Genotyping structural variants in pangenome graphs using the vg toolkit von Hickey, Glenn, Heller, David, Monlong, Jean, Sibbesen, Jonas A, Sirén, Jouni, Eizenga, Jordan, Dawson, Eric T, Garrison, Erik, Novak, Adam M, Paten, Benedict

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Pangenomics enables genotyping of known structural variants in 5202 diverse genomes von Sirén, Jouni, Monlong, Jean, Chang, Xian, Novak, Adam M, Eizenga, Jordan M, Markello, Charles, Sibbesen, Jonas A, Hickey, Glenn, Chang, Pi-Chuan, Carroll, Andrew, Gupta, Namrata, Gabriel, Stacey, Blackwell, Thomas W, Ratan, Aakrosh, Taylor, Kent D, Rich, Stephen S, Rotter, Jerome I, Haussler, David, Garrison, Erik, Paten, Benedict

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Pangenome Graphs von Eizenga, Jordan M, Novak, Adam M, Sibbesen, Jonas A, Heumos, Simon, Ghaffaari, Ali, Hickey, Glenn, Chang, Xian, Seaman, Josiah D, Rounthwaite, Robin, Ebler, Jana, Rautiainen, Mikko, Garg, Shilpa, Paten, Benedict, Marschall, Tobias, Sirén, Jouni, Garrison, Erik

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Bayesian transcriptome assembly von Maretty, Lasse, Sibbesen, Jonas Andreas, Krogh, Anders

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Haplotype-aware pantranscriptome analyses using spliced pangenome graphs von Sibbesen, Jonas A., Eizenga, Jordan M., Novak, Adam M., Sirén, Jouni, Chang, Xian, Garrison, Erik, Paten, Benedict

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Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology von Lemay, Marc-André, Sibbesen, Jonas A, Torkamaneh, Davoud, Hamel, Jérémie, Levesque, Roger C, Belzile, François

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Accurate genotyping across variant classes and lengths using variant graphs von Sibbesen, Jonas Andreas, Maretty, Lasse, Krogh, Anders

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A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved] von Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter A, Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne E, Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas A, Markello, Charles J, Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard R, Lin, Michael F, Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Monlong, Jean, Musunuri, Rajeeva L, Sagayaradj, Sagayamary, Novak, Adam M, Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz J, Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki T, Zeng, Qiandong, Zook, Justin M, Paten, Benedict, Busby, Ben

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A strategy for building and using a human reference pangenome [version 1; peer review: 1 approved, 1 approved with reservations] von Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter A, Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne E, Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas A, Markello, Charles J, Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard R, Lin, Michael F, Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Monlong, Jean, Musunuri, Rajeeva L, Sagayaradj, Sagayamary, Novak, Adam M, Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz J, Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki T, Zeng, Qiandong, Zook, Justin M, Paten, Benedict, Busby, Ben

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RNA Sequencing of Trigeminal Ganglia in Rattus Norvegicus after Glyceryl Trinitrate Infusion with Relevance to Migraine von Hougaard Pedersen, Sara, Maretty, Lasse, Ramachandran, Roshni, Sibbesen, Jonas Andreas, Yakimov, Victor, Elgaard-Christensen, Rikke, Hansen, Thomas Folkmann, Krogh, Anders, Olesen, Jes, Jansen-Olesen, Inger

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A draft human pangenome reference von Liao, Wen-Wei, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cook, Daniel E., Cook-Deegan, Robert M., Diekhans, Mark, Ebert, Peter, Fedrigo, Olivier, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Koenig, Barbara A., Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M. D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J. P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, Paten, Benedict

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Sequencing and de novo assembly of 150 genomes from Denmark as a population reference von Maretty, Lasse, Jensen, Jacob Malte, Petersen, Bent, Sibbesen, Jonas Andreas, Liu, Siyang, Villesen, Palle, Skov, Laurits, Belling, Kirstine, Theil Have, Christian, Izarzugaza, Jose M. G., Grosjean, Marie, Bork-Jensen, Jette, Grove, Jakob, Als, Thomas D., Huang, Shujia, Chang, Yuqi, Xu, Ruiqi, Ye, Weijian, Rao, Junhua, Guo, Xiaosen, Sun, Jihua, Cao, Hongzhi, Ye, Chen, van Beusekom, Johan, Espeseth, Thomas, Flindt, Esben, Friborg, Rune M., Halager, Anders E., Le Hellard, Stephanie, Hultman, Christina M., Lescai, Francesco, Li, Shengting, Lund, Ole, Løngren, Peter, Mailund, Thomas, Matey-Hernandez, Maria Luisa, Mors, Ole, Pedersen, Christian N. S., Sicheritz-Pontén, Thomas, Sullivan, Patrick, Syed, Ali, Westergaard, David, Yadav, Rachita, Li, Ning, Xu, Xun, Hansen, Torben, Krogh, Anders, Bolund, Lars, Sørensen, Thorkild I. A., Pedersen, Oluf, Gupta, Ramneek, Rasmussen, Simon, Besenbacher, Søren, Børglum, Anders D., Wang, Jun, Eiberg, Hans, Kristiansen, Karsten, Brunak, Søren, Schierup, Mikkel Heide

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Proteomic changes upon treatment with semaglutide in individuals with obesity von Maretty, Lasse, Gill, Dipender, Simonsen, Lotte, Soh, Keng, Zagkos, Loukas, Galanakis, Michael, Sibbesen, Jonas, Iglesias, Miquel Triana, Secher, Anna, Valkenborg, Dirk, Purnell, Jonathan Q., Knudsen, Lotte Bjerre, Tahrani, Abd A., Geybels, Milan

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Next-generation biology: Sequencing and data analysis approaches for non-model organisms von da Fonseca, Rute R., Albrechtsen, Anders, Themudo, Gonçalo Espregueira, Ramos-Madrigal, Jazmín, Sibbesen, Jonas Andreas, Maretty, Lasse, Zepeda-Mendoza, M. Lisandra, Campos, Paula F., Heller, Rasmus, Pereira, Ricardo J.

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Pangenomics enables genotyping known structural variants in 5,202 diverse genomes von Sirén, Jouni, Monlong, Jean, Chang, Xian, Novak, Adam M., Eizenga, Jordan M., Markello, Charles, Sibbesen, Jonas A., Hickey, Glenn, Chang, Pi-Chuan, Carroll, Andrew, Gupta, Namrata, Gabriel, Stacey, Blackwell, Thomas W., Ratan, Aakrosh, Taylor, Kent D., Rich, Stephen S., Rotter, Jerome I., Haussler, David, Garrison, Erik, Paten, Benedict

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Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection von Dialdestoro, Kevin, Sibbesen, Jonas Andreas, Maretty, Lasse, Raghwani, Jayna, Gall, Astrid, Kellam, Paul, Pybus, Oliver G, Hein, Jotun, Jenkins, Paul A

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Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios von Matey-Hernandez, Maria Luisa, Brunak, Søren, Izarzugaza, Jose M G

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Assembly and analysis of 100 full MHC haplotypes from the Danish population von Jensen, Jacob M, Villesen, Palle, Friborg, Rune M, Mailund, Thomas, Besenbacher, Søren, Schierup, Mikkel H

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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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Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale von Liu, Siyang, Huang, Shujia, Rao, Junhua, Ye, Weijian, Krogh, Anders, Wang, Jun

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