RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites von Engreitz, Jesse M., Sirokman, Klara, McDonel, Patrick, Shishkin, Alexander A., Surka, Christine, Russell, Pamela, Grossman, Sharon R., Chow, Amy Y., Guttman, Mitchell, Lander, Eric S.

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Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus von Quinodoz, Sofia A., Ollikainen, Noah, Tabak, Barbara, Palla, Ali, Schmidt, Jan Marten, Detmar, Elizabeth, Lai, Mason M., Shishkin, Alexander A., Bhat, Prashant, Takei, Yodai, Trinh, Vickie, Aznauryan, Erik, Russell, Pamela, Cheng, Christine, Jovanovic, Marko, Chow, Amy, Cai, Long, McDonel, Patrick, Garber, Manuel, Guttman, Mitchell

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Genetic and epigenetic fine mapping of causal autoimmune disease variants von Farh, Kyle Kai-How, Marson, Alexander, Zhu, Jiang, Kleinewietfeld, Markus, Housley, William J., Beik, Samantha, Shoresh, Noam, Whitton, Holly, Ryan, Russell J. H., Shishkin, Alexander A., Hatan, Meital, Carrasco-Alfonso, Marlene J., Mayer, Dita, Luckey, C. John, Patsopoulos, Nikolaos A., De Jager, Philip L., Kuchroo, Vijay K., Epstein, Charles B., Daly, Mark J., Hafler, David A., Bernstein, Bradley E.

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The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3 von McHugh, Colleen A., Chen, Chun-Kan, Chow, Amy, Surka, Christine F., Tran, Christina, McDonel, Patrick, Pandya-Jones, Amy, Blanco, Mario, Burghard, Christina, Moradian, Annie, Sweredoski, Michael J., Shishkin, Alexander A., Su, Julia, Lander, Eric S., Hess, Sonja, Plath, Kathrin, Guttman, Mitchell

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Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP) von Van Nostrand, Eric L, Pratt, Gabriel A, Shishkin, Alexander A, Gelboin-Burkhart, Chelsea, Fang, Mark Y, Sundararaman, Balaji, Blue, Steven M, Nguyen, Thai B, Surka, Christine, Elkins, Keri, Stanton, Rebecca, Rigo, Frank, Guttman, Mitchell, Yeo, Gene W

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Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells von Gifford, Casey A., Ziller, Michael J., Gu, Hongcang, Trapnell, Cole, Donaghey, Julie, Tsankov, Alexander, Shalek, Alex K., Kelley, David R., Shishkin, Alexander A., Issner, Robbyn, Zhang, Xiaolan, Coyne, Michael, Fostel, Jennifer L., Holmes, Laurie, Meldrim, Jim, Guttman, Mitchell, Epstein, Charles, Park, Hongkun, Kohlbacher, Oliver, Rinn, John, Gnirke, Andreas, Lander, Eric S., Bernstein, Bradley E., Meissner, Alexander

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Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs von Chen, Jenny, Shishkin, Alexander A, Zhu, Xiaopeng, Kadri, Sabah, Maza, Itay, Guttman, Mitchell, Hanna, Jacob H, Regev, Aviv, Garber, Manuel

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The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome von Engreitz, Jesse M, Pandya-Jones, Amy, McDonel, Patrick, Shishkin, Alexander, Sirokman, Klara, Surka, Christine, Kadri, Sabah, Xing, Jeffrey, Goren, Alon, Lander, Eric S, Plath, Kathrin, Guttman, Mitchell

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Simultaneous generation of many RNA-seq libraries in a single reaction von Shishkin, Alexander A, Giannoukos, Georgia, Kucukural, Alper, Ciulla, Dawn, Busby, Michele, Surka, Christine, Chen, Jenny, Bhattacharyya, Roby P, Rudy, Robert F, Patel, Milesh M, Novod, Nathaniel, Hung, Deborah T, Gnirke, Andreas, Garber, Manuel, Guttman, Mitchell, Livny, Jonathan

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Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors von Wheeler, Emily C., Vu, Anthony Q., Einstein, Jaclyn M., DiSalvo, Matthew, Ahmed, Noorsher, Van Nostrand, Eric L., Shishkin, Alexander A., Jin, Wenhao, Allbritton, Nancy L., Yeo, Gene W.

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Genome-wide Screen Identifies Pathways that Govern GAA/TTC Repeat Fragility and Expansions in Dividing and Nondividing Yeast Cells von Zhang, Yu, Shishkin, Alexander A., Nishida, Yuri, Marcinkowski-Desmond, Dana, Saini, Natalie, Volkov, Kirill V., Mirkin, Sergei M., Lobachev, Kirill S.

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Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq von Blue, Steven M., Yee, Brian A., Pratt, Gabriel A., Mueller, Jasmine R., Park, Samuel S., Shishkin, Alexander A., Starner, Anne C., Van Nostrand, Eric L., Yeo, Gene W.

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Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions von Van Nostrand, Eric L., Shishkin, Alexander A., Pratt, Gabriel A., Nguyen, Thai B., Yeo, Gene W.

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Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale von Zhukov, Dmitriy V, Khorosheva, Eugenia M, Khazaei, Tahmineh, Du, Wenbin, Selck, David A, Shishkin, Alexander A, Ismagilov, Rustem F

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Genome rearrangements caused by interstitial telomeric sequences in yeast von Aksenova, Anna Y., Greenwell, Patricia W., Dominska, Margaret, Shishkin, Alexander A., Kim, Jane C., Petes, Thomas D., Mirkin, Sergei M.

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Role of DNA Polymerases in Repeat-Mediated Genome Instability von Shah, Kartik A., Shishkin, Alexander A., Voineagu, Irina, Pavlov, Youri I., Shcherbakova, Polina V., Mirkin, Sergei M.

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Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility von Mirkin, Sergei M, Voineagu, Irina, Surka, Christine F, Shishkin, Alexander A, Krasilnikova, Maria M

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Expansion of Interstitial Telomeric Sequences in Yeast von Aksenova, Anna Y., Han, Gil, Shishkin, Alexander A., Volkov, Kirill V., Mirkin, Sergei M.

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Large-Scale Expansions of Friedreich's Ataxia GAA Repeats in Yeast von Shishkin, Alexander A., Voineagu, Irina, Matera, Robert, Cherng, Nicole, Chernet, Brook T., Krasilnikova, Maria M., Narayanan, Vidhya, Lobachev, Kirill S., Mirkin, Sergei M.

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Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML von Krivdova, Gabriela, Voisin, Veronique, Schoof, Erwin M., Marhon, Sajid A., Murison, Alex, McLeod, Jessica L., Gabra, Martino M., Zeng, Andy G.X., Aigner, Stefan, Yee, Brian A., Shishkin, Alexander A., Van Nostrand, Eric L., Hermans, Karin G., Trotman-Grant, Aaron C., Mbong, Nathan, Kennedy, James A., Gan, Olga I., Wagenblast, Elvin, De Carvalho, Daniel D., Salmena, Leonardo, Minden, Mark D., Bader, Gary D., Yeo, Gene W., Dick, John E., Lechman, Eric R.

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