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Friedman, Nir, Regev, Aviv, Grabherr, Manfred G, Haas, Brian J, Yassour, Moran, Levin, Joshua Z, Thompson, Dawn A, Amit, Ido, Adiconis, Xian, Fan, Lin, Raychowdhury, Raktima, Zeng, Qiandong, Chen, Zehua, Mauceli, Evan, Hacohen, Nir, Gnirke, Andreas, Rhind, Nicholas, di Palma, Federica, Birren, Bruce W, Nusbaum, Chad, Lindblad-Toh, Kerstin
Published in Nature biotechnology (01.07.2011)
Published in Nature biotechnology (01.07.2011)
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Comprehensive comparative analysis of strand-specific RNA sequencing methods
Levin, Joshua Z, Regev, Aviv, Yassour, Moran, Adiconis, Xian, Nusbaum, Chad, Thompson, Dawn Anne, Friedman, Nir, Gnirke, Andreas
Published in Nature methods (01.09.2010)
Published in Nature methods (01.09.2010)
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Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Sanborn, Adrian L., Rao, Suhas S. P., Huang, Su-Chen, Durand, Neva C., Huntley, Miriam H., Jewett, Andrew I., Bochkov, Ivan D., Chinnappan, Dharmaraj, Cutkosky, Ashok, Li, Jian, Geeting, Kristopher P., Gnirke, Andreas, Melnikov, Alexandre, McKenna, Doug, Stamenova, Elena K., Lander, Eric S., Aiden, Erez Lieberman
Published in Proceedings of the National Academy of Sciences - PNAS (24.11.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (24.11.2015)
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Transcription factor binding dynamics during human ES cell differentiation
Tsankov, Alexander M., Gu, Hongcang, Akopian, Veronika, Ziller, Michael J., Donaghey, Julie, Amit, Ido, Gnirke, Andreas, Meissner, Alexander
Published in Nature (London) (19.02.2015)
Published in Nature (London) (19.02.2015)
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Smart-RRBS for single-cell methylome and transcriptome analysis
Gu, Hongcang, Raman, Ayush T., Wang, Xiaoxue, Gaiti, Federico, Chaligne, Ronan, Mohammad, Arman W., Arczewska, Aleksandra, Smith, Zachary D., Landau, Dan A., Aryee, Martin J., Meissner, Alexander, Gnirke, Andreas
Published in Nature protocols (01.08.2021)
Published in Nature protocols (01.08.2021)
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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, Philip L., Rosen, Evan D., Bennett, David A., Bernstein, Bradley E., Gnirke, Andreas, Meissner, Alexander
Published in Nature (London) (22.08.2013)
Published in Nature (London) (22.08.2013)
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Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer
Smith, Zachary D., Shi, Jiantao, Gu, Hongcang, Donaghey, Julie, Clement, Kendell, Cacchiarelli, Davide, Gnirke, Andreas, Michor, Franziska, Meissner, Alexander
Published in Nature (London) (28.09.2017)
Published in Nature (London) (28.09.2017)
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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Shalek, Alex K., Satija, Rahul, Adiconis, Xian, Gertner, Rona S., Gaublomme, Jellert T., Raychowdhury, Raktima, Schwartz, Schraga, Yosef, Nir, Malboeuf, Christine, Lu, Diana, Trombetta, John J., Gennert, Dave, Gnirke, Andreas, Goren, Alon, Hacohen, Nir, Levin, Joshua Z., Park, Hongkun, Regev, Aviv
Published in Nature (London) (13.06.2013)
Published in Nature (London) (13.06.2013)
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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
Published in Nature genetics (01.05.2015)
Published in Nature genetics (01.05.2015)
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Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
Bock, Christoph, Kiskinis, Evangelos, Verstappen, Griet, Gu, Hongcang, Boulting, Gabriella, Smith, Zachary D., Ziller, Michael, Croft, Gist F., Amoroso, Mackenzie W., Oakley, Derek H., Gnirke, Andreas, Eggan, Kevin, Meissner, Alexander
Published in Cell (04.02.2011)
Published in Cell (04.02.2011)
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Comparative analysis of RNA sequencing methods for degraded or low-input samples
