Publications 2016–2021

Publications

Papers from 2016 to 2021. Current and former lab members are in bold.

2021

  1. The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus

    Karimi MM, Guo Y, Cui X, Pallikonda HA, Horková V, Wang YF, Gil SR, …

    Nature Communications 12:99

  2. 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, Di Gregorio A, Zawadzki T, … Karimi MM, …

    Nature Metabolism 3:1091–1108

  3. CpG islands shape the epigenome landscape

    Papin C, Le Gras S, Ibrahim A, Salem H, Karimi MM, Stoll I, Ugrinova I, …

    Journal of Molecular Biology 433(6):166659

  4. iNucs: inter-nucleosome interactions

    Oveisi M, Shukla M, Seymen N, Ohno M, Taniguchi Y, Nahata S, Loos R, … Karimi MM, …

    Bioinformatics 37(23):4562–4563

2020

  1. Surveillance of cohesin-supported chromosome structure controls meiotic progression

    Castellano-Pozo M, Pacheco S, Sioutas G, Jaso-Tamame AL, Dore MH, … Karimi MM, …

    Nature Communications 11:4345

  2. Evolution of an amniote-specific mechanism for modulating ubiquitin signaling via phosphoregulation of the E2 enzyme UBE2D3

    Roman-Trufero M, Ito CM, Pedebos C, Magdalou I, Wang YF, Karimi MM, …

    Molecular Biology and Evolution 37(7):1986–2001

2019

  1. LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq

    Babaian A, Thompson IR, Lever J, Gagnier L, Karimi MM, Mager DL

    Bioinformatics

  2. Hepatocyte nuclear factor 4-alpha is essential for the active epigenetic state at enhancers in mouse liver

    Thakur A, Wong JCH, Wang EY, Lotto J, Kim D, Cheng JC, Mingay M, … Karimi MM, …

    Hepatology 70(4):1360–1376

  3. FACT mediates cohesin function on chromatin

    Garcia-Luis J, Lazar-Stefanita L, Gutierrez-Escribano P, Thierry A, … Karimi MM, …

    Nature Structural & Molecular Biology 26(10):970–979

2018

  1. 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, … Karimi MM, …

    Nature Communications 9:3331

  2. Inhibition of methyltransferase Setd7 allows the in vitro expansion of myogenic stem cells with improved therapeutic potential

    Judson RN, Quarta M, Oudhoff MJ, Soliman H, Yi L, Chang CK, Loi G, … Karimi MM, …

    Cell Stem Cell 22(2):177–190

  3. H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2

    Chen CCL, Goyal P, Karimi MM, Abildgaard MH, Kimura H, Lorincz MC

    Genome Research 28(1):37–51

  4. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs

    Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y

    eLife 7:e33084

  5. 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 AB, … Karimi MM, …

    BMC Genomics 19:463

  6. Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates

    Webster P, Dawes J, Dewchand H, Takacs K, Iadarola B, Bolt B, … Karimi MM, …

    Nature Communications 9

2017

  1. On the role of H3.3 in retroviral silencing

    Wolf G, Rebollo R, Karimi MM, Ewing AD, Kamada R, Wu W, Wu B, …

    Nature 548(7665):E1–E3

  2. A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer

    Lock FE, Babaian A, Zhang Y, Gagnier L, Kuah S, Weberling A, … Karimi MM, …

    PLoS One 12(7):e0180659

2016

  1. Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma

    Babaian A, Romanish MT, Gagnier L, Kuo LY, Karimi MM, Steidl C, …

    Oncogene 35(19):2542–2546

  2. Activation of endogenous retroviruses in Dnmt1−/− ESCs involves disruption of SETDB1-mediated repression by NP95 binding to hemimethylated DNA

    Sharif J, Endo TA, Nakayama M, Karimi MM, Shimada M, Katsuyama K, …

    Cell Stem Cell 19(1):81–94

  3. ChAsE: chromatin analysis and exploration tool

    Younesy H, Nielsen CB, Lorincz MC, Jones SJM, Karimi MM, Möller T

    Bioinformatics 32(21):3324–3326

For a complete list, see Mehdi’s Google Scholar profile.