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Biblio
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2006
G. Jin
,
Nakhleh, L.
,
Snir, S.
, and
Tuller, T.
,
“
Maximum likelihood of phylogenetic networks
”
,
Bioinformatics
, vol. 22, pp. 2604-2611, 2006.
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2010
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.
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tcbb-Metric.pdf
(287.01 KB)
2012
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.
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ParkNakhleh.pdf
(289.57 KB)
2013
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.
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BerestovskyEtAl13.pdf
(1.66 MB)
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.
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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.
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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.
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SaxerEtAl-PLoSGenetics2014.pdf
(1.99 MB)
2015
Y. Yu
and
Nakhleh, L.
,
“
A Maximum Pseudo-likelihood Approach for Phylogenetic Networks
”
,
BMC Genomics
, vol. 16, no. Suppl 10, p. S10, 2015.
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YuNakhleh-BMCGenomics2015.pdf
(1.75 MB)
2016
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.
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ZafarEtAl-NMETH2016.pdf
(1.51 MB)
2018
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.
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GrindelEtAl.pdf
(2.28 MB)