Search Results - "Alexandersson, Marina"

Applications of generalized pair hidden Markov models to alignment and gene finding problems by Pachter, Lior, Alexandersson, Marina, Cawley, Simon

“…Hidden Markov models (HMMs) have been successfully applied to a variety of problems in molecular biology, ranging from alignment problems to gene finding and…”
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Genome sequence of the Brown Norway rat yields insights into mammalian evolution by Gibbs, Richard A, Weinstock, George M, Metzker, Michael L, Muzny, Donna M, Sodergren, Erica J, Scherer, Steven, Scott, Graham, Steffen, David, Worley, Kim C, Burch, Paula E, Okwuonu, Geoffrey, Hines, Sandra, Lewis, Lora, DeRamo, Christine, Delgado, Oliver, Dugan-Rocha, Shannon, Miner, George, Morgan, Margaret, Hawes, Alicia, Gill, Rachel, Celera, Holt, Robert A, Adams, Mark D, Amanatides, Peter G, Baden-Tillson, Holly, Barnstead, Mary, Chin, Soo, Evans, Cheryl A, Ferriera, Steve, Fosler, Carl, Glodek, Anna, Gu, Zhiping, Jennings, Don, Kraft, Cheryl L, Nguyen, Trixie, Pfannkoch, Cynthia M, Sitter, Cynthia, Sutton, Granger G, Venter, J Craig, Woodage, Trevor, Smith, Douglas, Lee, Hong-Mei, Gustafson, Erik, Cahill, Patrick, Kana, Arnold, Doucette-Stamm, Lynn, Weinstock, Keith, Fechtel, Kim, Weiss, Robert B, Dunn, Diane M, Green, Eric D, Blakesley, Robert W, Bouffard, Gerard G, De Jong, Pieter J, Osoegawa, Kazutoyo, Zhu, Baoli, Marra, Marco, Schein, Jacqueline, Bosdet, Ian, Fjell, Chris, Jones, Steven, Krzywinski, Martin, Mathewson, Carrie, Siddiqui, Asim, Wye, Natasja, McPherson, John, Zhao, Shaying, Fraser, Claire M, Shetty, Jyoti, Shatsman, Sofiya, Geer, Keita, Chen, Yixin, Abramzon, Sofyia, Nierman, William C, Havlak, Paul H, Chen, Rui, Durbin, K James, Simons, Rain, Ren, Yanru, Song, Xing-Zhi, Li, Bingshan, Liu, Yue, Qin, Xiang, Cawley, Simon, Cooney, A J, D'Souza, Lisa M, Martin, Kirt, Wu, Jia Qian, Gonzalez-Garay, Manuel L, Jackson, Andrew R, Kalafus, Kenneth J, McLeod, Michael P, Milosavljevic, Aleksandar, Virk, Davinder, Volkov, Andrei, Wheeler, David A, Zhang, Zhengdong, Bailey, Jeffrey A, Eichler, Evan E

“…The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human…”
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Initial sequencing and comparative analysis of the mouse genome by Waterston, Robert H, Lindblad-Toh, Kerstin, Birney, Ewan, Rogers, Jane, Abril, Josep F, Agarwal, Pankaj, Agarwala, Richa, Ainscough, Rachel, Alexandersson, Marina, An, Peter, Antonarakis, Stylianos E, Attwood, John, Baertsch, Robert, Bailey, Jonathon, Barlow, Karen, Beck, Stephan, Berry, Eric, Birren, Bruce, Bloom, Toby, Bork, Peer, Botcherby, Marc, Bray, Nicolas, Brent, Michael R, Brown, Daniel G, Brown, Stephen D, Bult, Carol, Burton, John, Butler, Jonathan, Campbell, Robert D, Carninci, Piero, Cawley, Simon, Chiaromonte, Francesca, Chinwalla, Asif T, Church, Deanna M, Clamp, Michele, Clee, Christopher, Collins, Francis S, Cook, Lisa L, Copley, Richard R, Coulson, Alan, Couronne, Olivier, Cuff, James, Curwen, Val, Cutts, Tim, Daly, Mark, David, Robert, Davies, Joy, Delehaunty, Kimberly D, Deri, Justin, Dermitzakis, Emmanouil T, Dewey, Colin, Dickens, Nicholas J, Diekhans, Mark, Dodge, Sheila, Dubchak, Inna, Dunn, Diane M, Eddy, Sean R, Elnitski, Laura, Emes, Richard D, Eswara, Pallavi, Eyras, Eduardo, Felsenfeld, Adam, Fewell, Ginger A, Flicek, Paul, Foley, Karen, Frankel, Wayne N, Fulton, Lucinda A, Fulton, Robert S, Furey, Terrence S, Gage, Diane, Gibbs, Richard A, Glusman, Gustavo, Gnerre, Sante, Goldman, Nick, Goodstadt, Leo, Grafham, Darren, Graves, Tina A, Green, Eric D, Gregory, Simon, Guigó, Roderic, Guyer, Mark, Hardison, Ross C, Haussler, David, Hayashizaki, Yoshihide, Hillier, LaDeana W, Hinrichs, Angela, Hlavina, Wratko, Holzer, Timothy, Hsu, Fan, Hua, Axin, Hubbard, Tim, Hunt, Adrienne, Jackson, Ian, Jaffe, David B, Johnson, L Steven, Jones, Matthew, Jones, Thomas A, Joy, Ann, Kamal, Michael, Karlsson, Elinor K

“…The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical…”
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SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model by Alexandersson, Marina, Cawley, Simon, Pachter, Lior

“…Comparative-based gene recognition is driven by the principle that conserved regions between related organisms are more likely than divergent regions to be…”
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On the existence of the stable birth-type distribution in a general branching process cell cycle model with unequal cell division by Alexandersson, Marina

“…We use multi-type branching process theory to construct a cell population model, general enough to include a large class of such models, and we use an abstract…”
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Existence of the Stable Birth Type Distribution in a General Branching Process Cell Cycle Model with Unequal Cell Division by Alexandersson, Marina

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Bioinformatic identification of polymerizing and transmembrane mucins in the puffer fish Fugu rubripes by Lang, Tiange, Alexandersson, Marina, Hansson, Gunnar C., Samuelsson, Tore

“…Mucins are large glycoproteins characterized by mucin domains that show little sequence conservation and are rich in the amino acids Ser, Thr, and Pro. To…”
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On the existence of the stable birth-type distribution in a general branching process cell cycle model with unequal cell division by Alexandersson, Marina

“…We use multi-type branching process theory to construct a cell population model, general enough to include a large class of such models, and we use an abstract…”
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SLAM webserver for comparative gene finding and alignment by Cawley, Simon, Pachter, Lior, Alexandersson, Marina

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Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat by Dewey, Colin, Wu, Jia Qian, Cawley, Simon, Alexandersson, Marina, Gibbs, Richard, Pachter, Lior

“…We describe a new method for simultaneously identifying novel homologous genes with identical structure in the human, mouse, and rat genomes by combining…”
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SLAM web server for comparative gene finding and alignment by Cawley, Simon, Pachter, Lior, Alexandersson, Marina

“…SLAM is a program that simultaneously aligns and annotates pairs of homologous sequences. The SLAM web server integrates SLAM with repeat masking tools and the…”
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Picking alignments from (Steiner) trees by Lam, Fumei, Alexandersson, Marina, Pachter, Lior

“…The application of Needleman-Wunsch alignment techniques to biological sequences is complicated by two serious problems when the sequences are long: the…”
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