Adiconis, Xian, Borges-Rivera, Diego, Satija, Rahul, DeLuca, David S, Busby, Michele A, Berlin, Aaron M, Sivachenko, Andrey, Thompson, Dawn Anne, Wysoker, Alec, Fennell, Timothy, Gnirke, Andreas, Pochet, Nathalie, Regev, Aviv, Levin, Joshua Z
Published in Nature methods (01.07.2013)
Published in Nature methods (01.07.2013)
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DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells
Bock, Christoph, Beerman, Isabel, Lien, Wen-Hui, Smith, Zachary D., Gu, Hongcang, Boyle, Patrick, Gnirke, Andreas, Fuchs, Elaine, Rossi, Derrick J., Meissner, Alexander
Published in Molecular cell (24.08.2012)
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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
Melnikov, Alexandre, Murugan, Anand, Zhang, Xiaolan, Tesileanu, Tiberiu, Wang, Li, Rogov, Peter, Feizi, Soheil, Gnirke, Andreas, Callan, Curtis G, Kinney, Justin B, Kellis, Manolis, Lander, Eric S, Mikkelsen, Tarjei S
Published in Nature biotechnology (01.03.2012)
Published in Nature biotechnology (01.03.2012)
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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Guttman, Mitchell, Garber, Manuel, Regev, Aviv, Levin, Joshua Z, Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J, Gnirke, Andreas, Nusbaum, Chad, Rinn, John L, Lander, Eric S
Published in Nature biotechnology (01.05.2010)
Published in Nature biotechnology (01.05.2010)
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Quantitative comparison of genome-wide DNA methylation mapping technologies
Brinkman, Arie B, Meissner, Alexander, Gu, Hongcang, Müller, Fabian, Bock, Christoph, Jäger, Natalie, Tomazou, Eleni M, Stunnenberg, Hendrik G, Gnirke, Andreas, Simmer, Femke
Published in Nature biotechnology (01.10.2010)
Published in Nature biotechnology (01.10.2010)
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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J, Burton, Joshua N, Walker, Bruce J, Sharpe, Ted, Hall, Giles, Shea, Terrance P, Sykes, Sean, Berlin, Aaron M, Aird, Daniel, Costello, Maura, Daza, Riza, Williams, Louise, Nicol, Robert, Gnirke, Andreas, Nusbaum, Chad, Lander, Eric S, Jaffe, David B
Published in Proceedings of the National Academy of Sciences - PNAS (25.01.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (25.01.2011)
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Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinopathy
Dvela-Levitt, Moran, Kost-Alimova, Maria, Emani, Maheswarareddy, Kohnert, Eva, Thompson, Rebecca, Sidhom, Eriene-Heidi, Rivadeneira, Ana, Sahakian, Nareh, Roignot, Julie, Papagregoriou, Gregory, Montesinos, Monica S., Clark, Abbe R., McKinney, David, Gutierrez, Juan, Roth, Mark, Ronco, Lucienne, Elonga, Esther, Carter, Todd A., Gnirke, Andreas, Melanson, Michelle, Hartland, Kate, Wieder, Nicolas, Hsu, Jane C.-H., Deltas, Constantinos, Hughey, Rebecca, Bleyer, Anthony J., Kmoch, Stanislav, Živná, Martina, Barešova, Veronika, Kota, Savithri, Schlondorff, Johannes, Heiman, Myriam, Alper, Seth L., Wagner, Florence, Weins, Astrid, Golub, Todd R., Lander, Eric S., Greka, Anna
Published in Cell (25.07.2019)
Published in Cell (25.07.2019)
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Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
Pastore, Alessandro, Gaiti, Federico, Lu, Sydney X., Brand, Ryan M., Kulm, Scott, Chaligne, Ronan, Gu, Hongcang, Huang, Kevin Y., Stamenova, Elena K., Béguelin, Wendy, Jiang, Yanwen, Schulman, Rafael C., Kim, Kyu-Tae, Alonso, Alicia, Allan, John N., Furman, Richard R., Gnirke, Andreas, Wu, Catherine J., Melnick, Ari M., Meissner, Alexander, Bernstein, Bradley E., Abdel-Wahab, Omar, Landau, Dan A.
Published in Nature communications (23.04.2019)
Published in Nature communications (23.04.2019)
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Genetic determinants and epigenetic effects of pioneer-factor occupancy
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
Published in Nature genetics (01.02.2018)
Published in Nature genetics (01.02.2018)
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