Dense and accurate whole-chromosome haplotyping of individual genomes von Porubsky, David, Garg, Shilpa, Sanders, Ashley D., Korbel, Jan O., Guryev, Victor, Lansdorp, Peter M., Marschall, Tobias

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Characterizing polymorphic inversions in human genomes by single-cell sequencing von Sanders, Ashley D, Hills, Mark, Porubský, David, Guryev, Victor, Falconer, Ester, Lansdorp, Peter M

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

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Inversion polymorphism in a complete human genome assembly von Porubsky, David, Harvey, William T, Rozanski, Allison N, Ebler, Jana, Höps, Wolfram, Ashraf, Hufsah, Hasenfeld, Patrick, Paten, Benedict, Sanders, Ashley D, Marschall, Tobias, Korbel, Jan O, Eichler, Evan E

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DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution von Falconer, Ester, Hills, Mark, Naumann, Ulrike, Poon, Steven S S, Chavez, Elizabeth A, Sanders, Ashley D, Zhao, Yongjun, Hirst, Martin, Lansdorp, Peter M

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The Prognostic Impact of CD163-Positive Macrophages in Follicular Lymphoma: A Study from the BC Cancer Agency and the Lymphoma Study Association von Kridel, Robert, Xerri, Luc, Gelas-Dore, Bénédicte, Tan, King, Feugier, Pierre, Vawda, Ayesha, Canioni, Danielle, Farinha, Pedro, Boussetta, Sami, Moccia, Alden A, Brice, Pauline, Chavez, Elizabeth A, Kyle, Alastair H, Scott, David W, Sanders, Ashley D, Fabiani, Bettina, Slack, Graham W, Minchinton, Andrew I, Haioun, Corinne, Connors, Joseph M, Sehn, Laurie H, Steidl, Christian, Gascoyne, Randy D, Salles, Gilles

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Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data von Hills, Mark, Falconer, Ester, O'Neill, Kieran, Sanders, Ashley D., Howe, Kerstin, Guryev, Victor, Lansdorp, Peter M.

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Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus von Maggiolini, Flavia A M, Cantsilieris, Stuart, D'Addabbo, Pietro, Manganelli, Michele, Coe, Bradley P, Dumont, Beth L, Sanders, Ashley D, Pang, Andy Wing Chun, Vollger, Mitchell R, Palumbo, Orazio, Palumbo, Pietro, Accadia, Maria, Carella, Massimo, Eichler, Evan E, Antonacci, Francesca

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Essential role for Ptpn11 in survival of hematopoietic stem and progenitor cells von Chan, Gordon, Cheung, Laurene S., Yang, Wentian, Milyavsky, Michael, Sanders, Ashley D., Gu, Shengqing, Hong, Wan Xing, Liu, Aurora X., Wang, Xiaonan, Barbara, Mary, Sharma, Tarun, Gavin, Joehleen, Kutok, Jeffery L., Iscove, Norman N., Shannon, Kevin M., Dick, John E., Neel, Benjamin G., Braun, Benjamin S.

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Adult spinal cord radial glia display a unique progenitor phenotype von Petit, Audrey, Sanders, Ashley D, Kennedy, Timothy E, Tetzlaff, Wolfram, Glattfelder, Katie J, Dalley, Rachel A, Puchalski, Ralph B, Jones, Allan R, Roskams, A Jane

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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads von Porubsky, David, Ebert, Peter, Audano, Peter A., Vollger, Mitchell R., Harvey, William T., Marijon, Pierre, Ebler, Jana, Munson, Katherine M., Sorensen, Melanie, Sulovari, Arvis, Haukness, Marina, Ghareghani, Maryam, Lansdorp, Peter M., Paten, Benedict, Devine, Scott E., Sanders, Ashley D., Lee, Charles, Chaisson, Mark J. P., Korbel, Jan O., Eichler, Evan E., Marschall, Tobias

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breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data von Porubsky, David, Sanders, Ashley D, Taudt, Aaron, Colomé-Tatché, Maria, Lansdorp, Peter M, Guryev, Victor

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ASHLEYS: automated quality control for single-cell Strand-seq data von Gros, Christina, Sanders, Ashley D, Korbel, Jan O, Marschall, Tobias, Ebert, Peter

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Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders von Porubsky, David, Höps, Wolfram, Ashraf, Hufsah, Hsieh, PingHsun, Rodriguez-Martin, Bernardo, Yilmaz, Feyza, Ebler, Jana, Hallast, Pille, Maria Maggiolini, Flavia Angela, Harvey, William T., Henning, Barbara, Audano, Peter A., Gordon, David S., Ebert, Peter, Hasenfeld, Patrick, Benito, Eva, Zhu, Qihui, Lee, Charles, Antonacci, Francesca, Steinrücken, Matthias, Beck, Christine R., Sanders, Ashley D., Marschall, Tobias, Eichler, Evan E., Korbel, Jan O.

