Works by Spivakov, Mikhail

Results: 24

A Comparison of Peak Callers Used for DNase-Seq Data.

Published in:

PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0096303

By:

Koohy, Hashem;
Down, Thomas A.;
Spivakov, Mikhail;
Hubbard, Tim

Publication type:

Article

Publisher Correction: Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07887-3

By:

Dobnikar, Lina;
Taylor, Annabel L.;
Chappell, Joel;
Oldach, Phoebe;
Harman, Jennifer L.;
Oerton, Erin;
Dzierzak, Elaine;
Bennett, Martin R.;
Spivakov, Mikhail;
Jørgensen, Helle F.

Publication type:

Article

Author Correction: Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07399-0

By:

Choy, Mun-Kit;
Javierre, Biola M.;
Williams, Simon G.;
Baross, Stephanie L.;
Liu, Yingjuan;
Wingett, Steven W.;
Akbarov, Artur;
Wallace, Chris;
Freire-Pritchett, Paula;
Rugg-Gunn, Peter J.;
Spivakov, Mikhail;
Fraser, Peter;
Keavney, Bernard D.

Publication type:

Article

Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06891-x

By:

Dobnikar, Lina;
Taylor, Annabel L.;
Chappell, Joel;
Oldach, Phoebe;
Harman, Jennifer L.;
Oerton, Erin;
Dzierzak, Elaine;
Bennett, Martin R.;
Spivakov, Mikhail;
Jørgensen, Helle F.

Publication type:

Article

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-04931-0

By:

Mun-Kit Choy;
Javierre, Biola M.;
Williams, Simon G.;
Baross, Stephanie L.;
Yingjuan Liu;
Wingett, Steven W.;
Akbarov, Artur;
Wallace, Chris;
Freire-Pritchett, Paula;
Rugg-Gunn, Peter J.;
Spivakov, Mikhail;
Fraser, Peter;
Keavney, Bernard D.

Publication type:

Article

Distinct Promoters Mediate the Regulation of Ebf1 Gene Expression by Interleukin-7 and Pax5.

Published in:

Molecular & Cellular Biology, 2007, v. 27, n. 2, p. 14, doi. 10.1128/MCB.01192-06

By:

Roessler, Stephanie;
Györy, Ildiko;
Imhof, Sascha;
Spivakov, Mikhail;
Williams, Ruth R.;
Busslinger, Meinrad;
Fisher, Amanda G.;
Grosschedl, Rudolf

Publication type:

Article

Epigenetic signatures of stem-cell identity.

Published in:

2007

By:

Spivakov, Mikhail;
Fisher, Amanda G.

Publication type:

journal article

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

Published in:

BioEssays, 2014, v. 36, n. 8, p. 798, doi. 10.1002/bies.201400036

By:

Spivakov, Mikhail

Publication type:

Article

Genetic coupling of enhancer activity and connectivity in gene expression control.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-55900-3

By:

Ray-Jones, Helen;
Sung, Chak Kei;
Chan, Lai Ting;
Haglund, Alexander;
Artemov, Pavel;
Della Rosa, Monica;
Ruje, Luminita;
Burden, Frances;
Kreuzhuber, Roman;
Litovskikh, Anna;
Weyenbergh, Eline;
Brusselaers, Zoï;
Tan, Vanessa Xue Hui;
Frontini, Mattia;
Wallace, Chris;
Malysheva, Valeriya;
Bottolo, Leonardo;
Vigorito, Elena;
Spivakov, Mikhail

Publication type:

Article

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells.

Published in:

Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1489-y

By:

Koohy, Hashem;
Bolland, Daniel J.;
Matheson, Louise S.;
Schoenfelder, Stefan;
Stellato, Claudia;
Dimond, Andrew;
Várnai, Csilla;
Chovanec, Peter;
Chessa, Tamara;
Denizot, Jeremy;
Manzano Garcia, Raquel;
Wingett, Steven W.;
Freire-Pritchett, Paula;
Nagano, Takashi;
Hawkins, Phillip;
Stephens, Len;
Elderkin, Sarah;
Spivakov, Mikhail;
Fraser, Peter;
Corcoran, Anne E.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2020, v. 48, n. 6, p. 2866, doi. 10.1093/nar/gkaa123

By:

Mitchelmore, Joanna;
Grinberg, Nastasiya F;
Wallace, Chris;
Spivakov, Mikhail

Publication type:

Article

Cellular mechanisms of oligoclonal vascular smooth muscle cell expansion in cardiovascular disease.

Published in:

Cardiovascular Research, 2023, v. 119, n. 5, p. 1279, doi. 10.1093/cvr/cvac138

By:

Worssam, Matt D;
Lambert, Jordi;
Oc, Sebnem;
Taylor, James C K;
Taylor, Annabel L;
Dobnikar, Lina;
Chappell, Joel;
Harman, Jennifer L;
Figg, Nichola L;
Finigan, Alison;
Foote, Kirsty;
Uryga, Anna K;
Bennett, Martin R;
Spivakov, Mikhail;
Jørgensen, Helle F

Publication type:

Article

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

Published in:

Genome Biology, 2012, v. 13, n. 9, p. 1, doi. 10.1186/gb-2012-13-9-r49

By:

Spivakov, Mikhail;
Akhtar, Junaid;
Kheradpour, Pouya;
Beal, Kathryn;
Girardot, Charles;
Koscielny, Gautier;
Herrero, Javier;
Kellis, Manolis;
Furlong, Eileen E.M.;
Birney, Ewan

Publication type:

Article

A Dynamic Switch in the Replication Timing of Key Regulator Genes in Embryonic Stem Cells upon Neural Induction.

