Cuartero S, Weiss FD, Dharmalingam G, Guo Y, Ing-Simmons E, Masella S, Robles-Rebollo I, Xiao X, Wang YF, Barozzi I, Djeghloul D, Amano MT, Niskanen H, Petretto E, Dowell RD, Tachibana K, Kaikkonen MU, Nasmyth KA, Lenhard B, Natoli G, Fisher AG, Merkenschlager M. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat Immunol. 2018 Sep;19(9):932-941. doi: 10.1038/s41590-018-0184-1

Albert JR, Koike T, Younesy H, Thompson R, Bogutz AB, Karimi MM*, Lorincz MC* (*Co-corresponding author). Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA). BMC Genomics 15;19(1):463. doi: 10.1186/s12864-018-4835-2 (2018).

Cantone I, Dharmalingam G, Chan YW, Kohler AC, Lenhard B, Merkenschlager M, Fisher AG. Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation. Genome Biol. 2017 Jan 25;18(1):2.

Hudry B, Khadayate S, Miguel-Aliaga I. The sexual identity of adult intestinal stem cells controls organ size and plasticity. Nature. 2016 Feb;530(7590):344-8.

Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM*, Möller T* (*Co-corresponding author). ChAsE: chromatin analysis and exploration tool. Bioinformatics. 2016 Nov 1;32(21):3324-3326.

Younesy H, Möller T, Lorincz MC, Karimi MM*, Jones SJ* (*Co-corresponding author). VisRseq: R-based visual framework for analysis of sequencing data. BMC Bioinformatics. 2015;16 Suppl 11:S2.

Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM*, Jones SJ* (*Co-corresponding author). ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics. 2014 Apr 15;30(8):1172-1174.

Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, Lorincz MC. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell. 2011 Jun 3;8(6):676-87.

2018

Cuartero S, Weiss FD, Dharmalingam G, Guo Y, Ing-Simmons E, Masella S, Robles-Rebollo I, Xiao X, Wang YF, Barozzi I, Djeghloul D, Amano MT, Niskanen H, Petretto E, Dowell RD, Tachibana K, Kaikkonen MU, Nasmyth KA, Lenhard B, Natoli G, Fisher AG, Merkenschlager M. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat Immunol. 2018 Sep;19(9):932-941. doi: 10.1038/s41590-018-0184-1

Webster P, Dawes J, Dewchand H, Takacs K, Iadarola B, Bolt B, Caceres J, Kaczor J, Dharmalingam G, Dore M, Game L, Adejumo T, Elliott J, Naresh K, Karimi MM, Rekopoulou K, Tan G, Paccanaro A, Uren A. Subclonal mutation selection in mouse lymphoma genesis identifies known cancer loci and suggests novel candidates. Nature Communications 9;9(1):2649. doi: 10.1038/s41467-018-05069-9 (2018).

Brind'Amour J, Kobayashi K, Albert JR, Shirane K, Sakashita A, Kamio A, Bogutz A, Koike T, Karimi MM, Lefebvre L, Kono T, Lorincz MC. LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. In presse in Nature Communications.

Albert JR, Koike T, Younesy H, Thompson R, Bogutz AB, Karimi MM*, Lorincz MC* (*Co-corresponding author). Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA). BMC Genomics 15;19(1):463. doi: 10.1186/s12864-018-4835-2 (2018).

Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. eLife 2018;7:e33084 DOI: 10.7554/eLife.33084 (2018).

Georgilis A, Klotz S, Hanley CJ, Herranz N, Weirich B, Morancho B, Leote AC, D'Artista L, Gallage S, Seehawer M, Carroll T, Dharmalingam G, Wee KB, Mellone M, Pombo J, Heide D, Guccione E, Arribas J, Barbosa-Morais NL, Heikenwalder M, Thomas GJ, Zender L, Gil J. PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells. Cancer Cell. 2018 Jul 9;34(1):85-102.e9.

Hill PWS, Leitch HG, Requena CE, Sun Z, Amouroux R, Roman-Trufero M, Borkowska M, Terragni J, Vaisvila R, Linnett S, Bagci H, Dharmalingham G, Haberle V, Lenhard B, Zheng Y, Pradhan S, Hajkova P. Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte. Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte. Nature. 2018 Mar 15;555(7696):392-396.

