Dr Mohammad Mahdi Karimi
Senior Lecturer in Bioinformatics
Research interests
- Biomedical and life sciences
Biography
Dr Mohammad Mahdi Karimi holds a B.Sc. degree in Biomedical Engineering from Tehran Polytechnic (2002), an M.Sc. degree in Biomedical Engineering from University of Tehran (2004), and a PhD degree in Computing Science from Simon Fraser University, Burnaby, Canada (2009). He has since served as an MSFHR Research Associate at the University of British Columbia, a Research Scientist at Canada's Michael Smith Genome Sciences Centre, and the Head of Bioinformatics at MRC London Institute of Medical Science, before joining King's. He is one of the team leaders to develop the Epigenomic Data Coordination Centre for Canada.
His main research interest is to provide visual analytics and machine learning solutions for multi-omics data integration and analysis towards the discovery of diagnostic and therapeutic targets and predictive models for haematological malignancies.
Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs
Thoms, J. A. I., Yan, F., Hampton, H. R., Davidson, S., Joshi, S., Saw, J., Sarowar, C. H., Lim, X. Y., Nunez, A. C., Kakadia, P. M., Bhuyan, G. S., Zou, X., Nguyen, M., Ghodousi, E. S., Koch, F. C., Vafaee, F., Thompson, I. R., Karimi, M. M., Pickford, R. & Raftery, M. J. & 30 others, Hough, S., Buckland, G., Bailey, M., Ghodke, Y., Absar, N., Vaughan, L., Pasalic, L., Fong, C. Y., Kenealy, M., Hiwase, D. K., Stoddart, R. I., Mohammed, S., Lee, L., Passam, F. H., Larsen, S. R., Spring, K. J., Skarratt, K. K., Rebeiro, P., Presgrave, P., Stevenson, W. S., Ling, S., Tiley, C., Fuller, S. J., Roncolato, F., Enjeti, A. K., Hoenemann, D., Lemech, C., Jolly, C. J., Bohlander, S. K. & Curtis, D. J., 31 Dec 2025, In: Nature communications. 16, 1, 4451.Research output: Contribution to journal › Article › peer-review
Transposable elements as novel therapeutic targets for PARPi-induced synthetic lethality in PcG-mutated blood cancer
Zeisig, B., Tsai, C.-T., Virely, C., Fung, T. K. K., Akin, A. T., Troadec, E., Jiao, B., Thompson, R., Lau, P. N. I., Li, N., Charalambous, A., Bomfim, L., Lynch, J., Georgiou, A., Hoogeboom, R., Lynn, C., Zhang, S. Y., Patten, P. E., Fisher, C. & Schuh, A. & 4 others, Ogawa, S., Mufti, G. J., Karimi, M. M. & So, C. W. E., 25 Jun 2025, (E-pub ahead of print) In: Blood.Research output: Contribution to journal › Article › peer-review
A 5:2 intermittent fasting regimen ameliorates NASH and fibrosis and blunts HCC development via hepatic PPARα and PCK1
Gallage, S., Ali, A., Barragan Avila, J. E., Seymen, N., Ramadori, P., Joerke, V., Zizmare, L., Aicher, D., Gopalsamy, I. K., Fong, W., Kosla, J., Focaccia, E., Li, X., Yousuf, S., Sijmonsma, T., Rahbari, M., Kommoss, K. S., Billeter, A., Prokosch, S. & Rothermel, U. & 14 others, Mueller, F., Hetzer, J., Heide, D., Schinkel, B., Machauer, T., Pichler, B., Malek, N. P., Longerich, T., Roth, S., Rose, A. J., Schwenck, J., Trautwein, C., Karimi, M. M. & Heikenwalder, M., 4 Jun 2024, In: CELL METABOLISM. 36, 6, p. 1371-1393.e7Research output: Contribution to journal › Article › peer-review
Expression of most retrotransposons in human blood correlates with biological aging
Tsai, Y.-T., Seymen, N., Thompson, I. R., Zou, X., Mumtaz, W., Gerlevik, S., Mufti, G. J., Karimi, M. M., Dang, W. (Editor) & Marston, A. L. (Editor), 17 Oct 2024, (E-pub ahead of print) In: eLife. 13, p. RP96575Research output: Contribution to journal › Article › peer-review
Identification of novel myelodysplastic syndromes prognostic subgroups by integration of inflammation, cell-type composition, and immune signatures in the bone marrow
Gerlevik, S., Seymen, N., Hama, S., Mumtaz, W., Thompson, I. R., Jalili, S. R., Kaya, D. E., Iacoangeli, A., Pellagatti, A., Boultwood, J., Napolitani, G., Mufti, G. J., Karimi, M. M. & Rath, S. (Editor), 1 Sept 2024, In: eLife. 13, p. RP97096Research output: Contribution to journal › Article › peer-review
MCM2-7 loading-dependent ORC release ensures genome-wide origin licensing
Reuter, L. M., Khadayate, S. P., Mossler, A., Liebl, K., Faull, S. V., Karimi, M. M. & Speck, C., Dec 2024, In: Nature communications. 15, 1, 7306.Research output: Contribution to journal › Article › peer-review
ModEx: a general purpose computer model exploration system
Younesy, H., Pober, J., Möller, T. & Karimi, M. M., 2023, In: Frontiers in Bioinformatics. 3, 1153800.Research output: Contribution to journal › Article › peer-review