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Computational pan-genomics: status, promises and challenges von Marschall, Tobias, Marz, Manja, Abeel, Thomas, Dijkstra, Louis, Dutilh, Bas E, Ghaffaari, Ali, Kersey, Paul, Kloosterman, Wigard P, Mäkinen, Veli, Novak, Adam M, Paten, Benedict, Porubsky, David, Rivals, Eric, Alkan, Can, Baaijens, Jasmijn A, Paul I W De Bakker, Boeva, Valentina, Bonnal, Raoul J P, Chiaromonte, Francesca, Chikhi, Rayan, Ciccarelli, Francesca D, Cijvat, Robin, Datema, Erwin, Van Duijn, Cornelia M, Eichler, Evan E, Ernst, Corinna, Eskin, Eleazar, Garrison, Erik, El-Kebir, Mohammed, Klau, Gunnar W, Korbel, Jan O, Eric-Wubbo Lameijer, Langmead, Benjamin, Martin, Marcel, Medvedev, Paul, Mu, John C, Neerincx, Pieter, Ouwens, Klaasjan, Peterlongo, Pierre, Pisanti, Nadia, Rahmann, Sven, Raphael, Ben, Reinert, Knut, de Ridder, Dick, de Ridder, Jeroen, Schlesner, Matthias, Schulz-Trieglaff, Ole, Sanders, Ashley D, Sheikhizadeh, Siavash, Shneider, Carl, Smit, Sandra, Valenzuela, Daniel, Wang, Jiayin, Wessels, Lodewyk, Zhang, Ying, Guryev, Victor, Vandin, Fabio, Ye, Kai, Schönhuth, Alexander

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Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs von Sanders, Ashley D, Falconer, Ester, Hills, Mark, Spierings, Diana C J, Lansdorp, Peter M

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Gaps and complex structurally variant loci in phased genome assemblies von Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E

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Recurrent inversion toggling and great ape genome evolution von Porubsky, David, Sanders, Ashley D., Höps, Wolfram, Hsieh, PingHsun, Sulovari, Arvis, Li, Ruiyang, Mercuri, Ludovica, Sorensen, Melanie, Murali, Shwetha C., Gordon, David, Cantsilieris, Stuart, Pollen, Alex A., Ventura, Mario, Antonacci, Francesca, Marschall, Tobias, Korbel, Jan O., Eichler, Evan E.

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Familial long-read sequencing increases yield of de novo mutations von Noyes, Michelle D., Harvey, William T., Porubsky, David, Sulovari, Arvis, Li, Ruiyang, Rose, Nicholas R., Audano, Peter A., Munson, Katherine M., Lewis, Alexandra P., Hoekzema, Kendra, Mantere, Tuomo, Graves-Lindsay, Tina A., Sanders, Ashley D., Goodwin, Sara, Kramer, Melissa, Mokrab, Younes, Zody, Michael C., Hoischen, Alexander, Korbel, Jan O., McCombie, W. Richard, Eichler, Evan E.

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Functional analysis of structural variants in single cells using Strand-seq von Jeong, Hyobin, Grimes, Karen, Rauwolf, Kerstin K., Bruch, Peter-Martin, Rausch, Tobias, Hasenfeld, Patrick, Benito, Eva, Roider, Tobias, Sabarinathan, Radhakrishnan, Porubsky, David, Herbst, Sophie A., Erarslan-Uysal, Büşra, Jann, Johann-Christoph, Marschall, Tobias, Nowak, Daniel, Bourquin, Jean-Pierre, Kulozik, Andreas E., Dietrich, Sascha, Bornhauser, Beat, Sanders, Ashley D., Korbel, Jan O.

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