Modern technologies and algorithms for scaffolding assembled genomes.

by Jay Ghurye, Mihai Pop
Published 2019-06-01

MetaCarvel: linking assembly graph motifs to biological variants

by Jay Ghurye, Todd Treangen, Marcus Fedarko, W. Judson Hervey, Mihai Pop
Published 2019-08-01

Scaffolding of long read assemblies using long range contact information

by Jay Ghurye, Mihai Pop, Sergey Koren, Derek Bickhart, Chen-Shan Chin
Published 2017-07-01

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

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

Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water

by Prachi Kulkarni, Nathan D. Olson, Nathan D. Olson, Anthony Q. Bui, Rhodel N. Bradshaw, Laura P. Del Collo, Lauren E. Hittle, Eric T. Handy, Joseph N. Paulson, Jay Ghurye, Daniel J. Nasko, Cheryl East, Jo Ann Van Kessel, Kalmia E. Kniel, Pei C. Chiu, Emmanuel F. Mongodin, Mihai Pop, Manan Sharma, Amy R. Sapkota
Published 2020-11-01

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

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

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

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College P...

by Jacquelyn S. Meisel, Daniel J. Nasko, Brian Brubach, Victoria Cepeda-Espinoza, Jessica Chopyk, Héctor Corrada-Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D. Olson, Nidhi Shah, Sarah M. Allard, Adam L. Bazinet, Nicholas H. Bergman, Alexis Brown, J. Gregory Caporaso, Sean Conlan, Jocelyne DiRuggiero, Samuel P. Forry, Nur A. Hasan, Jason Kralj, Paul M. Luethy, Donald K. Milton, Brian D. Ondov, Sarah Preheim, Shashikala Ratnayake, Stephanie M. Rogers, M. J. Rosovitz, Eric G. Sakowski, Nils Oliver Schliebs, Daniel D. Sommer, Krista L. Ternus, Gherman Uritskiy, Sean X. Zhang, Mihai Pop, Todd J. Treangen
Published 2018-11-01