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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Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects von de Soysa, T. Yvanka, Ranade, Sanjeev S., Okawa, Satoshi, Ravichandran, Srikanth, Huang, Yu, Salunga, Hazel T., Schricker, Amelia, del Sol, Antonio, Gifford, Casey A., Srivastava, Deepak

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Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells von Liao, Jing, Karnik, Rahul, Gu, Hongcang, Ziller, Michael J, Clement, Kendell, Tsankov, Alexander M, Akopian, Veronika, Gifford, Casey A, Donaghey, Julie, Galonska, Christina, Pop, Ramona, Reyon, Deepak, Tsai, Shengdar Q, Mallard, William, Joung, J Keith, Rinn, John L, Gnirke, Andreas, Meissner, Alexander

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A transcriptional switch governs fibroblast activation in heart disease von Alexanian, Michael, Przytycki, Pawel F., Micheletti, Rudi, Padmanabhan, Arun, Ye, Lin, Travers, Joshua G., Gonzalez-Teran, Barbara, Silva, Ana Catarina, Duan, Qiming, Ranade, Sanjeev S., Felix, Franco, Linares-Saldana, Ricardo, Li, Li, Lee, Clara Youngna, Sadagopan, Nandhini, Pelonero, Angelo, Huang, Yu, Andreoletti, Gaia, Jain, Rajan, McKinsey, Timothy A., Rosenfeld, Michael G., Gifford, Casey A., Pollard, Katherine S., Haldar, Saptarsi M., Srivastava, Deepak

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Network-based screen in iPSC-derived cells reveals therapeutic candidate for heart valve disease von Theodoris, Christina V, Zhou, Ping, Liu, Lei, Zhang, Yu, Nishino, Tomohiro, Huang, Yu, Kostina, Aleksandra, Ranade, Sanjeev S, Gifford, Casey A, Uspenskiy, Vladimir, Malashicheva, Anna, Ding, Sheng, Srivastava, Deepak

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Oligogenic inheritance of a human heart disease involving a genetic modifier von Gifford, Casey A., Ranade, Sanjeev S., Samarakoon, Ryan, Salunga, Hazel T., de Soysa, T. Yvanka, Huang, Yu, Zhou, Ping, Elfenbein, Aryé, Wyman, Stacia K., Bui, Yen Kim, Metzler, Kimberly R. Cordes, Ursell, Philip, Ivey, Kathryn N., Srivastava, Deepak

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A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells von Tsankov, Alexander M, Akopian, Veronika, Pop, Ramona, Chetty, Sundari, Gifford, Casey A, Daheron, Laurence, Tsankova, Nadejda M, Meissner, Alexander

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Genetic determinants and epigenetic effects of pioneer-factor occupancy von Donaghey, Julie, Thakurela, Sudhir, Charlton, Jocelyn, Chen, Jennifer S., Smith, Zachary D., Gu, Hongcang, Pop, Ramona, Clement, Kendell, Stamenova, Elena K., Karnik, Rahul, Kelley, David R., Gifford, Casey A., Cacchiarelli, Davide, Rinn, John L., Gnirke, Andreas, Ziller, Michael J., Meissner, Alexander

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Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming von Stone, Nicole R., Gifford, Casey A., Thomas, Reuben, Pratt, Karishma J.B., Samse-Knapp, Kaitlen, Mohamed, Tamer M.A., Radzinsky, Ethan M., Schricker, Amelia, Ye, Lin, Yu, Pengzhi, van Bemmel, Joke G., Ivey, Kathryn N., Pollard, Katherine S., Srivastava, Deepak

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Transcription factor protein interactomes reveal genetic determinants in heart disease von Gonzalez-Teran, Barbara, Pittman, Maureen, Felix, Franco, Thomas, Reuben, Richmond-Buccola, Desmond, Hüttenhain, Ruth, Choudhary, Krishna, Moroni, Elisabetta, Costa, Mauro W., Huang, Yu, Padmanabhan, Arun, Alexanian, Michael, Lee, Clara Youngna, Maven, Bonnie E.J., Samse-Knapp, Kaitlen, Morton, Sarah U., McGregor, Michael, Gifford, Casey A., Seidman, J.G., Seidman, Christine E., Gelb, Bruce D., Colombo, Giorgio, Conklin, Bruce R., Black, Brian L., Bruneau, Benoit G., Krogan, Nevan J., Pollard, Katherine S., Srivastava, Deepak