Mouse HP1γ regulates TRF1 expression and telomere stability
Stylianakis, E., Chan, J. P. K., Law, P. P., Jiang, Y., Khadayate, S., Karimi, M. M., Festenstein, R. & Vannier, J.-B., 15 Oct 2023, In: Life Sciences. 331, 122030.Research output: Contribution to journal › Article › peer-review
Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters
Robles-Rebollo, I., Cuartero, S., Canellas-Socias, A., Wells, S., Karimi, M. M., Mereu, E., Chivu, A. G., Heyn, H., Whilding, C., Dormann, D., Marguerat, S., Rioja, I., Prinjha, R. K., Stumpf, M. P. H., Fisher, A. G. & Merkenschlager, M., Dec 2022, In: Nature Communications. 13, 1, 4342.Research output: Contribution to journal › Article › peer-review
Spontaneous Cholemia in C57BL/6 Mice Predisposes to Liver Cancer in NASH
Gallage, S., Ali, A., Barragan avila, J. E., Herebian, D., Karimi, M. M., Irvine, E. E., Mchugh, D., Schneider, A. T., Vucur, M., Keitel, V., Gil, J., Withers, D. J., Luedde, T. & Heikenwalder, M., 2022, In: Cellular and molecular gastroenterology and hepatology. 13, 3, p. 875-878Research output: Contribution to journal › Article › peer-review
Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development
Lima, A., Lubatti, G., Burgstaller, J., Hu, D., Green, A. P., Di Gregorio, A., Zawadzki, T., Pernaute, B., Mahammadov, E., Perez-Montero, S., Dore, M., Sanchez, J. M., Bowling, S., Sancho, M., Kolbe, T., Karimi, M. M., Carling, D., Jones, N., Srinivas, S. & Scialdone, A. & 1 others, Rodriguez, T. A., Aug 2021, In: Nature Metabolism. 3, 8, p. 1091-1108 18 p.Research output: Contribution to journal › Article › peer-review
INucs: Inter-nucleosome interactions
Oveisi, M., Shukla, M., Seymen, N., Ohno, M., Taniguchi, Y., Nahata, S., Loos, R., Mufti, G. J., Allshire, R. C., DImitrov, S. & Karimi, M. M., 1 Dec 2021, In: BIOINFORMATICS. 37, 23, p. 4562-4563 2 p.Research output: Contribution to journal › Article › peer-review
RUNX1 Regulates a Transcription Program That Affects the Dynamics of Cell Cycle Entry of Naive Resting B Cells
Thomsen, I., Kunowska, N., de Souza, R., Moody, A. M., Crawford, G., Wang, Y. F., Khadayate, S., Whilding, C., Strid, J., Karimi, M. M., Barr, A. R., Dillon, N. & Sabbattini, P., 15 Dec 2021, In: Journal of Immunology. 207, 12, p. 2976-2991 16 p.Research output: Contribution to journal › Article › peer-review
The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus
Karimi, M. M., Guo, Y., Cui, X., Pallikonda, H. A., Horková, V., Wang, Y. F., Gil, S. R., Rodriguez-Esteban, G., Robles-Rebollo, I., Bruno, L., Georgieva, R., Patel, B., Elliott, J., Dore, M. H., Dauphars, D., Krangel, M. S., Lenhard, B., Heyn, H., Fisher, A. G. & Štěpánek, O. & 1 others, Merkenschlager, M., Dec 2021, In: Nature Communications. 12, 1, 99.Research output: Contribution to journal › Article › peer-review
CpG Islands Shape the Epigenome Landscape
Papin, C., Le Gras, S., Ibrahim, A., Salem, H., Karimi, M. M., Stoll, I., Ugrinova, I., Schröder, M., Fontaine-Pelletier, E., Omran, Z., Bronner, C., Dimitrov, S. & Hamiche, A., 2020, (Accepted/In press) In: Journal of Molecular Biology.Research output: Contribution to journal › Article › peer-review
Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3
Roman-trufero, M., Ito, C. M., Pedebos, C., Magdalou, I., Wang, Y.-F., Karimi, M. M., Moyon, B., Webster, Z., Di Gregorio, A., Azuara, V., Khalid, S., Speck, C., Rodriguez, T., Dillon, N. & Yeager, M. (Editor), 1 Jul 2020, In: Molecular Biology and Evolution. 37, 7, p. 1986-2001 16 p.Research output: Contribution to journal › Article › peer-review
Surveillance of cohesin-supported chromosome structure controls meiotic progression
Castellano-pozo, M., Pacheco, S., Sioutas, G., Jaso-tamame, A. L., Dore, M. H., Karimi, M. M. & Martinez-perez, E., 1 Dec 2020, In: Nature Communications. 11, 1, p. 4345 4345.Research output: Contribution to journal › Article › peer-review
FACT mediates cohesin function on chromatin
Garcia-luis, J., Lazar-stefanita, L., Gutierrez-escribano, P., Thierry, A., Cournac, A., García, A., González, S., Sánchez, M., Jarmuz, A., Montoya, A., Dore, M., Kramer, H., Karimi, M. M., Antequera, F., Koszul, R. & Aragon, L., 1 Oct 2019, In: NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 26, 10, p. 970-979 10 p.Research output: Contribution to journal › Article › peer-review
Hepatocyte Nuclear Factor 4-Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver
