Modern technologies and algorithms for scaffolding assembled genomes

Tekijä Ghurye, Jay, Pop, Mihai
Julkaisussa PLoS Comput Biol (2019)

Metagenomic Assembly: Overview, Challenges and Applications

Tekijä Ghurye, Jay S., Cepeda-Espinoza, Victoria, Pop, Mihai
Julkaisussa Yale J Biol Med (2016)

Scaffolding of long read assemblies using long range contact information

Tekijä Ghurye, Jay, Pop, Mihai, Koren, Sergey, Bickhart, Derek, Chin, Chen-Shan
Julkaisussa BMC Genomics (2017)

MetaCarvel: linking assembly graph motifs to biological variants

Tekijä Ghurye, Jay, Treangen, Todd, Fedarko, Marcus, Hervey, W. Judson, Pop, Mihai
Julkaisussa Genome Biol (2019)

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

Tekijä Ghurye, Jay, Koren, Sergey, Small, Scott T, Redmond, Seth, Howell, Paul, Phillippy, Adam M, Besansky, Nora J
Julkaisussa Gigascience (2019)

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

Tekijä Ghurye, Jay, Rhie, Arang, Walenz, Brian P., Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M., Koren, Sergey
Julkaisussa PLoS Comput Biol (2019)

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

Tekijä Olson, Nathan D, Treangen, Todd J, Hill, Christopher M, Cepeda-Espinoza, Victoria, Ghurye, Jay, Koren, Sergey, Pop, Mihai
Julkaisussa Brief Bioinform (2017)

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

Tekijä Liu, Ruijie, Low, Wai Yee, Tearle, Rick, Koren, Sergey, Ghurye, Jay, Rhie, Arang, Phillippy, Adam M., Rosen, Benjamin D., Bickhart, Derek M., Smith, Timothy P. L., Hiendleder, Stefan, Williams, John L.
Julkaisussa BMC Genomics (2019)

Chromosome-scale, haplotype-resolved assembly of human genomes

Tekijä Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., Li, Heng
Julkaisussa Nat Biotechnol (2020)

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

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

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

Tekijä Low, Wai Yee, Tearle, Rick, Liu, Ruijie, Koren, Sergey, Rhie, Arang, Bickhart, Derek M., Rosen, Benjamin D., Kronenberg, Zev N., Kingan, Sarah B., Tseng, Elizabeth, Thibaud-Nissen, Françoise, Martin, Fergal J., Billis, Konstantinos, Ghurye, Jay, Hastie, Alex R., Lee, Joyce, Pang, Andy W. C., Heaton, Michael P., Phillippy, Adam M., Hiendleder, Stefan, Smith, Timothy P. L., Williams, John L.
Julkaisussa Nat Commun (2020)

Improved reference genome of the arboviral vector Aedes albopictus

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

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

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

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...

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

De novo assembly of the cattle reference genome with single-molecule sequencing

Tekijä Rosen, Benjamin D, Bickhart, Derek M, Schnabel, Robert D, Koren, Sergey, Elsik, Christine G, Tseng, Elizabeth, Rowan, Troy N, Low, Wai Y, Zimin, Aleksey, Couldrey, Christine, Hall, Richard, Li, Wenli, Rhie, Arang, Ghurye, Jay, McKay, Stephanie D, Thibaud-Nissen, Françoise, Hoffman, Jinna, Murdoch, Brenda M, Snelling, Warren M, McDaneld, Tara G, Hammond, John A, Schwartz, John C, Nandolo, Wilson, Hagen, Darren E, Dreischer, Christian, Schultheiss, Sebastian J, Schroeder, Steven G, Phillippy, Adam M, Cole, John B, Van Tassell, Curtis P, Liu, George, Smith, Timothy P L, Medrano, Juan F
Julkaisussa Gigascience (2020)

Towards complete and error-free genome assemblies of all vertebrate species

Tekijä Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C., Lama, Tanya M., Grutzner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E., Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C., Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D.
Julkaisussa Nature (2021)