Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Lorig-Roach, Ryan, Meredith, Melissa, Monlong, Jean, Jain, Miten, Olsen, Hugh E, McNulty, Brandy, Porubsky, David, Montague, Tessa G, Lucas, Julian K, Condon, Chris, Eizenga, Jordan M, Juul, Sissel, McKenzie, Sean K, Simmonds, Sara E, Park, Jimin, Asri, Mobin, Koren, Sergey, Eichler, Evan E, Axel, Richard, Martin, Bruce, Carnevali, Paolo, Miga, Karen H, Paten, Benedict
Published in Genome research (01.03.2024)
Published in Genome research (01.03.2024)
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Journal Article
Semi-automated assembly of high-quality diploid human reference genomes
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.
Published in Nature (London) (17.11.2022)
Published in Nature (London) (17.11.2022)
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Journal Article
Increased mutation and gene conversion within human segmental duplications
Vollger, Mitchell R., Dishuck, Philip C., Harvey, William T., DeWitt, William S., Guitart, Xavi, Goldberg, Michael E., Rozanski, Allison N., Lucas, Julian, Asri, Mobin, Munson, Katherine M., Lewis, Alexandra P., Hoekzema, Kendra, Logsdon, Glennis A., Porubsky, David, Paten, Benedict, Harris, Kelley, Hsieh, PingHsun, Eichler, Evan E.
Published in Nature (London) (11.05.2023)
Published in Nature (London) (11.05.2023)
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Journal Article
The variation and evolution of complete human centromeres
Logsdon, Glennis A., Rozanski, Allison N., Ryabov, Fedor, Potapova, Tamara, Shepelev, Valery A., Catacchio, Claudia R., Porubsky, David, Mao, Yafei, Yoo, DongAhn, Rautiainen, Mikko, Koren, Sergey, Nurk, Sergey, Lucas, Julian K., Hoekzema, Kendra, Munson, Katherine M., Gerton, Jennifer L., Phillippy, Adam M., Ventura, Mario, Alexandrov, Ivan A., Eichler, Evan E.
Published in Nature (London) (02.05.2024)
Published in Nature (London) (02.05.2024)
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Journal Article
Transcription initiation by human RNA polymerase II visualized at single-molecule resolution
Revyakin, Andrey, Zhang, Zhengjian, Coleman, Robert A, Li, Yan, Inouye, Carla, Lucas, Julian K, Park, Sang-Ryul, Chu, Steven, Tjian, Robert
Published in Genes & development (01.08.2012)
Published in Genes & development (01.08.2012)
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Journal Article
Structural and molecular characterization of lopinavir and ivermectin as breast cancer resistance protein (BCRP/ABCG2) inhibitors
Dutra, Julia de Paula, Scheiffer, Gustavo, Kronenberger, Thales, Gomes, Lucas Julian Cruz, Zanzarini, Isadora, Dos Santos, Kelly Karoline, Tonduru, Arun K, Poso, Antti, Rego, Fabiane Gomes de Moraes, Picheth, Geraldo, Valdameri, Glaucio, Moure, Vivian Rotuno
Published in EXCLI journal (01.01.2023)
Published in EXCLI journal (01.01.2023)
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Development and Clinical Validation of a Blood Test for Early Detection of Colorectal Adenomas and Cancer for Screening and Postpolypectomy Surveillance
Friedland, Shai, Watson, Drew, Pan, Jennifer, Chen, Yu, Nimgaonkar, Ashish, Gulzar, Zulfiqar, Atkins, Alexander, Gupta, Pratyush, Lucas, Julian, Lai, Jr-Ming, Hsieh, Huangpin, Su, Stephen, Gupta, Samir, Sninsky, John J., Mei, Rui
Published in Gastro hep advances (2022)
Published in Gastro hep advances (2022)
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Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Cheng, Haoyu, Asri, Mobin, Lucas, Julian, Koren, Sergey, Li, Heng
Published in Nature methods (01.06.2024)
Published in Nature methods (01.06.2024)
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Journal Article
The complete sequence of a human Y chromosome
Rhie, Arang, Nurk, Sergey, Cechova, Monika, Hoyt, Savannah J., Taylor, Dylan J., Altemose, Nicolas, Hook, Paul W., Koren, Sergey, Rautiainen, Mikko, Alexandrov, Ivan A., Allen, Jamie, Asri, Mobin, Bzikadze, Andrey V., Chen, Nae-Chyun, Chin, Chen-Shan, Diekhans, Mark, Flicek, Paul, Formenti, Giulio, Fungtammasan, Arkarachai, Garcia Giron, Carlos, Garrison, Erik, Gershman, Ariel, Gerton, Jennifer L., Grady, Patrick G. S., Guarracino, Andrea, Haggerty, Leanne, Halabian, Reza, Hansen, Nancy F., Harris, Robert, Hartley, Gabrielle A., Harvey, William T., Haukness, Marina, Heinz, Jakob, Hourlier, Thibaut, Hubley, Robert M., Hunt, Sarah E., Hwang, Stephen, Jain, Miten, Kesharwani, Rupesh K., Lewis, Alexandra P., Li, Heng, Logsdon, Glennis A., Lucas, Julian K., Makalowski, Wojciech, Markovic, Christopher, Martin, Fergal J., Mc Cartney, Ann M., McCoy, Rajiv C., McDaniel, Jennifer, McNulty, Brandy M., Medvedev, Paul, Mikheenko, Alla, Munson, Katherine M., Murphy, Terence D., Olsen, Hugh E., Olson, Nathan D., Paulin, Luis F., Porubsky, David, Potapova, Tamara, Ryabov, Fedor, Salzberg, Steven L., Sauria, Michael E. G., Sedlazeck, Fritz J., Shafin, Kishwar, Shepelev, Valery A., Shumate, Alaina, Storer, Jessica M., Surapaneni, Likhitha, Taravella Oill, Angela M., Thibaud-Nissen, Françoise, Timp, Winston, Tomaszkiewicz, Marta, Vollger, Mitchell R., Walenz, Brian P., Watwood, Allison C., Weissensteiner, Matthias H., Wenger, Aaron M., Wilson, Melissa A., Zarate, Samantha, Zhu, Yiming, Zook, Justin M., Eichler, Evan E., O’Neill, Rachel J., Schatz, Michael C., Miga, Karen H., Makova, Kateryna D., Phillippy, Adam M.
Published in Nature (London) (14.09.2023)
Published in Nature (London) (14.09.2023)
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Journal Article
Complete genomic and epigenetic maps of human centromeres
Altemose, Nicolas, Logsdon, Glennis A, Bzikadze, Andrey V, Sidhwani, Pragya, Langley, Sasha A, Caldas, Gina V, Hoyt, Savannah J, Uralsky, Lev, Ryabov, Fedor D, Shew, Colin J, Sauria, Michael E G, Borchers, Matthew, Gershman, Ariel, Mikheenko, Alla, Shepelev, Valery A, Dvorkina, Tatiana, Kunyavskaya, Olga, Vollger, Mitchell R, Rhie, Arang, McCartney, Ann M, Asri, Mobin, Lorig-Roach, Ryan, Shafin, Kishwar, Lucas, Julian K, Aganezov, Sergey, Olson, Daniel, de Lima, Leonardo Gomes, Potapova, Tamara, Hartley, Gabrielle A, Haukness, Marina, Kerpedjiev, Peter, Gusev, Fedor, Tigyi, Kristof, Brooks, Shelise, Young, Alice, Nurk, Sergey, Koren, Sergey, Salama, Sofie R, Paten, Benedict, Rogaev, Evgeny I, Streets, Aaron, Karpen, Gary H, Dernburg, Abby F, Sullivan, Beth A, Straight, Aaron F, Wheeler, Travis J, Gerton, Jennifer L, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Dennis, Megan Y, O'Neill, Rachel J, Zook, Justin M, Schatz, Michael C, Pevzner, Pavel A, Diekhans, Mark, Langley, Charles H, Alexandrov, Ivan A, Miga, Karen H
Published in Science (American Association for the Advancement of Science) (01.04.2022)
Published in Science (American Association for the Advancement of Science) (01.04.2022)
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Journal Article
The Human Pangenome Project: a global resource to map genomic diversity
Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A., Lucas, Julian K., Phillippy, Adam M., Popejoy, Alice B., Asri, Mobin, Carson, Caryn, Chaisson, Mark J. P., Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L., Fulton, Robert S., Garrison, Erik P., Garrison, Nanibaa’ A., Graves-Lindsay, Tina A., Ji, Hanlee, Kenny, Eimear E., Koenig, Barbara A., Li, Daofeng, Marschall, Tobias, McMichael, Joshua F., Novak, Adam M., Purushotham, Deepak, Schneider, Valerie A., Schultz, Baergen I., Smith, Michael W., Sofia, Heidi J., Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H., Paten, Benedict, Jarvis, Erich D., Hall, Ira M., Eichler, Evan E., Haussler, David
Published in Nature (London) (21.04.2022)
Published in Nature (London) (21.04.2022)
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Pangenome graph construction from genome alignments with Minigraph-Cactus
Hickey, Glenn, Monlong, Jean, Ebler, Jana, Novak, Adam M., Eizenga, Jordan M., Gao, Yan, Marschall, Tobias, Li, Heng, Paten, Benedict
Published in Nature biotechnology (01.04.2024)
Published in Nature biotechnology (01.04.2024)
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Journal Article
Recombination between heterologous human acrocentric chromosomes
Guarracino, Andrea, Buonaiuto, Silvia, de Lima, Leonardo Gomes, Potapova, Tamara, Rhie, Arang, Koren, Sergey, Rubinstein, Boris, Fischer, Christian, Gerton, Jennifer L., Phillippy, Adam M., Colonna, Vincenza, Garrison, Erik
Published in Nature (London) (11.05.2023)
Published in Nature (London) (11.05.2023)
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Journal Article
Abstract 2241: Comparison of rare pathogenic germline variants associated with cancer predisposition syndrome in Taiwan and USA populations
Gulzar, Zulfiqar, Lucas, Julian, Atkins, Alex, Su, stephen, Segurado, Oscar, Mei, Rui
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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Abstract 3652: Analytical validation of a novel circulating tumor DNA detection platform for targeted and immunotherapy selection