Thakur, A., Wong, J. C. H., Wang, E. Y., Lotto, J., Kim, D., Cheng, J.-C., Mingay, M., Cullum, R., Moudgil, V., Ahmed, N., Tsai, S.-H., Wei, W., Walsh, C. P., Stephan, T., Bilenky, M., Fuglerud, B. M., Karimi, M. M., Gonzalez, F. J., Hirst, M. & Hoodless, P. A., Oct 2019, In: Hepatology. 70, 4, p. 1360-1376 17 p.Research output: Contribution to journal › Article › peer-review
Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver
Thakur, A., Wong, J. C. H., Wang, E. Y., Lotto, J., Kim, D., Cheng, J., Mingay, M., Cullum, R., Moudgil, V., Ahmed, N., Tsai, S., Wei, W., Walsh, C. P., Stephan, T., Bilenky, M., Fuglerud, B. M., Karimi, M. M., Gonzalez, F. J., Hirst, M. & Hoodless, P. A., 1 Oct 2019, In: Hepatology. 70, 4, p. 1360-1376Research output: Contribution to journal › Article › peer-review
LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq
Babaian, A., Thompson, I. R., Lever, J., Gagnier, L., Karimi, M. M., Mager, D. L. & Berger, B. (Editor), 1 Oct 2019, In: BIOINFORMATICS. 35, 19, p. 3839-3841 3 p.Research output: Contribution to journal › Article › peer-review
Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)
Richard Albert, J., Koike, T., Younesy, H., Thompson, R., Bogutz, A. B., Karimi, M. M. & Lorincz, M. C., 15 Jun 2018, In: BMC GENOMICS. 19, 1, p. 463Research output: Contribution to journal › Article › peer-review
H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2
Chen, C. C. L., Goyal, P., Karimi, M. M., Abildgaard, M. H., Kimura, H. & Lorincz, M. C., Jan 2018, In: Genome Research. 28, 1, p. 37-51 15 p.Research output: Contribution to journal › Article › peer-review
Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential
Judson, R. N., Quarta, M., Oudhoff, M. J., Soliman, H., Yi, L., Chang, C. K., Loi, G., Vander Werff, R., Cait, A., Hamer, M., Blonigan, J., Paine, P., Doan, L. T. N., Groppa, E., He, W., Su, L., Zhang, R. H., Xu, P., Eisner, C. & Low, M. & 6 others, Barta, I., Lewis, C.-A. B., Zaph, C., Karimi, M. M., Rando, T. A. & Rossi, F. M., 1 Feb 2018, In: Cell Stem Cell. 22, 2, p. 177-190.e7Research output: Contribution to journal › Article › peer-review
LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation
Brind’amour, J., Kobayashi, H., Richard Albert, J., Shirane, K., Sakashita, A., Kamio, A., Bogutz, A., Koike, T., Karimi, M. M., Lefebvre, L., Kono, T. & Lorincz, M. C., 1 Dec 2018, In: Nature Communications. 9, 1, p. 3331Research output: Contribution to journal › Article › peer-review
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
Ward, M. C., Zhao, S., Luo, K., Pavlovic, B. J., Karimi, M. M., Stephens, M. & Gilad, Y., 12 Apr 2018, In: eLife. 7Research output: Contribution to journal › Article › peer-review
Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates
Webster, P., Dawes, J. C., Dewchand, H., Takacs, K., Iadarola, B., Bolt, B. J., Caceres, J. J., Kaczor, J., Dharmalingam, G., Dore, M., Game, L., Adejumo, T., Elliott, J., Naresh, K., Karimi, M., Rekopoulou, K., Tan, G., Paccanaro, A. & Uren, A. G., 1 Dec 2018, In: Nature Communications. 9, 1Research output: Contribution to journal › Article › peer-review
A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer
Lock, F. E., Babaian, A., Zhang, Y., Gagnier, L., Kuah, S., Weberling, A., Karimi, M. M., Mager, D. L. & Schmitz, J. (Editor), 2017, In: PLoS ONE. 12, 7, p. e0180659Research output: Contribution to journal › Article › peer-review
On the role of H3.3 in retroviral silencing
Wolf, G., Rebollo, R., Karimi, M. M., Ewing, A. D., Kamada, R., Wu, W., Wu, B., Bachu, M., Ozato, K., Faulkner, G. J., Mager, D. L., Lorincz, M. C. & Macfarlan, T. S., 2 Aug 2017, In: Nature. 548, 7665, p. E1-E3Research output: Contribution to journal › Article › peer-review
Activation of Endogenous Retroviruses in Dnmt1(-/-) ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA
Sharif, J., Endo, T., Nakayama, M., Karimi, M., Shimada, M., Katsuyama, K., Goyal, P., Brind’amour, J., Sun, M.-A., Sun, Z., Ishikura, T., Mizutani-koseki, Y., Ohara, O., Shinkai, Y., Nakanishi, M., Xie, H., Lorincz, M. & Koseki, H., 7 Jul 2016, In: Cell Stem Cell. 19, 1, p. 81-94 14 p.Research output: Contribution to journal › Article › peer-review
ChAsE: chromatin analysis and exploration tool: chromatin analysis and exploration tool
Younesy, H., Nielsen, C. B., Lorincz, M. C., Jones, S. J. M., Karimi, M. M. & Möller, T., 1 Nov 2016, In: BIOINFORMATICS. 32, 21, p. 3324-3326 3 p.Research output: Contribution to journal › Article › peer-review
Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma
