Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes
Brannan, Kristopher W., Chaim, Isaac A., Marina, Ryan J., Yee, Brian A., Kofman, Eric R., Lorenz, Daniel A., Jagannatha, Pratibha, Dong, Kevin D., Madrigal, Assael A., Underwood, Jason G., Yeo, Gene W.
Published in Nature methods (01.05.2021)
Published in Nature methods (01.05.2021)
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Characterization of the human ESC transcriptome by hybrid sequencing
Au, Kin Fai, Sebastiano, Vittorio, Afshar, Pegah Tootoonchi, Durruthy, Jens Durruthy, Lee, Lawrence, Williams, Brian A, van Bakel, Harm, Schadt, Eric E, Reijo-Pera, Renee A, Underwood, Jason G, Wong, Wing Hung
Published in Proceedings of the National Academy of Sciences - PNAS (10.12.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (10.12.2013)
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Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation
Fiddes, Ian T, Armstrong, Joel, Diekhans, Mark, Nachtweide, Stefanie, Kronenberg, Zev N, Underwood, Jason G, Gordon, David, Earl, Dent, Keane, Thomas, Eichler, Evan E, Haussler, David, Stanke, Mario, Paten, Benedict
Published in Genome research (01.07.2018)
Published in Genome research (01.07.2018)
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Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing
Weirather, Jason L, Afshar, Pegah Tootoonchi, Clark, Tyson A, Tseng, Elizabeth, Powers, Linda S, Underwood, Jason G, Zabner, Joseph, Korlach, Jonas, Wong, Wing Hung, Au, Kin Fai
Published in Nucleic acids research (15.10.2015)
Published in Nucleic acids research (15.10.2015)
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FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
Salama, Sofie R, Underwood, Jason G, Uzilov, Andrew V, Katzman, Sol, Onodera, Courtney S, Mainzer, Jacob E, Mathews, David H, Lowe, Todd M, Haussler, David
Published in Nature methods (01.12.2010)
Published in Nature methods (01.12.2010)
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Massively multiplex single-molecule oligonucleosome footprinting
Abdulhay, Nour J, McNally, Colin P, Hsieh, Laura J, Kasinathan, Sivakanthan, Keith, Aidan, Estes, Laurel S, Karimzadeh, Mehran, Underwood, Jason G, Goodarzi, Hani, Narlikar, Geeta J, Ramani, Vijay
Published in eLife (02.12.2020)
Published in eLife (02.12.2020)
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Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes
Hsieh, PingHsun, Vollger, Mitchell R, Dang, Vy, Porubsky, David, Baker, Carl, Cantsilieris, Stuart, Hoekzema, Kendra, Lewis, Alexandra P, Munson, Katherine M, Sorensen, Melanie, Kronenberg, Zev N, Murali, Shwetha, Nelson, Bradley J, Chiatante, Giorgia, Maggiolini, Flavia Angela Maria, Blanché, Hélène, Underwood, Jason G, Antonacci, Francesca, Deleuze, Jean-François, Eichler, Evan E
Published in Science (American Association for the Advancement of Science) (18.10.2019)
Published in Science (American Association for the Advancement of Science) (18.10.2019)
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Transcriptional fates of human-specific segmental duplications in brain
Dougherty, Max L, Underwood, Jason G, Nelson, Bradley J, Tseng, Elizabeth, Munson, Katherine M, Penn, Osnat, Nowakowski, Tomasz J, Pollen, Alex A, Eichler, Evan E
Published in Genome research (01.10.2018)
Published in Genome research (01.10.2018)
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ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms
Sheynkman, Gloria M., Tuttle, Katharine S., Laval, Florent, Tseng, Elizabeth, Underwood, Jason G., Yu, Liang, Dong, Da, Smith, Melissa L., Sebra, Robert, Willems, Luc, Hao, Tong, Calderwood, Michael A., Hill, David E., Vidal, Marc
Published in Nature communications (11.05.2020)
Published in Nature communications (11.05.2020)
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Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans
Hsieh, PingHsun, Dang, Vy, Vollger, Mitchell R., Mao, Yafei, Huang, Tzu-Hsueh, Dishuck, Philip C., Baker, Carl, Cantsilieris, Stuart, Lewis, Alexandra P., Munson, Katherine M., Sorensen, Melanie, Welch, AnneMarie E., Underwood, Jason G., Eichler, Evan E.
Published in Nature communications (25.08.2021)
Published in Nature communications (25.08.2021)
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Long-read sequencing of chicken transcripts and identification of new transcript isoforms
Thomas, Sean, Underwood, Jason G, Tseng, Elizabeth, Holloway, Alisha K
Published in PloS one (01.04.2014)
Published in PloS one (01.04.2014)
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An evolutionary driver of interspersed segmental duplications in primates
Cantsilieris, Stuart, Sunkin, Susan M, Johnson, Matthew E, Anaclerio, Fabio, Huddleston, John, Baker, Carl, Dougherty, Max L, Underwood, Jason G, Sulovari, Arvis, Hsieh, PingHsun, Mao, Yafei, Catacchio, Claudia Rita, Malig, Maika, Welch, AnneMarie E, Sorensen, Melanie, Munson, Katherine M, Jiang, Weihong, Girirajan, Santhosh, Ventura, Mario, Lamb, Bruce T, Conlon, Ronald A, Eichler, Evan E
Published in Genome Biology (10.08.2020)
Published in Genome Biology (10.08.2020)
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