Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes von Shafin, Kishwar, Pesout, Trevor, Lorig-Roach, Ryan, Haukness, Marina, Olsen, Hugh E., Bosworth, Colleen, Armstrong, Joel, Tigyi, Kristof, Maurer, Nicholas, Koren, Sergey, Sedlazeck, Fritz J., Marschall, Tobias, Mayes, Simon, Costa, Vania, Zook, Justin M., Liu, Kelvin J., Kilburn, Duncan, Sorensen, Melanie, Munson, Katy M., Vollger, Mitchell R., Monlong, Jean, Garrison, Erik, Eichler, Evan E., Salama, Sofie, Haussler, David, Green, Richard E., Akeson, Mark, Phillippy, Adam, Miga, Karen H., Carnevali, Paolo, Jain, Miten, Paten, Benedict

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Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads von Shafin, Kishwar, Pesout, Trevor, Chang, Pi-Chuan, Nattestad, Maria, Kolesnikov, Alexey, Goel, Sidharth, Baid, Gunjan, Kolmogorov, Mikhail, Eizenga, Jordan M., Miga, Karen H., Carnevali, Paolo, Jain, Miten, Carroll, Andrew, Paten, Benedict

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Semi-automated assembly of high-quality diploid human reference genomes von Jarvis, Erich D., Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R., Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A., Carnevali, Paolo, Chaisson, Mark J. P., Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S., Fulton, Lucinda L., Garg, Shilpa, Gerton, Jennifer L., Ghurye, Jay, Granat, Anastasiya, Green, Richard E., Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B., Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O., Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W., McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E., Olson, Nathan D., Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L., Sanders, Ashley D., Schatz, Michael C., Schmitt, Anthony, Schneider, Valerie A., Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O., Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V., Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M., Eichler, Evan E., Phillippy, Adam M., Paten, Benedict, Howe, Kerstin, Miga, Karen H.

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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation von Kolmogorov, Mikhail, Billingsley, Kimberley J., Mastoras, Mira, Meredith, Melissa, Monlong, Jean, Lorig-Roach, Ryan, Asri, Mobin, Alvarez Jerez, Pilar, Malik, Laksh, Dewan, Ramita, Reed, Xylena, Genner, Rylee M., Daida, Kensuke, Behera, Sairam, Shafin, Kishwar, Pesout, Trevor, Prabakaran, Jeshuwin, Carnevali, Paolo, Yang, Jianzhi, Rhie, Arang, Scholz, Sonja W., Traynor, Bryan J., Miga, Karen H., Jain, Miten, Timp, Winston, Phillippy, Adam M., Chaisson, Mark, Sedlazeck, Fritz J., Blauwendraat, Cornelis, Paten, Benedict

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The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients von Jiang, Zhaoshi, Jhunjhunwala, Suchit, Liu, Jinfeng, Haverty, Peter M, Kennemer, Michael I, Guan, Yinghui, Lee, William, Carnevali, Paolo, Stinson, Jeremy, Johnson, Stephanie, Diao, Jingyu, Yeung, Stacy, Jubb, Adrian, Ye, Weilan, Wu, Thomas D, Kapadia, Sharookh B, de Sauvage, Frederic J, Gentleman, Robert C, Stern, Howard M, Seshagiri, Somasekar, Pant, Krishna P, Modrusan, Zora, Ballinger, Dennis G, Zhang, Zemin

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Phased nanopore assembly with Shasta and modular graph phasing with GFAse von Lorig-Roach, Ryan, Meredith, Melissa, Monlong, Jean, Jain, Miten, Olsen, Hugh E, McNulty, Brandy, Porubsky, David, Montague, Tessa G, Lucas, Julian K, Condon, Chris, Eizenga, Jordan M, Juul, Sissel, McKenzie, Sean K, Simmonds, Sara E, Park, Jimin, Asri, Mobin, Koren, Sergey, Eichler, Evan E, Axel, Richard, Martin, Bruce, Carnevali, Paolo, Miga, Karen H, Paten, Benedict

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Computational techniques for human genome resequencing using mated gapped reads von Carnevali, Paolo, Baccash, Jonathan, Halpern, Aaron L, Nazarenko, Igor, Nilsen, Geoffrey B, Pant, Krishna P, Ebert, Jessica C, Brownley, Anushka, Morenzoni, Matt, Karpinchyk, Vitali, Martin, Bruce, Ballinger, Dennis G, Drmanac, Radoje

