Petter S. Woll, Emanuele Azzoni, Alice Giustacchini, Michael Lutteropp, Tiphaine Bouriez-Jones, Harsh Vaidya, Adam J. Mead, Deborah Atkinson, Charlotta Böiers, Joana Carrelha, Iain C. Macaulay, Roger Patient, Frederic Geissmann, Claus Nerlov, Rickard Sandberg, Marella F.T.R. de Bruijn, C. Clare Blackburn, Isabelle Godin, Sten Eirik W. Jacobsen. Initial seeding of the embryonic thymus by immune-restricted lympho-myeloid progenitors, Nature Immunology, doi:10.1038/ni.3576

Lynn Quek,  Georg W. Otto, Catherine Garnett,  Ludovic Lhermitte, Dimitris Karamitros, Bilyana Stoilova,  I-Jun Lau, Jessica Doondeea,  Batchimeg Usukhbayar, Alison Kennedy, Marlen Metzner,  Nicolas Goardon, Adam Ivey,  Christopher Allen,  Rosemary Gale,  Benjamin Davies, Alexander Sternberg,  Sally Killick, Hannah Hunter, Paul Cahalin, Andrew Price, Andrew Carr,  Mike Griffiths, Paul Virgo,  Stephen Mackinnon, David Grimwade, Sylvie Freeman, Nigel Russell,  Charles Craddock, Adam Mead,  Andrew Peniket,  Catherine Porcher, Paresh Vyas, Genetically distinct leukemic stem cells in human CD34− acute myeloid leukemia are arrested at a hemopoietic precursor-like stagem, The Journal of Experimental Medicine, DOI: 10.1084/jem.20151775, 2016

 
Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Rantalainen M, Pawitan Y. Beta-Poisson model for single-cell RNA-seq data analyses. Bioinformatics. 2016 Jul 15;32(14):2128-35. doi: 10.1093/bioinformatics/btw202. 
 
Wills QF, Boothe T, Asadi A, Ao Z, Warnock GL, Kieffer TJ, Johnson JD.
Statistical approaches and software for clustering islet cell functional heterogeneityIslets. 2016 Mar 3;8(2):48-56. doi: 10.1080/19382014.2016.1150664.

Psaila, B., Barkas, B.*, Iskander, D.*, Roy, A., Anderson, S., Ashley, N., Caputo, V.S., Lichtenberg, J., Loaiza, S., Bodine, D., Karadimitris, A., Mead, A.J.* and Roberts, I.* Single-cell profiling of human megakaryocyte-erythroid progenitors identifies distinct megakaryocyte and erythoid differentiation pathways. Genome Biology, 2016; 17:83 DOI: 10.1186/s13059-016-0939-7

Grover, A.*, Sanjuan-Pla, A.*, Thongjuea, S., Carrelha, J., Giustacchini, A., Gambardella, A., Macaulay, I., Mancini, E., Luis, T., Mead, A.J., Jacobsen, S.E.* and Nerlov, C.* Single cell global gene profiling reveals molecular and functional platelet bias of aged hematopoietic stem cells. Nature Communications, 20167, Article number: 11075, doi:10.1038/ncomms11075

Drissen, R., Buza-Vidas, N., Thongjuea, S., Giustacchini, A., Mead, A.J., Mancini, E., Lutteropp, M., Grover, A., Jacobsen, S.E.* and Nerlov, C*. Single cell RNA sequencing of hematopoietic progenitors identifies distinct myeloid differentiation pathways. Nature Immunology 17, 666–676 (2016) doi:10.1038/ni.3412

Handel, A.E., Chintawar, S., Lalic, T., Whiteley, E., Vowles, J., Giustacchini, A., Argoud, K., Sopp, P., Nakanishi, M., Bowden, R. et al. (2016) Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics. Human molecular genetics, 25, 989-1000.

Buono, M., Facchini, R., Matsuoka, S., Thongjuea, S., Waithe, D., Luis, T.C., Giustacchini, A., Besmer, P., Mead, A.J., Jacobsen, S.E.* and Nerlov, C.*. (2016) A dynamic niche provides Kit ligand in a stage-specific manner to the earliest thymocyte progenitors. Nature cell biology, 18, 157-167.

