Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus

par Cone, Kelsey R., Kronenberg, Zev N., Yandell, Mark, Elde, Nels C.
Publié dans J Virol (2017)

Wham: Identifying Structural Variants of Biological Consequence

par Kronenberg, Zev N., Osborne, Edward J., Cone, Kelsey R., Kennedy, Brett J., Domyan, Eric T., Shapiro, Michael D., Elde, Nels C., Yandell, Mark
Publié dans PLoS Comput Biol (2015)

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

par 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
Publié dans Genome Res (2018)

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

par He, Yaoxi, Luo, Xin, Zhou, Bin, Hu, Ting, Meng, Xiaoyu, Audano, Peter A., Kronenberg, Zev N., Eichler, Evan E., Jin, Jie, Guo, Yongbo, Yang, Yanan, Qi, Xuebin, Su, Bing
Publié dans Nat Commun (2019)

Genomic patterns of de novo mutation in simplex autism

par Turner, Tychele N., Coe, Bradley P., Dickel, Diane E., Hoekzema, Kendra, Nelson, Bradley J., Zody, Michael C., Kronenberg, Zev N., Hormozdiari, Fereydoun, Raja, Archana, Pennacchio, Len A., Darnell, Robert B., Eichler, Evan E.
Publié dans Cell (2017)

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

par Mohajeri, Kiana, Cantsilieris, Stuart, Huddleston, John, Nelson, Bradley J., Coe, Bradley P., Campbell, Catarina D., Baker, Carl, Harshman, Lana, Munson, Katherine M., Kronenberg, Zev N., Kremitzki, Milinn, Raja, Archana, Catacchio, Claudia Rita, Graves, Tina A., Wilson, Richard K., Ventura, Mario, Eichler, Evan E.
Publié dans Genome Res (2016)

Discovery and genotyping of structural variation from long-read haploid genome sequence data

par Huddleston, John, Chaisson, Mark J.P., Steinberg, Karyn Meltz, Warren, Wes, Hoekzema, Kendra, Gordon, David, Graves-Lindsay, Tina A., Munson, Katherine M., Kronenberg, Zev N., Vives, Laura, Peluso, Paul, Boitano, Matthew, Chin, Chen-Shin, Korlach, Jonas, Wilson, Richard K., Eichler, Evan E.
Publié dans Genome Res (2017)

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data

par Huddleston, John, Chaisson, Mark J.P., Steinberg, Karyn Meltz, Warren, Wes, Hoekzema, Kendra, Gordon, David, Graves-Lindsay, Tina A., Munson, Katherine M., Kronenberg, Zev N., Vives, Laura, Peluso, Paul, Boitano, Matthew, Chin, Chen-Shin, Korlach, Jonas, Wilson, Richard K., Eichler, Evan E.
Publié dans Genome Res (2018)

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads

par VOLLGER, MITCHELL R., LOGSDON, GLENNIS A., AUDANO, PETER A., SULOVARI, ARVIS, PORUBSKY, DAVID, PELUSO, PAUL, WENGER, AARON M., CONCEPCION, GREGORY T., KRONENBERG, ZEV N., MUNSON, KATHERINE M., BAKER, CARL, SANDERS, ASHLEY D., SPIERINGS, DIANA C.J., LANSDORP, PETER M., SURTI, URVASHI, HUNKAPILLER, MICHAEL W., EICHLER, EVAN E.
Publié dans Ann Hum Genet (2019)

Long-read sequence assembly of the gorilla genome

par Gordon, David, Huddleston, John, Chaisson, Mark J. P., Hill, Christopher M., Kronenberg, Zev N., Munson, Katherine M., Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W., Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K., Haussler, David, Chin, Chen-Shan, Eichler, Evan E.
Publié dans Science (2016)

Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

par 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.
Publié dans Science (2019)

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

par Kronenberg, Zev N., Rhie, Arang, Koren, Sergey, Concepcion, Gregory T., Peluso, Paul, Munson, Katherine M., Porubsky, David, Kuhn, Kristen, Mueller, Kathryn A., Low, Wai Yee, Hiendleder, Stefan, Fedrigo, Olivier, Liachko, Ivan, Hall, Richard J., Phillippy, Adam M., Eichler, Evan E., Williams, John L., Smith, Timothy P. L., Jarvis, Erich D., Sullivan, Shawn T., Kingan, Sarah B.
Publié dans Nat Commun (2021)

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

par Pollen, Alex A., Bhaduri, Aparna, Andrews, Madeline G., Nowakowski, Tomasz J., Meyerson, Olivia S., Mostajo-Radji, Mohammed A., Di Lullo, Elizabeth, Alvarado, Beatriz, Bedolli, Melanie, Dougherty, Max L., Fiddes, Ian T., Kronenberg, Zev N., Shuga, Joe, Leyrat, Anne A., West, Jay A., Bershteyn, Marina, Lowe, Craig B., Pavlovic, Bryan J., Salama, Sofie R., Haussler, David, Eichler, Evan E., Kriegstein, Arnold R.
Publié dans Cell (2019)