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Clinical and genetic analysis of a rare syndrome associated with neoteny von Walker, Richard F, Ciotlos, Serban, Mao, Qing, Chin, Robert, Drmanac, Snezana, Barua, Nina, Agarwal, Misha R, Zhang, Rebecca Yu, Li, Zhenyu, Wu, Michelle Ka Yan, Sun, Kevin, Lee, Katharine, Nguyen, Staci, Liu, Jia Sophie, Carnevali, Paolo, Drmanac, Radoje, Peters, Brock A

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Fragment-Based Computation of Binding Free Energies by Systematic Sampling von Clark, Matthew, Meshkat, Siavash, Talbot, George T, Carnevali, Paolo, Wiseman, Jeffrey S

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The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes von Mao, Qing, Ciotlos, Serban, Zhang, Rebecca Yu, Ball, Madeleine P, Chin, Robert, Carnevali, Paolo, Barua, Nina, Nguyen, Staci, Agarwal, Misha R, Clegg, Tom, Connelly, Abram, Vandewege, Ward, Zaranek, Alexander Wait, Estep, Preston W, Church, George M, Drmanac, Radoje, Peters, Brock A

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Abstract 4821: Somatic variation scoring and validation for large-scale cancer genome sequencing von Pant, Krishna P., Lincoln, Steve, Baccash, Jonathan, Halpern, Aaron L., Nazarenko, Igor, Carnevali, Paolo, Ballinger, Dennis G.

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Fast Protein Structure Prediction Using Monte Carlo Simulations with Modal Moves von Carnevali, Paolo, Tóth, Gergely, Toubassi, Garrick, Meshkat, Siavash N

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The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes von Mao, Qing, Ciotlos, Serban, Zhang, Rebecca Yu, Ball, Madeleine P, Chin, Robert, Carnevali, Paolo, Barua, Nina, Nguyen, Staci, Agarwal, Misha R, Clegg, Tom, Connelly, Abram, Vandewege, Ward, Zaranek, Alexander Wait, Estep, Preston W, Church, George M, Drmanac, Radoje, Peters, Brock A

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Endoscopic multiple metal stenting for the treatment of enteral leaks near the biliary orifice: A novel effective rescue procedure von Mutignani, Massimiliano, Dioscoridi, Lorenzo, Dokas, Stefanos, Aseni, Paolo, Carnevali, Pietro, Forti, Edoardo, Manta, Raffaele, Sica, Mariano, Tringali, Alberto, Pugliese, Francesco

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Endoscopic multiple metal stenting for the treatment of enteral leaks near the biliary orifice: A novel effective rescue procedure von Massimiliano Mutignani Lorenzo Dioscoridi Stefanos Dokas Paolo Aseni Pietro Carnevali Edoardo Forti Raffaele Manta Mariano Sica Alberto Tringali Francesco Pugliese

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IDENTIFYING REARRANGEMENTS IN A SEQUENCED GENOME von NAZARENKO, IGOR, HALPERN, AARON L, CARNEVALI, PAOLO

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METHOD AND SYSTEM FOR CALLING VARIATIONS IN A SAMPLE POLYNUCLEOTIDE SEQUENCE WITH RESPECT TO A REFERENCE POLYNUCLEOTIDE SEQUENCE von NILSEN, Geoffrey, BACCASH, Jonathan, M, NAZARENKO, Igor, HALPERN, Aaron, L, DRMANAC, Radoje, CARNEVALI, Paolo, MARTIN, Bruce

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IDENTIFYING REARRANGEMENTS IN A SEQUENCED GENOME von NAZARENKO, IGOR, HALPERN, AARON L, CARNEVALI, PAOLO

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DETERMINING VARIANTS IN A GENOME OF A HETEROGENEOUS SAMPLE von PANT, KRISHNA, BACCASH, JONATHAN, TIAN, CHAO, HALPERN, AARON, CARNEVALI, PAOLO

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FREMGANGSMÅDE OG SYSTEM TIL AT HENTE VARIATIONER I EN PRØVEPOLYNUKLEOTIDSEKVENS I FORHOLD TIL EN REFERENCEPOLYNUKLEOTIDSEKVENS von Baccash, Jonathan, M, Carnevali, Paolo, Nazarenko, Igor, Drmanac, Radoje, Martin, Bruce, Halpern, Aaron, L, Nilsen Geoffrey

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