Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic von Greer, Stephanie U, Botello, Jacquelin, Hongo, Donna, Levy, Brynn, Shah, Premal, Rabinowitz, Matthew, Miller, Danny E, Im, Kate, Kumar, Akash

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Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases von Greer, Stephanie U, Nadauld, Lincoln D, Lau, Billy T, Chen, Jiamin, Wood-Bouwens, Christina, Ford, James M, Kuo, Calvin J, Ji, Hanlee P

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Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62 von Greer, Stephanie U., Chen, Jiamin, Ogmundsdottir, Margret H., Ayala, Carlos, Lau, Billy T., Delacruz, Richard Glenn C., Sandoval, Imelda T., Kristjansdottir, Sigrun, Jones, David A., Haslem, Derrick S., Romero, Robin, Fulde, Gail, Bell, John M., Jonasson, Jon G., Steingrimsson, Eirikur, Ji, Hanlee P., Nadauld, Lincoln D.

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Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8 von Shin, Giwon, Greer, Stephanie U., Hopmans, Erik, Grimes, Susan M., Lee, Hojoon, Zhao, Lan, Miotke, Laura, Suarez, Carlos, Almeda, Alison F., Haraldsdottir, Sigurdis, Ji, Hanlee P.

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Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant von Greer, Stephanie U, Wright, Stephen I, Eckert, Christopher G

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Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562 von Zhou, Bo, Ho, Steve S, Greer, Stephanie U, Zhu, Xiaowei, Bell, John M, Arthur, Joseph G, Spies, Noah, Zhang, Xianglong, Byeon, Seunggyu, Pattni, Reenal, Ben-Efraim, Noa, Haney, Michael S, Haraksingh, Rajini R, Song, Giltae, Ji, Hanlee P, Perrin, Dimitri, Wong, Wing H, Abyzov, Alexej, Urban, Alexander E

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Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy von Bell, John M., Lau, Billy T., Greer, Stephanie U., Wood-Bouwens, Christina, Xia, Li C., Connolly, Ian D., Gephart, Melanie H., Ji, Hanlee P.

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Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2 von Zhou, Bo, Ho, Steve S, Greer, Stephanie U, Spies, Noah, Bell, John M, Zhang, Xianglong, Zhu, Xiaowei, Arthur, Joseph G, Byeon, Seunggyu, Pattni, Reenal, Saha, Ishan, Huang, Yiling, Song, Giltae, Perrin, Dimitri, Wong, Wing H, Ji, Hanlee P, Abyzov, Alexej, Urban, Alexander E

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KmerKeys: a web resource for searching indexed genome assemblies and variants von Pavlichin, Dmitri S, Lee, HoJoon, Greer, Stephanie U, Grimes, Susan M, Weissman, Tsachy, Ji, Hanlee P

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Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints von Zhou, Bo, Purmann, Carolin, Guo, Hanmin, Shin, GiWon, Huang, Yiling, Pattni, Reenal, Meng, Qingxi, Greer, Stephanie U, Roychowdhury, Tanmoy, Wood, Raegan N, Ho, Marcus, Dohna, Heinrich Zu, Abyzov, Alexej, Hallmayer, Joachim F, Wong, Wing H, Ji, Hanlee P, Urban, Alexander E

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Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes von Shin, GiWon, Greer, Stephanie U, Xia, Li C, Lee, HoJoon, Zhou, Jun, Boles, T Christian, Ji, Hanlee P

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Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy von Bell, John M, Lau, Billy T, Greer, Stephanie U, Wood-Bouwens, Christina, Xia, Li C, Connolly, Ian D, Gephart, Melanie H, Ji, Hanlee P

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Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow‐sorting approach von Lorber, Thomas, Andor, Noemi, Dietsche, Tanja, Perrina, Valeria, Juskevicius, Darius, Pereira, Karen, Greer, Stephanie U, Krause, Arthur, Müller, David C, Savic Prince, Spasenija, Lardinois, Didier, Barrett, Michael T, Ruiz, Christian, Bubendorf, Lukas

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Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer von Xia, Li C., Van Hummelen, Paul, Kubit, Matthew, Lee, HoJoon, Bell, John M., Grimes, Susan M., Wood-Bouwens, Christina, Greer, Stephanie U., Barker, Tyler, Haslem, Derrick S., Ford, James M., Fulde, Gail, Ji, Hanlee P., Nadauld, Lincoln D.

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Characterization of the consensus mucosal microbiome of colorectal cancer von Zhao, Lan, Grimes, Susan M, Greer, Stephanie U, Kubit, Matthew, Lee, HoJoon, Nadauld, Lincoln D, Ji, Hanlee P

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Abstract 1298: Mapping the comprehensive landscape of missense-mutation neoantigens across the human genome von Lee, HoJoon, Greer, Stephanie U., Ji, Hanlee P.

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Abstract 1280: Chromosome-scale haplotyping enables comprehensive discovery of cancer rearrangements and germline-related susceptibility mutations von Greer, Stephanie U., Lau, Billy T., Nadauld, Lincoln D., Ji, Hanlee P.

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Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome von Lee, HoJoon, Greer, Stephanie U, Pavlichin, Dmitri S, Zhou, Bo, Urban, Alexander E, Weissman, Tsachy, Ji, Hanlee P

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Additional file 1 of Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic von Greer, Stephanie U., Botello, Jacquelin, Hongo, Donna, Levy, Brynn, Shah, Premal, Rabinowitz, Matthew, Miller, Danny E., Im, Kate, Kumar, Akash

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Additional file 3 of Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8 von Shin, GiWon, Greer, Stephanie U., Hopmans, Erik, Grimes, Susan M., Lee, HoJoon, Zhao, Lan, Miotke, Laura, Suarez, Carlos, Almeda, Alison F., Haraldsdottir, Sigurdis, Ji, Hanlee P.

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