Babaian, A., Romanish, M. T., Gagnier, L., Kuo, L. Y., Karimi, M. M., Steidl, C. & Mager, D. L., 1 May 2016, In: Oncogene. 35, 19, p. 2542-2546Research output: Contribution to journal › Article › peer-review
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
Brind’amour, J., Liu, S., Hudson, M., Chen, C., Karimi, M. M. & Lorincz, M. C., 1 May 2015, In: Nature Communications. 6, 1, 6033.Research output: Contribution to journal › Article › peer-review
hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells
Thompson, P. J., Dulberg, V., Moon, K.-M., Foster, L. J., Chen, C., Karimi, M. M., Lorincz, M. C. & Barsh, G. S. (Editor), Jan 2015, In: PLoS Genetics. 11, 1, p. e1004933Research output: Contribution to journal › Article › peer-review
VisRseq: R-based visual framework for analysis of sequencing data
Younesy, H., Möller, T., Lorincz, M. C., Karimi, M. M. & Jones, S. J. M., 2015, In: BMC Bioinformatics. 16 Suppl 11, p. S2Research output: Contribution to journal › Article › peer-review
ALEA: a toolbox for allele-specific epigenomics analysis
Younesy, H., Möller, T., Heravi-moussavi, A., Cheng, J. B., Costello, J. F., Lorincz, M. C., Karimi, M. M. & Jones, S. J. M., 15 Apr 2014, In: BIOINFORMATICS. 30, 8, p. 1172-1174 3 p.Research output: Contribution to journal › Article › peer-review
Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma
Lock, F. E., Rebollo, R., Miceli-royer, K., Gagnier, L., Kuah, S., Babaian, A., Sistiaga-poveda, M., Lai, C. B., Nemirovsky, O., Serrano, I., Steidl, C., Karimi, M. M. & Mager, D. L., 26 Aug 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 34, p. E3534-43Research output: Contribution to journal › Article › peer-review
Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells
Liu, S., Brind’amour, J., Karimi, M. M., Shirane, K., Bogutz, A., Lefebvre, L., Sasaki, H., Shinkai, Y. & Lorincz, M. C., 15 Sept 2014, In: Genes & development. 28, 18, p. 2041-55 15 p.Research output: Contribution to journal › Article › peer-review
An Interactive Analysis and Exploration Tool for Epigenomic Data
Younesy, H., Nielsen, C. B., Möller, T., Alder, O., Cullum, R., Lorincz, M. C., Karimi, M. M. & Jones, S. J. M., 1 Jun 2013, In: COMPUTER GRAPHICS FORUM. 32, 3pt1, p. 91-100Research output: Contribution to journal › Article › peer-review
Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells
Maksakova, I. A., Thompson, P. J., Goyal, P., Jones, S. J., Singh, P. B., Karimi, M. M. & Lorincz, M. C., 4 Jun 2013, In: Epigenetics & Chromatin. 6, 1, p. 15Research output: Contribution to journal › Article › peer-review
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells
Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., Lorincz, M. C. & Ramalho-Santos, M., 8 Aug 2013, In: Nature. 500, 7461, p. 222-6 5 p.Research output: Contribution to journal › Article › peer-review
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs
Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M. & Lorincz, M. C., 3 Jun 2011, In: Cell Stem Cell. 8, 6, p. 676-87 12 p.Research output: Contribution to journal › Article › peer-review
Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms
Rebollo, R., Karimi, M. M., Bilenky, M., Gagnier, L., Miceli-Royer, K., Zhang, Y., Goyal, P., Keane, T. M., Jones, S., Hirst, M., Lorincz, M. C. & Mager, D. L., Sept 2011, In: PLoS Genetics. 7, 9, p. e1002301Research output: Contribution to journal › Article › peer-review
Haplotype inferring via galled-tree networks is NP-complete
Gupta, A., Karimi, M. M., Manuch, J., Stacho, L. & Zhao, X., Oct 2010, In: Journal of Computational Biology. 17, 10, p. 1435-49 15 p.Research output: Contribution to journal › Article › peer-review
Minimum cost homomorphisms to locally semicomplete digraphs and quasi-transitive digraphs
Gupta, A., Gutin, G., Karimi, M., Kim, E. J. & Rafiey, A., 1 Feb 2010, In: Australasian Journal of Combinatorics. 46, p. 227-232 6 p.Research output: Contribution to journal › Article › peer-review
Minimum cost homomorphisms to oriented cycles with some loops
Karimi, M. & Gupta, A., 1 Dec 2009, Theory of Computing 2009 - Proceedings of the Fifteenth Computing: The Australasian Theory Symposium, CATS 2009. (Conferences in Research and Practice in Information Technology Series; vol. 94).Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review
Minimum cost homomorphism dichotomy for locally in-semicomplete digraphs