Judson RN, Quarta M, Oudhoff MJ, Soliman H, Yi L, Chang CK, Loi G, Vander Werff R, Cait A, Hamer M, Blonigan J, Paine P, Doan LTN, Groppa E, He WJ, Su L, Zhang RH, Xu P, Eisner C, Low M, Barta I, Lewis CAB, Zaph C, Karimi MM, Rando TA, Rossi FM. Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential. Cell Stem Cell 22, 1–14 February 1, 2018.


2017

Chen CCL, Goyal P, Karimi MM, Abildgaard MH, Kimura H, Lorincz MC. H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2. Genome Research. 2017 December 11, 2017, doi:10.1101/gr.224717.117.

Wolf G, Rebollo R, Karimi MM, Ewing AD, Kamada R, Wu W, Wu B, Bachu M, Ozato K, Faulkner GF, Mager DL, Lorincz MC, Macfarlan TS. On the role of H3.3 in retroviral silencing. Nature. 2017 doi:10.1038/nature23277.

Fisher CL, Marks H, Cho LT, Andrews R, Wormald S, Carroll T, Iyer V, Tate P, Rosen B, Stunnenberg HG, Fisher AG, Skarnes WC. An efficient method for generation of bi-allelic null mutant mouse embryonic stem cells and its application for investigating epigenetic modifiers. Nucleic Acids Res. 2017 Dec 1;45(21):e174.

Aarts M, Georgilis A, Beniazza M, Beolchi P, Banito A, Carroll T, Kulisic M, Kaemena DF, Dharmalingam G, Martin N, Reik W, Zuber J, Kaji K, Chandra T, Gil J. Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence. Genes Dev. 2017 Oct 15;31(20):2085-2098.

Clements MP, Byrne E, Camarillo Guerrero LF, Cattin AL, Zakka L, Ashraf A, Burden JJ, Khadayate S, Lloyd AC, Marguerat S, Parrinello S. The Wound Microenvironment Reprograms Schwann Cells to Invasive Mesenchymal-like Cells to Drive Peripheral Nerve Regeneration. Neuron. 2017 Sep 27;96(1):98-114.e7.

Lock FE, Babaian A, Zhang Y, Gagnier L, Kuah S, Weberling A, Karimi MM, Mager DL, A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer. PLoS One, Jul 17;12(7):e0180659.

Liang Z, Brown KE, Carroll T, Taylor B, Vidal IF, Hendrich B, Rueda D, Fisher AG, Merkenschlager M. A high-resolution map of transcriptional repression. Elife. 2017 Mar 20;6. pii: e22767.

Cantone I, Dharmalingam G, Chan YW, Kohler AC, Lenhard B, Merkenschlager M, Fisher AG. Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation. Genome Biol. 2017 Jan 25;18(1):2.


2016

Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM*, Möller T*. ChAsE: chromatin analysis and exploration tool. Bioinformatics. 2016 Nov 1;32(21):3324-3326.

Tordella L, Khan S, Hohmeyer A, Banito A, Klotz S, Raguz S, Martin N, Dhamarlingam G, Carroll T, González Meljem JM, Deswal S, Martínez-Barbera JP, García-Escudero R, Zuber J, Zender L, Gil J. SWI/SNF regulates a transcriptional program that induces senescence to prevent liver cancer. Genes Dev. 2016 Oct 1;30(19):2187-2198.

Cantone I, Bagci H, Dormann D, Dharmalingam G, Nesterova T, Brockdorff N, Rougeulle C, Vallot C, Heard E, Chaligne R, Merkenschlager M, Fisher AG. Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming. Nat Commun. 2016 Aug 10;7:12354.

Krusche B, Ottone C, Clements MP, Johnstone ER, Goetsch K, Lieven H, Mota SG, Singh P, Khadayate S, Ashraf A, Davies T, Pollard SM, De Paola V, Roncaroli F, Martinez-Torrecuadrada J, Bertone P, Parrinello S. EphrinB2 drives perivascular invasion and proliferation of glioblastoma stem-like cells. Elife. 2016 Jun 28;5. pii: e14845.

