Biblio

Export 108 results:

Author Keyword Title Type [ Year

]

2014

S. Iadevaia, Nakhleh, L., Azencott, R., and Ram, P. T., “Mapping network motif tunability and robustness in the design of synthetic signaling circuits”, PLoS One, vol. 9, no. 3, p. e91743, 2014.

IadevaiaEtAl-PLoSOne14.pdf (1.01 MB)

Y. Yu, Dong, J., Liu, K., and Nakhleh, L., “Maximum Likelihood Inference of Reticulate Evolutionary Histories”, Proceedings of the National Academy of Sciences, vol. 111, no. 46, pp. 16448-16453, 2014.

PNAS-2014-YuEtAl.pdf (1.55 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.

SaxerEtAl-PLoSGenetics2014.pdf (1.99 MB)

X. Fan, Zhou, W., Chong, Z., Nakhleh, L., and Chen, K., “Towards accurate characterization of clonal heterogeneity based on structural variation”, BMC Bioinformatics, vol. 15, p. 299, 2014.

FanEtAl2014.pdf (2.04 MB)

2013

T. Ruths and Nakhleh, L., “Boosting forward-time population genetic simulators through genotype compression”, BMC Bioinformatics, vol. 14, p. 192, 2013.

RuthsNakhleh-BMCBioinfo13.pdf (680.55 KB)

L. Nakhleh, “Computational approaches to species phylogeny inference and gene tree reconciliation”, Trends in Ecology and Evolution, vol. 28, no. 12, pp. 719-728, 2013.

TREE-Nakhleh13.pdf (559.43 KB)

N. Berestovsky and Nakhleh, L., “An Evaluation of Methods for Inferring Boolean Networks from Time-series Data”, PLoS One, vol. 8, p. e66031, 2013.

BerestovskyNakhleh-PLoSOne13.pdf (942.99 KB)

Y. Zhu, Lin, Z., and Nakhleh, L., “Evolution After Whole-genome Duplication: A Network Perspective”, G3: Genes | Genomes | Genetics, vol. 3, no. 11, pp. 2049-2057, 2013.

ZhuLinNakhleh13.pdf (1.18 MB)

F. Barbancon, Evans, S., Nakhleh, L., Ringe, D., and Warnow, T., “An experimental study comparing linguistic phylogenetic reconstruction methods”, Diachronica, vol. 30, no. 2, pp. 143-170, 2013.

Diachronica13.pdf (575.02 KB)

Y. Yu, Ristic, N., and Nakhleh, L., “Fast Algorithms and Heuristics for Phylogenomics under ILS and Hybridization”, BMC Bioinformatics, vol. 14, no. Suppl 15, p. S6, 2013.

YuRisticNakhleh13.pdf (1.68 MB)

N. Berestovsky, Zhou, W., Nagrath, D., and Nakhleh, L., “Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks”, PLoS Computational Biology, vol. 9, no. 11, p. e1003306, 2013.

BerestovskyEtAl13.pdf (1.66 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.

TIG2013.pdf (179.16 KB)

T. Ruths and Nakhleh, L., “Neutral forces acting on intragenomic variability shape the E. coli regulatory network topology”, Proceedings of the National Academy of Sciences, vol. 110, no. 19, pp. 7754-7759, 2013.

RuthsNakhleh-PNAS13.pdf (2.57 MB)

Y. Yu, Barnett, R. M., and Nakhleh, L., “Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting”, Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.

YuEtAl-SystBiol2013.pdf (1.55 MB)

2012

W. Zhou and Nakhleh, L., “Convergent evolution of modularity in metabolic networks through different community structures”, BMC Evolutionary Biology, vol. 12, p. 181, 2012.

ZhouNakhleh-BMCEvolBiol2012.pdf (1.88 MB)

Y. Zhu, Du, P., and Nakhleh, L., “Gene Duplicability-Connectivity-Complexity Across Organisms and a Neutral Evolutionary Explanation”, PLoS One, vol. 7, no. 9, p. e44491, 2012.

ZhuDuNakhleh.pdf (217.94 KB)

H. J. Park and Nakhleh, L., “Inference of Reticulate Evolutionary Histories by Maximum Likelihood: The Performance of Information Criteria”, BMC Bioinformatics, vol. 13, no. S19, p. S12, 2012.

ParkNakhleh-RECOMBCG12.pdf (754.52 KB)

H. J. Park and Nakhleh, L., “MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees”, The 8th International Symposium on Bioinformatics Research and Applications (ISBRA), vol. LNBI 7292. pp. 213-224, 2012.

ParkNakhleh.pdf (289.57 KB)

T. Ruths and Nakhleh, L., “ncDNA and drift drive binding site accumulation”, BMC Evolutionary Biology, vol. 12, p. 159, 2012.

RuthsNakhleh-BMCEvolBiol2012.pdf (659.08 KB)

N. Berestovsky, Fukui, R., and Nakhleh, L., “On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks.”, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. pp. 184-191, 2012.

BerestovskyFukuiNakhleh.pdf (2.77 MB)

S. Takuno, Kado, T., Sugino, R. P., Nakhleh, L., and Innan, H., “Population genomics in bacteria: A case study of Staphylococcus aureus.”, Molecular Biology and Evolution, vol. 29, no. 2, pp. 797-800, 2012.

TakunoEtAl-MBE11.pdf (933.28 KB)

Y. Yu, Degnan, J. H., and Nakhleh, L., “The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection”, PLoS Genetics, vol. 8, no. 4, p. e1002660, 2012.

YuDegnanNakhleh.pdf (483.41 KB)

W. Zhou and Nakhleh, L., “Quantifying And Assessing the Effect of Chemical Symmetry in Metabolic Pathways”, Journal of Chemical Information and Modeling, vol. 52, pp. 2684-2696, 2012.

ZhouNakhleh-JCIM2012.pdf (2.66 MB)

Y. Zhu and Nakhleh, L., “Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models”, Workshop on Algorithms in Bioinformatics, vol. LNBI 7534. pp. 57-68, 2012.

ZhuNakhleh-WABI12.pdf (1.53 MB)

2011

Y. Yu, Warnow, T., and Nakhleh, L., “Algorithms for MDC-based multi-locus phylogeny inference”, The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), vol. LNBI 6577. Lecture Notes in Bioinformatics, pp. 531-545, 2011.

YuWarnowNakhleh-RECOMB11.pdf (369.65 KB)

Pages