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

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

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

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

Development and evaluation of RNA-seq methods

by Levin, Joshua, Adiconis, Xian, Yassour, Moran, Thompson, Dawn, Guttman, Mitchell, Berger, Michael, Fan, Lin, Friedman, Nir, Nusbaum, Chad, Gnirke, Andreas, Regev, Aviv
Published 2010

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

Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

by Mattei, Josiemer, Parnell, Laurence D, Lai, Chao-Qiang, Garcia-Bailo, Bibiana, Adiconis, Xian, Shen, Jian, Arnett, Donna, Demissie, Serkalem, Tucker, Katherine L, Ordovas, Jose M
Published 2009

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

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

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

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

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

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

Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing

by Simmons, Sean K., Lithwick-Yanai, Gila, Adiconis, Xian, Oberstrass, Florian, Iremadze, Nika, Geiger-Schuller, Kathryn, Thakore, Pratiksha I., Frangieh, Chris J., Barad, Omer, Almogy, Gilad, Rozenblatt-Rosen, Orit, Regev, Aviv, Lipson, Doron, Levin, Joshua Z.
Published 2022

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

Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons

by Tekin, Halil, Simmons, Sean, Cummings, Beryl, Gao, Linyi, Adiconis, Xian, Hession, Cynthia C., Ghoshal, Ayan, Dionne, Danielle, Choudhury, Sourav R., Yesilyurt, Volkan, Sanjana, Neville E., Shi, Xi, Lu, Congyi, Heidenreich, Matthias, Pan, Jen Q, Levin, Joshua Z., Zhang, Feng
Published 2018

Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity

by Sorek, Matan, Oweis, Walaa, Nissim-Rafinia, Malka, Maman, Moria, Simon, Shahar, Hession, Cynthia C., Adiconis, Xian, Simmons, Sean K., Sanjana, Neville E., Shi, Xi, Lu, Congyi, Pan, Jen Q., Xu, Xiaohong, Pouladi, Mahmoud A., Ellerby, Lisa M., Zhang, Feng, Levin, Joshua Z., Meshorer, Eran
Published 2021

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

Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types

by Ximerakis, Methodios, Holton, Kristina M., Giadone, Richard M., Ozek, Ceren, Saxena, Monika, Santiago, Samara, Adiconis, Xian, Dionne, Danielle, Nguyen, Lan, Shah, Kavya M., Goldstein, Jill M., Gasperini, Caterina, Gampierakis, Ioannis A., Lipnick, Scott L., Simmons, Sean K., Buchanan, Sean M., Wagers, Amy J., Regev, Aviv, Levin, Joshua Z., Rubin, Lee L.
Published 2023

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

by Cuomo, Christina A., Bakkeren, Guus, Khalil, Hala Badr, Panwar, Vinay, Joly, David, Linning, Rob, Sakthikumar, Sharadha, Song, Xiao, Adiconis, Xian, Fan, Lin, Goldberg, Jonathan M., Levin, Joshua Z., Young, Sarah, Zeng, Qiandong, Anikster, Yehoshua, Bruce, Myron, Wang, Meinan, Yin, Chuntao, McCallum, Brent, Szabo, Les J., Hulbert, Scot, Chen, Xianming, Fellers, John P.
Published 2016