An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

por Timoshevskaya, Nataliya, Esşkut, Kaan i., Timoshevskiy, Vladimir A., Robb, Sofia M.C., Holt, Carson, Hess, Jon E., Parker, Hugo J., Baker, Cindy F., Miller, Allison K., Saraceno, Cody, Yandell, Mark, Krumlauf, Robb, Narum, Shawn R., Lampman, Ralph T., Gemmell, Neil J., Mountcastle, Jacquelyn, Haase, Bettina, Balacco, Jennifer R., Formenti, Giulio, Pelan, Sarah, Sims, Ying, Howe, Kerstin, Fedrigo, Olivier, Jarvis, Erich D., Smith, Jeramiah J.
Publicado 2023

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

por Toh, Huishi, Yang, Chentao, Formenti, Giulio, Raja, Kalpana, Yan, Lily, Tracey, Alan, Chow, William, Howe, Kerstin, Bergeron, Lucie A., Zhang, Guojie, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Fogg, John, Kirilenko, Bogdan, Munegowda, Chetan, Hiller, Michael, Jain, Aashish, Kihara, Daisuke, Rhie, Arang, Phillippy, Adam M., Swanson, Scott A., Jiang, Peng, Clegg, Dennis O., Jarvis, Erich D., Thomson, James A., Stewart, Ron, Chaisson, Mark J. P., Bukhman, Yury V.
Publicado 2022

The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes

por Bond, Donna M., Ortega-Recalde, Oscar, Laird, Melanie K., Hayakawa, Takashi, Richardson, Kyle S., Reese, Finlay.C. B., Kyle, Bruce, McIsaac-Williams, Brooke E., Robertson, Bruce C., van Heezik, Yolanda, Adams, Amy L., Chang, Wei-Shan, Haase, Bettina, Mountcastle, Jacquelyn, Driller, Maximilian, Collins, Joanna, Howe, Kerstin, Go, Yasuhiro, Thibaud-Nissen, Francoise, Lister, Nicholas C., Waters, Paul D., Fedrigo, Olivier, Jarvis, Erich D., Gemmell, Neil J., Alexander, Alana, Hore, Timothy A.
Publicado 2023

Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19

por Sahajpal, Nikhil Shri, Jill Lai, Chi-Yu, Hastie, Alex, Mondal, Ashis K., Dehkordi, Siavash Raeisi, van der Made, Caspar I., Fedrigo, Olivier, Al-Ajli, Farooq, Jalnapurkar, Sawan, Byrska-Bishop, Marta, Kanagal-Shamanna, Rashmi, Levy, Brynn, Schieck, Maximilian, Illig, Thomas, Bacanu, Silviu-Alin, Chou, Janet S., Randolph, Adrienne G., Rojiani, Amyn M., Zody, Michael C., Brownstein, Catherine A., Beggs, Alan H., Bafna, Vineet, Jarvis, Erich D., Hoischen, Alexander, Chaubey, Alka, Kolhe, Ravindra
Publicado 2022

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

por Joglekar, Anoushka, Prjibelski, Andrey, Mahfouz, Ahmed, Collier, Paul, Lin, Susan, Schlusche, Anna Katharina, Marrocco, Jordan, Williams, Stephen R., Haase, Bettina, Hayes, Ashley, Chew, Jennifer G., Weisenfeld, Neil I., Wong, Man Ying, Stein, Alexander N., Hardwick, Simon A., Hunt, Toby, Wang, Qi, Dieterich, Christoph, Bent, Zachary, Fedrigo, Olivier, Sloan, Steven A., Risso, Davide, Jarvis, Erich D., Flicek, Paul, Luo, Wenjie, Pitt, Geoffrey S., Frankish, Adam, Smit, August B., Ross, M. Elizabeth, Tilgner, Hagen U.
Publicado 2021

