Adam M Phillippy (Adam Phillippy)

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 107

Top Venues

Nature

bioRxiv : the preprint server for biology

Genome research

Nature biotechnology

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

Publications

Theodore S Kalbfleisch, Stephanie D McKay, Brenda M Murdoch, David L Adelson, Diego Almansa-Villa, Gabrielle M Becker, Linda M Beckett, María José Benítez-Galeano, Fernando Biase, Theresa M Casey, Edward Boyi Chuong, Emily Clark, Shannon M Clarke, Noelle Cockett, Christine Couldrey, Brian W Davis, Christine G Elsik, Thomas Faraut, Yahui Gao, Carine Genet, Patrick G S Grady, Jonathan Green, Richard Green, Dai-Lu Guan, Darren Erich Hagen, Gabrielle A Hartley, Michael P Heaton, Savannah J Hoyt, Wen Huang, Erich Jarvis, Jenna Kalleberg, Hasan Khatib, Klaus-Peter Koepfli, James Eugene Koltes, Sergey Koren, Christa Kuehn, Tosso Leeb, Alexander S Leonard, George E Liu, Wai Yee Low, Hunter McConnell, Kathryn McRae, Karen Miga, Michelle Mousel, Holly Neibergs, Temitayo Olagunju, Matt Pennell, Bruna Petry, Mirjam Pewsner, Adam M Phillippy, Brandon D Pickett, Paulene Pineda, Tamara Potapova, Satyanarayana Rachagani, Arang Rhie, Monique Rijnkels, Annie Robic, Nelida Rodriguez Osorio, Yana Safonova, Gustavo Schettini, Robert D Schnabel, Nagabhishek Sirpu Natesh, Morgan R Stegemiller, Jessica Storer, Paul Stothard, Caleb Stull, Gwenola Tosser-Klopp, German Matias Traglia, Christopher K Tuggle, Curtis P Van Tassell, Corey T Watson, Rosemarie Weikard, Klaus Wimmers, Shangqian Xie, Liu Yang, Timothy P L Smith, Rachel J O'Neill, Benjamin D Rosen
The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature genetics 56 (8) (2024)
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra A Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W Williams, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature biotechnology (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics (Oxford, England) 40 (5) (2024)
Alexander P Sweeten, Michael C Schatz, Adam M Phillippy
ModDotPlot-rapid and interactive visualization of tandem repeats. Bioinformatics (Oxford, England) 40 (8) (2024)
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra A Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W Williams, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature biotechnology 42 (3) (2024)
Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M Phillippy, Rayan Chikhi, Christopher Quince
High-quality metagenome assembly from long accurate reads with metaMDBG. Nature biotechnology (2024)
Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M Phillippy, Rayan Chikhi, Christopher Quince
High-quality metagenome assembly from long accurate reads with metaMDBG. Nature biotechnology (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics (Oxford, England) 40 (5) (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. 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)
Theodore S Kalbfleisch, Stephanie D McKay, Brenda M Murdoch, David L Adelson, Diego Almansa-Villa, Gabrielle M Becker, Linda M Beckett, María José Benítez-Galeano, Fernando Biase, Theresa M Casey, Edward Boyi Chuong, Emily Clark, Shannon M Clarke, Noelle Cockett, Christine Couldrey, Brian W Davis, Christine G Elsik, Thomas Faraut, Yahui Gao, Carine Genet, Patrick G S Grady, Jonathan Green, Richard Green, Dai-Lu Guan, Darren Erich Hagen, Gabrielle A Hartley, Michael P Heaton, Savannah J Hoyt, Wen Huang, Erich Jarvis, Jenna Kalleberg, Hasan Khatib, Klaus-Peter Koepfli, James Eugene Koltes, Sergey Koren, Christa Kuehn, Tosso Leeb, Alexander S Leonard, George E Liu, Wai Yee Low, Hunter McConnell, Kathryn McRae, Karen Miga, Michelle Mousel, Holly Neibergs, Temitayo Olagunju, Matt Pennell, Bruna Petry, Mirjam Pewsner, Adam M Phillippy, Brandon D Pickett, Paulene Pineda, Tamara Potapova, Satyanarayana Rachagani, Arang Rhie, Monique Rijnkels, Annie Robic, Nelida Rodriguez Osorio, Yana Safonova, Gustavo Schettini, Robert D Schnabel, Nagabhishek Sirpu Natesh, Morgan R Stegemiller, Jessica Storer, Paul Stothard, Caleb Stull, Gwenola Tosser-Klopp, German Matias Traglia, Christopher K Tuggle, Curtis P Van Tassell, Corey T Watson, Rosemarie Weikard, Klaus Wimmers, Shangqian Xie, Liu Yang, Timothy P L Smith, Rachel J O'Neill, Benjamin D Rosen