Published in:

Cell Cycle, 2004, v. 3, n. 12, p. 1645, doi. 10.4161/cc.3.12.1346

By:

Perry, Pascale;
Sauer, Stephan;
Billon, Nathalie;
Richardson, William D.;
Spivakov, Mikhail;
Warnes, Gary;
Livesey, Frederick J.;
Merkenschlager, Matthias;
Fisher, Amanda G.;
Azuara, Véronique

Publication type:

Article

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

Published in:

Bioinformatics, 2019, v. 35, n. 22, p. 4764, doi. 10.1093/bioinformatics/btz450

By:

Cairns, Jonathan;
Orchard, William R;
Malysheva, Valeriya;
Spivakov, Mikhail

Publication type:

Article

Chromosome contacts in activated T cells identify autoimmune disease candidate genes.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1285-0

By:

Burren, Oliver S.;
García, Arcadio Rubio;
Javierre, Biola-Maria;
Rainbow, Daniel B.;
Cairns, Jonathan;
Cooper, Nicholas J.;
Lambourne, John J.;
Schofield, Ellen;
Xaquin Castro Dopico;
Ferreira, Ricardo C.;
Coulson, Richard;
Burden, Frances;
Rowlston, Sophia P.;
Downes, Kate;
Wingett, Steven W.;
Frontini, Mattia;
Ouwehand, Willem H.;
Fraser, Peter;
Spivakov, Mikhail;
Todd, John A.

Publication type:

Article

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

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1003-3

By:

Pancaldi, Vera;
Carrillo-de-Santa-Pau, Enrique;
Javierre, Biola Maria;
Juan, David;
Fraser, Peter;
Spivakov, Mikhail;
Valencia, Alfonso;
Rico, Daniel

Publication type:

Article

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0992-2

By:

Cairns, Jonathan;
Freire-Pritchett, Paula;
Wingett, Steven W.;
Várnai, Csilla;
Dimond, Andrew;
Plagnol, Vincent;
Zerbino, Daniel;
Schoenfelder, Stefan;
Javierre, Biola-Maria;
Osborne, Cameron;
Fraser, Peter;
Spivakov, Mikhail

Publication type:

Article

Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.

Published in:

Nature Protocols, 2021, v. 16, n. 9, p. 4144, doi. 10.1038/s41596-021-00567-5

By:

Freire-Pritchett, Paula;
Ray-Jones, Helen;
Della Rosa, Monica;
Eijsbouts, Chris Q.;
Orchard, William R.;
Wingett, Steven W.;
Wallace, Chris;
Cairns, Jonathan;
Spivakov, Mikhail;
Malysheva, Valeriya

Publication type:

Article

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

Published in:

eLife, 2017, p. 1, doi. 10.7554/eLife.21926

By:

Freire-Pritchett, Paula;
Schoenfelder, Stefan;
Vá Rnai, Csilla;
Wingett, Steven W.;
Cairns, Jonathan;
Collier, Amanda J.;
García-Vílchez, Raquel;
Furlan-Magaril, Mayra;
Osborne, Cameron S.;
Fraser, Peter;
Rugg-Gunn, Peter J.;
Spivakov, Mikhail

Publication type:

Article

Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators.

Published in:

Nature Cell Biology, 2010, v. 12, n. 6, p. 618, doi. 10.1038/ncb2065

By:

Landeira, David;
Sauer, Stephan;
Poot, Raymond;
Dvorkina, Maria;
Mazzarella, Luca;
Jørgensen, Helle F.;
Pereira, C. Filipe;
Leleu, Marion;
Piccolo, Francesco M.;
Spivakov, Mikhail;
Brookes, Emily;
Pombo, Ana;
Fisher, Cynthia;
Skarnes, William C.;
Snoek, Tim;
Bezstarosti, Karel;
Demmers, Jeroen;
Klose, Robert J.;
Casanova, Miguel;
Tavares, Ligia

Publication type:

Article

Chromatin signatures of pluripotent cell lines.

Published in:

Nature Cell Biology, 2006, v. 8, n. 5, p. 532, doi. 10.1038/ncb1403

By:

Azuara, Véronique;
Perry, Pascale;
Sauer, Stephan;
Spivakov, Mikhail;
Jørgensen, Helle F.;
John, Rosalind M.;
Gouti, Mina;
Casanova, Miguel;
Warnes, Gary;
Merkenschlager, Matthias;
Fisher, Amanda G.

Publication type:

Article

Defining cell type with chromatin profiling.

Published in:

Nature Biotechnology, 2016, v. 34, n. 11, p. 1126, doi. 10.1038/nbt.3724

By:

Spivakov, Mikhail;
Fraser, Peter

Publication type:

Article

Transcriptional enhancers and their communication with gene promoters.

Published in:

2021

By:

Ray-Jones, Helen;
Spivakov, Mikhail

Publication type:

Literature Review