Now showing items 1-14 of 14

    • Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors 

      Edri, Reuven; Yaffe, Yakey; Ziller, Michael J.; Mutukula, Naresh; Volkman, Rotem; David, Eyal; Jacob-Hirsch, Jasmine; Malcov, Hagar; Levy, Carmit; Rechavi, Gideon; Gat-Viks, Irit; Meissner, Alexander; Elkabetz, Yechiel (Nature Pub. Group, 2015)
      Decoding heterogeneity of pluripotent stem cell (PSC)-derived neural progeny is fundamental for revealing the origin of diverse progenitors, for defining their lineages, and for identifying fate determinants driving ...
    • Charting a dynamic DNA methylation landscape of the human genome 

      Ziller, Michael J.; Gu, Hongcang; Müller, Fabian; Donaghey, Julie; Tsai, Linus T.-Y.; Kohlbacher, Oliver; De Jager, Phil L.; Rosen, Evan D.; Bennett, David A.; Bernstein, Bradley E.; Gnirke, Andreas; Meissner, Alexander (2013)
      DNA methylation is a defining feature of mammalian cellular identity and essential for normal development1,2. Most cell types, except germ cells and pre-implantation embryos3–5, display relatively stable DNA methylation ...
    • Coverage recommendations for methylation analysis by whole genome bisulfite sequencing 

      Ziller, Michael J.; Hansen, Kasper D.; Meissner, Alexander; Aryee, Martin J. (2014)
      Whole genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling but the associated high sequencing costs continue to limit its widespread application. We utilized several high coverage reference data ...
    • Epigenomics and Chromatin Dynamics 

      Akopian, Veronika; Chan, Michelle; Clement, Kendell; Galonska, Christina; Gifford, Casey; Lehtola, Elizabeth; Liao, Jing; Samavarchi-Tehrani, Payman; Sindhu, Camille; Smith, Zachary D; Tsankov, Alexander; Webster, Jamie Orme; Zhang, Yingying; Ziller, Michael Johannes; Meissner, Alexander (BioMed Central, 2012)
      A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012. This year's Joint Keystone Symposium on Epigenomics and Chromatin Dynamics was one of the largest ...
    • Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling 

      Boyle, Patrick; Clement, Kendell; Gu, Hongcang; Smith, Zachary D; Ziller, Michael Johannes; Fostel, Jennifer L; Holmes, Laurie; Meldrim, Jim; Kelley, Fontina; Gnirke, Andreas; Meissner, Alexander (BioMed Central, 2012)
      Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To ...
    • Information recovery from low coverage whole-genome bisulfite sequencing 

      Libertini, Emanuele; Heath, Simon C.; Hamoudi, Rifat A.; Gut, Marta; Ziller, Michael J.; Czyz, Agata; Ruotti, Victor; Stunnenberg, Hendrik G.; Frontini, Mattia; Ouwehand, Willem H.; Meissner, Alexander; Gut, Ivo G.; Beck, Stephan (Nature Publishing Group, 2016)
      The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important ...
    • Integrative analysis of 111 reference human epigenomes 

      Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Kheradpour, Pouya; Zhang, Zhizhuo; Heravi-Moussavi, Alireza; Liu, Yaping; Amin, Viren; Ziller, Michael J; Whitaker, John W; Schultz, Matthew D; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Wang, Jianrong; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Pfenning, Andreas; Wang, Xinchen; Claussnitzer, Melina; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven; Li, Wei; Marra, Marco; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, Manolis (2015)
      The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but a similar reference has lacked for epigenomic studies. To address this need, the NIH Roadmap ...
    • Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia 

      Landau, Dan Avi; Clement, Kendell; Ziller, Michael Johannes; Boyle, Patrick; Fan, Jean; Gu, Hongcang; Stevenson, Kristen; Sougnez, Carrie; Wang, Lili; Li, Shuqiang; Kotliar, Dylan; Zhang, Wandi; Ghandi, Mahmoud; Garraway, Levi Alexander; Fernandes, Stacey M.; Livak, Kenneth J.; Gabriel, Stacey; Gnirke, Andreas; Lander, Eric Steven; Brown, Jennifer Ruth; Neuberg, Donna S.; Kharchenko, Peter Vasili; Hacohen, Nir; Getz, Gad A; Meissner, Alexander; Wu, Catherine J. (Elsevier BV, 2014)
      Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic ...
    • Notch Inhibition Allows Oncogene-Independent Generation of iPS Cells 

      Ichida, Justin K.; TCW, Julia; Williams Gonzalez, Luis Alberto; Carter, Ava; Shi, Yingxiao; Moura, Marcelo T.; Ziller, Michael Johannes; Singh, Sean; Amabile, Giovanni; Bock, Christoph; Umezawa, Akihiro; Rubin, Lee; Bradner, James Elliott; Akutsu, Hidenori; Meissner, Alexander; Eggan, Kevin Carl (Nature Publishing Group, 2014)
      The reprogramming of somatic cells to pluripotency using defined transcription factors holds great promise for biomedicine. However, human reprogramming remains inefficient and relies either on the use of the potentially ...
    • Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1 

      Kiskinis, Evangelos; Sandoe, Jackson L; Williams, Lauren N.; Boulting, Gabriella Lutz; Moccia, Robert; Wainger, Brian Jason; Han, Steve Sang-woo; Peng, Theodore; Thams, Sebastian; Mikkilineni, Shravani; Mellin, Cassidy; Merkle, Florian Tobias; Davis-Dusenbery, B; Ziller, Michael Johannes; Oakley, Derek Hayden; Ichida, Justin; Di Costanzo, Stefania; Atwater, Nick; Maeder, M; Goodwin, Marcus; Nemesh, James; Handsaker, Robert E; Paull, Daniel; Noggle, Scott; McCarroll, Steven A.; Joung, Jae Keith; Woolf, Carl; Brown, Robert H; Eggan, Kevin Carl (Elsevier BV, 2014)
      Direct electrical recording and stimulation of neural activity using micro-fabricated silicon and metal micro-wire probes have contributed extensively to basic neuroscience and therapeutic applications; however, the ...
    • The systems biology simulation core algorithm 

      Keller, Roland; Dörr, Alexander; Tabira, Akito; Funahashi, Akira; Ziller, Michael J; Adams, Richard; Rodriguez, Nicolas; Novère, Nicolas Le; Hiroi, Noriko; Planatscher, Hannes; Zell, Andreas; Dräger, Andreas (BioMed Central, 2013)
      Background: With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems ...
    • Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells 

      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 (2015)
      DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Here we inactivated all three catalytically active DNA methyltransferases in human embryonic stem ...
    • Transcription factor binding dynamics during human ESC differentiation 

      Tsankov, Alexander M.; Gu, Hongcang; Akopian, Veronika; Ziller, Michael J.; Donaghey, Julie; Amit, Ido; Gnirke, Andreas; Meissner, Alexander (2015)
      Summary Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome wide ...
    • Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells 

      Gifford, Casey A.; Ziller, Michael Johannes; Gu, Hongcang; Trapnell, Cole; Donaghey, Julie A; Tsankov, Alexander; Shalek, Alex K.; Kelley, David Roy; Shishkin, Alexander A.; Issner, Robbyn; Zhang, Xiaolan; Coyne, Michael J.; Fostel, Jennifer L.; Holmes, Laurie; Meldrim, Jim; Guttman, Mitchell; Epstein, Charles; Park, Hongkun; Kohlbacher, Oliver; Rinn, John L; Gnirke, Andreas; Lander, Eric Steven; Bernstein, Bradley E.; Meissner, Alexander (Elsevier BV, 2013)
      Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive ...