Sökresultat - "Shumate, Alaina"

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 JP, 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

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A complete reference genome improves analysis of human genetic variation

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 EG, 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

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Epigenetic patterns in a complete human genome

Gershman, Ariel, Sauria, Michael EG, Guitart, Xavi, Vollger, Mitchell R, Hook, Paul W, Hoyt, Savannah J, Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey, Altemose, Nicolas, Caldas, Gina V, Logsdon, Glennis A, Rhie, Arang, Eichler, Evan E, Schatz, Michael C, O'Neill, Rachel J, Phillippy, Adam M, Miga, Karen H, Timp, Winston

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The complete sequence of a human genome

Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick GS, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian FA, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan MD, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O’Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H, Phillippy, Adam M

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The complete sequence of a human Y chromosome

Rhie, Arang, Nurk, Sergey^{Aff1, Aff51}, Cechova, Monika^{Aff2, Aff3}, Hoyt, Savannah J., Taylor, Dylan J., Altemose, Nicolas, Hook, Paul W., Koren, Sergey, Rautiainen, Mikko, Alexandrov, Ivan A.^{Aff8, Aff9, Aff52}, Allen, Jamie, Asri, Mobin, Bzikadze, Andrey V., Chen, Nae-Chyun, Chin, Chen-Shan^{Aff14, Aff15}, Diekhans, Mark, Flicek, Paul^{Aff10, Aff16}, Formenti, Giulio, Fungtammasan, Arkarachai, Garcia Giron, Carlos, Garrison, Erik, Gershman, Ariel, Gerton, Jennifer L.^{Aff20, Aff21}, Grady, Patrick G. S., Guarracino, Andrea^{Aff19, Aff22}, Haggerty, Leanne, Halabian, Reza, Hansen, Nancy F.^{Aff1, Aff24}, 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^{Aff31, Aff32}, Logsdon, Glennis A., Lucas, Julian K.^{Aff3, Aff11}, Makalowski, Wojciech, Markovic, Christopher, Martin, Fergal J., Mc Cartney, Ann M., McCoy, Rajiv C., McDaniel, Jennifer, McNulty, Brandy M.^{Aff3, Aff11}, Medvedev, Paul^{Aff35, Aff36, Aff37}, Mikheenko, Alla^{Aff9, Aff38}, Munson, Katherine M., Murphy, Terence D., Olsen, Hugh E.^{Aff3, Aff11}, Olson, Nathan D., Paulin, Luis F., Porubsky, David, Potapova, Tamara, Ryabov, Fedor, Salzberg, Steven L., Sauria, Michael E. G., Sedlazeck, Fritz J.^{Aff30, Aff42}, Shafin, Kishwar, Shepelev, Valery A., Shumate, Alaina, Storer, Jessica M., Surapaneni, Likhitha, Taravella Oill, Angela M., Thibaud-Nissen, Françoise, Timp, Winston, Tomaszkiewicz, Marta^{Aff25, Aff46}, 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.^{Aff26, Aff48}, O’Neill, Rachel J.^{Aff4, Aff49, Aff50}, Schatz, Michael C.^{Aff5, Aff13}, Miga, Karen H.^{Aff3, Aff11}, Makova, Kateryna D., Phillippy, Adam M.^{Aff1, IDs4158602306457y_cor87}

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

Varabyou, Ales^{Aff1, Aff2, Aff3, IDs13059023030884_cor1}, Sommer, Markus J.^{Aff1, Aff3}, Erdogdu, Beril^{Aff1, Aff3}, Shinder, Ida^{Aff1, Aff4}, Minkin, Ilia^{Aff1, Aff3}, Chao, Kuan-Hao^{Aff1, Aff2}, Park, Sukhwan^{Aff5, Aff6}, Heinz, Jakob^{Aff1, Aff3}, Pockrandt, Christopher^{Aff1, Aff3}, Shumate, Alaina^{Aff1, Aff3}, Rincon, Natalia^{Aff1, Aff3}, Puiu, Daniela^{Aff1, Aff3}, Steinegger, Martin^{Aff5, Aff6, Aff7}, Salzberg, Steven L.^{Aff1, Aff2, Aff3, Aff8, Aff9, IDs13059023030884_cor14}, Pertea, Mihaela^{Aff1, Aff2, Aff3, Aff8, IDs13059023030884_cor15}