Sharif J, Endo T, Nakayama M, Karimi MM, Shimada M, Katsuyama K, Goyal P, BrindAmour J, Sun M, Sun Z, Ishikura T, Mizutani-Koseki Y, Ohara O, Shinkai Y, Nakanishi M, Xie H, Lorincz MC & Koseki H. Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing. Cell Stem Cell. 2016 Jul 7;19(1):81-94.

Graham B, Marcais A, Dharmalingam G, Carroll T, Kanellopoulou C, Graumann J, Nesterova TB, Bermange A, Brazauskas P, Xella B, Kriaucionis S, Higgs DR, Brockdorff N, Mann M, Fisher AG, Merkenschlager M. MicroRNAs of the miR-290-295 Family Maintain Bivalency in Mouse Embryonic Stem Cells. Stem Cell Reports. 2016 May 10;6(5):635-42.

Babaian A, Romanish MT, Gagnier L, Kuo LY, Karimi MM, Steidl C, Mager DL. Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma. Oncogene. 2016 May 12;35(19):2542-6.

Hudry B, Khadayate S, Miguel-Aliaga I. The sexual identity of adult intestinal stem cells controls organ size and plasticity. Nature. 2016 Feb 18;530(7590):344-8.


2015

Tomlinson JA, Caplin B, Boruc O, Bruce-Cobbold C, Cutillas P, Dormann D, Faull P, Grossman RC, Khadayate S, Mas VR, Nitsch DD, Wang Z, Norman JT, Wilcox CS,Wheeler DC, Leiper J. Reduced Renal Methylarginine Metabolism Protects against Progressive Kidney Damage. J Am Soc Nephrol. 2015 Dec;26(12):3045-59.

Nashun B, Hill PW, Smallwood SA, Dharmalingam G, Amouroux R, Clark SJ, Sharma V, Ndjetehe E, Pelczar P, Festenstein RJ, Kelsey G, Hajkova P. Continuous Histone Replacement by Hira Is Essential for Normal Transcriptional Regulation and De Novo DNA Methylation during Mouse Oogenesis. Mol Cell. 2015 Nov 19;60(4):611-25.

Bitton DA, Schubert F, Dey S, Okoniewski M, Smith GC, Khadayate S, Pancaldi V, Wood V, Bähler J. AnGeLi: A Tool for the Analysis of Gene Lists from FissionYeast. Front Genet. 2015 Nov 16;6:330. doi: 10.3389/fgene.2015.00330. eCollection 2015.

Herranz N, Gallage S, Mellone M, Wuestefeld T, Klotz S, Hanley CJ, Raguz S, Acosta JC, Innes AJ, Banito A, Georgilis A, Montoya A, Wolter K, Dharmalingam G, Faull P, Carroll T, Martínez-Barbera JP, Cutillas P, Reisinger F, Heikenwalder M, Miller RA, Withers D, Zender L, Thomas GJ, Gil J. mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype. Nat Cell Biol. 2015 Sep;17(9).

Younesy H, Möller T, Lorincz MC, Karimi MM*, Jones SJ*. VisRseq: R-based visual framework for analysis of sequencing data.BMC Bioinformatics. 2015;16 Suppl 11:S2.

Landeira D, Bagci H, Malinowski AR, Brown KE, Soza-Ried J, Feytout A, Webster Z, Ndjetehe E, Cantone I, Asenjo HG, Brockdorff N, Carroll T, Merkenschlager M, Fisher AG. Jarid2 Coordinates Nanog Expression and PCP/Wnt Signaling Required for Efficient ESC Differentiation and Early Embryo Development. Cell Rep. 2015 Jul 28;12(4):573-86.

Lambden S, Kelly P, Ahmetaj-Shala B, Wang Z, Lee B, Nandi M, Torondel B,Delahaye M, Dowsett L, Piper S, Tomlinson J, Caplin B, Colman L, Boruc O,Slaviero A, Zhao L, Oliver E, Khadayate S, Singer M, Arrigoni F, Leiper J. Dimethylarginine dimethylaminohydrolase 2 regulates nitric oxide synthesis and hemodynamics and determines outcome in polymicrobial sepsis. Arterioscler Thromb.Vasc Biol. 2015 Jun;35(6):1382-92.

