Journal ArticleDOI
ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays.
Yifang Hu,Gordon K. Smyth +1 more
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TLDR
ELDA is a software application for limiting dilution analysis (LDA), with particular attention to the needs of stem cell assays, which is the first limiting dilutions analysis software to provide meaningful confidence intervals for all LDA data sets, including those with 0% or 100% responses.About:
This article is published in Journal of Immunological Methods.The article was published on 2009-08-15. It has received 1645 citations till now.read more
Citations
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Endothelial and perivascular cells maintain haematopoietic stem cells
TL;DR: HSCs reside in a perivascular niche in which multiple cell types express factors that promote HSC maintenance, and were depleted from bone marrow when Scf was deleted from endothelial cells or leptin receptor (Lepr)-expressing periv vascular stromal cells.
Journal ArticleDOI
Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia
Liran I. Shlush,Sasan Zandi,Amanda Mitchell,Weihsu Claire Chen,Joseph M. Brandwein,Vikas Gupta,James A. Kennedy,Aaron D. Schimmer,Andre C. Schuh,Karen W.L. Yee,Jessica McLeod,Monica Doedens,Jessie J. F. Medeiros,Rene Marke,Hyeoung Joon Kim,Kwon Lee,John Douglas Mcpherson,Thomas J. Hudson,Andrew M.K. Brown,Fouad Yousif,Quang M. Trinh,Lincoln Stein,Mark D. Minden,Jean C.Y. Wang,John E. Dick +24 more
TL;DR: Highly purified haematopoietic stem cells, progenitor and mature cell fractions from the blood of AML patients were found to contain recurrent DNMT3A mutations at high allele frequency, but without coincident NPM1 mutations (NPM1c) present in AML blasts.
Journal ArticleDOI
Normal and neoplastic nonstem cells can spontaneously convert to a stem-like state
Christine L. Chaffer,Ines Brueckmann,Christina Scheel,Alicia J. Kaestli,Paul A. Wiggins,Leonardo O. Rodrigues,Mary W. Brooks,Ferenc Reinhardt,Ying Su,Kornelia Polyak,Lisa M. Arendt,Charlotte Kuperwasser,Brian Bierie,Robert A. Weinberg +13 more
TL;DR: It is demonstrated that normal and CSC-like cells can arise de novo from more differentiated cell types and that hierarchical models of mammary stem cell biology should encompass bidirectional interconversions between stem and nonstem compartments.
Journal ArticleDOI
DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts.
David Roulois,Helen Loo Yau,Helen Loo Yau,Rajat Singhania,Yadong Wang,Arnavaz Danesh,Shu Yi Shen,Han Han,Gangning Liang,Peter A. Jones,Trevor J. Pugh,Trevor J. Pugh,Catherine A. O’Brien,Catherine A. O’Brien,Catherine A. O’Brien,Daniel D. De Carvalho,Daniel D. De Carvalho +16 more
TL;DR: It is demonstrated that low-dose 5-AZA-CdR targets colorectal cancer-initiating cells (CICs) by inducing viral mimicry, and the MDA5/MAVS/IRF7 pathway is highlighted as a potentially druggable target against CICs.
Journal ArticleDOI
Identification of the tumour transition states occurring during EMT
Ievgenia Pastushenko,Audrey Brisebarre,Alejandro Sifrim,Alejandro Sifrim,Marco Fioramonti,Tatiana Revenco,Soufiane Boumahdi,Alexandra Van Keymeulen,Daniel Brown,Virginie Moers,Sophie Lemaire,Sarah De Clercq,Esmeralda Minguijón,Cédric Balsat,Youri Sokolow,Christine Dubois,Florian De Cock,Samuel Scozzaro,Federico Sopena,Angel Lanas,Nicky D'Haene,Isabelle Salmon,Jean-Christophe Marine,Thierry Voet,Thierry Voet,Panagiota A. Sotiropoulou,Cédric Blanpain +26 more
TL;DR: A large panel of cell surface markers in skin and mammary primary tumours is screened, and the existence of multiple tumour subpopulations associated with different EMT stages are identified: from epithelial to completely mesenchymal states, passing through intermediate hybrid states.
References
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Book
Generalized Linear Models
Peter McCullagh,John A. Nelder +1 more
TL;DR: In this paper, a generalization of the analysis of variance is given for these models using log- likelihoods, illustrated by examples relating to four distributions; the Normal, Binomial (probit analysis, etc.), Poisson (contingency tables), and gamma (variance components).
Journal ArticleDOI
A Simple Sequentially Rejective Multiple Test Procedure
TL;DR: In this paper, a simple and widely accepted multiple test procedure of the sequentially rejective type is presented, i.e. hypotheses are rejected one at a time until no further rejections can be done.
Journal ArticleDOI
Generalized Linear Models
TL;DR: In this paper, the authors used iterative weighted linear regression to obtain maximum likelihood estimates of the parameters with observations distributed according to some exponential family and systematic effects that can be made linear by a suitable transformation.
Journal ArticleDOI
Generalized linear models. 2nd ed.
Peter McCullagh,John A. Nelder +1 more
TL;DR: A class of statistical models that generalizes classical linear models-extending them to include many other models useful in statistical analysis, of particular interest for statisticians in medicine, biology, agriculture, social science, and engineering.