Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes

by Melnikov, Alexandre, Rogov, Peter, Wang, Li, Gnirke, Andreas, Mikkelsen, Tarjei S.
Published 2014

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

by Meissner, Alexander, Gnirke, Andreas, Bell, George W., Ramsahoye, Bernard, Lander, Eric S., Jaenisch, Rudolf
Published 2005

A unique regulatory phase of DNA methylation in the early mammalian embryo

by Smith, Zachary D., Chan, Michelle M., Mikkelsen, Tarjei S., Gu, Hongcang, Gnirke, Andreas, Regev, Aviv, Meissner, Alexander
Published 2012

Targeted bisulfite sequencing of the dynamic DNA methylome

by Ziller, Michael J., Stamenova, Elena K., Gu, Hongcang, Gnirke, Andreas, Meissner, Alexander
Published 2016

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

by van Berkum, Nynke L., Lieberman-Aiden, Erez, Williams, Louise, Imakaev, Maxim, Gnirke, Andreas, Mirny, Leonid A., Dekker, Job, Lander, Eric S.
Published 2010

Transcription factor binding dynamics during human ESC differentiation

by Tsankov, Alexander M., Gu, Hongcang, Akopian, Veronika, Ziller, Michael J., Donaghey, Julie, Amit, Ido, Gnirke, Andreas, Meissner, Alexander
Published 2015

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

by Ziller, Michael J., Müller, Fabian, Liao, Jing, Zhang, Yingying, Gu, Hongcang, Bock, Christoph, Boyle, Patrick, Epstein, Charles B., Bernstein, Bradley E., Lengauer, Thomas, Gnirke, Andreas, Meissner, Alexander
Published 2011

Genome-wide mapping of DNA methylation: a quantitative technology comparison

by Bock, Christoph, Tomazou, Eleni M., Brinkman, Arjen, Müller, Fabian, Simmer, Femke, Gu, Hongcang, Jäger, Natalie, Gnirke, Andreas, Stunnenberg, Hendrik G., Meissner, Alexander
Published 2010

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

by Aird, Daniel, Ross, Michael G, Chen, Wei-Sheng, Danielsson, Maxwell, Fennell, Timothy, Russ, Carsten, Jaffe, David B, Nusbaum, Chad, Gnirke, Andreas
Published 2011

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
Published 2011

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, Soheil, Gnirke, Andreas, Callan, Curtis G., Kinney, Justin B., Kellis, Manolis, Lander, Eric S., Mikkelsen, Tarjei S.
Published 2012

RNA-Seq methods for imperfect samples: development, evaluation and applications

by Adiconis, Xian, Fan, Lin, DeLuca, David, Sivachenko, Andrey, Pochet, Nathalie, Berlin, Aaron, Young, Sarah, Getz, Gad, Regev, Aviv, Nusbaum, Chad, Gnirke, Andreas, Levin, Joshua Z
Published 2011

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

by Boyle, Patrick, Clement, Kendell, Gu, Hongcang, Smith, Zachary D, Ziller, Michael, Fostel, Jennifer L, Holmes, Laurie, Meldrim, Jim, Kelley, Fontina, Gnirke, Andreas, Meissner, Alexander
Published 2012

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, Schragi, Yosef, Nir, Malboeuf, Christine, Lu, Diana, Trombetta, John T., Gennert, Dave, Gnirke, Andreas, Goren, Alon, Hacohen, Nir, Levin, Joshua Z., Park, Hongkun, Regev, Aviv
Published 2013

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

by Giannoukos, Georgia, Ciulla, Dawn M, Huang, Katherine, Haas, Brian J, Izard, Jacques, Levin, Joshua Z, Livny, Jonathan, Earl, Ashlee M, Gevers, Dirk, Ward, Doyle V, Nusbaum, Chad, Birren, Bruce W, Gnirke, Andreas
Published 2012

Comprehensive 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.
Published 2013

Charting a dynamic DNA methylation landscape of the human genome

by 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
Published 2013

Hybrid selection for sequencing pathogen genomes from clinical samples

by Melnikov, Alexandre, Galinsky, Kevin, Rogov, Peter, Fennell, Timothy, Van Tyne, Daria, Russ, Carsten, Daniels, Rachel, Barnes, Kayla G, Bochicchio, James, Ndiaye, Daouda, Sene, Papa D, Wirth, Dyann F, Nusbaum, Chad, Volkman, Sarah K, Birren, Bruce W, Gnirke, Andreas, Neafsey, Daniel E
Published 2011

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

by Bergman, Casey M, Pfeiffer, Barret D, Rincón-Limas, Diego E, Hoskins, Roger A, Gnirke, Andreas, Mungall, Chris J, Wang, Adrienne M, Kronmiller, Brent, Pacleb, Joanne, Park, Soo, Stapleton, Mark, Wan, Kenneth, George, Reed A, de Jong, Pieter J, Botas, Juan, Rubin, Gerald M, Celniker, Susan E
Published 2002

Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

by 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, Friedman, Nir, Regev, Aviv
Published 2011