Bon H, Wadhwa K, Schreiner A, Osborne M, Carroll T, Ramos-Montoya A, Ross-Adams H, Visser M, Hoffmann R, Ahmed AA, Neal DE, Mills IG. Salt-inducible kinase 2 regulates mitotic progression and transcription in prostate cancer. Mol Cancer Res. 2015 Apr;13(4):620-35.

Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M. Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin. Genome Res. 2015 Apr;25(4):504-13. doi: 10.1101/gr.184986.114.

Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, Stojic L, Halim S, Vowler SL, Lynch AG, Delatte B, de Bony EJ, Colin L, Defrance M, Krueger F, Silva AL, Ten Hoopen R, Ibrahim AE, Fuks F, Murrell A. 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Genome Biol. 2015 Apr 1;16:69.

Blevins R, Bruno L, Carroll T, Elliott J, Marcais A, Loh C, Hertweck A, Krek A, Rajewsky N, Chen CZ, Fisher AG, Merkenschlager M.microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes. PLoS Genet. 2015 Feb 25;11(2).

Brind'Amour J, Liu S, Hudson M, Chen C, Karimi MM, Lorincz MC. An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat Commun. 2015 Jan 21;6:6033.

Thompson PJ, Dulberg V, Moon KM, Foster LJ, Chen C, Karimi MM, Lorincz MC. hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells. PLoS Genet. 2015 Jan 22;11(1):e1004933.

Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M. Initiation and maintenance of pluripotency gene expression in the absence of cohesin. Genes Dev. 2015 Jan 1;29(1):23-38.

Lavagnolli T, Gupta P, Hörmanseder E, Mira-Bontenbal H, Dharmalingam G, Carroll T, Gurdon JB, Fisher AG, Merkenschlager M. Initiation and maintenance of pluripotency gene expression in the absence of cohesin. Genes Dev. 2015 Jan 1;29(1):23-38.


2014

Marcais A, Blevins R, Graumann J, Feytout A, Dharmalingam G, Carroll T, Amado IF, Bruno L, Lee K, Walzer T, Mann M, Freitas AA, Boothby M, Fisher AG, Merkenschlager M. microRNA-mediated regulation of mTOR complex components facilitates discrimination between activation and anergy in CD4 T cells. J Exp Med. 2014 Oct 20;211(11):2281-95.

Liu S, Brind'Amour J, Karimi MM, Shirane K, Bogutz A, Lefebvre L, Sasaki H, Shinkai Y, Lorincz MC. Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells. Genes Dev. 2014 Sep 15;28(18):2041-55.

Lock FE, Rebollo R, Miceli-Royer K, Gagnier L, Kuah S, Babaian A, Sistiaga-Poveda M, Lai CB, Nemirovsky O, Serrano I, Steidl C, Karimi MM, Mager DL. Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):E3534-43.

Carroll TS,Rasinger JD, Lundebye AK, Hogstrand C. Cross-omics gene and protein expression profiling in juvenile female mice highlights disruption of calcium and zinc signalling in the brain following dietary exposure to CB-153, BDE-47, HBCD or TCDD. Toxicology. 2014 Jul 3;321:1-12.

Ramos-Montoya A, Lamb AD, Russell R, Carroll T, Jurmeister S, Galeano-Dalmau N, Massie CE, Boren J, Bon H, Theodorou V, Vias M, Shaw GL, Sharma NL, Ross-Adams H, Scott HE, Vowler SL, Howat WJ, Warren AY, Wooster RF, Mills IG, Neal DE. HES6 drives a critical AR transcriptional programme to induce castration-resistant prostate cancer through activation of an E2F1-mediated cell cycle network. EMBO Mol Med. 2014 May 1;6(5):651-61.

Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM*, Jones SJ*. ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics. 2014 Apr 15;30(8):1172-1174.

Carroll TS, Liang Z, Salama R, Stark R, de Santiago I. Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data. Front Genet. 2014 Apr 10;5:75.

