Predicting the functional effect of amino acid substitutions and indels von Choi, Yongwook, Sims, Gregory E, Murphy, Sean, Miller, Jason R, Chan, Agnes P

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Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq von Miller, Jason R, Adjeroh, Donald A

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Genomic insights into the Ixodes scapularis tick vector of Lyme disease von Gulia-Nuss, Monika, Nuss, Andrew B., Meyer, Jason M., Sonenshine, Daniel E., Roe, R. Michael, Waterhouse, Robert M., Sattelle, David B., de la Fuente, José, Ribeiro, Jose M., Megy, Karine, Thimmapuram, Jyothi, Miller, Jason R., Walenz, Brian P., Koren, Sergey, Hostetler, Jessica B., Thiagarajan, Mathangi, Joardar, Vinita S., Hannick, Linda I., Bidwell, Shelby, Hammond, Martin P., Young, Sarah, Zeng, Qiandong, Abrudan, Jenica L., Almeida, Francisca C., Ayllón, Nieves, Bhide, Ketaki, Bissinger, Brooke W., Bonzon-Kulichenko, Elena, Buckingham, Steven D., Caffrey, Daniel R., Caimano, Melissa J., Croset, Vincent, Driscoll, Timothy, Gilbert, Don, Gillespie, Joseph J., Giraldo-Calderón, Gloria I., Grabowski, Jeffrey M., Jiang, David, Khalil, Sayed M. S., Kim, Donghun, Kocan, Katherine M., Koči, Juraj, Kuhn, Richard J., Kurtti, Timothy J., Lees, Kristin, Lang, Emma G., Kennedy, Ryan C., Kwon, Hyeogsun, Perera, Rushika, Qi, Yumin, Radolf, Justin D., Sakamoto, Joyce M., Sánchez-Gracia, Alejandro, Severo, Maiara S., Silverman, Neal, Šimo, Ladislav, Tojo, Marta, Tornador, Cristian, Van Zee, Janice P., Vázquez, Jesús, Vieira, Filipe G., Villar, Margarita, Wespiser, Adam R., Yang, Yunlong, Zhu, Jiwei, Arensburger, Peter, Pietrantonio, Patricia V., Barker, Stephen C., Shao, Renfu, Zdobnov, Evgeny M., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Park, Yoonseong, Rozas, Julio, Benton, Richard, Pedra, Joao H. F., Nelson, David R., Unger, Maria F., Tubio, Jose M. C., Tu, Zhijian, Robertson, Hugh M., Shumway, Martin, Sutton, Granger, Wortman, Jennifer R., Lawson, Daniel, Wikel, Stephen K., Nene, Vishvanath M., Fraser, Claire M., Collins, Frank H., Birren, Bruce, Nelson, Karen E., Caler, Elisabet, Hill, Catherine A.

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Araport: the Arabidopsis information portal von Krishnakumar, Vivek, Hanlon, Matthew R, Contrino, Sergio, Ferlanti, Erik S, Karamycheva, Svetlana, Kim, Maria, Rosen, Benjamin D, Cheng, Chia-Yi, Moreira, Walter, Mock, Stephen A, Stubbs, Joseph, Sullivan, Julie M, Krampis, Konstantinos, Miller, Jason R, Micklem, Gos, Vaughn, Matthew, Town, Christopher D

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Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes von Zhou, Peng, Silverstein, Kevin A T, Ramaraj, Thiruvarangan, Guhlin, Joseph, Denny, Roxanne, Liu, Junqi, Farmer, Andrew D, Steele, Kelly P, Stupar, Robert M, Miller, Jason R, Tiffin, Peter, Mudge, Joann, Young, Nevin D

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Assembly algorithms for next-generation sequencing data von Miller, Jason R., Koren, Sergey, Sutton, Granger

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Evaluation of machine learning models that predict lncRNA subcellular localization von Miller, Jason R, Yi, Weijun, Adjeroh, Donald A

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Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation von Koren, Sergey, Walenz, Brian P, Berlin, Konstantin, Miller, Jason R, Bergman, Nicholas H, Phillippy, Adam M

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Multi-symptom Relief with Propylene Glycol-Hydroxypropyl-Guar Nanoemulsion Lubricant Eye Drops in Subjects with Dry Eye Disease: A Post-Marketing Prospective Study von Bickle, Katherine, Miller, Jason R., Tauber, Joseph, Awisi-Gyau, Deborah

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Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula von Moll, Karen M, Zhou, Peng, Ramaraj, Thiruvarangan, Fajardo, Diego, Devitt, Nicholas P, Sadowsky, Michael J, Stupar, Robert M, Tiffin, Peter, Miller, Jason R, Young, Nevin D, Silverstein, Kevin A T, Mudge, Joann

