Comprehensive comparative analysis of strand-specific RNA sequencing methods

by Levin, Joshua Z., Yassour, Moran, Adiconis, Xian, Nusbaum, Chad, Thompson, Dawn Anne, Friedman, Nir, Gnirke, Andreas, Regev, Aviv
Published 2010

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

by Matranga, Christian B., Gladden-Young, Adrianne, Qu, James, Winnicki, Sarah, Nosamiefan, Dolo, Levin, Joshua Z., Sabeti, Pardis C.
Published 2016

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
Published 2010

Use of the MS2 aptamer and coat protein for RNA localization in yeast: A response to “MS2 coat proteins bound to yeast mRNAs block 5′ to 3′ degradation and trap mRNA decay products...

by Haimovich, Gal, Zabezhinsky, Dmitry, Haas, Brian, Slobodin, Boris, Purushothaman, Pravinkumar, Fan, Lin, Levin, Joshua Z., Nusbaum, Chad, Gerst, Jeffrey E.
Published 2016

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

by Levin, Joshua Z, Berger, Michael F, Adiconis, Xian, Rogov, Peter, Melnikov, Alexandre, Fennell, Timothy, Nusbaum, Chad, Garraway, Levi A, Gnirke, Andreas
Published 2009

RNA-SeQC: RNA-seq metrics for quality control and process optimization

by DeLuca, David S., Levin, Joshua Z., Sivachenko, Andrey, Fennell, Timothy, Nazaire, Marc-Danie, Williams, Chris, Reich, Michael, Winckler, Wendy, Getz, Gad
Published 2012

Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA

by Miranda, Kevin C., Bond, Daniel T., Levin, Joshua Z., Adiconis, Xian, Sivachenko, Andrey, Russ, Carsten, Brown, Dennis, Nusbaum, Chad, Russo, Leileata M.
Published 2014

The effect of background noise and its removal on the analysis of single-cell expression data

by Janssen, Philipp, Kliesmete, Zane, Vieth, Beate, Adiconis, Xian, Simmons, Sean, Marshall, Jamie, McCabe, Cristin, Heyn, Holger, Levin, Joshua Z., Enard, Wolfgang, Hellmann, Ines
Published 2023

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

Lupus autoantibodies initiate a maladaptive equilibrium sustained by HMGB1:RAGE signaling and reversed by LAIR-1:C1q signaling

by Carroll, Kaitlin R., Mizrachi, Mark, Simmons, Sean, Toz, Bahtiyar, Wingard, Jeffrey, Tehrani, Nazila, Zarfeshani, Aida, Kello, Nina, Kowal, Czeslawa, Levin, Joshua Z., Volpe, Bruce T., Diamond, Betty
Published 2023

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

De novo assembly of highly diverse viral populations

by Yang, Xiao, Charlebois, Patrick, Gnerre, Sante, Coole, Matthew G, Lennon, Niall J, Levin, Joshua Z, Qu, James, Ryan, Elizabeth M, Zody, Michael C, Henn, Matthew R
Published 2012

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

by Velasco, Silvia, Kedaigle, Amanda J., Simmons, Sean K., Nash, Allison, Rocha, Marina, Quadrato, Giorgia, Paulsen, Bruna, Nguyen, Lan, Adiconis, Xian, Regev, Aviv, Levin, Joshua Z., Arlotta, Paola
Published 2019

Peptidomic discovery of short open reading frame-encoded peptides in human cells

by Slavoff, Sarah A., Mitchell, Andrew J., Schwaid, Adam G., Cabili, Moran N., Ma, Jiao, Levin, Joshua Z., Karger, Amir D., Budnik, Bogdan A., Rinn, John L., Saghatelian, Alan
Published 2012

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., Lander, Eric S., Regev, Aviv
Published 2010

Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development

by Zheng, Xinhe, Wu, Boli, Liu, Yuejia, Simmons, Sean K., Kim, Kwanho, Clarke, Grace S., Ashiq, Abdullah, Park, Joshua, Wang, Zhilin, Tong, Liqi, Wang, Qizhao, Xu, Xiangmin, Levin, Joshua Z., Jin, Xin
Published 2023

Comprehensive comparative analysis of 5’ end RNA sequencing methods

by Adiconis, Xian, Haber, Adam, Simmons, Sean K., Moonshine, Ami Levy, Ji, Zhe, Busby, Michele A., Shi, Xi, Jacques, Justin, Lancaster, Madeline A., Pan, Jen Q., Regev, Aviv, Levin, Joshua Z.
Published 2018

Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex

by Yuan, Wen, Ma, Sai, Brown, Juliana R., Kim, Kwanho, Murek, Vanessa, Trastulla, Lucia, Meissner, Alexander, Lodato, Simona, Shetty, Ashwin S., Levin, Joshua Z., Buenrostro, Jason D., Ziller, Michael J., Arlotta, Paola
Published 2022

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

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

by Cuomo, Christina A., Desjardins, Christopher A., Bakowski, Malina A., Goldberg, Jonathan, Ma, Amy T., Becnel, James J., Didier, Elizabeth S., Fan, Lin, Heiman, David I., Levin, Joshua Z., Young, Sarah, Zeng, Qiandong, Troemel, Emily R.
Published 2012