Sabbattini P, Sjoberg M, Nikic S, Frangini A, Holmqvist PH, Kunowska N, Carroll T, Brookes E, Arthur SJ, Pombo A, Dillon N. An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation. Mol Biol Cell. 2014 Mar;25(6):904-15.

Lamb AD,Ramos-Montoya A,Russell R,Carroll T,Massie CE,Shaw GL,Sharma NL,Warren AY,Mills IG,Neal DE. Role of Hes6 in castration-resistant prostate cancer. The Lancet 2014 Jan;383:S67.

Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, di Bernardo D. A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders. BMC Genomics. 2014;15 Suppl 3:S5.


2013

Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype. Robinson JL, Hickey TE, Warren AY, Vowler SL, Carroll T, Lamb AD, Papoutsoglou N, Neal DE, Tilley WD, Carroll JS. Oncogene. 2013 Dec 2.

Frangini A, Sjöberg M, Roman-Trufero M, Dharmalingam G, Haberle V, Bartke T, Lenhard B, Malumbres M, Vidal M, Dillon N. The aurora B kinase and the polycomb protein ring1B combine to regulate active promoters in quiescent lymphocytes. Mol Cell. 2013 Sep 12;51(5):647-61.

Blaschke K, Ebata KT, Karimi MM, Zepeda-Martínez JA, Goyal P, Mahapatra S, Tam A, Laird DJ, Hirst M, Rao A, Lorincz MC, Ramalho-Santos M. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature. 2013 Aug 8;500(7461):222-6.

Sadaie M, Salama R, Carroll T, Tomimatsu K, Chandra T, Young AR, Narita M, Pérez-Mancera PA, Bennett DC, Chong H, Kimura H, Narita M. Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence. Genes Dev. 2013 Aug 15;27(16):1800-8.

Acosta JC, Banito A, Wuestefeld T, Georgilis A, Janich P, Morton JP, Athineos D, Kang TW, Lasitschka F, Andrulis M, Pascual G, Morris KJ, Khan S, Jin H, Dharmalingam G, Snijders AP, Carroll T, Capper D, Pritchard C, Inman GJ, Longerich T, Sansom OJ, Benitah SA, Zender L, Gil J. A complex secretory program orchestrated by the inflammasome controls paracrine senescence. Nat Cell Biol. 2013 Aug;15(8):978-90.

Martin N, Raguz S, Dharmalingam G, Gil J. Co-regulation of senescence-associated genes by oncogenic homeobox proteins and polycomb repressive complexes. Cell Cycle. 2013 Jul 15;12(14):2194-9.

Chan PK, Torres R, Yandim C, Law PP, Khadayate S, Mauri M, Grosan C, Chapman-Rothe N, Giunti P, Pook M, Festenstein R. Heterochromatinization induced by GAA-repeat hyperexpansion in Friedreich's ataxia can be reduced upon HDAC inhibition by vitamin B3. Hum Mol Genet. 2013 Jul 1;22(13):2662-75.

Dietary exposure of juvenile female mice to polyhalogenated seafood contaminants (HBCD, BDE-47, PCB-153, TCDD): comparative assessment of effects in potential target tissues. Maranghi F, Tassinari R, Moracci G, Altieri I, Rasinger JD, Carroll TS, Hogstrand C, Lundebye AK, Mantovani A. Food Chem Toxicol. 2013 Jun;56:443-9.

Maksakova IA, Thompson PJ, Goyal P, Jones SJ, Singh PB, Karimi MM, Lorincz MC. Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics Chromatin. 2013 Jun 4;6(1):15.

