Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis by Meissner, Alexander, Gnirke, Andreas, Bell, George W., Ramsahoye, Bernard, Jaenisch, Rudolf, Lander, Eric Steven

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Comprehensive comparative analysis of strand-specific RNA sequencing methods by Regev, Aviv, Levin, Joshua Z., Yassour, Moran, Adiconis, Xian, Nusbaum, Chad, Thompson, Dawn Anne, Friedman, Nir, Gnirke, Andreas

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A unique regulatory phase of DNA methylation in the early mammalian embryo by Chan, Michelle Mei Wah, Regev, Aviv, Smith, Zachary D., Gu, Hongcang, Gnirke, Andreas, Meissner, Alexander, Mikkelsen, Tarjei Sigurd, 1978-

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Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species by Yassour, Moran, Pfiffner, Jenna, Levin, Joshua Z., Adiconis, Xian, Gnirke, Andreas, Nusbaum, Chad, Thompson, Dawn-Anne, Friedman, Nir, Regev, Aviv, Yassour, Moran

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Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution by Gu, Hongcang, Bock, Christoph, Jäger, Natalie, Smith, Zachary D., Tomazou, Eleni, Gnirke, Andreas, Meissner, Alexander, Mikkelsen, Tarjei Sigurd, 1978-, Lander, Eric Steven

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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes by van Berkum, Nynke L., Lieberman-Aiden, Erez, Williams, Louise, Gnirke, Andreas, Dekker, Job, Imakaev, Maksim Viktorovich, Mirny, Leonid A, Lander, Eric Steven

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Development and evaluation of RNA-seq methods by Levin, Joshua Z., Adiconis, Xian, Yassour, Moran, Thompson, Dawn, Guttman, Mitchell, Berger, Michael F., Fan, Lin, Friedman, Nir, Nusbaum, Chad, Gnirke, Andreas, Regev, Aviv

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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells by Rabani, Michal, Levin, Joshua Z., Fan, Lin, Adiconis, Xian, Raychowdhury, Raktima, Garber, Manuel, Gnirke, Andreas, Nusbaum, Chad, Hacohen, Nir, Friedman, Nir, Amit, Ido, Regev, Aviv

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Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs by Guttman, Mitchell, Garber, Manuel, Levin, Joshua Z., Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J., Gnirke, Andreas, Nusbaum, Chad, Rinn, John L., Regev, Aviv, Lander, Eric Steven

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Development and Validation of a Mass Spectrometry–Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease by Blumenstiel, Brendan, DeFelice, Matthew, Birsoy, Ozge, Bleyer, Anthony J., Kmoch, Stanislav, Carter, Todd A., Gnirke, Andreas, Kidd, Kendrah, Rehm, Heidi L., Ronco, Lucienne, Gabriel, Stacey, Lennon, Niall J., Lander, Eric Steven

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Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay by Melnikov, Alexandre, Murugan, Anand, Zhang, Xiaolan, Tesileanu, Tiberiu, Wang, Li, Rogov, Peter, Feizi-Khankandi, Soheil, Gnirke, Andreas, Callan Jr, Curtis G., Kinney, Justin B., Kellis, Manolis, Lander, Eric S., Mikkelsen, Tarjei Sigurd, 1978-

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Comparative analysis of RNA sequencing methods for degraded or low-input samples by 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.

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Comparative analysis of RNA sequencing methods for degraded or low-input samples by 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.

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells by Shalek, Alex K., Satija, Rahul, Adiconis, Xian, Gertner, Rona S., Gaublomme, Jellert T., Raychowdhury, Raktima, Schwartz, Schraga, Yosef, Nir, Malboeuf, Christine, Trombetta, John J., Gennert, David, Gnirke, Andreas, Goren, Alon, Hacohen, Nir, Levin, Joshua Z., Park, Hongkun, Regev, Aviv, Lu, Diana, Ph. D. Massachusetts Institute of Technology

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Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes by 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., Aiden, Erez Lieberman, Lander, Eric Steven

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High-quality draft assemblies of mammalian genomes from massively parallel sequence data by Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Felipe J., Burton, Joshua, 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, Jaffe, David B., Lander, Eric Steven

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ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth by Andersson, Leif, Hjalm, Goran, Andersson, Goran, Lindblad-Toh, Kerstin, Wadelius, Claes, Kullander, Klas, Zierath, Juleen R., Ponten, Fredrik, De, Sachinandan, Stromberg, Sara, Yan, Jie, Barres, Romain, Lindroth, Anders M., Gnirke, Andreas, Saenz-Vash, Veronica, Wang, Li, Zhang, Xiaolan, Larhammar, Martin, Wallerman, Ola, Jaffe, Jacob D., Jiang, Lin, Markljung, Ellen, Mikkelsen, Tarjei Sigurd, 1978-, Carr, Steven A, Lander, Eric Steven

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A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals by Garber, Manuel, Yosef, Nir, Goren, Alon, Raychowdhury, Raktima, Thielke, Anne, Guttman, Mitchell, Robinson, James, Minie, Brian, Chevrier, Nicolas, Itzhaki, Zohar, Blecher-Gonen, Ronnie, Bornstein, Chamutal, Amann-Zalcenstein, Daniela, Weiner, Assaf, Friedrich, Dennis C., Meldrim, James C., Ram, Oren, Cheng, Christine S., Gnirke, Andreas, Fisher, Sheila, Friedman, Nir, Wong, Bang, Bernstein, Bradley E., Nusbaum, Chad, Hacohen, Nir, Regev, Aviv, Amit, Ido

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Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia by Landau, Dan A., Clement, Kendell, Ziller, Michael J., Boyle, Patrick, Fan, Jean, Gu, Hongcang, Stevenson, Kristen, Sougnez, Carrie, Wang, Lili, Li, Shuqiang, Kotliar, Dylan, Zhang, Wandi, Ghandi, Mahmoud, Garraway, Levi, Fernandes, Stacey M., Livak, Kenneth J., Gabriel, Stacey, Gnirke, Andreas, Brown, Jennifer R., Neuberg, Donna, Kharchenko, Peter V., Hacohen, Nir, Getz, Gad, Meissner, Alexander, Wu, Catherine J., Lander, Eric Steven

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Integrative analysis of the melanoma transcriptome by Berger, Michael F., Levin, Joshua Z., Vijayendran, Krishna, Sivachenko, Andrey, Adiconis, Xian, Maguire, Jared, Johnson, Laura A., Robinson, James, Verhaak, Roel G., Sougnez, Carrie, Onofrio, Robert, Ziaugra, Liuda, Cibulskis, Kristian, Laine, Elisabeth, Barretina, Jordi, Winckler, Wendy, Fisher, David E., Getz, Gad, Meyerson, Matthew L., Jaffe, David B., Gabriel, Stacey B., Dummer, Reinhard, Gnirke, Andreas, Nusbaum, Chad, Garraway, Levi A., Lander, Eric Steven

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