Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen L, Yan Y, Ecker S, Burden F, Farrow S, Farr B, Iotchkova V, Elding H, Mead D, Tardaguila M, Ponstingl H, Richardson D, Datta A, Flicek P, Clarke L, Downes K, Pastinen T, Fraser P, Frontini M^, Javierre BM^, Spivakov M^, Soranzo N^. Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility. bioRxiv, 2019. doi: 10.1101/620260. ^ – joint senior and corresponding authors.

Mitchelmore J, Grinberg N, Wallace C, Spivakov M. Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters. bioRxiv, 2019. doi: 10.1101/620062.

Malysheva V, Mendoza-Parra MA, Blum M, Spivakov M, Gronemeyer H. Gene regulatory network reconstruction incorporating 3D chromosomal architecture reveals key transcription factors and DNA elements driving neural lineage commitment. bioRxiv, 2019. doi: 10.1101/303842.


Cairns J* / Orchard WR* / Malysheva V*, Spivakov M. Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data. Bioinformatics, 2019. AOP doi: 10.1093/bioinformatics/btz450.


Dobnikar L* / Taylor AL*, Chappell J, Oldach P, Harman JL, Oerton E, Dzierzak E, Bennett MR, Spivakov M^, Jørgensen HF^. Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels. Nature Communications, 2018. 9:4567. * – joint first authors, ^ – joint corresponding authors and supervisors.

Koohy H* / Bolland DJ* / Matheson LS, Schoenfelder S, Stellato C, Dimond A, Várnai C, Chovanec P, Chessa T, Denizot J, Garcia RM, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE^, Varga-Weisz PD^. Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells. Genome Biology, 2018. 19:126. * – joint first authors, ^ – joint corresponding authors.

Choy M-K^, Javierre B-M, Williams S, Baross S, Liu Y, Wingett S, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn P, Spivakov M, Fraser P^, Keavney B^. Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks. Nature Communications, 2018. 9:2526. ^ – joint corresponding authors.


Freire-Pritchett P* / Schoenfelder S*, Várnai C, Wingett SW, Cairns J, Collier AJ, García-Vílchez R, Furlan-Magaril M, Osborne CS, Fraser P, Rugg-Gunn PJ^, Spivakov M^. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. eLife. 2017. doi: 10.7554/eLife.21926.
* – joint first authors, ^ – joint corresponding authors.

Burren OS* / Garcia AR* / Javierre B-M* / Rainbow DB*, Cairns J, Cooper NJ, Lambourne JJ, Schofield E, Dopico XC, Ferreira RC, Coulson R, Burden F, Rowlston SP, Downes K, Wingett SW, Frontini M, Ouwehand WH, Fraser P, Spivakov M, Todd JA^, Wicker LS^, Cutler AJ^, Wallace C^. Chromosome contacts in activated T cells identify autoimmune disease-candidate genes. Genome Biology. 2017. 18:165. * – joint first authors, ^ – joint corresponding authors.

Petersen R* / Lambourne JJ* / Javierre B-M* / Luigi Grassi*, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts A-S, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide M-E, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M^, Ouwehand WH#, Astle WJ#, Downes K#, Kostadima M^#, Frontini M^#. Platelet function is modified by common sequence variation in megakaryocyte super enhancers. Nature Communications. 2017. doi:10.1038/ncomms16058. * – joint first authors, # – jointly supervised the work, ^ – joint corresponding authors.

Rubin A* / Barajas B* / Furlan-Magaril M*, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature Genetics. 2017. doi:10.1038/ng.3935 * Joint first authors.

Siersbæk R* / Madsen JGS* / Javierre B-M* / Nielsen R*, Bagge EK, Cairns J, Wingett SW, Traynor S, Spivakov M, Fraser P^, Mandrup M^. Dynamic rewiring of promoter-Anchored chromatin loops during adipocyte differentiation. Molecular Cell. 2017. doi: 10.1016/j.molcel.2017.04.010. * – joint first authors, ^ – joint corresponding authors.


Javierre B-M* / Burren OS* / Wilder SP* / Kreuzhuber R* / Hill SM*, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, The BLUEPRINT Consortium , Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M^ / Wallace C^ / Spivakov M^# / Fraser P^. Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters Cell. 2016. 147:1369–1384. * – joint first authors, ^ – joint corresponding authors, # – lead contact.
•  Minireview presenting this paper.    •  Interview to Cambridge TV.

Cairns J* / Freire-Pritchett P*, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre B-M, Osborne C, Fraser P, Spivakov M. CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data. Genome Biology. 2016. 17:127. PMID: 27306882. F1000 Prime recommended paper. * – joint first authors.

Bolland DJ* / Koohy H*, Wood AL, Matheson LS, Krueger F, Stubbington MJT, Baizan-Edge A, Chovanec P, Stubbs BA, Tabbada K, Andrews SR, Spivakov M^ / Corcoran AE^. Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination. Cell Reports. 2016. 15(11):2475–2487. PMID: 27264181. * – joint first authors; ^ – joint corresponding authors. F1000 Prime recommended paper.

