Skip to main content
CS Bioinformatics Group
Main menu
About
Contact
Members
Projects
Publications
Software
Support
You are here
Home
Bioinformatics Group
About
Contact
Login
Members
Projects
Publications
Authors
Keywords
Software
Student Awards
Support
User login
NetID Login
For NetID Login, click the login button below. You will be sent to a secure Rice login page.
For NetID Login, click the login button below. You will be sent to a secure Rice login page.
Username
*
Password
*
Request new password
NetID Login
Biblio
Export 20 results:
BibTeX
RTF
Tagged
EndNote XML
RIS
Author
Keyword
Title
Type
[
Year
]
Filters:
Author
is
Luay Nakhleh
[Clear All Filters]
2011
Y. Yu
,
Warnow, T.
, and
Nakhleh, L.
,
“
Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles
”
,
Journal of Computational Biology
, vol. 18, no. 11, pp. 1543-1559, 2011.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
YuWarnowNakhleh-JCB11.pdf
(419.4 KB)
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
RuthsNakhleh-BMCEvolBiol2012.pdf
(659.08 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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
ZhouNakhleh-JCIM2012.pdf
(2.66 MB)
2013
T. Ruths
and
Nakhleh, L.
,
“
Boosting forward-time population genetic simulators through genotype compression
”
,
BMC Bioinformatics
, vol. 14, p. 192, 2013.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
ZhuLinNakhleh13.pdf
(1.18 MB)
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
YuEtAl-SystBiol2013.pdf
(1.55 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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
PNAS-2014-YuEtAl.pdf
(1.55 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.
Google Scholar
BibTeX
RTF
Tagged
EndNote XML
RIS
FanEtAl2014.pdf
(2.04 MB)