Jouni Sirén

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 19

Top Topics

Induced Pluripotent Stem Cells

Single Molecule

Top Venues

bioRxiv : the preprint server for biology

Science (New York, N.Y.)

This page only lists publications with an associated author ORCID identifier.

Publications

Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized pangenome references. Nature methods (2024)
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang, Erik Garrison, Benedict Paten
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods 20 (2) (2023)
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang, Erik Garrison, Benedict Paten
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods 20 (2) (2023)
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang, Erik Garrison, Benedict Paten
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods (2023)
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K Lucas, Jean Monlong, Haley J Abel, Silvia Buonaiuto, Xian H Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M Eizenga, Xiaowen Feng, Christian Fischer, Robert S Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J Martin, Matthew W Mitchell, Katherine M Munson, Moses Njagi Mwaniki, Adam M Novak, Hugh E Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R Vollger, Lucinda L Antonacci-Fulton, Gunjan Baid, Carl A Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E Cook, Robert M Cook-Deegan, Omar E Cornejo, Mark E Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa' A Garrison, Carlos Garcia Giron, Richard E Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P Ji, Eimear E Kenny, Barbara A Koenig, Alexey Kolesnikov, Jan O Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D Olson, Alice B Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A Regier, Arang Rhie, Samuel Sacco, Ashley D Sanders, Valerie A Schneider, Baergen I Schultz, Kishwar Shafin, Michael W Smith, Heidi J Sofia, Ahmad N Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian P Walenz, Jonathan M D Wood, Aleksey V Zimin, Guillaume Bourque, Mark J P Chaisson, Paul Flicek, Adam M Phillippy, Justin M Zook, Evan E Eichler, David Haussler, Ting Wang, Erich D Jarvis, Karen H Miga, Erik P Garrison, Tobias Marschall, Ira M Hall, Heng Li, Benedict Paten
A draft human pangenome reference. Nature 617 (7960) (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang, Erik Garrison, Benedict Paten
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods 20 (2) (2023)
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K Lucas, Jean Monlong, Haley J Abel, Silvia Buonaiuto, Xian H Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M Eizenga, Xiaowen Feng, Christian Fischer, Robert S Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J Martin, Matthew W Mitchell, Katherine M Munson, Moses Njagi Mwaniki, Adam M Novak, Hugh E Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R Vollger, Lucinda L Antonacci-Fulton, Gunjan Baid, Carl A Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E Cook, Robert M Cook-Deegan, Omar E Cornejo, Mark E Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa' A Garrison, Carlos Garcia Giron, Richard E Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P Ji, Eimear E Kenny, Barbara A Koenig, Alexey Kolesnikov, Jan O Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D Olson, Alice B Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A Regier, Arang Rhie, Samuel Sacco, Ashley D Sanders, Valerie A Schneider, Baergen I Schultz, Kishwar Shafin, Michael W Smith, Heidi J Sofia, Ahmad N Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian P Walenz, Jonathan M D Wood, Aleksey V Zimin, Guillaume Bourque, Mark J P Chaisson, Paul Flicek, Adam M Phillippy, Justin M Zook, Evan E Eichler, David Haussler, Ting Wang, Erich D Jarvis, Karen H Miga, Erik P Garrison, Tobias Marschall, Ira M Hall, Heng Li, Benedict Paten
A draft human pangenome reference. Nature 617 (7960) (2023)
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang, Erik Garrison, Benedict Paten
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods 20 (2) (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K Lucas, Jean Monlong, Haley J Abel, Silvia Buonaiuto, Xian H Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M Eizenga, Xiaowen Feng, Christian Fischer, Robert S Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J Martin, Matthew W Mitchell, Katherine M Munson, Moses Njagi Mwaniki, Adam M Novak, Hugh E Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R Vollger, Lucinda L Antonacci-Fulton, Gunjan Baid, Carl A Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E Cook, Robert M Cook-Deegan, Omar E Cornejo, Mark E Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa' A Garrison, Carlos Garcia Giron, Richard E Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P Ji, Eimear E Kenny, Barbara A Koenig, Alexey Kolesnikov, Jan O Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D Olson, Alice B Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A Regier, Arang Rhie, Samuel Sacco, Ashley D Sanders, Valerie A Schneider, Baergen I Schultz, Kishwar Shafin, Michael W Smith, Heidi J Sofia, Ahmad N Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian P Walenz, Jonathan M D Wood, Aleksey V Zimin, Guillaume Bourque, Mark J P Chaisson, Paul Flicek, Adam M Phillippy, Justin M Zook, Evan E Eichler, David Haussler, Ting Wang, Erich D Jarvis, Karen H Miga, Erik P Garrison, Tobias Marschall, Ira M Hall, Heng Li, Benedict Paten
A draft human pangenome reference. Nature 617 (7960) (2023)
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K Lucas, Jean Monlong, Haley J Abel, Silvia Buonaiuto, Xian H Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M Eizenga, Xiaowen Feng, Christian Fischer, Robert S Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J Martin, Matthew W Mitchell, Katherine M Munson, Moses Njagi Mwaniki, Adam M Novak, Hugh E Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R Vollger, Lucinda L Antonacci-Fulton, Gunjan Baid, Carl A Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E Cook, Robert M Cook-Deegan, Omar E Cornejo, Mark E Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa' A Garrison, Carlos Garcia Giron, Richard E Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P Ji, Eimear E Kenny, Barbara A Koenig, Alexey Kolesnikov, Jan O Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D Olson, Alice B Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A Regier, Arang Rhie, Samuel Sacco, Ashley D Sanders, Valerie A Schneider, Baergen I Schultz, Kishwar Shafin, Michael W Smith, Heidi J Sofia, Ahmad N Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian P Walenz, Jonathan M D Wood, Aleksey V Zimin, Guillaume Bourque, Mark J P Chaisson, Paul Flicek, Adam M Phillippy, Justin M Zook, Evan E Eichler, David Haussler, Ting Wang, Erich D Jarvis, Karen H Miga, Erik P Garrison, Tobias Marschall, Ira M Hall, Heng Li, Benedict Paten
A draft human pangenome reference. Nature 617 (7960) (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang, Erik Garrison, Benedict Paten
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods 20 (2) (2023)
Jonas A Sibbesen, Jordan M Eizenga, Adam M Novak, Jouni Sirén, Xian Chang, Erik Garrison, Benedict Paten
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods 20 (2) (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Jouni Sirén, Benedict Paten
GBZ file format for pangenome graphs. Bioinformatics (Oxford, England) 38 (22) (2022)
Jouni Sirén, Jean Monlong, Xian Chang, Adam M Novak, Jordan M Eizenga, Charles Markello, Jonas A Sibbesen, Glenn Hickey, Pi-Chuan Chang, Andrew Carroll, Namrata Gupta, Stacey Gabriel, Thomas W Blackwell, Aakrosh Ratan, Kent D Taylor, Stephen S Rich, Jerome I Rotter, David Haussler, Erik Garrison, Benedict Paten
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science (New York, N.Y.) 374 (6574) (2021)