Benedict Paten

ORCID

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 95

Top Venues

Nature

Science (New York, N.Y.)

bioRxiv : the preprint server for biology

Nature methods

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

Publications

Siavash Mirarab, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey, Guangii Chen, Nadolina Brajuka, Olivier Fedrigo, Giulio Formenti, Jochen B W Wolf, Kerstin Howe, Agostinho Antunes, Mikkel Heide Schierup, Benedict Paten, Erich D Jarvis, Guojie Zhang, Edward L Braun
A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Rylee Genner, Stuart Akeson, Melissa Meredith, Pilar Alvarez Jerez, Laksh Malik, Breeana Baker, Abigail Miano-Burkhardt, null null, Benedict Paten, Kimberley J Billingsley, Cornelis Blauwendraat, Miten Jain
Assessing methylation detection for primary human tissue using Nanopore sequencing. bioRxiv : the preprint server for biology (2024)
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John E Gorzynski, Sneha Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Local read haplotagging enables accurate long-read small variant calling. Nature communications 15 (1) (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016) (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016) (2024)
Siavash Mirarab, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey, Guangii Chen, Nadolina Brajuka, Olivier Fedrigo, Giulio Formenti, Jochen B W Wolf, Kerstin Howe, Agostinho Antunes, Mikkel Heide Schierup, Benedict Paten, Erich D Jarvis, Guojie Zhang, Edward L Braun
A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature (2024)
Jimin Park, Daniel E Cook, Pi-Chuan Chang, Alexey Kolesnikov, Lucas Brambrink, Juan Carlos Mier, Joshua Gardner, Brandy McNulty, Samuel Sacco, Ayse Keskus, Asher Bryant, Tanveer Ahmad, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Helland, Byunggil Yoo, Irina Pushel, Lisa A Lansdon, Chengpeng Bi, Adam Walter, Margaret Gibson, Tomi Pastinen, Midhat S Farooqi, Nicolas Robine, Karen H Miga, Andrew Carroll, Mikhail Kolmogorov, Benedict Paten, Kishwar Shafin
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies. bioRxiv : the preprint server for biology (2024)
Siavash Mirarab, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey, Guangii Chen, Nadolina Brajuka, Olivier Fedrigo, Giulio Formenti, Jochen B W Wolf, Kerstin Howe, Agostinho Antunes, Mikkel Heide Schierup, Benedict Paten, Erich D Jarvis, Guojie Zhang, Edward L Braun
A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Siavash Mirarab, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey, Guangii Chen, Nadolina Brajuka, Olivier Fedrigo, Giulio Formenti, Jochen B W Wolf, Kerstin Howe, Agostinho Antunes, Mikkel Heide Schierup, Benedict Paten, Erich D Jarvis, Guojie Zhang, Edward L Braun
A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Rylee Genner, Stuart Akeson, Melissa Meredith, Pilar Alvarez Jerez, Laksh Malik, Breeana Baker, Abigail Miano-Burkhardt, null null, Benedict Paten, Kimberley J Billingsley, Cornelis Blauwendraat, Miten Jain
Assessing methylation detection for primary human tissue using Nanopore sequencing. bioRxiv : the preprint server for biology (2024)
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John E Gorzynski, Sneha Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Local read haplotagging enables accurate long-read small variant calling. Nature communications 15 (1) (2024)
Rylee Genner, Stuart Akeson, Melissa Meredith, Pilar Alvarez Jerez, Laksh Malik, Breeana Baker, Abigail Miano-Burkhardt, null null, Benedict Paten, Kimberley J Billingsley, Cornelis Blauwendraat, Miten Jain
Assessing methylation detection for primary human tissue using Nanopore sequencing. bioRxiv : the preprint server for biology (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016) (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016) (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016) (2024)
DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A Logsdon, Steven Jared Solar, Dmitry Antipov, Brandon D Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M Storer, Jiadong Lin, Abigail N Sequeira, Riley J Mangan, Glenn Hickey, Graciela Monfort Anez, Parithi Balachandran, Anton Bankevich, Christine R Beck, Arjun Biddanda, Matthew Borchers, Gerard G Bouffard, Emry Brannan, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Yongwook Choi, Juyun Crawford, Mark Diekhans, Eric Engelbrecht, Cedric Feschotte, Giulio Formenti, Gage H Garcia, Luciana de Gennaro, David M Gilbert, Richard E Green, Andrea Guarracino, Ishaan Gupta, Diana Haddad, Junmin Han, Robert S Harris, Gabrielle A Hartley, William T Harvey, Michael Hiller, Kendra Hoekzema, Marlys L Houck, Hyeonsoo Jeong, Kaivan Kamali, Manolis Kellis, Bryce Kille, Chul Lee, Youngho Lee, William D Lees, Alexandra P Lewis, Qiuhui Li, Mark Loftus, Yong Hwee Eddie Loh, Hailey Loucks, Jian Ma, Yafei Mao, Juan F I Martinez, Patrick Masterson, Rajiv C McCoy, Barbara McGrath, Sean McKinney, Britta S Meyer, Karen H Miga, Saswat Kumar Mohanty, Katherine M Munson, Karol Pal, Matthew W Pennell, Pavel A Pevzner, David Porubsky, Tamara Potapova, Francisca R Ringeling, Joana L Rocha, Oliver A Ryder, Samuel Sacco, Swati Saha, Takayo Sasaki, Michael C Schatz, Nicholas J Schork, Cole Shanks, Linnéa Smeds, Dongmin R Son, Cynthia Steiner, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Edmundo Torres-González, Mihir Trivedi, Wenjie Wei, Julie Wertz, Muyu Yang, Panpan Zhang, Shilong Zhang, Yang Zhang, Zhenmiao Zhang, Sarah A Zhao, Yixin Zhu, Erich D Jarvis, Jennifer L Gerton, Iker Rivas-González, Benedict Paten, Zachary Alfano Szpiech, Christian D Huber, Tobias L Lenz, Miriam K Konkel, Soojin V Yi, Stefan Canzar, Corey T Watson, Peter H Sudmant, Erin K Molloy, Erik Garrison, Craig B Lowe, Mario Ventura, Rachel J O'Neill, Sergey Koren, Kateryna D Makova, Adam M Phillippy, Evan E Eichler
Complete sequencing of ape genomes. bioRxiv : the preprint server for biology (2024)
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)
Rylee Genner, Stuart Akeson, Melissa Meredith, Pilar Alvarez Jerez, Laksh Malik, Breeana Baker, Abigail Miano-Burkhardt, null null, Benedict Paten, Kimberley J Billingsley, Cornelis Blauwendraat, Miten Jain
Assessing methylation detection for primary human tissue using Nanopore sequencing. bioRxiv : the preprint server for biology (2024)
Siavash Mirarab, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey, Guangii Chen, Nadolina Brajuka, Olivier Fedrigo, Giulio Formenti, Jochen B W Wolf, Kerstin Howe, Agostinho Antunes, Mikkel Heide Schierup, Benedict Paten, Erich D Jarvis, Guojie Zhang, Edward L Braun
A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016) (2024)
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John E Gorzynski, Sneha Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Local read haplotagging enables accurate long-read small variant calling. Nature communications 15 (1) (2024)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark E Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara A Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, null Sweetalana, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016) (2024)
Shloka Negi, Sarah L Stenton, Seth I Berger, Brandy McNulty, Ivo Violich, Joshua Gardner, Todd Hillaker, Sara M O'Rourke, Melanie C O'Leary, Elizabeth Carbonell, Christina A Austin-Tse, Gabrielle T Lemire, Jillian Serrano, Brian Mangilog, Grace E VanNoy, Mikhail Kolmogorov, Eric Vilain, Anne H O'Donnell-Luria, Emmanuèle C Délot, Karen H Miga, Jean Monlong, Benedict Paten
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. medRxiv : the preprint server for health sciences (2024)
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Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas W Maurer, Sergey Koren, Fritz J Sedlazeck, Tobias Marschall, Simon Mayes, Vania Costa, Justin M Zook, Kelvin J Liu, Duncan Kilburn, Melanie Sorensen, Katherine M Munson, Mitchell R Vollger, Jean Monlong, Erik Garrison, Evan E Eichler, Sofie Salama, David Haussler, Richard E Green, Mark Akeson, Adam M Phillippy, Karen H Miga, Paolo Carnevali, Miten Jain, Benedict Paten
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature biotechnology 38 (9) (2020)
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon, Valerie A Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G Bouffard, Alexander M Chang, Nancy F Hansen, Amy B Wilfert, Françoise Thibaud-Nissen, Anthony D Schmitt, Jon-Matthew Belton, Siddarth Selvaraj, Megan Y Dennis, Daniela C Soto, Ruta Sahasrabudhe, Gulhan Kaya, Josh Quick, Nicholas J Loman, Nadine Holmes, Matthew William Loose, Urvashi Surti, Rosa Ana Risques, Tina A Graves Lindsay, Robert Fulton, Ira M Hall, Benedict Paten, Kerstin Howe, Winston Timp, Alice Young, May Christine V Malicdan, Pavel A Pevzner, Jennifer L Gerton, Beth A Sullivan, Evan E Eichler, Adam M Phillippy
Telomere-to-telomere assembly of a complete human X chromosome. Nature 585 (7823) (2020)

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Benedict Paten