Gupta, A., Karimi, M., Kim, E. J. & Rafiey, A., 22 Sept 2008, Combinatorial Optimization and Applications - Second International Conference, COCOA 2008, Proceedings. p. 374-383 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5165 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review
Minimum cost homomorphisms to reflexive digraphs
Gupta, A., Hell, P., Karimi, M. & Rafiey, A., 12 May 2008, LATIN 2008: Theoretical Informatics - 8th Latin American Symposium, Proceedings. p. 182-193 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4957 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review
Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs
Thoms, J. A. I., Yan, F., Hampton, H. R., Davidson, S., Joshi, S., Saw, J., Sarowar, C. H., Lim, X. Y., Nunez, A. C., Kakadia, P. M., Bhuyan, G. S., Zou, X., Nguyen, M., Ghodousi, E. S., Koch, F. C., Vafaee, F., Thompson, I. R., Karimi, M. M., Pickford, R. & Raftery, M. J. & 30 others, Hough, S., Buckland, G., Bailey, M., Ghodke, Y., Absar, N., Vaughan, L., Pasalic, L., Fong, C. Y., Kenealy, M., Hiwase, D. K., Stoddart, R. I., Mohammed, S., Lee, L., Passam, F. H., Larsen, S. R., Spring, K. J., Skarratt, K. K., Rebeiro, P., Presgrave, P., Stevenson, W. S., Ling, S., Tiley, C., Fuller, S. J., Roncolato, F., Enjeti, A. K., Hoenemann, D., Lemech, C., Jolly, C. J., Bohlander, S. K. & Curtis, D. J., 31 Dec 2025, In: Nature communications. 16, 1, 4451.Research output: Contribution to journal › Article › peer-review
Transposable elements as novel therapeutic targets for PARPi-induced synthetic lethality in PcG-mutated blood cancer
Zeisig, B., Tsai, C.-T., Virely, C., Fung, T. K. K., Akin, A. T., Troadec, E., Jiao, B., Thompson, R., Lau, P. N. I., Li, N., Charalambous, A., Bomfim, L., Lynch, J., Georgiou, A., Hoogeboom, R., Lynn, C., Zhang, S. Y., Patten, P. E., Fisher, C. & Schuh, A. & 4 others, Ogawa, S., Mufti, G. J., Karimi, M. M. & So, C. W. E., 25 Jun 2025, (E-pub ahead of print) In: Blood.Research output: Contribution to journal › Article › peer-review
A 5:2 intermittent fasting regimen ameliorates NASH and fibrosis and blunts HCC development via hepatic PPARα and PCK1
Gallage, S., Ali, A., Barragan Avila, J. E., Seymen, N., Ramadori, P., Joerke, V., Zizmare, L., Aicher, D., Gopalsamy, I. K., Fong, W., Kosla, J., Focaccia, E., Li, X., Yousuf, S., Sijmonsma, T., Rahbari, M., Kommoss, K. S., Billeter, A., Prokosch, S. & Rothermel, U. & 14 others, Mueller, F., Hetzer, J., Heide, D., Schinkel, B., Machauer, T., Pichler, B., Malek, N. P., Longerich, T., Roth, S., Rose, A. J., Schwenck, J., Trautwein, C., Karimi, M. M. & Heikenwalder, M., 4 Jun 2024, In: CELL METABOLISM. 36, 6, p. 1371-1393.e7Research output: Contribution to journal › Article › peer-review
Expression of most retrotransposons in human blood correlates with biological aging
Tsai, Y.-T., Seymen, N., Thompson, I. R., Zou, X., Mumtaz, W., Gerlevik, S., Mufti, G. J., Karimi, M. M., Dang, W. (Editor) & Marston, A. L. (Editor), 17 Oct 2024, (E-pub ahead of print) In: eLife. 13, p. RP96575Research output: Contribution to journal › Article › peer-review
Identification of novel myelodysplastic syndromes prognostic subgroups by integration of inflammation, cell-type composition, and immune signatures in the bone marrow
Gerlevik, S., Seymen, N., Hama, S., Mumtaz, W., Thompson, I. R., Jalili, S. R., Kaya, D. E., Iacoangeli, A., Pellagatti, A., Boultwood, J., Napolitani, G., Mufti, G. J., Karimi, M. M. & Rath, S. (Editor), 1 Sept 2024, In: eLife. 13, p. RP97096Research output: Contribution to journal › Article › peer-review
MCM2-7 loading-dependent ORC release ensures genome-wide origin licensing
Reuter, L. M., Khadayate, S. P., Mossler, A., Liebl, K., Faull, S. V., Karimi, M. M. & Speck, C., Dec 2024, In: Nature communications. 15, 1, 7306.Research output: Contribution to journal › Article › peer-review
ModEx: a general purpose computer model exploration system
Younesy, H., Pober, J., Möller, T. & Karimi, M. M., 2023, In: Frontiers in Bioinformatics. 3, 1153800.Research output: Contribution to journal › Article › peer-review
Mouse HP1γ regulates TRF1 expression and telomere stability
Stylianakis, E., Chan, J. P. K., Law, P. P., Jiang, Y., Khadayate, S., Karimi, M. M., Festenstein, R. & Vannier, J.-B., 15 Oct 2023, In: Life Sciences. 331, 122030.Research output: Contribution to journal › Article › peer-review
Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters
