Publications by authors named "Mikhail Spivakov"

37Publications

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers.

Cell Rep 2020 Jul;32(3):107929

Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.107929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383238PMC
July 2020

Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.

Nucleic Acids Res 2020 04;48(6):2866-2879

Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.

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http://dx.doi.org/10.1093/nar/gkaa123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102942PMC
April 2020

Silencers in the spotlight.

Nat Genet 2020 03;52(3):244-245

MRC London Institute of Medical Sciences, London, UK.

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http://dx.doi.org/10.1038/s41588-020-0583-8DOI Listing
March 2020

Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data.

Bioinformatics 2019 11;35(22):4764-4766

Regulatory Genomics Group, Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853696PMC
November 2019

Defining cell type with chromatin profiling.

Nat Biotechnol 2016 11;34(11):1126-1128

Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/nbt.3724DOI Listing
November 2016

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.

Genome Biol 2016 07 8;17(1):152. Epub 2016 Jul 8.

Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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http://dx.doi.org/10.1186/s13059-016-1003-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939006PMC
July 2016

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model.

Blood 2016 Mar 25;127(13):e12-23. Epub 2016 Jan 25.

Department of Haematology, Wellcome Trust and Medical Research Council Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom; and.

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http://dx.doi.org/10.1182/blood-2015-10-677393DOI Listing
March 2016

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency.

Cell Stem Cell 2015 Dec;17(6):748-757

Radboud University, Faculty of Science, Department of Molecular Biology, 6525GA Nijmegen, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.11.010DOI Listing
December 2015

Spurious transcription factor binding: non-functional or genetically redundant?

Authors:
Mikhail Spivakov

Bioessays 2014 Aug 30;36(8):798-806. Epub 2014 May 30.

Babraham Institute, Cambridge, UK.

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http://dx.doi.org/10.1002/bies.201400036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230394PMC
August 2014

A comparison of peak callers used for DNase-Seq data.

PLoS One 2014 8;9(5):e96303. Epub 2014 May 8.

The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096303PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014496PMC
October 2015

Analysis of variation at transcription factor binding sites in Drosophila and humans.

Genome Biol 2012 Sep 28;13(9):R49. Epub 2012 Sep 28.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

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http://dx.doi.org/10.1186/gb-2012-13-9-r49DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491393PMC
September 2012

A transcription factor collective defines cardiac cell fate and reflects lineage history.

Cell 2012 Feb;148(3):473-86

Genome Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.cell.2012.01.030DOI Listing
February 2012

T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR.

Proc Natl Acad Sci U S A 2008 Jun 28;105(22):7797-802. Epub 2008 May 28.

Lymphocyte Development Group, Medical Research Council Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0800928105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2409380PMC
June 2008

Epigenetic signatures of stem-cell identity.

Nat Rev Genet 2007 Apr;8(4):263-71

Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.

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http://regulatorygenomicsgroup.org/resources/spivakov_fisher
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http://dx.doi.org/10.1038/nrg2046DOI Listing
April 2007

Distinct promoters mediate the regulation of Ebf1 gene expression by interleukin-7 and Pax5.

Mol Cell Biol 2007 Jan 13;27(2):579-94. Epub 2006 Nov 13.

Max Planck Institute of Immunobiology, Department of Cellular and Molecular Immunology, 79108 Freiburg, Germany.

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http://dx.doi.org/10.1128/MCB.01192-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800812PMC
January 2007

Chromatin signatures of pluripotent cell lines.

Nat Cell Biol 2006 May 29;8(5):532-8. Epub 2006 Mar 29.

Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK.

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http://dx.doi.org/10.1038/ncb1403DOI Listing
May 2006

A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction.

Cell Cycle 2004 Dec 4;3(12):1645-50. Epub 2004 Dec 4.

Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London, UK.

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December 2004