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2017

Functional and transcriptional heterogeneity of human hemopoietic lympho-myeloid progenitors at the single cell level.

Karamitros D. et al,  (2017) Nature Immunology, In Press

 

Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

Giustacchini A. et al, (2017), Nat Med., Jun;23(6):692-702. doi: 10.1038/nm.4336

 

switchde: inference of switch-like differential expression along single-cell trajectories

Campbell KR, Yau C, (2017),  Bioinformatics, Apr 15;33(8):1241-1242. doi: 10.1093/bioinformatics/btw798

 

Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers

Campbell KR, Yau C,  (2017), Wellcome Open Res. 2017 Mar 15;2:19. doi: 10.12688/wellcomeopenres.11087.1

 

The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq

Wills QF. et al, (2017),  BMC Genomics, Jan 7;18(1):53. doi: 10.1186/s12864-016-3445-0

 

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

McCarthy DJ. et al, (2017), Bioinformatics, Apr 15;33(8):1179-1186. doi: 10.1093/bioinformatics/btw777

 

Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation

Mead AJ. et al, (2017) J Exp Med, Jul 3;214(7):2005-2021. doi: 10.1084/jem.20161418

 

2016

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference

Campbell, K. C. and Yau, C, (2016),  PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1005212

 

pcaReduce: hierarchical clustering of single cell transcriptional profiles

Zurauskiene, J. and Yau, C, (2016), BMC Bioinformatics, DOI: 10.1186/s12859-016-0984-y

 

Initial seeding of the embryonic thymus by immune-restricted lympho-myeloid progenitors

Luis TC. et al, (2016), Nature Immunology, doi:10.1038/ni.3576

 

Genetically distinct leukemic stem cells in human CD34− acute myeloid leukemia are arrested at a hemopoietic precursor-like stagem

Quek L. et al, (2016), The Journal of Experimental Medicine, DOI: 10.1084/jem.20151775

 

Beta-Poisson model for single-cell RNA-seq data analyses

Vu TN. et al, (2016), Bioinformatics, Jul 15;32(14):2128-35. doi: 10.1093/bioinformatics/btw202

 

Statistical approaches and software for clustering islet cell functional heterogeneity

Wills QF, et al, (2-16) Islets, Mar 3;8(2):48-56. doi: 10.1080/19382014.2016.1150664

 

Single-cell profiling of human megakaryocyte-erythroid progenitors identifies distinct megakaryocyte and erythoid differentiation pathways

Psaila, B. et al, (2016), Genome Biology, 17:83 DOI: 10.1186/s13059-016-0939-7

 

Single cell global gene profiling reveals molecular and functional platelet bias of aged hematopoietic stem cells

Grover, A. et al, (2016), Nature Communications, 7, Article number: 11075, doi:10.1038/ncomms11075

 

Single cell RNA sequencing of hematopoietic progenitors identifies distinct myeloid differentiation pathways

Drissen, R.et al, (2016),  Nature Immunology 17, 666–676 doi:10.1038/ni.3412

 

Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics

Handel, A.E. et al, (2016) Human molecular genetics, 25, 989-1000

 

A dynamic niche provides Kit ligand in a stage-specific manner to the earliest thymocyte progenitors

Buono, M. et al, (2016), Nature cell biology, 18, 157-167

 

2015

Application of single-cell genomics in cancer: promise and challenges

Wills, Q.F. and Mead, A.J. (2015), Human molecular genetics, 24, R74-84

 

Studying epigenomics in single cells: what is feasible and what can we learn?

Wills, Q.F., Higgs, D.R. and Mead, A.J. (2015)  Epigenomics, 7, 1231-1234

 

Expanded GAA repeats impair FXN gene expression and reposition the FXN locus to the nuclear lamina in single cells

Silva, A.M. et al, (2015), Human molecular genetics, 24, 3457-3471

 

Dimensionality reduction for zero-inflated single-cell gene expression analysis

Pierson, E. and Yau, C. (2015), ZIFA: Genome biology, 16, 241

 

CalQuo: automated, simultaneous single-cell and population-level quantification of global intracellular Ca(2+) responses

Fritzsche, M.et al, (2015), Scientific reports, 5, 16487

 

2014

Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo

Woll, P.S. et al, (2014), Cancer Cell, 25, 794-808

 

Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification

Wilkinson, A.C. et al, (2014), Development, 141, 4018-4030

 

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data

Tang, X. et al, (2014), Nucleic Acids Research, 42, e172

 

Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

Sansom, S.N.et al, (2014), Genome Research, 24, 1918-1931

 

Erythropoietin guides multipotent hematopoietic progenitor cells toward an erythroid fate

Grover, A.et al, (2014), The Journal of Experimental Medicine, 211, 181-188.

 

2013

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

Wills, Q.F.et al, (2013), Nature Biotechnology, 31, 748-752.

 

Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level

Swiers, G. et al, (2013), Nature Communications, 4, 2924.

 

Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy

Sanjuan-Pla, A. et al, (2013), Nature, 502, 232-236.

 

Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells

Livak, K.J. et al, (2013), Methods, 59, 71-79.

 

Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells

Boiers, C. et al, (2013), Cell Stem Cell, 13, 535-548.

 

2012

The earliest thymic T cell progenitors sustain B cell and myeloid lineage potential

Luc, S. et al, (2012), Nature Immunology, 13, 412-419.