Robles-Rebollo, I., Cuartero, S., Canellas-Socias, A., Wells, S., Karimi, M. M., Mereu, E., Chivu, A. G., Heyn, H., Whilding, C., Dormann, D., Marguerat, S., Rioja, I., Prinjha, R. K., Stumpf, M. P. H., Fisher, A. G. & Merkenschlager, M., Dec 2022, In: Nature Communications. 13, 1, 4342.Research output: Contribution to journal › Article › peer-review
Spontaneous Cholemia in C57BL/6 Mice Predisposes to Liver Cancer in NASH
Gallage, S., Ali, A., Barragan avila, J. E., Herebian, D., Karimi, M. M., Irvine, E. E., Mchugh, D., Schneider, A. T., Vucur, M., Keitel, V., Gil, J., Withers, D. J., Luedde, T. & Heikenwalder, M., 2022, In: Cellular and molecular gastroenterology and hepatology. 13, 3, p. 875-878Research output: Contribution to journal › Article › peer-review
Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development
Lima, A., Lubatti, G., Burgstaller, J., Hu, D., Green, A. P., Di Gregorio, A., Zawadzki, T., Pernaute, B., Mahammadov, E., Perez-Montero, S., Dore, M., Sanchez, J. M., Bowling, S., Sancho, M., Kolbe, T., Karimi, M. M., Carling, D., Jones, N., Srinivas, S. & Scialdone, A. & 1 others, Rodriguez, T. A., Aug 2021, In: Nature Metabolism. 3, 8, p. 1091-1108 18 p.Research output: Contribution to journal › Article › peer-review
INucs: Inter-nucleosome interactions
Oveisi, M., Shukla, M., Seymen, N., Ohno, M., Taniguchi, Y., Nahata, S., Loos, R., Mufti, G. J., Allshire, R. C., DImitrov, S. & Karimi, M. M., 1 Dec 2021, In: BIOINFORMATICS. 37, 23, p. 4562-4563 2 p.Research output: Contribution to journal › Article › peer-review
RUNX1 Regulates a Transcription Program That Affects the Dynamics of Cell Cycle Entry of Naive Resting B Cells
Thomsen, I., Kunowska, N., de Souza, R., Moody, A. M., Crawford, G., Wang, Y. F., Khadayate, S., Whilding, C., Strid, J., Karimi, M. M., Barr, A. R., Dillon, N. & Sabbattini, P., 15 Dec 2021, In: Journal of Immunology. 207, 12, p. 2976-2991 16 p.Research output: Contribution to journal › Article › peer-review
The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus
Karimi, M. M., Guo, Y., Cui, X., Pallikonda, H. A., Horková, V., Wang, Y. F., Gil, S. R., Rodriguez-Esteban, G., Robles-Rebollo, I., Bruno, L., Georgieva, R., Patel, B., Elliott, J., Dore, M. H., Dauphars, D., Krangel, M. S., Lenhard, B., Heyn, H., Fisher, A. G. & Štěpánek, O. & 1 others, Merkenschlager, M., Dec 2021, In: Nature Communications. 12, 1, 99.Research output: Contribution to journal › Article › peer-review
CpG Islands Shape the Epigenome Landscape
Papin, C., Le Gras, S., Ibrahim, A., Salem, H., Karimi, M. M., Stoll, I., Ugrinova, I., Schröder, M., Fontaine-Pelletier, E., Omran, Z., Bronner, C., Dimitrov, S. & Hamiche, A., 2020, (Accepted/In press) In: Journal of Molecular Biology.Research output: Contribution to journal › Article › peer-review
Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3
Roman-trufero, M., Ito, C. M., Pedebos, C., Magdalou, I., Wang, Y.-F., Karimi, M. M., Moyon, B., Webster, Z., Di Gregorio, A., Azuara, V., Khalid, S., Speck, C., Rodriguez, T., Dillon, N. & Yeager, M. (Editor), 1 Jul 2020, In: Molecular Biology and Evolution. 37, 7, p. 1986-2001 16 p.Research output: Contribution to journal › Article › peer-review
Surveillance of cohesin-supported chromosome structure controls meiotic progression
Castellano-pozo, M., Pacheco, S., Sioutas, G., Jaso-tamame, A. L., Dore, M. H., Karimi, M. M. & Martinez-perez, E., 1 Dec 2020, In: Nature Communications. 11, 1, p. 4345 4345.Research output: Contribution to journal › Article › peer-review
FACT mediates cohesin function on chromatin
Garcia-luis, J., Lazar-stefanita, L., Gutierrez-escribano, P., Thierry, A., Cournac, A., García, A., González, S., Sánchez, M., Jarmuz, A., Montoya, A., Dore, M., Kramer, H., Karimi, M. M., Antequera, F., Koszul, R. & Aragon, L., 1 Oct 2019, In: NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 26, 10, p. 970-979 10 p.Research output: Contribution to journal › Article › peer-review
Hepatocyte Nuclear Factor 4-Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver
Thakur, A., Wong, J. C. H., Wang, E. Y., Lotto, J., Kim, D., Cheng, J.-C., Mingay, M., Cullum, R., Moudgil, V., Ahmed, N., Tsai, S.-H., Wei, W., Walsh, C. P., Stephan, T., Bilenky, M., Fuglerud, B. M., Karimi, M. M., Gonzalez, F. J., Hirst, M. & Hoodless, P. A., Oct 2019, In: Hepatology. 70, 4, p. 1360-1376 17 p.Research output: Contribution to journal › Article › peer-review
Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver