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

par Low, Wai Yee, Tearle, Rick, Liu, Ruijie, Koren, Sergey, Rhie, Arang, Bickhart, Derek M., Rosen, Benjamin D., Kronenberg, Zev N., Kingan, Sarah B., Tseng, Elizabeth, Thibaud-Nissen, Françoise, Martin, Fergal J., Billis, Konstantinos, Ghurye, Jay, Hastie, Alex R., Lee, Joyce, Pang, Andy W. C., Heaton, Michael P., Phillippy, Adam M., Hiendleder, Stefan, Smith, Timothy P. L., Williams, John L.
Publié dans Nat Commun (2020)

De novo genic mutations among a Chinese autism spectrum disorder cohort

par Wang, Tianyun, Guo, Hui, Xiong, Bo, Stessman, Holly A.F., Wu, Huidan, Coe, Bradley P., Turner, Tychele N., Liu, Yanling, Zhao, Wenjing, Hoekzema, Kendra, Vives, Laura, Xia, Lu, Tang, Meina, Ou, Jianjun, Chen, Biyuan, Shen, Yidong, Xun, Guanglei, Long, Min, Lin, Janice, Kronenberg, Zev N., Peng, Yu, Bai, Ting, Li, Honghui, Ke, Xiaoyan, Hu, Zhengmao, Zhao, Jingping, Zou, Xiaobing, Xia, Kun, Eichler, Evan E.
Publié dans Nat Commun (2016)

High-resolution comparative analysis of great ape genomes

par Kronenberg, Zev N., Fiddes, Ian T., Gordon, David, Murali, Shwetha, Cantsilieris, Stuart, Meyerson, Olivia S., Underwood, Jason G., Nelson, Bradley J., Chaisson, Mark J.P., Dougherty, Max L., Munson, Katherine M., Hastie, Alex R., Diekhans, Mark, Hormozdiari, Fereydoun, Lorusso, Nicola, Hoekzema, Kendra, Qiu, Ruolan, Clark, Karen, Raja, Archana, Welch, AnneMarie E., Sorensen, Melanie, Baker, Carl, Fulton, Robert S., Armstrong, Joel, Graves-Lindsay, Tina A., Denli, Ahmet M., Hoppe, Emma R., Hsieh, PingHsun, Hill, Christopher M., Pang, Andy Wing Chun, Lee, Joyce, Lam, Ernest T., Dutcher, Susan K., Gage, Fred H., Warren, Wesley C., Shendure, Jay, Haussler, David, Schneider, Valerie A., Cao, Han, Ventura, Mario, Wilson, Richard K., Paten, Benedict, Pollen, Alex, Eichler, Evan E.
Publié dans Science (2018)

Multi-platform discovery of haplotype-resolved structural variation in human genomes

par Chaisson, Mark J. P., Sanders, Ashley D., Zhao, Xuefang, Malhotra, Ankit, Porubsky, David, Rausch, Tobias, Gardner, Eugene J., Rodriguez, Oscar L., Guo, Li, Collins, Ryan L., Fan, Xian, Wen, Jia, Handsaker, Robert E., Fairley, Susan, Kronenberg, Zev N., Kong, Xiangmeng, Hormozdiari, Fereydoun, Lee, Dillon, Wenger, Aaron M., Hastie, Alex R., Antaki, Danny, Anantharaman, Thomas, Audano, Peter A., Brand, Harrison, Cantsilieris, Stuart, Cao, Han, Cerveira, Eliza, Chen, Chong, Chen, Xintong, Chin, Chen-Shan, Chong, Zechen, Chuang, Nelson T., Lambert, Christine C., Church, Deanna M., Clarke, Laura, Farrell, Andrew, Flores, Joey, Galeev, Timur, Gorkin, David U., Gujral, Madhusudan, Guryev, Victor, Heaton, William Haynes, Korlach, Jonas, Kumar, Sushant, Kwon, Jee Young, Lam, Ernest T., Lee, Jong Eun, Lee, Joyce, Lee, Wan-Ping, Lee, Sau Peng, Li, Shantao, Marks, Patrick, Viaud-Martinez, Karine, Meiers, Sascha, Munson, Katherine M., Navarro, Fabio C. P., Nelson, Bradley J., Nodzak, Conor, Noor, Amina, Kyriazopoulou-Panagiotopoulou, Sofia, Pang, Andy W. C., Qiu, Yunjiang, Rosanio, Gabriel, Ryan, Mallory, Stütz, Adrian, Spierings, Diana C. J., Ward, Alistair, Welch, AnneMarie E., Xiao, Ming, Xu, Wei, Zhang, Chengsheng, Zhu, Qihui, Zheng-Bradley, Xiangqun, Lowy, Ernesto, Yakneen, Sergei, McCarroll, Steven, Jun, Goo, Ding, Li, Koh, Chong Lek, Ren, Bing, Flicek, Paul, Chen, Ken, Gerstein, Mark B., Kwok, Pui-Yan, Lansdorp, Peter M., Marth, Gabor T., Sebat, Jonathan, Shi, Xinghua, Bashir, Ali, Ye, Kai, Devine, Scott E., Talkowski, Michael E., Mills, Ryan E., Marschall, Tobias, Korbel, Jan O., Eichler, Evan E., Lee, Charles
Publié dans Nat Commun (2019)