Biblio

Export 22 results:
Author Keyword Title [ Type(Desc)] Year
Filters: First Letter Of Last Name is M  [Clear All Filters]
Conference Paper
L. Nakhleh, Moret, B. M. E., Roshan, U., John, S. K., Sun, J., and Warnow, T., “The Accuracy of Phylogenetic Methods for Large Datasets”, in Proc.\ 7th Pacific Symp. on Biocomputing ({PSB02}), 2002, vol. 7, pp. 211-222.
C. R. Linder, Moret, B. M. E., Nakhleh, L., and Warnow, T., “Network (reticulate) evolution: biology, models, and algorithms”, in The Ninth Pacific Symposium on Biocomputing (PSB), 2004.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance”, in Proceedings of the International Symposium on Bioinformatics Research and Applications, 2007, vol. 4463, pp. 61-72.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., “The Performance of Phylogenetic Methods on Trees of Bounded Diameter”, in First International Workshop on Algorithms in Bioinformatics (WABI 01), 2001, vol. Lecture Notes in Computer Science 2149, pp. 214–226.
C. Coarfa, Dotsenko, Y., Mellor-Crummey, J., Nakhleh, L., and Roshan, U., “PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction”, in Proceedigns of the First IEEE Workshop on High Performance Computing in Medicine and Biology, 2005, vol. 2, pp. 346-350.
L. Nakhleh, Jin, G., Zhao, F., and Mellor-Crummey, J., “Reconstructing phylogenetic networks using maximum parsimony”, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), 2005, pp. 93-102.
L. Nakhleh, Miranker, D., Barbancon, F., Piel, W. H., and Donoghue, M. J., “Requirements of Phylogenetic Databases”, in Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2003), 2003, pp. 141-148.
L. Nakhleh, Sun, J., Warnow, T., Linder, R., Moret, B. M. E., and Tholse, A., “Towards the development of tools for evaluating phylogenetic network reconstruction methods”, in Proc.\ 8th Pacific Symp. on Biocomputing ({PSB03}), 2003, pp. 315–326.
Journal Article
J. Zhu, Wen, D., Yu, Y., Meudt, H., and Nakhleh, L., “Bayesian inference of phylogenetic networks from bi-allelic genetic markers”, PLoS Computational Biology, vol. 14, no. 1, p. e1005932, 2018.PDF icon ZhuEtAl-PLoSCB18.pdf (10.6 MB)
G. A. Bravo, Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F. P., Wiedenhoeft, J., .Willows-Munro, S., and Edwards, S. V., “Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics”, PeerJ, vol. 7, p. e6399, 2019.PDF icon PeerJ2019.pdf (3.72 MB)
G. A. Bravo, Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F. P., Wiedenhoeft, J., .Willows-Munro, S., and Edwards, S. V., “Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics”, PeerJ, vol. 7, p. e6399, 2019.PDF icon PeerJ2019.pdf (3.72 MB)
Y. Lu, Muller, M., Smith, D., Dutta, B., Mourov, K., Iadevaia, S., Ruths, D., Tseng, J. - T., Yu, S., Yu, Q., Nakhleh, L., Balazsi, G., Donnelly, J., Schurdak, M., Morgan-Lappe, S., Fesik, S., Ram, P. T., and Mills, G. B., “Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling”, Oncogene, vol. 30, pp. 4567-4577, 2011.PDF icon Oncogene2011.pdf (905.3 KB)
Y. Lu, Muller, M., Smith, D., Dutta, B., Mourov, K., Iadevaia, S., Ruths, D., Tseng, J. - T., Yu, S., Yu, Q., Nakhleh, L., Balazsi, G., Donnelly, J., Schurdak, M., Morgan-Lappe, S., Fesik, S., Ram, P. T., and Mills, G. B., “Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling”, Oncogene, vol. 30, pp. 4567-4577, 2011.PDF icon Oncogene2011.pdf (905.3 KB)
Y. Lu, Muller, M., Smith, D., Dutta, B., Mourov, K., Iadevaia, S., Ruths, D., Tseng, J. - T., Yu, S., Yu, Q., Nakhleh, L., Balazsi, G., Donnelly, J., Schurdak, M., Morgan-Lappe, S., Fesik, S., Ram, P. T., and Mills, G. B., “Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling”, Oncogene, vol. 30, pp. 4567-4577, 2011.PDF icon Oncogene2011.pdf (905.3 KB)
Y. Lu, Muller, M., Smith, D., Dutta, B., Mourov, K., Iadevaia, S., Ruths, D., Tseng, J. - T., Yu, S., Yu, Q., Nakhleh, L., Balazsi, G., Donnelly, J., Schurdak, M., Morgan-Lappe, S., Fesik, S., Ram, P. T., and Mills, G. B., “Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling”, Oncogene, vol. 30, pp. 4567-4577, 2011.PDF icon Oncogene2011.pdf (905.3 KB)
B. J. Grindel, Martinez, J. R., Tellman, T. V., Harrington, D. A., Zafar, H., Nakhleh, L., Chung, L., and Farach-Carson, M. C., “Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells”, Scientific Reports, vol. 8, p. 7262, 2018.PDF icon GrindelEtAl.pdf (2.28 MB)
G. Saxer, Krepps, M. D., Merkley, E. D., Ansong, C., Kaiser, B. L. Deatherage, Valovska, M. - T., Ristic, N., Yeh, P. T., Prakash, V. P., Leiser, O. P., Nakhleh, L., Gibbons, H. S., Kreuzer, H. W., and Shamoo, Y., “Mutations in global regulators lead to metabolic selection during adaptation to complex environments”, PLoS Genetics, vol. 10, no. 12, p. e1004872, 2014.PDF icon SaxerEtAl-PLoSGenetics2014.pdf (1.99 MB)
E. Bapteste, van Iersel, L., Janke, A., Kelchner, S., Kelk, S., McInerney, J. O., Morrison, D. A., Nakhleh, L., Steel, M., Stougie, L., and Whitfield, J., “Networks: Expanding evolutionary thinking”, Trends in Genetics, vol. 29, no. 8, pp. 439-441, 2013.PDF icon TIG2013.pdf (179.16 KB)
E. Bapteste, van Iersel, L., Janke, A., Kelchner, S., Kelk, S., McInerney, J. O., Morrison, D. A., Nakhleh, L., Steel, M., Stougie, L., and Whitfield, J., “Networks: Expanding evolutionary thinking”, Trends in Genetics, vol. 29, no. 8, pp. 439-441, 2013.PDF icon TIG2013.pdf (179.16 KB)
B. M. E. Moret, Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., Sun, J., and Timme, R., “Phylogenetic networks: modeling, reconstructibility, and accuracy”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, pp. 13–23, 2004.
Y. Dotsenko, Coarfa, C., Nakhleh, L., Mellor-Crummey, J., and Roshan, U., “PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction”, International Journal on Bioinformatics Research and Applications, vol. 2, pp. 407-419, 2006.
D. Ruths, Muller, M., Tseng, J. T., Nakhleh, L., and Ram, P. T., “The Signaling Petri Net-based Simulator: A Non-parametric Strategy for Characterizing the Dynamics of Cell-specific Signaling Networks”, PLoS Computational Biology, vol. 4, p. e1000005, 2008.