Chen H, We Y, Ruje L, Wan Q, Spivakov M, Glebov O. Rapid long-range synaptic remodeling in hyperacute ischemic stroke. bioRxiv 2024 doi: https://doi.org/10.1101/2024.12.12.628225.

Ng HL, Glaser TL, Robinson ME, Cosgun KN, Malysheva V, …, Sun L, Spivakov M, Mueschen M, Feldhahn N. Unraveling BCR::ABL1-driven enhancer activation and transcriptional reprogramming in Ph B-ALL. Research square 2024, doi: 10.21203/rs.3.rs-5326686/v1.

Tardaguila M, Von Schiller D, Colombo M, Gori I, Coomber EL, Vanderstichele T, Benaglio P, Chiereghin C, Gerety S, Vuckovic D, Landini A, Clerici G, Albers P, Ray-Jones H, Burnham KL, Tokolyi A, Persyn E, Spivakov M, Sankaran VG, Walter K, Kundu K, Pirastu N, Inouye M, Paul DS, Davenport EE, Sahlén P, Watt S, Soranzo N. Variant-to-function dissection of rare non-coding GWAS loci with high impact on blood traits. bioRxiv 2024. doi: 10.1101/2024.08.05.606572.

Ray-Jones H#, Sung CK, Chan LT, Haglund A, Artemov P, Della Rosa M, Burden F, …, Frontini
M, Wallace C, Malysheva V$, Bottolo L$#, Vigorito E$, Spivakov M$#. Shared and distinct molecular effects of regulatory genetic variants provide insight into mechanisms of distal
enhancer-promoter communication. bioRxiv, 2023. doi: 2023.08.04.551251. (# Joint corresponding authors; $ Joint supervisors).

Malysheva V / Ray-Jones H, Cazares TA / Clay O / Ohayon D / Artemov P, Wayman JA, Della Rosa M, Petitjean C, Booth C, Ellaway JIJ, Orchard W, Chen X, Parameswaran S, Nagano T, Fraser P, Schoenfelder S, Weirauch M, Kottyan LC, Smith DF, Powell N, Weimer J, Wallace C, Miraldi ER, Waggoner S, Spivakov M. High-resolution promoter interaction analysis in Type 3 Innate Lymphoid Cells implicates Batten Disease gene CLN3 in Crohn’s Disease aetiology. bioRxiv, 2022. doi: 10.1101/2022.10.19.512842.

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.

Lambert J / Oc S, Worssam MD, Häußler D, Figg NL, Baxter R, Foote K, Finigan A, Mahbubani, KT, Bennett MR, Krüger A, Spivakov M, Jørgensen HF. Network-based prioritisation and validation of novel regulators of vascular smooth muscle cell proliferation in disease. Nature Cardiovascular Research, 2024. https://doi.org/10.1038/s44161-024-00474-4

Worssam MD / Lambert J / Oc S, Taylor AL, Dobnikar L, Chappell J, Harman JL, Figg NL, Finigan A, Foote K, Uryga AK, Bennett MR, Spivakov M, Jørgensen HF. Cellular mechanisms of oligoclonal vascular smooth muscle cell expansion in cardiovascular disease. Cardiovascular Res, 2022. AOP doi: 10.1093/cvr/cvac138.

Ray-Jones H, Spivakov M. Brief encounters: The relationship between enhancer proximity and gene expression. Dev Cell, 2022. 57: 1439-1441. doi: 10.1016/j.devcel.2022.05.020 (A news & views article).

Thiecke M / Yang E, Burren O, Ray-Jones H#, Spivakov M#. Prioritization of putative target genes underpinning COVID-19 host genetic traits based on high-resolution 3D chromosomal topology. Front Genet, 2021. 12:745672. https://doi.org/10.3389/fgene.2021.745672.

Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci, 2021. 8:6453-6485. (A review article).

Freire-Pritchett P / Ray-Jones H, Della Rosa M, Eijsbouts C, Orchard WR, Wingett SW, Wallace C, Cairns J, Spivakov M#, Malysheva V#. Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools. Nature Protocols, 2021. 16: 4144–4176. # – joint corresponding authors with a postdoc in the lab.

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#^. Genetic perturbation in PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease. Nature Communications, 2021. 12:2298. # – joint senior authors, ^ – joint corresponding authors.

Ho JSY* / Mok BW-Y*, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zeyu Z, Zheng S, Zhao N, White K, Ray-Jones H, Malysheva V, Thiecke MJ, Lau S-Y, Liu H, Zhang AJ, Lee AC-Y, Liu W-C, Jangra S, Escalera A, Aydillo T, Melo BS, Guccione E, Sebra R, Shum E, Bakker J, Kaufman DA, Moreira AL, Carossino M, Balasuriya UBR, Byun M, Albrecht RA, Schotsaert M, Garcia-Sastre A, Chanda SK, Miraldi ER, Jeyasekharan AD, TenOever BR, Spivakov M, Weirauch MT, Heinz S, Chen H, Benner C, Richt JA, Marazzi I. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell, 2021. AOP DOI: https://doi.org/10.1016/j.cell.2021.03.051. * – joint first authors. • Press release.

Malysheva V, Schoenfelder S, Spivakov M, Nagano T, Fraser P. Novel method. Patent application WO/2021/064430, international filing date 05.10.2020, publication date 08.04.2021. (International patent application).

Thiecke M* / Wutz G*, Muhar M, Tang W, Bevan S, Malysheva V, Stocsits R, Neumann T, Zuber J, Fraser P, Schoenfelder S, Peters J-M#, Spivakov M#^. Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers. Cell Reports, 2020. 32, 107929. * – joint first authors, # – joint senior authors, ^ – corresponding author.

Mitchelmore J, Grinberg N, Wallace C, Spivakov M. Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters. Nucleic Acids Res, 2020. AOP doi: 10.1093/nar/gkaa123.

Della Rosa M, Spivakov M. Silencers in the spotlight. Nat Genet, 2020. AOP doi:10.1038/s41588-020-0583-8. (A News and Views article).description

Cairns J* / Orchard WR* / Malysheva V*, Spivakov M. Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data. Bioinformatics, 2019. 35:4764–4766.

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.

Item descriptionFreire-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.

Item 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. http://dx.doi.org/10.1093/bioinformatics/btw173. 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. http://dx.doi.org/10.1182/blood-2015-10-677393. PMID: 26809507.description

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. description

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.description

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.escription

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. description