Evolutionary and biomedical insights from a marmoset diploid genome assembly

por Yang, Chentao, Zhou, Yang, Marcus, Stephanie, Formenti, Giulio, Bergeron, Lucie A., Song, Zhenzhen, Bi, Xupeng, Bergman, Juraj, Rousselle, Marjolaine Marie C., Zhou, Chengran, Zhou, Long, Deng, Yuan, Fang, Miaoquan, Xie, Duo, Zhu, Yuanzhen, Tan, Shangjin, Mountcastle, Jacquelyn, Haase, Bettina, Balacco, Jennifer, Wood, Jonathan, Chow, William, Rhie, Arang, Pippel, Martin, Fabiszak, Margaret M., Koren, Sergey, Fedrigo, Olivier, Freiwald, Winrich A., Howe, Kerstin, Yang, Huanming, Phillippy, Adam M., Schierup, Mikkel Heide, Jarvis, Erich D., Zhang, Guojie
Publicado 2021

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

por Hardwick, Simon A., Hu, Wen, Joglekar, Anoushka, Fan, Li, Collier, Paul G., Foord, Careen, Balacco, Jennifer, Lanjewar, Samantha, Sampson, Maureen McGuirk, Koopmans, Frank, Prjibelski, Andrey D., Mikheenko, Alla, Belchikov, Natan, Jarroux, Julien, Lucas, Anne Bergstrom, Palkovits, Miklós, Luo, Wenjie, Milner, Teresa A., Ndhlovu, Lishomwa C., Smit, August B., Trojanowski, John Q., Lee, Virginia M. Y., Fedrigo, Olivier, Sloan, Steven A., Tombácz, Dóra, Ross, M. Elizabeth, Jarvis, Erich, Boldogkői, Zsolt, Gan, Li, Tilgner, Hagen U.
Publicado 2022

Six reference-quality genomes reveal evolution of bat adaptations

por Jebb, David, Huang, Zixia, Pippel, Martin, Hughes, Graham M., Lavrichenko, Ksenia, Devanna, Paolo, Winkler, Sylke, Jermiin, Lars S., Skirmuntt, Emilia C., Katzourakis, Aris, Burkitt-Gray, Lucy, Ray, David A., Sullivan, Kevin A. M., Roscito, Juliana G., Kirilenko, Bogdan M., Dávalos, Liliana M., Corthals, Angelique P., Power, Megan L., Jones, Gareth, Ransome, Roger D., Dechmann, Dina K. N., Locatelli, Andrea G., Puechmaille, Sébastien J., Fedrigo, Olivier, Jarvis, Erich D., Hiller, Michael, Vernes, Sonja C., Myers, Eugene W., Teeling, Emma C.
Publicado 2020

A chromosome-level reference genome and pangenome for barn swallow population genomics

por Secomandi, Simona, Gallo, Guido R., Sozzoni, Marcella, Iannucci, Alessio, Galati, Elena, Abueg, Linelle, Balacco, Jennifer, Caprioli, Manuela, Chow, William, Ciofi, Claudio, Collins, Joanna, Fedrigo, Olivier, Ferretti, Luca, Fungtammasan, Arkarachai, Haase, Bettina, Howe, Kerstin, Kwak, Woori, Lombardo, Gianluca, Masterson, Patrick, Messina, Graziella, Møller, Anders P., Mountcastle, Jacquelyn, Mousseau, Timothy A., Obiol, Joan Ferrer, Olivieri, Anna, Rhie, Arang, Rubolini, Diego, Saclier, Marielle, Stanyon, Roscoe, Stucki, David, Thibaud-Nissen, Françoise, Torrance, James, Torroni, Antonio, Weber, Kristina, Ambrosini, Roberto, Bonisoli-Alquati, Andrea, Jarvis, Erich D., Gianfranceschi, Luca, Formenti, Giulio
Publicado 2023