Gupta, Pratyush, Lucas, Julian, Atkins, Alex, Tsai, Wen-Sy, Marfatia, Twinkal, Chang, Shih-En, Segurado, Oscar, Mei, Rui
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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Improving the efficiency of clerking patients under an acute medical admission by introducing allied healthcare professionals to the clerking process
Srivastava, Sonam, Mohamed, Ahmed, Julian, Lucas, Edries, Mohamed, Jalal, Mujtaba, Ali, Freyaa, Alkaabi, Ibrahim, Patel, Hiten, Patel, Nikhil
Published in Future healthcare journal (01.04.2024)
Published in Future healthcare journal (01.04.2024)
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A sensitive and quantitative multimodal blood test for the detection of colorectal adenomas and cancer: Correlation with size and number of polyps
Friedland, Shai, Pan, Jennifer Y., Watson, Drew, Chen, Yu, Nimgaonkar, Ashish, Gulzar, Zulfiqar, Gupta, Pratyush, Lucas, Julian, Atkins, Alex, Lai, Jr-Ming, Hsieh, Ben, Su, Stephen, Lim, Austin, Ciu, Iris, Setthasap, Ploy, Sninsky, John J., Mei, Rui
Published in Journal of clinical oncology (20.05.2020)
Published in Journal of clinical oncology (20.05.2020)
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575 A HIGHLY SENSITIVE AND QUANTITATIVE MULTIMODAL BLOOD TEST FOR THE DETECTION OF COLORECTAL ADENOMAS AND CANCER
Friedland, Shai, Watson, Drew, Pan, Jennifer Y., Chen, Yu, Nimgaonkar, Ashish, Gulzar, Zulfiqar, Gupta, Pratyush, Lucas, Julian, Atkins, Alexander, Lai, Jr-Ming, Hsieh, Huangpin B., Su, Stephen, Lim, Austin, Chu, Iris, Setthasap, Ploy, Sninsky, John, Mei, Rui
Published in Gastroenterology (New York, N.Y. 1943) (01.05.2020)
Published in Gastroenterology (New York, N.Y. 1943) (01.05.2020)
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Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
Schatz, Michael C., Philippakis, Anthony A., Afgan, Enis, Banks, Eric, Carey, Vincent J., Carroll, Robert J., Culotti, Alessandro, Ellrott, Kyle, Goecks, Jeremy, Grossman, Robert L., Hall, Ira M., Hansen, Kasper D., Lawson, Jonathan, Leek, Jeffrey T., Luria, Anne O’Donnell, Mosher, Stephen, Morgan, Martin, Nekrutenko, Anton, O’Connor, Brian D., Osborn, Kevin, Paten, Benedict, Patterson, Candace, Tan, Frederick J., Taylor, Casey Overby, Vessio, Jennifer, Waldron, Levi, Wang, Ting, Wuichet, Kristin, Baumann, Alexander, Rula, Andrew, Kovalsy, Anton, Bernard, Clare, Caetano-Anollés, Derek, Van der Auwera, Geraldine A., Canas, Justin, Yuksel, Kaan, Herman, Kate, Taylor, M. Morgan, Simeon, Marianie, Baumann, Michael, Wang, Qi, Title, Robert, Munshi, Ruchi, Chaluvadi, Sushma, Reeves, Valerie, Disman, William, Thomas, Salin, Hajian, Allie, Kiernan, Elizabeth, Gupta, Namrata, Vosburg, Trish, Geistlinger, Ludwig, Ramos, Marcel, Oh, Sehyun, Rogers, Dave, McDade, Frances, Hastie, Mim, Turaga, Nitesh, Ostrovsky, Alexander, Mahmoud, Alexandru, Baker, Dannon, Clements, Dave, Cox, Katherine E.L., Suderman, Keith, Kucher, Nataliya, Golitsynskiy, Sergey, Zarate, Samantha, Wheelan, Sarah J., Kammers, Kai, Stevens, Ana, Hutter, Carolyn, Wellington, Christopher, Ghanaim, Elena M., Wiley, Ken L., Sen, Shurjo K., Di Francesco, Valentina, s Yuen, Deni, Walsh, Brian, Sargent, Luke, Jalili, Vahid, Chilton, John, Shepherd, Lori, Stubbs, B.J., O’Farrell, Ash, Vizzier, Benton A., Overbeck, Charles, Reid, Charles, Steinberg, David Charles, Sheets, Elizabeth A., Lucas, Julian, Blauvelt, Lon, Cabansay, Louise, Warren, Noah, Hannafious, Brian, Harris, Tim, Reddy, Radhika, Torstenson, Eric, Banasiewicz, M. Katie, Abel, Haley J., Walker, Jason
Published in Cell genomics (12.01.2022)
Published in Cell genomics (12.01.2022)
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