2015

Wills, Q.F. and Mead, A.J. (2015) Application of single-cell genomics in cancer: promise and challenges. Human molecular genetics, 24, R74-84.

Wills, Q.F., Higgs, D.R. and Mead, A.J. (2015) Studying epigenomics in single cells: what is feasible and what can we learn? Epigenomics, 7, 1231-1234.

Silva, A.M., Brown, J.M., Buckle, V.J., Wade-Martins, R. and Lufino, M.M. (2015) Expanded GAA repeats impair FXN gene expression and reposition the FXN locus to the nuclear lamina in single cells. Human molecular genetics, 24, 3457-3471.

Pierson, E. and Yau, C. (2015) ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome biology, 16, 241.

Fritzsche, M., Fernandes, R.A., Colin-York, H., Santos, A.M., Lee, S.F., Lagerholm, B.C., Davis, S.J. and Eggeling, C. (2015) CalQuo: automated, simultaneous single-cell and population-level quantification of global intracellular Ca(2+) responses. Scientific reports, 5, 16487.

2014

Woll, P.S., Kjallquist, U., Chowdhury, O., Doolittle, H., Wedge, D.C., Thongjuea, S., Erlandsson, R., Ngara, M., Anderson, K., Deng, Q. et al. (2014) Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo. Cancer cell, 25, 794-808.

Wilkinson, A.C., Kawata, V.K., Schutte, J., Gao, X., Antoniou, S., Baumann, C., Woodhouse, S., Hannah, R., Tanaka, Y., Swiers, G. et al. (2014) Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification. Development, 141, 4018-4030.

Tang, X., Baheti, S., Shameer, K., Thompson, K.J., Wills, Q., Niu, N., Holcomb, I.N., Boutet, S.C., Ramakrishnan, R., Kachergus, J.M. et al. (2014) The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. Nucleic acids research, 42, e172.

Sansom, S.N., Shikama-Dorn, N., Zhanybekova, S., Nusspaumer, G., Macaulay, I.C., Deadman, M.E., Heger, A., Ponting, C.P. and Hollander, G.A. (2014) Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. Genome research, 24, 1918-1931.

Grover, A., Mancini, E., Moore, S., Mead, A.J., Atkinson, D., Rasmussen, K.D., O'Carroll, D., Jacobsen, S.E. and Nerlov, C. (2014) Erythropoietin guides multipotent hematopoietic progenitor cells toward an erythroid fate. The Journal of experimental medicine, 211, 181-188.

2013

Wills, Q.F., Livak, K.J., Tipping, A.J., Enver, T., Goldson, A.J., Sexton, D.W. and Holmes, C. (2013) Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nature biotechnology, 31, 748-752.

Swiers, G., Baumann, C., O'Rourke, J., Giannoulatou, E., Taylor, S., Joshi, A., Moignard, V., Pina, C., Bee, T., Kokkaliaris, K.D. et al. (2013) Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level. Nature communications, 4, 2924.

Sanjuan-Pla, A., Macaulay, I.C., Jensen, C.T., Woll, P.S., Luis, T.C., Mead, A., Moore, S., Carella, C., Matsuoka, S., Bouriez Jones, T. et al. (2013) Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy. Nature, 502, 232-236.

Livak, K.J., Wills, Q.F., Tipping, A.J., Datta, K., Mittal, R., Goldson, A.J., Sexton, D.W. and Holmes, C.C. (2013) Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells. Methods, 59, 71-79.

Boiers, C., Carrelha, J., Lutteropp, M., Luc, S., Green, J.C., Azzoni, E., Woll, P.S., Mead, A.J., Hultquist, A., Swiers, G. et al. (2013) Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells. Cell stem cell, 13, 535-548.

2012

Luc, S., Luis, T.C., Boukarabila, H., Macaulay, I.C., Buza-Vidas, N., Bouriez-Jones, T., Lutteropp, M., Woll, P.S., Loughran, S.J., Mead, A.J. et al. (2012) Nature immunology, 13, 412-419.