Thakur, A., Wong, J. C. H., Wang, E. Y., Lotto, J., Kim, D., Cheng, J., Mingay, M., Cullum, R., Moudgil, V., Ahmed, N., Tsai, S., Wei, W., Walsh, C. P., Stephan, T., Bilenky, M., Fuglerud, B. M., Karimi, M. M., Gonzalez, F. J., Hirst, M. & Hoodless, P. A., 1 Oct 2019, In: Hepatology. 70, 4, p. 1360-1376Research output: Contribution to journal › Article › peer-review
LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq
Babaian, A., Thompson, I. R., Lever, J., Gagnier, L., Karimi, M. M., Mager, D. L. & Berger, B. (Editor), 1 Oct 2019, In: BIOINFORMATICS. 35, 19, p. 3839-3841 3 p.Research output: Contribution to journal › Article › peer-review
Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)
Richard Albert, J., Koike, T., Younesy, H., Thompson, R., Bogutz, A. B., Karimi, M. M. & Lorincz, M. C., 15 Jun 2018, In: BMC GENOMICS. 19, 1, p. 463Research output: Contribution to journal › Article › peer-review
H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2
Chen, C. C. L., Goyal, P., Karimi, M. M., Abildgaard, M. H., Kimura, H. & Lorincz, M. C., Jan 2018, In: Genome Research. 28, 1, p. 37-51 15 p.Research output: Contribution to journal › Article › peer-review
Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential
Judson, R. N., Quarta, M., Oudhoff, M. J., Soliman, H., Yi, L., Chang, C. K., Loi, G., Vander Werff, R., Cait, A., Hamer, M., Blonigan, J., Paine, P., Doan, L. T. N., Groppa, E., He, W., Su, L., Zhang, R. H., Xu, P., Eisner, C. & Low, M. & 6 others, Barta, I., Lewis, C.-A. B., Zaph, C., Karimi, M. M., Rando, T. A. & Rossi, F. M., 1 Feb 2018, In: Cell Stem Cell. 22, 2, p. 177-190.e7Research output: Contribution to journal › Article › peer-review
LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation
Brind’amour, J., Kobayashi, H., Richard Albert, J., Shirane, K., Sakashita, A., Kamio, A., Bogutz, A., Koike, T., Karimi, M. M., Lefebvre, L., Kono, T. & Lorincz, M. C., 1 Dec 2018, In: Nature Communications. 9, 1, p. 3331Research output: Contribution to journal › Article › peer-review
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
Ward, M. C., Zhao, S., Luo, K., Pavlovic, B. J., Karimi, M. M., Stephens, M. & Gilad, Y., 12 Apr 2018, In: eLife. 7Research output: Contribution to journal › Article › peer-review
Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates
Webster, P., Dawes, J. C., Dewchand, H., Takacs, K., Iadarola, B., Bolt, B. J., Caceres, J. J., Kaczor, J., Dharmalingam, G., Dore, M., Game, L., Adejumo, T., Elliott, J., Naresh, K., Karimi, M., Rekopoulou, K., Tan, G., Paccanaro, A. & Uren, A. G., 1 Dec 2018, In: Nature Communications. 9, 1Research output: Contribution to journal › Article › peer-review
A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer
Lock, F. E., Babaian, A., Zhang, Y., Gagnier, L., Kuah, S., Weberling, A., Karimi, M. M., Mager, D. L. & Schmitz, J. (Editor), 2017, In: PLoS ONE. 12, 7, p. e0180659Research output: Contribution to journal › Article › peer-review
On the role of H3.3 in retroviral silencing
Wolf, G., Rebollo, R., Karimi, M. M., Ewing, A. D., Kamada, R., Wu, W., Wu, B., Bachu, M., Ozato, K., Faulkner, G. J., Mager, D. L., Lorincz, M. C. & Macfarlan, T. S., 2 Aug 2017, In: Nature. 548, 7665, p. E1-E3Research output: Contribution to journal › Article › peer-review
Activation of Endogenous Retroviruses in Dnmt1(-/-) ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA
Sharif, J., Endo, T., Nakayama, M., Karimi, M., Shimada, M., Katsuyama, K., Goyal, P., Brind’amour, J., Sun, M.-A., Sun, Z., Ishikura, T., Mizutani-koseki, Y., Ohara, O., Shinkai, Y., Nakanishi, M., Xie, H., Lorincz, M. & Koseki, H., 7 Jul 2016, In: Cell Stem Cell. 19, 1, p. 81-94 14 p.Research output: Contribution to journal › Article › peer-review
ChAsE: chromatin analysis and exploration tool: chromatin analysis and exploration tool
Younesy, H., Nielsen, C. B., Lorincz, M. C., Jones, S. J. M., Karimi, M. M. & Möller, T., 1 Nov 2016, In: BIOINFORMATICS. 32, 21, p. 3324-3326 3 p.Research output: Contribution to journal › Article › peer-review
Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma
Babaian, A., Romanish, M. T., Gagnier, L., Kuo, L. Y., Karimi, M. M., Steidl, C. & Mager, D. L., 1 May 2016, In: Oncogene. 35, 19, p. 2542-2546Research output: Contribution to journal › Article › peer-review
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
Brind’amour, J., Liu, S., Hudson, M., Chen, C., Karimi, M. M. & Lorincz, M. C., 1 May 2015, In: Nature Communications. 6, 1, 6033.Research output: Contribution to journal › Article › peer-review
hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells
