Search Results - "Kirsche, Melanie"

Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing by Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C, Soyk, Sebastian

“…Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for…”
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Paragraph: a graph-based structural variant genotyper for short-read sequence data by Chen, Sai, Krusche, Peter, Dolzhenko, Egor, Sherman, Rachel M, Petrovski, Roman, Schlesinger, Felix, Kirsche, Melanie, Bentley, David R, Schatz, Michael C, Sedlazeck, Fritz J, Eberle, Michael A

“…Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical…”
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Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing by Aganezov, Sergey, Goodwin, Sara, Sherman, Rachel M, Sedlazeck, Fritz J, Arun, Gayatri, Bhatia, Sonam, Lee, Isac, Kirsche, Melanie, Wappel, Robert, Kramer, Melissa, Kostroff, Karen, Spector, David L, Timp, Winston, McCombie, W Richard, Schatz, Michael C

“…Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic…”
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A diploid assembly-based benchmark for variants in the major histocompatibility complex by Chin, Chen-Shan, Wagner, Justin, Zeng, Qiandong, Garrison, Erik, Garg, Shilpa, Fungtammasan, Arkarachai, Rautiainen, Mikko, Aganezov, Sergey, Kirsche, Melanie, Zarate, Samantha, Schatz, Michael C., Xiao, Chunlin, Rowell, William J., Markello, Charles, Farek, Jesse, Sedlazeck, Fritz J., Bansal, Vikas, Yoo, Byunggil, Miller, Neil, Zhou, Xin, Carroll, Andrew, Barrio, Alvaro Martinez, Salit, Marc, Marschall, Tobias, Dilthey, Alexander T., Zook, Justin M.

“…Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct…”
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Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area by Thielen, Peter M, Wohl, Shirlee, Mehoke, Thomas, Ramakrishnan, Srividya, Kirsche, Melanie, Falade-Nwulia, Oluwaseun, Trovão, Nídia S, Ernlund, Amanda, Howser, Craig, Sadowski, Norah, Morris, C Paul, Hopkins, Mark, Schwartz, Matthew, Fan, Yunfan, Gniazdowski, Victoria, Lessler, Justin, Sauer, Lauren, Schatz, Michael C, Evans, Jared D, Ray, Stuart C, Timp, Winston, Mostafa, Heba H

“…The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within…”
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Sapling: accelerating suffix array queries with learned data models by Kirsche, Melanie, Das, Arun, Schatz, Michael C

“…Abstract Motivation As genomic data becomes more abundant, efficient algorithms and data structures for sequence alignment become increasingly important. The…”
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Jasmine and Iris: population-scale structural variant comparison and analysis by Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Battle, Alexis, Aganezov, Sergey, Schatz, Michael C.

“…The availability of long reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through…”
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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato by Alonge, Michael, Wang, Xingang, Benoit, Matthias, Soyk, Sebastian, Pereira, Lara, Zhang, Lei, Suresh, Hamsini, Ramakrishnan, Srividya, Maumus, Florian, Ciren, Danielle, Levy, Yuval, Harel, Tom Hai, Shalev-Schlosser, Gili, Amsellem, Ziva, Razifard, Hamid, Caicedo, Ana L., Tieman, Denise M., Klee, Harry, Kirsche, Melanie, Aganezov, Sergey, Ranallo-Benavidez, T. Rhyker, Lemmon, Zachary H., Kim, Jennifer, Robitaille, Gina, Kramer, Melissa, Goodwin, Sara, McCombie, W. Richard, Hutton, Samuel, Van Eck, Joyce, Gillis, Jesse, Eshed, Yuval, Sedlazeck, Fritz J., van der Knaap, Esther, Schatz, Michael C., Lippman, Zachary B.

“…Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of…”
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A complete reference genome improves analysis of human genetic variation by Aganezov, Sergey, Yan, Stephanie M, Soto, Daniela C, Kirsche, Melanie, Zarate, Samantha, Avdeyev, Pavel, Taylor, Dylan J, Shafin, Kishwar, Shumate, Alaina, Xiao, Chunlin, Wagner, Justin, McDaniel, Jennifer, Olson, Nathan D, Sauria, Michael E G, Vollger, Mitchell R, Rhie, Arang, Meredith, Melissa, Martin, Skylar, Lee, Joyce, Koren, Sergey, Rosenfeld, Jeffrey A, Paten, Benedict, Layer, Ryan, Chin, Chen-Shan, Sedlazeck, Fritz J, Hansen, Nancy F, Miller, Danny E, Phillippy, Adam M, Miga, Karen H, McCoy, Rajiv C, Dennis, Megan Y, Zook, Justin M, Schatz, Michael C

“…Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors,…”
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Semi-automated assembly of high-quality diploid human reference genomes by 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.

“…The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1 , 2 …”
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Democratizing long-read genome assembly by Kirsche, Melanie, Schatz, Michael C

“…De novo assembled genomes serve as the backbone for modern genomics. In an article in this issue of Cell Systems, Ekim et al. present the mdBG assembler that…”
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Benchmarking challenging small variants with linked and long reads by Wagner, Justin, Olson, Nathan D., Harris, Lindsay, Khan, Ziad, Farek, Jesse, Mahmoud, Medhat, Stankovic, Ana, Kovacevic, Vladimir, Yoo, Byunggil, Miller, Neil, Rosenfeld, Jeffrey A., Ni, Bohan, Zarate, Samantha, Kirsche, Melanie, Aganezov, Sergey, Schatz, Michael C., Narzisi, Giuseppe, Byrska-Bishop, Marta, Clarke, Wayne, Evani, Uday S., Markello, Charles, Shafin, Kishwar, Zhou, Xin, Sidow, Arend, Bansal, Vikas, Ebert, Peter, Marschall, Tobias, Lansdorp, Peter, Hanlon, Vincent, Mattsson, Carl-Adam, Barrio, Alvaro Martinez, Fiddes, Ian T., Xiao, Chunlin, Fungtammasan, Arkarachai, Chin, Chen-Shan, Wenger, Aaron M., Rowell, William J., Sedlazeck, Fritz J., Carroll, Andrew, Salit, Marc, Zook, Justin M.

“…Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use…”
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