Variation graph toolkit improves read mapping by representing genetic variation in the reference

by Garrison, Erik, Sirén, Jouni, Novak, Adam M, Hickey, Glenn, Eizenga, Jordan M, Dawson, Eric T, Jones, William, Garg, Shilpa, Markello, Charles, Lin, Michael F, Paten, Benedict, Durbin, Richard
Published in Nature biotechnology

Haplotype-aware graph indexes

by Sirén, Jouni, Garrison, Erik, Novak, Adam M, Paten, Benedict, Durbin, Richard
Published in Bioinformatics

Indexing Graphs for Path Queries with Applications in Genome Research

by Siren, Jouni, Valimaki, Niko, Makinen, Veli
Published in IEEE/ACM transactions on computational biology and bioinformatics

Genotyping structural variants in pangenome graphs using the vg toolkit

by Hickey, Glenn, Heller, David, Monlong, Jean, Sibbesen, Jonas A, Sirén, Jouni, Eizenga, Jordan, Dawson, Eric T, Garrison, Erik, Novak, Adam M, Paten, Benedict
Published in Genome Biology

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

by 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
Published in Science (American Association for the Advancement of Science)

Wheeler graphs: A framework for BWT-based data structures

by Gagie, Travis, Manzini, Giovanni, Sirén, Jouni
Published in Theoretical computer science

GBZ file format for pangenome graphs

by Sirén, Jouni, Paten, Benedict
Published in Bioinformatics (Oxford, England)

Distance indexing and seed clustering in sequence graphs

by Chang, Xian, Eizenga, Jordan, Novak, Adam M, Sirén, Jouni, Paten, Benedict
Published in Bioinformatics (Oxford, England)

Computational graph pangenomics: a tutorial on data structures and their applications

by Baaijens, Jasmijn A., Bonizzoni, Paola, Boucher, Christina, Della Vedova, Gianluca, Pirola, Yuri, Rizzi, Raffaella, Sirén, Jouni
Published in Natural computing

Relative Suffix Trees

by Farruggia, Andrea, Gagie, Travis, Navarro, Gonzalo, Puglisi, Simon J, Sirén, Jouni
Published in Computer journal

A draft human pangenome reference

by Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Baid, Gunjan, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Diekhans, Mark, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa' A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lewis, Alexandra P, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Walenz, Brian, Wood, Jonathan M D, Zimin, Aleksey V, Bourque, Guillaume, Chaisson, Mark J P, Flicek, Paul, Zook, Justin M, Eichler, Evan E, Haussler, David, Wang, Ting, Jarvis, Erich D, Miga, Karen H, Garrison, Erik, Hall, Ira M, Paten, Benedict
Published in Nature (London)

Distribution-Aware Compressed Full-Text Indexes

by Ferragina, Paolo, Sirén, Jouni, Venturini, Rossano
Published in Algorithmica

Document retrieval on repetitive string collections

by Gagie, Travis, Hartikainen, Aleksi, Karhu, Kalle, Kärkkäinen, Juha, Navarro, Gonzalo, Puglisi, Simon J., Sirén, Jouni
Published in Information retrieval (Boston)

Pangenome graph construction from genome alignments with Minigraph-Cactus

by Hickey, Glenn, Monlong, Jean, Ebler, Jana, Novak, Adam M, Eizenga, Jordan M, Gao, Yan, Marschall, Tobias, Li, Heng, Paten, Benedict
Published in Nature biotechnology

Recombination between heterologous human acrocentric chromosomes

by Guarracino, Andrea, Buonaiuto, Silvia, de Lima, Leonardo Gomes, Potapova, Tamara, Rhie, Arang, Koren, Sergey, Rubinstein, Boris, Fischer, Christian, Gerton, Jennifer L, Phillippy, Adam M, Colonna, Vincenza, Garrison, Erik
Published in Nature (London)

Fast in-memory XPath search using compressed indexes

by Arroyuelo, Diego, Claude, Francisco, Maneth, Sebastian, Maakinen, Veli, Navarro, Gonzalo, Kim Nguyen, Siren, Jouni, Valimaki, Niko

Increased mutation and gene conversion within human segmental duplications

by Vollger, Mitchell R, Dishuck, Philip C, Harvey, William T, DeWitt, William S, Guitart, Xavi, Goldberg, Michael E, Rozanski, Allison N, Lucas, Julian, Asri, Mobin, Munson, Katherine M, Lewis, Alexandra P, Hoekzema, Kendra, Logsdon, Glennis A, Porubsky, David, Paten, Benedict, Harris, Kelley, Hsieh, PingHsun, Eichler, Evan E
Published in Nature (London)

Gaps and complex structurally variant loci in phased genome assemblies

by 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
Published in Genome research

Pangenomics enables genotyping known structural variants in 5,202 diverse genomes

by 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
Published in Science (American Association for the Advancement of Science)

A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved]

by 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
Published in F1000 research