by Shumate, Alaina, Salzberg, Steven L
Published in Bioinformatics (19.07.2021)

by Shumate, Alaina, Wong, Brandon, Pertea, Geo, Pertea, Mihaela
Published in PLoS computational biology (01.06.2022)

by Pertea, Mihaela, Shumate, Alaina, Pertea, Geo, Varabyou, Ales, Breitwieser, Florian P., Chang, Yu-Chi, Madugundu, Anil K., Pandey, Akhilesh, Salzberg, Steven L.
Published in Genome Biology (28.11.2018)

by Shumate, Alaina, Salzberg, Steven
Published in F1000 research (2022)

by Gershman, Ariel, Sauria, Michael E. G., 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
Published in Science (American Association for the Advancement of Science) (01.04.2022)

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.
Published in Science (American Association for the Advancement of Science) (01.04.2022)

by 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., Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Narzisi, Giuseppe, Evani, Uday Shanker, Clarke, Wayne E., Lee, Joyce, Mason, Christopher E., Lincoln, Stephen E., Miga, Karen H., Ebbert, Mark T. W., Shumate, Alaina, Li, Heng, Chin, Chen-Shan, Zook, Justin M., Sedlazeck, Fritz J.
Published in Nature biotechnology (01.05.2022)

by Alonge, Michael, Shumate, Alaina, Puiu, Daniela, Zimin, Aleksey V, Salzberg, Steven L
Published in Genetics (Austin) (01.10.2020)

by Shumate, Alaina, Zimin, Aleksey V., Sherman, Rachel M., Puiu, Daniela, Wagner, Justin M., Olson, Nathan D., Pertea, Mihaela, Salit, Marc L., Zook, Justin M., Salzberg, Steven L.
Published in Genome Biology (02.06.2020)

by Varabyou, Ales, Sommer, Markus J., Erdogdu, Beril, Shinder, Ida, Minkin, Ilia, Chao, Kuan-Hao, Park, Sukhwan, Heinz, Jakob, Pockrandt, Christopher, Shumate, Alaina, Rincon, Natalia, Puiu, Daniela, Steinegger, Martin, Salzberg, Steven L., Pertea, Mihaela
Published in Genome Biology (30.10.2023)

by Puiu, Daniela, Zimin, Aleksey, Shumate, Alaina, Ge, Yuchen, Qiu, Jiabin, Bhaskaran, Manoj, Salzberg, Steven L
Published in F1000 research (2020)

by Shumate, Alaina, Salzberg, Steven
Published in F1000 research (2022)

by Dohlman, Anders B., Mjelle, Robin, Wood, Henry, Lee, Iris, Jiang, Kevin, Shurberg, Ethan, Shumate, Alaina, Sanders, Blake, Qiao, Guanxi, Hirshman, Jodi, Cherniack, Andrew, Quirke, Phil, Meyerson, Matthew
Published in Cancer research (Chicago, Ill.) (21.04.2025)

by Chao, Kuan-Hao, Heinz, Jakob M., Hoh, Celine, Mao, Alan, Shumate, Alaina, Pertea, Mihaela, Salzberg, Steven L.
Published in Genome research (01.02.2025)

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.
Published in Nature (London) (17.11.2022)

by Zimin, Aleksey V, Shumate, Alaina, Shinder, Ida, Heinz, Jakob, Puiu, Daniela, Pertea, Mihaela, Salzberg, Steven L
Published in Genetics (Austin) (04.02.2022)

by Mc Cartney, Ann M., Shafin, Kishwar, Alonge, Michael, Bzikadze, Andrey V., Formenti, Giulio, Fungtammasan, Arkarachai, Howe, Kerstin, Jain, Chirag, Koren, Sergey, Logsdon, Glennis A., Miga, Karen H., Mikheenko, Alla, Paten, Benedict, Shumate, Alaina, Soto, Daniela C., Sović, Ivan, Wood, Jonathan M. D., Zook, Justin M., Phillippy, Adam M., Rhie, Arang
Published in Nature methods (01.06.2022)

by Shumate, Alaina, Salzberg, Steven
Published in bioRxiv (26.06.2020)

by 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)

by Alonge, Michael, Shumate, Alaina, Puiu, Daniela, Zimin, Aleksey V, Salzberg, Steven L
Published in Genetics (Austin) (01.10.2020)