French JD, Ghoussaini M, Edwards SL, Meyer KB, Michailidou K, Ahmed S, Khan S, Maranian MJ, O'Reilly M, Hillman KM, Betts JA, Carroll T, Bailey PJ, Dicks E, Beesley J, Tyrer J, Maia AT, Beck A, Knoblauch NW, Chen C, Kraft P, Barnes D, González-Neira A, Alonso MR, Herrero D, Tessier DC, Vincent D, Bacot F, Luccarini C, Baynes C, Conroy D, Dennis J, Bolla MK, Wang Q, Hopper JL, Southey MC, Schmidt MK, Broeks A, Verhoef S, Cornelissen S, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Fasching PA, Loehberg CR, Ekici AB, Beckmann MW, Peto J, dos Santos Silva I, Johnson N, Aitken Z, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, Marme F, Schneeweiss A, Sohn C, Burwinkel B, Guénel P, Truong T, Laurent-Puig P, Menegaux F, Bojesen SE, Nordestgaard BG, Nielsen SF, Flyger H, Milne RL, Zamora MP, Arias Perez JI, Benitez J, Anton-Culver H, Brenner H, Müller H, Arndt V, Stegmaier C, Meindl A, Lichtner P, Schmutzler RK, Engel C, Brauch H, Hamann U, Justenhoven C; GENICA Network, Aaltonen K, Heikkilä P, Aittomäki K, Blomqvist C, Matsuo K, Ito H, Iwata H, Sueta A, Bogdanova NV, Antonenkova NN, Dörk T, Lindblom A, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM; kConFab Investigators, Wu AH, Tseng CC, Van Den Berg D, Stram DO, Lambrechts D, Peeters S, Smeets A, Floris G, Chang-Claude J, Rudolph A, Nickels S, Flesch-Janys D, Radice P, Peterlongo P, Bonanni B, Sardella D, Couch FJ, Wang X, Pankratz VS, Lee A, Giles GG, Severi G, Baglietto L, Haiman CA, Henderson BE, Schumacher F, Le Marchand L, Simard J, Goldberg MS, Labrèche F, Dumont M, Teo SH, Yip CH, Ng CH, Vithana EN, Kristensen V, Zheng W, Deming-Halverson S, Shrubsole M, Long J, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Andrulis IL, Knight JA, Glendon G, Mulligan AM, Devilee P, Seynaeve C, García-Closas M, Figueroa J, Chanock SJ, Lissowska J, Czene K, Klevebring D, Schoof N, Hooning MJ, Martens JW, Collée JM, Tilanus-Linthorst M, Hall P, Li J, Liu J, Humphreys K, Shu XO, Lu W, Gao YT, Cai H, Cox A, Balasubramanian SP, Blot W, Signorello LB, Cai Q, Pharoah PD, Healey CS, Shah M, Pooley KA, Kang D, Yoo KY, Noh DY, Hartman M, Miao H, Sng JH, Sim X, Jakubowska A, Lubinski J, Jaworska-Bieniek K, Durda K, Sangrajrang S, Gaborieau V, McKay J, Toland AE, Ambrosone CB, Yannoukakos D, Godwin AK, Shen CY, Hsiung CN, Wu PE, Chen ST, Swerdlow A, Ashworth A, Orr N, Schoemaker MJ, Ponder BA, Nevanlinna H, Brown MA, Chenevix-Trench G, Easton DF, Dunning AM. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. Am J Hum Genet. 2013 Apr 4;92(4):489-503.

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.

Leitch HG, McEwen KR, Turp A, Encheva V, Carroll T, Grabole N, Mansfield W, Nashun B, Knezovich JG, Smith A, Surani MA, Hajkova P. Naive pluripotency is associated with global DNA hypomethylation. Nat Struct Mol Biol. 2013 Mar;20(3):311-6.

Martin N, Popov N, Aguilo F, O'Loghlen A, Raguz S, Snijders AP, Dharmalingam G, Li S, Thymiakou E, Carroll T, Zeisig BB, So CW, Peters G, Episkopou V, Walsh MJ, Gil J. Interplay between Homeobox proteins and Polycomb repressive complexes in p16INK⁴a regulation. EMBO J. 2013 Apr 3;32(7):982-95.

Peluso I, Conte I, Testa F, Dharmalingam G, Pizzo M, Collin RW, Meola N, Barbato S, Mutarelli M, Ziviello C, Barbarulo AM, Nigro V, Melone MA; European Retinal Disease Consortium, Simonelli F, Banfi S. The ADAMTS18 gene is responsible for autosomal recessive early onset severe retinal dystrophy. Orphanet J Rare Dis. 2013 Jan 28;8:16.