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Hybrid assembly with long and short reads improves discovery of gene family expansions von Miller, Jason R, Zhou, Peng, Mudge, Joann, Gurtowski, James, Lee, Hayan, Ramaraj, Thiruvarangan, Walenz, Brian P, Liu, Junqi, Stupar, Robert M, Denny, Roxanne, Song, Li, Singh, Namrata, Maron, Lyza G, McCouch, Susan R, McCombie, W Richard, Schatz, Michael C, Tiffin, Peter, Young, Nevin D, Silverstein, Kevin A T

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New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information von Lorenzi, Hernan A, Puiu, Daniela, Miller, Jason R, Brinkac, Lauren M, Amedeo, Paolo, Hall, Neil, Caler, Elisabet V

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ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery von Krishnakumar, Vivek, Contrino, Sergio, Cheng, Chia-Yi, Belyaeva, Irina, Ferlanti, Erik S, Miller, Jason R, Vaughn, Matthew W, Micklem, Gos, Town, Christopher D, Chan, Agnes P

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A draft genome sequence for the Ixodes scapularis cell line, ISE6 [version 1; peer review: 2 approved] von Miller, Jason R, Koren, Sergey, Dilley, Kari A, Harkins, Derek M, Stockwell, Timothy B, Shabman, Reed S, Sutton, Granger G

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Association of Vitamin D With Stress Fractures: A Retrospective Cohort Study von Miller, Jason R., DPM, FACFAS, Dunn, Karl W., DPM, AACFAS, Ciliberti, Louis J., DPM, AACFAS, Patel, Rikhil D., DPM, Swanson, Brock A., DPM

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The Atlantic salmon genome provides insights into rediploidization von Lien, Sigbjørn, Koop, Ben F., Sandve, Simen R., Miller, Jason R., Kent, Matthew P., Nome, Torfinn, Hvidsten, Torgeir R., Leong, Jong S., Minkley, David R., Zimin, Aleksey, Grammes, Fabian, Grove, Harald, Gjuvsland, Arne, Walenz, Brian, Hermansen, Russell A., von Schalburg, Kris, Rondeau, Eric B., Di Genova, Alex, Samy, Jeevan K. A., Olav Vik, Jon, Vigeland, Magnus D., Caler, Lis, Grimholt, Unni, Jentoft, Sissel, Inge Våge, Dag, de Jong, Pieter, Moen, Thomas, Baranski, Matthew, Palti, Yniv, Smith, Douglas R., Yorke, James A., Nederbragt, Alexander J., Tooming-Klunderud, Ave, Jakobsen, Kjetill S., Jiang, Xuanting, Fan, Dingding, Hu, Yan, Liberles, David A., Vidal, Rodrigo, Iturra, Patricia, Jones, Steven J. M., Jonassen, Inge, Maass, Alejandro, Omholt, Stig W., Davidson, William S.

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Regulation of Parent-of-Origin Allelic Expression in the Endosperm von Hornslien, Karina S, Miller, Jason R, Grini, Paul E

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An algorithm for automated closure during assembly von Koren, Sergey, Miller, Jason R, Walenz, Brian P, Sutton, Granger

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Aggressive assembly of pyrosequencing reads with mates von Miller, Jason R., Delcher, Arthur L., Koren, Sergey, Venter, Eli, Walenz, Brian P., Brownley, Anushka, Johnson, Justin, Li, Kelvin, Mobarry, Clark, Sutton, Granger

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Whole-Genome Shotgun Assembly and Comparison of Human Genome Assemblies von Istrail, Sorin, Sutton, Granger G., Florea, Liliana, Halpern, Aaron L., Mobarry, Clark M., Lippert, Ross, Walenz, Brian, Shatkay, Hagit, Dew, Ian, Miller, Jason R., Flanigan, Michael J., Edwards, Nathan J., Bolanos, Randall, Fasulo, Daniel, Halldorsson, Bjarni V., Hannenhalli, Sridhar, Turner, Russell, Yooseph, Shibu, Lu, Fu, Nusskern, Deborah R., Shue, Bixiong Chris, Zheng, Xiangqun Holly, Zhong, Fei, Delcher, Arthur L., Huson, Daniel H., Kravitz, Saul A., Mouchard, Laurent, Reinert, Knut, Remington, Karin A., Clark, Andrew G., Waterman, Michael S., Eichler, Evan E., Adams, Mark D., Hunkapiller, Michael W., Myers, Eugene W., Venter, J. Craig

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