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Mc Cartney, Ann M., Shafin, Kishwar, Alonge, Michael, Bzikadze, Andrey V., Formenti, Giulio, Fungtammasan, Arkarachai, Howe, Kerstin, Jain, Chirag^{Aff1, Aff8}, Koren, Sergey, Logsdon, Glennis A., Miga, Karen H.^{Aff2, Aff10}, Mikheenko, Alla, Paten, Benedict, Shumate, Alaina, Soto, Daniela C., Sović, Ivan^{Aff14, Aff15}, Wood, Jonathan M. D., Zook, Justin M., Phillippy, Adam M.^{Aff1, IDs41592022014403_cor19}, Rhie, Arang^{Aff1, IDs41592022014403_cor20}

Curated variation benchmarks for challenging medically relevant autosomal genes

Wagner, Justin, Olson, Nathan D., Harris, Lindsay, McDaniel, Jennifer, Cheng, Haoyu, Fungtammasan, Arkarachai, Hwang, Yih-Chii, Gupta, Richa, Wenger, Aaron M., Rowell, William J., Khan, Ziad M., Farek, Jesse, Zhu, Yiming, Pisupati, Aishwarya, Mahmoud, Medhat, Xiao, Chunlin, Yoo, Byunggil, Sahraeian, Sayed Mohammad Ebrahim, Miller, Danny E.^{Aff9, Aff10}, Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos^{Aff11, Aff12, Aff13}, Narzisi, Giuseppe, Evani, Uday Shanker, Clarke, Wayne E., Lee, Joyce, Mason, Christopher E., Lincoln, Stephen E., Miga, Karen H., Ebbert, Mark T. W.^{Aff19, Aff20, Aff21}, Shumate, Alaina^{Aff22, Aff23}, Li, Heng, Chin, Chen-Shan^{Aff3, IDs41587021011581_cor35}, Zook, Justin M.^{Aff1, IDs41587021011581_cor36}, Sedlazeck, Fritz J.^{Aff5, IDs41587021011581_cor37}

Improved transcriptome assembly using a hybrid of long and short reads with StringTie.

Shumate, Alaina^1,2 (AUTHOR), Wong, Brandon^1,2,3,4 (AUTHOR), Pertea, Geo⁵ (AUTHOR), Pertea, Mihaela^1,2,3 (AUTHOR) mpertea@jhu.edu

Assembly and annotation of an Ashkenazi human reference genome

Shumate, Alaina^{Aff1, Aff2}, Zimin, Aleksey V.^{Aff1, Aff2}, Sherman, Rachel M.^{Aff1, Aff3}, Puiu, Daniela^{Aff1, Aff3}, Wagner, Justin M., Olson, Nathan D., Pertea, Mihaela^{Aff1, Aff2}, Salit, Marc L., Zook, Justin M., Salzberg, Steven L.^{Aff1, Aff2, Aff3, Aff6}

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

Pertea, Mihaela^{Aff1, Aff3}, Shumate, Alaina^{Aff1, Aff2}, Pertea, Geo, Varabyou, Ales^{Aff1, Aff3}, Breitwieser, Florian P., Chang, Yu-Chi, Madugundu, Anil K.^{Aff4, Aff5, Aff6, Aff8}, Pandey, Akhilesh^{Aff4, Aff7, Aff8}, Salzberg, Steven L.^{Aff1, Aff2, Aff3, Aff9}

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Combining DNA and protein alignments to improve genome annotation with LiftOn.

Chao KH; Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA; kh.chao@cs.jhu.edu salzberg@jhu.edu.; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA., Heinz JM; Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA., Hoh C; Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA., Mao A; Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA., Shumate A; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA., Pertea M; Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA., Salzberg SL; Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA; kh.chao@cs.jhu.edu salzberg@jhu.edu.; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.; Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21211, USA.

Journal Article , 2025

Combining DNA and protein alignments to improve genome annotation with LiftOn.

Chao KH; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA., Heinz JM; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA., Hoh C; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA., Mao A; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA., Shumate A; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA., Pertea M; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA., Salzberg SL; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA.; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.; Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA.

Preprint; Journal Article , 2024

LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies.

Shumate A; Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.; Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA., Salzberg S; Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.; Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.; Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.; Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.

Journal Article; Comparative Study , 2024

The genome of the American groundhog, Marmota monax .

Puiu D; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.; Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA., Zimin A; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.; Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA., Shumate A; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.; Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA., Ge Y; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA., Qiu J; Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA., Bhaskaran M; Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA., Salzberg SL; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.; Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21211, USA.; Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, USA.

Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't , 2020