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Dissecting neural differentiation regulatory networks through epigenetic footprinting von Ziller, Michael J., Edri, Reuven, Yaffe, Yakey, Donaghey, Julie, Pop, Ramona, Mallard, William, Issner, Robbyn, Gifford, Casey A., Goren, Alon, Xing, Jeffrey, Gu, Hongcang, Cacchiarelli, Davide, Tsankov, Alexander M., Epstein, Charles, Rinn, John L., Mikkelsen, Tarjei S., Kohlbacher, Oliver, Gnirke, Andreas, Bernstein, Bradley E., Elkabetz, Yechiel, Meissner, Alexander

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Differentiation of V2a interneurons from human pluripotent stem cells von Butts, Jessica C., McCreedy, Dylan A., Martinez-Vargas, Jorge Alexis, Mendoza-Camacho, Frederico N., Hookway, Tracy A., Gifford, Casey A., Taneja, Praveen, Noble-Haeusslein, Linda, McDevitt, Todd C.

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Threonine phosphorylation post-translationally regulates protein secretion in Pseudomonas aeruginosa von Mougous, Joseph D., Gifford, Casey A., Ramsdell, Talia L., Mekalanos, John J.

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SARS-CoV-2 Susceptibility and ACE2 Gene Variations Within Diverse Ethnic Backgrounds von Vadgama, Nirmal, Kreymerman, Alexander, Campbell, Jackie, Shamardina, Olga, Brugger, Christiane, Research Consortium, Genomics England, Deaconescu, Alexandra M, Lee, Richard T, Penkett, Christopher J, Gifford, Casey A, Mercola, Mark, Nasir, Jamal, Karakikes, Ioannis

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Transcriptional and Chromatin Dynamics of Muscle Regeneration after Severe Trauma von Aguilar, Carlos A., Pop, Ramona, Shcherbina, Anna, Watts, Alain, Matheny, Ronald W., Cacchiarelli, Davide, Han, Woojin M., Shin, Eunjung, Nakhai, Shadi A., Jang, Young C., Carrigan, Christopher T., Gifford, Casey A., Kottke, Melissa A., Cesana, Marcella, Lee, Jackson, Urso, Maria L., Meissner, Alexander

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Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency von Cacchiarelli, Davide, Trapnell, Cole, Ziller, Michael J., Soumillon, Magali, Cesana, Marcella, Karnik, Rahul, Donaghey, Julie, Smith, Zachary D., Ratanasirintrawoot, Sutheera, Zhang, Xiaolan, Ho Sui, Shannan J., Wu, Zhaoting, Akopian, Veronika, Gifford, Casey A., Doench, John, Rinn, John L., Daley, George Q., Meissner, Alexander, Lander, Eric S., Mikkelsen, Tarjei S.

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Heart disease modelling adds a Notch to its belt von Gifford, Casey A., Srivastava, Deepak

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Epigenetic obstacles encountered by transcription factors: reprogramming against all odds von Gifford, Casey A, Meissner, Alexander

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Transcription Factor GATA4 Regulates Cell Type–Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell–Derived Cardiac Progenitors von Zhu, Lili, Choudhary, Krishna, Gonzalez-Teran, Barbara, Ang, Yen-Sin, Thomas, Reuben, Stone, Nicole R., Liu, Lei, Zhou, Ping, Zhu, Chenchen, Ruan, Hongmei, Huang, Yu, Jin, Shibo, Pelonero, Angelo, Koback, Frances, Padmanabhan, Arun, Sadagopan, Nandhini, Hsu, Austin, Costa, Mauro W., Gifford, Casey A., van Bemmel, Joke G., Hüttenhain, Ruth, Vedantham, Vasanth, Conklin, Bruce R., Black, Brian L., Bruneau, Benoit G., Steinmetz, Lars, Krogan, Nevan J., Pollard, Katherine S., Srivastava, Deepak

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Virulence Locus of Pseudomonas aeruginosa Encodes a Protein Secretion Apparatus von Mougous, Joseph D, Cuff, Marianne E, Raunser, Stefan, Shen, Aimee, Zhou, Min, Gifford, Casey A, Goodman, Andrew L, Joachimiak, Grazyna, Ordoñez, Claudia L, Lory, Stephen, Walz, Thomas, Joachimiak, Andrzej, Mekalanos, John J

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