Variation in predicted COVID-19 risk among lemurs and lorises

por Melin, Amanda D., Orkin, Joseph D., Janiak, Mareike C., Valenzuela, Alejandro, Kuderna, Lukas, Marrone, Frank, Ramangason, Hasinala, Horvath, Julie E., Roos, Christian, Kitchener, Andrew C., Khor, Chiea Chuen, Lim, Weng Khong, Lee, Jessica G. H., Tan, Patrick, Umapathy, Govindhaswamy, Raveendran, Muthuswamy, Harris, R. Alan, Gut, Ivo, Gut, Marta, Lizano, Esther, Nadler, Tilo, Zinner, Dietmar, Johnson, Steig E., Jarvis, Erich D., Fedrigo, Olivier, Wu, Dongdong, Zhang, Guojie, Farh, Kyle Kai-How, Rogers, Jeffrey, Marques-Bonet, Tomas, Navarro, Arcadi, Juan, David, Arora, Paramjit S., Higham, James P.
Publicado 2021

Reference genome and demographic history of the most endangered marine mammal, the vaquita

por Morin, Phillip A., Archer, Frederick I., Avila, Catherine D., Balacco, Jennifer R., Bukhman, Yury V., Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A., Fungtammasan, Arkarachai, Gulland, Frances M. D., Haase, Bettina, Peter Heide‐Jorgensen, Mads, Houck, Marlys L., Howe, Kerstin, Misuraca, Ann C., Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas‐Bracho, Lorenzo, Rowles, Teri K., Ryder, Oliver A., Smith, Cynthia R., Stevenson, Sacha, Taylor, Barbara L., Teilmann, Jonas, Torrance, James, Wells, Randall S., Westgate, Andrew J., Jarvis, Erich D.
Publicado 2020

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

por Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D., Rabbani, Keon, Balacco, Jennifer R., Chaisson, Mark, Cheng, Haoyu, Collins, Joanna, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O'Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Waterhouse, Robert M., Phillippy, Adam M., Jarvis, Erich D., Schatz, Michael C., Nekrutenko, Anton, Formenti, Giulio
Publicado 2023

Platypus and echidna genomes reveal mammalian biology and evolution

por Zhou, Yang, Shearwin-Whyatt, Linda, Li, Jing, Song, Zhenzhen, Hayakawa, Takashi, Stevens, David, Fenelon, Jane C., Peel, Emma, Cheng, Yuanyuan, Pajpach, Filip, Bradley, Natasha, Suzuki, Hikoyu, Nikaido, Masato, Damas, Joana, Daish, Tasman, Perry, Tahlia, Zhu, Zexian, Geng, Yuncong, Rhie, Arang, Sims, Ying, Wood, Jonathan, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Li, Qiye, Yang, Huanming, Wang, Jian, Johnston, Stephen D., Phillippy, Adam M., Howe, Kerstin, Jarvis, Erich D., Ryder, Oliver A., Kaessmann, Henrik, Donnelly, Peter, Korlach, Jonas, Lewin, Harris A., Graves, Jennifer, Belov, Katherine, Renfree, Marilyn B., Grutzner, Frank, Zhou, Qi, Zhang, Guojie
Publicado 2021

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

por Formenti, Giulio, Rhie, Arang, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Kwak, Woori, Korlach, Jonas, Fungtammasan, Arkarachai, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., Jarvis, Erich D.
Publicado 2021

Population genomics of the critically endangered kākāpō

por Dussex, Nicolas, van der Valk, Tom, Morales, Hernán E., Wheat, Christopher W., Díez-del-Molino, David, von Seth, Johanna, Foster, Yasmin, Kutschera, Verena E., Guschanski, Katerina, Rhie, Arang, Phillippy, Adam M., Korlach, Jonas, Howe, Kerstin, Chow, William, Pelan, Sarah, Mendes Damas, Joanna D., Lewin, Harris A., Hastie, Alex R., Formenti, Giulio, Fedrigo, Olivier, Guhlin, Joseph, Harrop, Thomas W.R., Le Lec, Marissa F., Dearden, Peter K., Haggerty, Leanne, Martin, Fergal J., Kodali, Vamsi, Thibaud-Nissen, Françoise, Iorns, David, Knapp, Michael, Gemmell, Neil J., Robertson, Fiona, Moorhouse, Ron, Digby, Andrew, Eason, Daryl, Vercoe, Deidre, Howard, Jason, Jarvis, Erich D., Robertson, Bruce C., Dalén, Love
Publicado 2021