The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature genetics (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)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Alexander P Sweeten, Michael C Schatz, Adam M Phillippy
ModDotPlot - Rapid and interactive visualization of complex repeats. bioRxiv : the preprint server for biology (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature 629 (8010) (2024)
Alexander P Sweeten, Michael C Schatz, Adam M Phillippy
ModDotPlot-rapid and interactive visualization of tandem repeats. Bioinformatics (Oxford, England) 40 (8) (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. Genome research (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature 629 (8010) (2024)
Sergey Koren, Zhigui Bao, Andrea Guarracino, Shujun Ou, Sara Goodwin, Katharine M Jenike, Julian Lucas, Brandy McNulty, Jimin Park, Mikko Rautianinen, Arang Rhie, Dick Roelofs, Harrie Schneiders, Ilse Vrijenhoek, Koen Nijbroek, Doreen Ware, Michael C Schatz, Erik P Garrison, Sanwen Huang, William Richard McCombie, Karen H Miga, Alexander H J Wittenberg, Adam M Phillippy
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. bioRxiv : the preprint server for biology (2024)
Alexander P Sweeten, Michael C Schatz, Adam M Phillippy
ModDotPlot-Rapid and interactive visualization of complex repeats. bioRxiv : the preprint server for biology (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature 629 (8010) (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature 629 (8010) (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature 629 (8010) (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjoern Andreas Gruening, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R Balacco, Mark J P Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra A Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O'Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W Williams, Robert M Waterhouse, Adam M Phillippy, Erich D Jarvis, Michael C Schatz, Anton Nekrutenko, Giulio Formenti
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature biotechnology (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature (2024)
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew L Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome research 34 (3) (2024)
Alexander P Sweeten, Michael C Schatz, Adam M Phillippy
ModDotPlot-Rapid and interactive visualization of complex repeats. bioRxiv : the preprint server for biology (2024)
Glennis A Logsdon, Allison N Rozanski, Fedor D Ryabov, Tamara A Potapova, Valery A Shepelev, Claudia Rita Catacchio, David Porubsky, Yafei Mao, DongAhn Yoo, Mikko Rautiainen, Sergey Koren, Sergey Nurk, Julian K Lucas, Kendra Hoekzema, Katherine M Munson, Jennifer L Gerton, Adam M Phillippy, Mario Ventura, Ivan A Alexandrov, Evan E Eichler
The variation and evolution of complete human centromeres. Nature 629 (8010) (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)
Alexander P Sweeten, Michael C Schatz, Adam M Phillippy
ModDotPlot - Rapid and interactive visualization of complex repeats. 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 630 (8016) (2024)
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Chentao Yang, Yang Zhou, Stephanie Marcus, Giulio Formenti, Lucie A Bergeron, Zhenzhen Song, Xupeng Bi, Juraj Bergman, Marjolaine Marie C Rousselle, Chengran Zhou, Long Zhou, Yuan Deng, Miaoquan Fang, Duo Xie, Yuanzhen Zhu, Shangjin Tan, Jacquelyn Mountcastle, Bettina Haase, Jennifer Balacco, Jonathan Wood, William Chow, Arang Rhie, Martin Pippel, Margaret M Fabiszak, Sergey Koren, Olivier Fedrigo, Winrich A Freiwald, Kerstin Howe, Huanming Yang, Adam M Phillippy, Mikkel Heide Schierup, Erich D Jarvis, Guo-Jie Zhang
Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature 594 (7862) (2021)
Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L Gedman, Lindsey J Cantin, Françoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C Vernes, Tanya M Lama, Frank Grützner, Wesley C Warren, Christopher N Balakrishnan, David W Burt, Julia M George, Matthew T Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce C Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F Kautt, Paolo Franchini, Harry William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J P Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B Kingan, Richard J Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E Green, Nicholas H Putnam, Ivo Glynne Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E Dagnew, Dengfeng Guan, Sarah E London, David