Thompson, P. J., Dulberg, V., Moon, K.-M., Foster, L. J., Chen, C., Karimi, M. M., Lorincz, M. C. & Barsh, G. S. (Editor), Jan 2015, In: PLoS Genetics. 11, 1, p. e1004933Research output: Contribution to journal › Article › peer-review
VisRseq: R-based visual framework for analysis of sequencing data
Younesy, H., Möller, T., Lorincz, M. C., Karimi, M. M. & Jones, S. J. M., 2015, In: BMC Bioinformatics. 16 Suppl 11, p. S2Research output: Contribution to journal › Article › peer-review
ALEA: a toolbox for allele-specific epigenomics analysis
Younesy, H., Möller, T., Heravi-moussavi, A., Cheng, J. B., Costello, J. F., Lorincz, M. C., Karimi, M. M. & Jones, S. J. M., 15 Apr 2014, In: BIOINFORMATICS. 30, 8, p. 1172-1174 3 p.Research output: Contribution to journal › Article › peer-review
Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma
Lock, F. E., Rebollo, R., Miceli-royer, K., Gagnier, L., Kuah, S., Babaian, A., Sistiaga-poveda, M., Lai, C. B., Nemirovsky, O., Serrano, I., Steidl, C., Karimi, M. M. & Mager, D. L., 26 Aug 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 34, p. E3534-43Research output: Contribution to journal › Article › peer-review
Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells
Liu, S., Brind’amour, J., Karimi, M. M., Shirane, K., Bogutz, A., Lefebvre, L., Sasaki, H., Shinkai, Y. & Lorincz, M. C., 15 Sept 2014, In: Genes & development. 28, 18, p. 2041-55 15 p.Research output: Contribution to journal › Article › peer-review
An Interactive Analysis and Exploration Tool for Epigenomic Data
Younesy, H., Nielsen, C. B., Möller, T., Alder, O., Cullum, R., Lorincz, M. C., Karimi, M. M. & Jones, S. J. M., 1 Jun 2013, In: COMPUTER GRAPHICS FORUM. 32, 3pt1, p. 91-100Research output: Contribution to journal › Article › peer-review
Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells
Maksakova, I. A., Thompson, P. J., Goyal, P., Jones, S. J., Singh, P. B., Karimi, M. M. & Lorincz, M. C., 4 Jun 2013, In: Epigenetics & Chromatin. 6, 1, p. 15Research output: Contribution to journal › Article › peer-review
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells
Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., Lorincz, M. C. & Ramalho-Santos, M., 8 Aug 2013, In: Nature. 500, 7461, p. 222-6 5 p.Research output: Contribution to journal › Article › peer-review
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs
Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M. & Lorincz, M. C., 3 Jun 2011, In: Cell Stem Cell. 8, 6, p. 676-87 12 p.Research output: Contribution to journal › Article › peer-review
Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms
Rebollo, R., Karimi, M. M., Bilenky, M., Gagnier, L., Miceli-Royer, K., Zhang, Y., Goyal, P., Keane, T. M., Jones, S., Hirst, M., Lorincz, M. C. & Mager, D. L., Sept 2011, In: PLoS Genetics. 7, 9, p. e1002301Research output: Contribution to journal › Article › peer-review
Haplotype inferring via galled-tree networks is NP-complete
Gupta, A., Karimi, M. M., Manuch, J., Stacho, L. & Zhao, X., Oct 2010, In: Journal of Computational Biology. 17, 10, p. 1435-49 15 p.Research output: Contribution to journal › Article › peer-review
Minimum cost homomorphisms to locally semicomplete digraphs and quasi-transitive digraphs
Gupta, A., Gutin, G., Karimi, M., Kim, E. J. & Rafiey, A., 1 Feb 2010, In: Australasian Journal of Combinatorics. 46, p. 227-232 6 p.Research output: Contribution to journal › Article › peer-review
Minimum cost homomorphisms to oriented cycles with some loops
Karimi, M. & Gupta, A., 1 Dec 2009, Theory of Computing 2009 - Proceedings of the Fifteenth Computing: The Australasian Theory Symposium, CATS 2009. (Conferences in Research and Practice in Information Technology Series; vol. 94).Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review
Minimum cost homomorphism dichotomy for locally in-semicomplete digraphs
Gupta, A., Karimi, M., Kim, E. J. & Rafiey, A., 22 Sept 2008, Combinatorial Optimization and Applications - Second International Conference, COCOA 2008, Proceedings. p. 374-383 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5165 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review
Minimum cost homomorphisms to reflexive digraphs
Gupta, A., Hell, P., Karimi, M. & Rafiey, A., 12 May 2008, LATIN 2008: Theoretical Informatics - 8th Latin American Symposium, Proceedings. p. 182-193 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4957 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review