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Unraveling intratumoral heterogeneity through high-sensitivity single-cell mutational analysis and parallel RNA sequencing.

Rodriguez-Meira A. et al, (2019), Molecular Cell, In Press.


Expression of the plasma cell transcriptional regulator Blimp-1 by dark zone germinal center B cells during periods of proliferation.

Radtke D. et al, (2019), Front Immunol, doi: 10.3389/fimmu.2018.03106


From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo.

Lukoseviciute M. et al (2018), Dev Cell, Dec 3;47(5):608-628.e6. doi: 10.1016/j.devcel.2018.11.009.


Does osteogenic potential of clonal human bone marrow mesenchymal stem/stromal cells correlate with their vascular supportive ability?

Merryweather-Clarke AT. et al, (2018), Stem Cell Res Ther, Dec 19;9(1):351. doi: 10.1186/s13287-018-1095-7.


Invasive salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets.

Aulicino A. et al, (2018), Nat Commun, Nov 19;9(1):4883. doi: 10.1038/s41467-018-07329-0.


Structural remodeling of the human colonic mesenchyme in inflammatory bowel disease.

Kinchen J. et al, (2018), Cell, Oct 4;175(2):372-386.e17. doi: 10.1016/j.cell.2018.08.067. 


Single-molecule DNA-mapping and whole-genome sequencing of individual cells.

Marie R. et al, (2018), Proc Natl Acad USA, Oct 30;115(44):11192-11197. doi: 10.1073/pnas.1804194115. 


Germinal center B cells replace their antigen receptors in dark zones and fail light zone entry when immunoglobulin gene mutations are damaging.

Stewart I. et al, (2018), Immunity, Sep 18;49(3):477-489.e7.  doi: 10.1016/j.immuni.2018.08.025.


Kit ligand has a critical role in mouse yolk sac and aorta-gonad-mesonephros hematopoiesis.

Azzoni E. et al, (2018), EMBO Reports, doi: 10.15252/embr.201745477


Hierarchically related lineage-restricted fates of multipotent haematopoietic  stem cells.

Carrelha J. et al, (2018), Nature, Feb 1;554(7690):106-111. doi: 10.1038/nature25455.  


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



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, 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



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, al, (2015), Scientific reports, 5, 16487



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, al, (2014), Genome Research, 24, 1918-1931


Erythropoietin guides multipotent hematopoietic progenitor cells toward an erythroid fate

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



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

Wills, 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.



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

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