F Clayton, Claudio V Mello, Samantha R Friedrich, Peter V Lovell, Ekaterina Osipova, Farooq O Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S Harris, Kateryna D Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal J Martin, Kevin Howe, Paul Flicek, Brian P Walenz, Woori Kwak, Hiram Clawson, Mark E Diekhans, Luis Nassar, Benedict Paten, Robert H S Kraus, Andrew J Crawford, Marcus Thomas Pius Gilbert, Guo-Jie Zhang, Byrappa Venkatesh, Robert W Murphy, Klaus-Peter Koepfli, Joshua D Kapp, Warren E Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A Ryder, David Haussler, Stephen J O'Brien, Jonas Korlach, Harris A Lewin, Kerstin Howe, Eugene W Myers, Richard Durbin, Adam M Phillippy, Erich D Jarvis
Towards complete and error-free genome assemblies of all vertebrate species. Nature 592 (7856) (2021)
Zev N Kronenberg, Arang Rhie, Sergey Koren, Gregory T Concepcion, Paul Peluso, Katherine M Munson, David Porubsky, Kristen Kuhn, Kathryn A Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo, Ivan Liachko, Richard J Hall, Adam M Phillippy, Evan E Eichler, John Lewis Williams, Timothy P L Smith, Erich D Jarvis, Shawn T Sullivan, Sarah B Kingan
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nature communications 12 (1) (2021)
Shujun Ou, Jianing Liu, Kapeel M Chougule, Arkarachai Fungtammasan, Arun S Seetharam, Joshua C Stein, Victor Llaca, Nancy Manchanda, Amanda M Gilbert, Sharon Wei, Chen-Shan Chin, David E Hufnagel, Sarah Pedersen, Samantha J Snodgrass, Kevin Fengler, Margaret R Woodhouse, Brian P Walenz, Sergey Koren, Adam M Phillippy, Brett T Hannigan, R Kelly Dawe, Candice N Hirsch, Matthew B Hufford, Doreen H Ware
Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature communications 11 (1) (2020)
Wai Yee Low, Rick Tearle, Ruijie Liu, Sergey Koren, Arang Rhie, Derek M Bickhart, Benjamin D Rosen, Zev N Kronenberg, Sarah B Kingan, Elizabeth Tseng, Françoise Thibaud-Nissen, Fergal J Martin, Konstantinos Billis, Jay Ghurye, Alex R Hastie, Joyce Lee, Andy Wing Chun Pang, Michael P Heaton, Adam M Phillippy, Stefan Hiendleder, Timothy P L Smith, John Lewis Williams
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature communications 11 (1) (2020)
Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome research 30 (9) (2020)
Phillip A Morin, Frederick I Archer, Catherine D Avila, Jennifer R Balacco, Yury V Bukhman, William Chow, Olivier Fedrigo, Giulio Formenti, Julie A Fronczek, Arkarachai Fungtammasan, Frances M D Gulland, Bettina Haase, Mads Peter Heide-Jørgensen, Marlys L Houck, Kerstin Howe, Ann C Misuraca, Jacquelyn Mountcastle, Whitney Musser, Sadye Paez, Sarah E Pelan, Adam M Phillippy, Arang Rhie, Jacqueline A Robinson, Lorenzo Rojas-Bracho, Teri K Rowles, Oliver A Ryder, Cynthia R Smith, Sacha Stevenson, Barbara L Taylor, Jonas Teilmann, James W Torrance, Randall S Wells, Andrew J Westgate, Erich D Jarvis
Reference genome and demographic history of the most endangered marine mammal, the vaquita. Molecular ecology resources 21 (4) (2020)
Justin M Zook, Nancy F Hansen, Nathan D Olson, Lesley Chapman, May Christine V Malicdan, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M Phillippy, Paul C Boutros, Sayed Mohammad E Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T Fiddes, Alvaro Martinez Barrio, Jeremiah Wala, Andrew Carroll, Noushin Ghaffari, Oscar L Rodriguez, Ali Bashir, Shaun Jackman, John J Farrell, Aaron M Wenger, Can Alkan, Arda Söylev, Michael C Schatz, Shilpa Garg, George M Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C English, Jeffrey A Rosenfeld, Weichen Zhou, Ryan E Mills, Jay M Sage, Jennifer R Davis, Michael D Kaiser, John S Oliver, Anthony P Catalano, Mark J P Chaisson, Noah Spies, Fritz J Sedlazeck, Marc Salit
A robust benchmark for detection of germline large deletions and insertions. Nature biotechnology 38 (11) (2020)
Maxwell J Scott, Joshua B Benoit, Rebecca J Davis, Samuel T Bailey, Virag Varga, Ellen O Martinson, Paul V Hickner, Zainulabeuddin Syed, Gisele A Cardoso, Tatiana Teixeira Torres, Matthew T Weirauch, Elizabeth H Scholl, Adam M Phillippy, Agustin Sagel, Mario Vasquez, Gladys Quintero, Steven R Skoda
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. Communications biology 3 (1) (2020)

Adam M Phillippy.css-eqlu8i{font-size:small;padding-left:4px;} (Adam Phillippy)

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Adam M Phillippy (Adam Phillippy)