Journal Article
G. Jin, Nakhleh, L., Snir, S., and Tuller, T.,
“Inferring phylogenetic networks by the maximum parsimony criterion: a case study”,
Molecular Biology and Evolution, vol. 24, pp. 324-337, 2007.
D. Wen, Yu, Y., Zhu, J., and Nakhleh, L.,
“Inferring phylogenetic networks using PhyloNet”,
Systematic Biology, vol. 67, no. 4, pp. 735-740, 2018.
phylonet3.pdf (144.21 KB) K. Liu, Steinberg, E., Yozzo, A., Song, Y., Kohn, M. H., and Nakhleh, L.,
“Interspecific introgressive origin of genomic diversity in the house mouse”,
Proceedings of the National Academy of Sciences, vol. 112, no. 1, pp. 196-201, 2015.
LiuEtAl-PNAS2014.pdf (24.54 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.
Oncogene2011.pdf (905.3 KB) 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) 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.
GrindelEtAl.pdf (2.28 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. Jin, Nakhleh, L., Snir, S., and Tuller, T.,
“Maximum likelihood of phylogenetic networks”,
Bioinformatics, vol. 22, pp. 2604-2611, 2006.
L. Nakhleh,
“A metric on the space of reduced phylogenetic networks”,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, pp. 218-222, 2010.
tcbb-Metric.pdf (287.01 KB) 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) H. Zafar, Wang, Y., Nakhleh, L., Navin, N., and Chen, K.,
“Monovar: single nucleotide variant detection in single cells”,
Nature Methods, vol. 13, no. 6, pp. 505-507, 2016.
ZafarEtAl-NMETH2016.pdf (1.51 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) 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) 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) G. Jin, Nakhleh, L., Snir, S., and Tuller, T.,
“Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic”,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 495-505, 2009.
L. Nakhleh, Ringe, D., and Warnow, T.,
“Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages”,
LANGUAGE, Journal of the Linguistic Society of America, vol. 81, pp. 382-420, 2005.
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.
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)