Spivakov M, Fraser P. Defining cell type with chromatin profiling. Nature Biotechnology. 2016. 34(11):1126-1128. PMID: 27824844. (A News and Views article).

Pancaldi V, Carrillo-de-Santa-Pau E, Javierre B-M, Juan D, Fraser P, Spivakov M, Valencia A, Rico D. Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity. Genome Biology. 2016. 17:152. PMID: 27391817.

Schofield EC, Carver T, Achuthan P, Freire-Pritchett P, Spivakov M, Todd JA and Burren OS. CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets. Bioinformatics. 2016. PMID: 27153610.

Wilson N, Schoenfelder S, Hannah R, Castillo MS, Schütte J, Ladopoulos V, Mitchelmore J, Goode DK, Calero-Nieto FJ, Moignard V, Wilkinson AC, Jimenez-Madrid I, Kinston S, Spivakov M, Fraser P, Göttgens B. Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model. Blood. 2016. 127:e12-e23. PMID: 26809507.


Joshi O* / Wang SY*, Kuznetsova T, Atlasi Y, Peng T, Fabre PJ, Habibi E, Shaik J, Saeed S, Handoko L, Richmond T, Spivakov M, Burgess D, Stunnenberg HG. Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency. Cell Stem Cell. 2015. 17(6):748–757. PMID: 26637943.

Petrini E, Baillet V, Cridge J, Hogan CJ, Guillaume C, Ke H, Brandetti E, Walker S, Koohy H, Spivakov M, Varga-Weisz P. A novel phosphate-starvation response in fission yeast requires the endocytic function of Myosin I. Journal of Cell Science. 2015. 128(20):3707-13. PMID: 26345368.


Spivakov M. Spurious transcription factor binding: Non-functional or genetically redundant? BioEssays. 2014 36(8):798-806. PMID: 24888900.

Koohy H, Down T, Spivakov M, Hubbard T. A comparison of peak callers used for DNase-seq data. PLOS ONE. 2014 9(5):e96303. 10.1371/journal.pone.0096303. PMID: 24810143.

Spivakov M* / Auer TO*, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J. Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish. G3. 2014 4(3):433-445. 10.1534/g3.113.008722. PMID: 24408034. * – joint first authors.

Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Nesterova TB, Green C, Otte AP, Schermelleh L, Brockdorff N. Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy. PNAS. 2014 111(6):2235-2240. 10.1073/pnas.1312951111. PMID: 24469834.


Ferreirós-Vidal I, Carroll T, Taylor B, Terry A, Liang Z, Bruno L, Dharmalingam G, Khadayate S, Cobb BS, Smale ST, Spivakov M, Srivastava P, Petretto E, Fisher AG, Merkenschlager M. Genome-wide identification of Ikaros targets elucidates its contribution to mouse B-cell lineage specification and pre-B-cell differentiation. Blood. 2013 Mar 7;121(10):1769-82. PMID: 23303821.


Spivakov M^, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E^. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol. 2012 Sep 28;13(9):R49. PMID: 22950968. ^ – joint corresponding authors.

Junion G* / Spivakov M*, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell. 2012 Feb 3;148(3):473-86. PMID: 22304916. * – joint first authors.


Landeira D* / Sauer S*, Poot R, Dvorkina M, Mazzarella L, Jørgensen HF, Pereira CF, Leleu M, Piccolo FM, Spivakov M, Brookes E, Pombo A, Fisher C, Skarnes WC, Snoek T, Bezstarosti K, Demmers J, Klose RJ, Casanova M, Tavares L, Brockdorff N, Merkenschlager M, Fisher AG. 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. Nat Cell Biol. 2010 Jun;12(6):618-24. PMID: 20473294.

Sauer S, Bruno L, Hertweck A, Finlay D, Leleu M, Spivakov M, Knight ZA, Cobb BS, Cantrell D, O’Connor E, Shokat KM, Fisher AG, Merkenschlager M. T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR. Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7797-802. PMID: 18509048.

Parelho V* / Hadjur S*, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C, Webster Z, Nesterova T, Cobb BS, Yokomori K, Dillon N, Aragon L, Fisher AG, Merkenschlager M. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell. 2008 Feb 8;132(3):422-33. PMID: 18237772. recommended paper.

Jørgensen HF, Azuara V, Amoils S, Spivakov M, Terry A, Nesterova T, Cobb BS, Ramsahoye B, Merkenschlager M, Fisher AG. The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells. Genome Biol. 2007;8(8):R169. PMID: 17705870.

Spivakov M, Fisher AG. Epigenetic signatures of stem-cell identity. Nat Rev Genet. 2007 Apr;8(4):263-71. Review. PMID: 17363975.

* – joint first authors.
^ – joint corresponding authors.