Hamid Younesy, Cydney Nielsen, Torsten Möller, Olivia Alder, Rebecca Cullum, Matthew Lorincz, Mohammad M. Karimi, Steven M. Jones. An interactive analysis & exploration tool for epigenetic data. Computer Graphics Forum (EuroVis) 32 (number 3), 92–93 (2013).


2012

Haubner BJ, Adamowicz-Brice M, Khadayate S, Tiefenthaler V, Metzler B, Aitman T, Penninger JM. Complete cardiac regeneration in a mouse model of myocardial infarction. Aging (Albany NY). 2012 Dec;4(12):966-77.

Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell. 2012 Jul 27;47(2):203-14.

Gennarino VA, D'Angelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges R, Mutarelli M, Belcastro V, Ballabio A, Verde P, Sardiello M, Banfi S. Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res. 2012 Jun;22(6):1163-72.

Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell. 2012 Feb 3;10(2):157-70.

O'Loghlen A, Muñoz-Cabello AM, Gaspar-Maia A, Wu HA, Banito A, Kunowska N, Racek T, Pemberton HN, Beolchi P, Lavial F, Masui O, Vermeulen M, Carroll T, Graumann J, Heard E, Dillon N, Azuara V, Snijders AP, Peters G, Bernstein E, Gil J. MicroRNA regulation of Cbx7 mediates a switch of Polycomb orthologs during ESC differentiation. Cell Stem Cell. 2012 Jan 6;10(1):33-46.


2011

Belcastro V, Siciliano V, Gregoretti F, Mithbaokar P, Dharmalingam G, Berlingieri S, Iorio F, Oliva G, Polishchuck R, Brunetti-Pierri N, di Bernardo D. Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. Nucleic Acids Res. 2011 Nov 1;39(20):8677-88.

Cerebral gene expression and neurobehavioural development after perinatal exposure to an environmentally relevant polybrominated diphenylether (BDE47). Haave M, Folven KI, Carroll T, Glover C, Heegaard E, Brattelid T, Hogstrand C, Lundebye AK. Cell Biol Toxicol. 2011 Oct;27(5):343-61.

Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, Goyal P, Keane TM, Jones S, Hirst M, Lorincz MC, Mager DL. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet. 2011 Sep;7(9):e1002301.

Seitan VC, Hao B, Tachibana-Konwalski K, Lavagnolli T, Mira-Bontenbal H, Brown KE, Teng G, Carroll T, Terry A, Horan K, Marks H, Adams DJ, Schatz DG, Aragon L, Fisher AG, Krangel MS, Nasmyth K, Merkenschlager M. A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation. Nature. 2011 Aug 10;476(7361):467-71.

Gennarino VA, Sardiello M, Mutarelli M, Dharmalingam G, Maselli V, Lago G, Banfi S. HOCTAR database: a unique resource for microRNA target prediction. Gene. 2011 Jul 1;480(1-2):51-8.

Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, Lorincz MC. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell. 2011 Jun 3;8(6):676-87.


2010

Arvind Gupta, Gregory Gutin, Mohammad M. Karimi, Eun J. Kim, Arash Rafiey. Minimum Cost Homomorphisms to Locally Semicomplete and Quasi-Transitive Digraphs. The Australasian Journal of Combinatorics, 46:217-232 (2010).

Arvind Gupta*, Mohammad M. Karimi*, Jan Manuch, Ladislav Stacho L, Xiaohong Zhao Haplotype Inferring via Galled-Tree Networks Is NP-Complete. Journal of Computational Biology 17(10): 1317-1331 (2010).


2009

Tassinari R,Maranghi F,Moracci G,Rasinger J,Carroll T,Hogstrand C,Haave H,Lundebye A,Mantovani A,Macrì A. Histopathological effects on target organ maturation in juvenile female mice upon exposure to 2,3,7,8TCDD, PCB153, PBDE-47 or HBCD through a salmon-based diet Reproductive Toxicology - REPROD TOXICOL. 01/2009; 28(2):127-127.


2007

Gonzalez D, Bowen AJ, Carroll TS, Conlan RS. The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription. Mol Cell Biol. 2007 Aug;27(15):5306-15.