A draft genome sequence of the elusive giant squid, Architeuthis dux

por da Fonseca, Rute R, Couto, Alvarina, Machado, Andre M, Brejova, Brona, Albertin, Carolin B, Silva, Filipe, Gardner, Paul, Baril, Tobias, Hayward, Alex, Campos, Alexandre, Ribeiro, Ângela M, Barrio-Hernandez, Inigo, Hoving, Henk-Jan, Tafur-Jimenez, Ricardo, Chu, Chong, Frazão, Barbara, Petersen, Bent, Peñaloza, Fernando, Musacchia, Francesco, Alexander, Graham C, Osório, Hugo, Winkelmann, Inger, Simakov, Oleg, Rasmussen, Simon, Rahman, M Ziaur, Pisani, Davide, Vinther, Jakob, Jarvis, Erich, Zhang, Guojie, Strugnell, Jan M, Castro, L Filipe C, Fedrigo, Olivier, Patricio, Mateus, Li, Qiye, Rocha, Sara, Antunes, Agostinho, Wu, Yufeng, Ma, Bin, Sanges, Remo, Vinar, Tomas, Blagoev, Blagoy, Sicheritz-Ponten, Thomas, Nielsen, Rasmus, Gilbert, M Thomas P
Publicado 2020

The swan genome and transcriptome, it is not all black and white

por Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., Short, Kirsty R.
Publicado 2023

Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

por Bentley, Blair P., Carrasco-Valenzuela, Tomás, Ramos, Elisa K. S., Pawar, Harvinder, Souza Arantes, Larissa, Alexander, Alana, Banerjee, Shreya M., Masterson, Patrick, Kuhlwilm, Martin, Pippel, Martin, Mountcastle, Jacquelyn, Haase, Bettina, Uliano-Silva, Marcela, Formenti, Giulio, Howe, Kerstin, Chow, William, Tracey, Alan, Sims, Ying, Pelan, Sarah, Wood, Jonathan, Yetsko, Kelsey, Perrault, Justin R., Stewart, Kelly, Benson, Scott R., Levy, Yaniv, Todd, Erica V., Shaffer, H. Bradley, Scott, Peter, Henen, Brian T., Murphy, Robert W., Mohr, David W., Scott, Alan F., Duffy, David J., Gemmell, Neil J., Suh, Alexander, Winkler, Sylke, Thibaud-Nissen, Françoise, Nery, Mariana F., Marques-Bonet, Tomas, Antunes, Agostinho, Tikochinski, Yaron, Dutton, Peter H., Fedrigo, Olivier, Myers, Eugene W., Jarvis, Erich D., Mazzoni, Camila J., Komoroske, Lisa M.
Publicado 2023

Semi-automated assembly of high-quality diploid human reference genomes

por Jarvis, Erich D., Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R., Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A., Carnevali, Paolo, Chaisson, Mark J. P., Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S., Fulton, Lucinda L., Garg, Shilpa, Gerton, Jennifer L., Ghurye, Jay, Granat, Anastasiya, Green, Richard E., Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B., Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O., Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W., McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E., Olson, Nathan D., Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L., Sanders, Ashley D., Schatz, Michael C., Schmitt, Anthony, Schneider, Valerie A., Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O., Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V., Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M., Eichler, Evan E., Phillippy, Adam M., Paten, Benedict, Howe, Kerstin, Miga, Karen H.
Publicado 2022

The Earth BioGenome Project 2020: Starting the clock

por Lewin, Harris A., Richards, Stephen, Lieberman Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie
Publicado 2022