An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations von Brind’Amour, Julie, Liu, Sheng, Hudson, Matthew, Chen, Carol, Karimi, Mohammad M., Lorincz, Matthew C.

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DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs von Karimi, Mohammad M., Goyal, Preeti, Maksakova, Irina A., Bilenky, Misha, Leung, Danny, Tang, Jie Xin, Shinkai, Yoichi, Mager, Dixie L., Jones, Steven, Hirst, Martin, Lorincz, Matthew C.

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Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells von Liu, Sheng, Brind'Amour, Julie, Karimi, Mohammad M, Shirane, Kenjiro, Bogutz, Aaron, Lefebvre, Louis, Sasaki, Hiroyuki, Shinkai, Yoichi, Lorincz, Matthew C

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The Induced Heating–Healing of Inductive Warm-Mix Asphalt Mixture Containing Copper-Slag Filler von Fakhri, Mansour, Javadi, Sajad, Norouzi, Mohammad Amin, Bahmai, Behnam Baveli, Karimi, Mohammad M.

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Activation of Endogenous Retroviruses in Dnmt1−/− ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA von Sharif, Jafar, Endo, Takaho A., Nakayama, Manabu, Karimi, Mohammad M., Shimada, Midori, Katsuyama, Kayoko, Goyal, Preeti, Brind’Amour, Julie, Sun, Ming-An, Sun, Zhixiong, Ishikura, Tomoyuki, Mizutani-Koseki, Yoko, Ohara, Osamu, Shinkai, Yoichi, Nakanishi, Makoto, Xie, Hehuang, Lorincz, Matthew C., Koseki, Haruhiko

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LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation von Brind’Amour, Julie, Kobayashi, Hisato, Richard Albert, Julien, Shirane, Kenjiro, Sakashita, Akihiko, Kamio, Asuka, Bogutz, Aaron, Koike, Tasuku, Karimi, Mohammad M., Lefebvre, Louis, Kono, Tomohiro, Lorincz, Matthew C.

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hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells von Thompson, Peter J, Dulberg, Vered, Moon, Kyung-Mee, Foster, Leonard J, Chen, Carol, Karimi, Mohammad M, Lorincz, Matthew C

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LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq von Babaian, Artem, Thompson, I Richard, Lever, Jake, Gagnier, Liane, Karimi, Mohammad M, Mager, Dixie L

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Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms von Rebollo, Rita, Karimi, Mohammad M, Bilenky, Misha, Gagnier, Liane, Miceli-Royer, Katharine, Zhang, Ying, Goyal, Preeti, Keane, Thomas M, Jones, Steven, Hirst, Martin, Lorincz, Matthew C, Mager, Dixie L

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MCM2-7 loading-dependent ORC release ensures genome-wide origin licensing von Reuter, L. Maximilian, Khadayate, Sanjay P., Mossler, Audrey, Liebl, Korbinian, Faull, Sarah V., Karimi, Mohammad M., Speck, Christian

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Surveillance of cohesin-supported chromosome structure controls meiotic progression von Castellano-Pozo, Maikel, Pacheco, Sarai, Sioutas, Georgios, Jaso-Tamame, Angel Luis, Dore, Marian H., Karimi, Mohammad M., Martinez-Perez, Enrique

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Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters von Robles-Rebollo, Irene, Cuartero, Sergi, Canellas-Socias, Adria, Wells, Sarah, Karimi, Mohammad M., Mereu, Elisabetta, Chivu, Alexandra G., Heyn, Holger, Whilding, Chad, Dormann, Dirk, Marguerat, Samuel, Rioja, Inmaculada, Prinjha, Rab K., Stumpf, Michael P. H., Fisher, Amanda G., Merkenschlager, Matthias

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The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus von Karimi, Mohammad M., Guo, Ya, Cui, Xiaokai, Pallikonda, Husayn A., Horková, Veronika, Wang, Yi-Fang, Gil, Sara Ruiz, Rodriguez-Esteban, Gustavo, Robles-Rebollo, Irene, Bruno, Ludovica, Georgieva, Radina, Patel, Bhavik, Elliott, James, Dore, Marian H., Dauphars, Danielle, Krangel, Michael S., Lenhard, Boris, Heyn, Holger, Fisher, Amanda G., Štěpánek, Ondřej, Merkenschlager, Matthias

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ChAsE: chromatin analysis and exploration tool von Younesy, Hamid, Nielsen, Cydney B, Lorincz, Matthew C, Jones, Steven J M, Karimi, Mohammad M, Möller, Torsten

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Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells von Maksakova, Irina A, Thompson, Peter J, Goyal, Preeti, Jones, Steven Jm, Singh, Prim B, Karimi, Mohammad M, Lorincz, Matthew C

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A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer von Lock, Frances E, Babaian, Artem, Zhang, Ying, Gagnier, Liane, Kuah, Sabrina, Weberling, Antonia, Karimi, Mohammad M, Mager, Dixie L

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VisRseq: R-based visual framework for analysis of sequencing data von Younesy, Hamid, Möller, Torsten, Lorincz, Matthew C, Karimi, Mohammad M, Jones, Steven J M

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A New Ensemble Prediction Method for Reclaimed Asphalt Pavement (RAP) Mixtures Containing Different Constituents von Ghavami, Sadegh, Alipour, Zeynab, Naseri, Hamed, Jahanbakhsh, Hamid, Karimi, Mohammad M.

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Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA) von Richard Albert, Julien, Koike, Tasuku, Younesy, Hamid, Thompson, Richard, Bogutz, Aaron B, Karimi, Mohammad M, Lorincz, Matthew C

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Induction heating and healing of carbon black modified asphalt concrete under microwave radiation von Jahanbakhsh, Hamid, Karimi, Mohammad M., Jahangiri, Behnam, Nejad, F. Moghadas

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