Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

by Alexander T. Dilthey, Chirag Jain, Sergey Koren, Adam M. Phillippy
Published 2019-07-01

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

by Arang Rhie, Brian P. Walenz, Sergey Koren, Adam M. Phillippy
Published 2020-09-01

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

by Daniel J. Nasko, Sergey Koren, Adam M. Phillippy, Todd J. Treangen
Published 2018-10-01

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

by Chirag Jain, Luis M. Rodriguez-R, Adam M. Phillippy, Konstantinos T. Konstantinidis, Srinivas Aluru
Published 2018-11-01

Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru.

by Todd J Treangen, George Schoeler, Adam M Phillippy, Nicholas H Bergman, Michael J Turell
Published 2016-04-01

MUMmer4: A fast and versatile genome alignment system.

by Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin
Published 2018-01-01

Integrating Hi-C links with assembly graphs for chromosome-scale assembly.

by Jay Ghurye, Arang Rhie, Brian P Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M Phillippy, Sergey Koren
Published 2019-08-01

Mash Screen: high-throughput sequence containment estimation for genome discovery

by Brian D. Ondov, Gabriel J. Starrett, Anna Sappington, Aleksandra Kostic, Sergey Koren, Christopher B. Buck, Adam M. Phillippy
Published 2019-11-01

Comprehensive DNA signature discovery and validation.

by Adam M Phillippy, Jacquline A Mason, Kunmi Ayanbule, Daniel D Sommer, Elisa Taviani, Anwar Huq, Rita R Colwell, Ivor T Knight, Steven L Salzberg
Published 2007-05-01

The whale shark genome reveals patterns of vertebrate gene family evolution

by Milton Tan, Anthony K Redmond, Helen Dooley, Ryo Nozu, Keiichi Sato, Shigehiro Kuraku, Sergey Koren, Adam M Phillippy, Alistair DM Dove, Timothy Read
Published 2021-08-01

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes

by Ruijie Liu, Wai Yee Low, Rick Tearle, Sergey Koren, Jay Ghurye, Arang Rhie, Adam M. Phillippy, Benjamin D. Rosen, Derek M. Bickhart, Timothy P. L. Smith, Stefan Hiendleder, John L. Williams
Published 2019-12-01

The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

by Jung-Hyun Kim, Vladimir N. Noskov, Aleksey Y. Ogurtsov, Ramaiah Nagaraja, Nikolai Petrov, Mikhail Liskovykh, Brian P. Walenz, Hee-Sheung Lee, Natalay Kouprina, Adam M. Phillippy, Svetlana A. Shabalina, David Schlessinger, Vladimir Larionov
Published 2021-02-01

Molecular Epidemiologic Investigation of an Anthrax Outbreak among Heroin Users, Europe

by Erin P. Price, Meagan L. Seymour, Derek S. Sarovich, Jennie Latham, Spenser R. Wolken, Joanne Mason, Gemma Vincent, Kevin P. Drees, Stephen M. Beckstrom-Sternberg, Adam M. Phillippy, Sergey Koren, Richard T. Okinaka, Wai-Kwan Chung, James M. Schupp, David M. Wagner, Richard Vipond, Jeffrey T. Foster, Nicholas H. Bergman, James Burans, Talima Pearson, Tim Brooks, Paul Keim
Published 2012-08-01

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

by 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 L. Williams, Timothy P. L. Smith, Erich D. Jarvis, Shawn T. Sullivan, Sarah B. Kingan
Published 2021-04-01

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

by 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 Woodhouse, Brian P. Walenz, Sergey Koren, Adam M. Phillippy, Brett T. Hannigan, R. Kelly Dawe, Candice N. Hirsch, Matthew B. Hufford, Doreen Ware
Published 2020-05-01

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

by 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 W. C. Pang, Michael P. Heaton, Adam M. Phillippy, Stefan Hiendleder, Timothy P. L. Smith, John L. Williams
Published 2020-04-01

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

by Derek M. Bickhart, Mick Watson, Sergey Koren, Kevin Panke-Buisse, Laura M. Cersosimo, Maximilian O. Press, Curtis P. Van Tassell, Jo Ann S. Van Kessel, Bradd J. Haley, Seon Woo Kim, Cheryl Heiner, Garret Suen, Kiranmayee Bakshy, Ivan Liachko, Shawn T. Sullivan, Phillip R. Myer, Jay Ghurye, Mihai Pop, Paul J. Weimer, Adam M. Phillippy, Timothy P. L. Smith
Published 2019-08-01

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

by Robert M. Waterhouse, Sergey Aganezov, Yoann Anselmetti, Jiyoung Lee, Livio Ruzzante, Maarten J. M. F. Reijnders, Romain Feron, Sèverine Bérard, Phillip George, Matthew W. Hahn, Paul I. Howell, Maryam Kamali, Sergey Koren, Daniel Lawson, Gareth Maslen, Ashley Peery, Adam M. Phillippy, Maria V. Sharakhova, Eric Tannier, Maria F. Unger, Simo V. Zhang, Max A. Alekseyev, Nora J. Besansky, Cedric Chauve, Scott J. Emrich, Igor V. Sharakhov
Published 2020-01-01

Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

by Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud-Nissen, James K. Biedler, Flavia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna-Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Dmitry A. Karagodin, Jeremy Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos A. Papathanos, Ronald P. Van Rij, Omar S. Akbari, Jeffrey Powell, Adam M. Phillippy, Mariangela Bonizzoni
Published 2021-07-01

Improved reference genome of the arboviral vector Aedes albopictus

by Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud-Nissen, James K. Biedler, Flavia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna-Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Dmitry A. Karagodin, Jeremy Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos A. Papathanos, Ronald P. Van Rij, Omar S. Akbari, Jeffrey Powell, Adam M. Phillippy, Mariangela Bonizzoni
Published 2020-08-01