 |
|
Posters and Surveys
| 3 |
C.R. Linder, B.M.E. Moret, L. Nakhleh, and T. Warnow,
"Network (Reticulate) Evolution: Biology, Models, and
Algorithms." A tutorial presented at The Ninth Pacific
Symposium on Biocomputing
(PSB 2004). |
 |
| 2 |
L. Nakhleh, T. Warnow, and C.R. Linder,
"Reconstructing Reticulate Evolution in Species."
Poster at the RECOMB IMA Workshop on Comparative Genomics, Minneapolis,
MN, October 2003. |
|
| 1 |
R. Kalra, K. St. John, L. Nakhleh, and T. Warnow,
"Applications of Clustering and Visualization to Phylogeny."
Poster at the European Conference on Computational Biology
(ECCB 2003). |
|
In Print or Press
| 43 |
C. Than, G. Jin, and L. Nakhleh,
"Integrating Sequence and Topology for Efficient and Accurate Detection of
Horizontal Gene Transfer."
Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop.
Lecture Notes in Bioinformatics (LNBI #5267), 113-127,
2008. |
|
| 42 |
C. Than, D. Ruths, and L. Nakhleh,
"PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships."
BMC Bioinformatics, 9:322, 2008. |
|
| 41 |
D. Ruths, L. Nakhleh, and P.T. Ram,
"Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle."
BMC Systems Biology, 2:76, 2008. |
|
| 40 |
I. Kanj, L. Nakhleh, C. Than, and
G. Xia,
"Seeing the Trees and Their Branches in the Network is Hard."
Theoretical Computer Science (TCS), 401: 153-164, 2008. |
|
| 39 |
C. Than, R. Sugino, H. Innan, and
L. Nakhleh,
"Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data."
The 16th Annual International Conference on Intelligent Systems for
Molecular Biology (ISMB). Bioinformatics, 24: i123-i131, 2008. |
|
| 38 |
D. Ruths, M. Muller, J.T. Tseng,
L. Nakhleh, and P.T. Ram,
"The Signaling Petri Net-based Simulator: A Non-parametric
Strategy for Characterizing the Dynamics of Cell-specific Signaling
Networks."
PLoS Computational Biology, 4(2): e1000005, 2008. |
|
| 37 |
I. Kanj, L. Nakhleh, and G. Xia,
"The Compatibility of
Binary Characters on Phylogenetic Networks: Complexity and Parameterized
Algorithms." Algorithmica, 51: 99-128, 2008. |
|
| 36 |
C. Than and L. Nakhleh,
"SPR-based Tree Reconciliation: Non-binary Trees and Multiple
Solutions."
Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC),
251-260, 2008. |
|
| 35 |
I. Kanj, L. Nakhleh, C. Than, and
G. Xia,
"Seeing the Trees and Their Branches in the Network is Hard."
Proceedings of the Tenth Italian Conference on Theoretical
Computer Science (ICTCS), 82-93, 2007. |
|
| 34 |
C. Than, D. Ruths, H. Innan, and L. Nakhleh,
"Confounding Factors in HGT Detection: Statistical Error,
Coalescent Effects, and Multiple Solutions." Journal of Computational
Biology, 14(4): 517-535, 2007. |
|
| 33 |
G. Jin, L. Nakhleh, S. Snir, and T. Tuller,
"A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance."
Proceedings of the International Symposium on Bioinformatics Research and
Applications (ISBRA). Lecture Notes in Bioinformatics (LNBI #4463), 61-72,
2007. |
|
| 32 |
D. Ruths, J.T. Tseng, L. Nakhleh, and P.T. Ram,
"De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis."
Proceedings of the RECOMB Satellite Workshop on Systems Biology and
Proteomics. Lecture Notes in Bioinformatics (LNBI #4205), 108-118,
2007. |
|
| 31 |
G. Jin, L. Nakhleh, S. Snir, and T. Tuller,
"Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study."
Molecular Biology and Evolution, 24(1): 324-337, 2007. |
|
| 30 |
G. Jin, L. Nakhleh, S. Snir, and T. Tuller,
"Maximum Likelihood of Phylogenetic Networks."
Bioinformatics, 22(21): 2604-2611, 2006. (The supplementary material
contains the proofs and more technical details.) |
|
| 29 |
C. Than, D. Ruths, H. Innan, and L. Nakhleh,
"Identifiability Issues in Phylogeny-based Detection of Horizontal Gene Transfer." Proceedings of the Fourth RECOMB Comparative
Genomics Satellite Workshop. Lecture Notes in Bioinformatics (LNBI 4205),
215-229, 2006. [Typo in formula (1) on page 223: the
summation should be a product.] |
|
| 28 |
D. Ruths, L. Nakhleh, M.S. Iyengar, S.A.G. Reddy, and P.T. Ram,
"Graph-theoretic Hypothesis Generation in Biological Signaling
Networks." Journal of Computational Biology, 13(9): 1546-1557, 2006. |
|
| 27 |
G. Jin, L. Nakhleh, S. Snir, and
T. Tuller, "Efficient Parsimony-based Methods for Phylogenetic Network
Reconstruction." Bioinformatics, 23:e123-e128, 2006.
(Proceedings of the European Conference on Computational
Biology (ECCB 2006)). |
|
| 26 |
T. Shigaki, I. Rees, L. Nakhleh,
and K. Hirschi,
"Identification of Three Distinct Phylogenetic Groups of CAX
Cation/Proton Antiporters."
Journal of Molecular Evolution, 63:815-825, 2006. |
|
| 25 |
I. Kanj, L. Nakhleh, and G. Xia,
"Reconstructing Evolution of Natural Languages: Complexity and
Parameterized Algorithms."
Proceedings of the 12th Annual International Computing
and Combinatorics Conference (COCOON 2006). Lecture Notes in Computer Science (LNCS #4112), 299-308, 2006. |
|
| 24 |
Y. Dotsenko, C. Coarfa, L. Nakhleh, J. Mellor-Crummey, and U.
Roshan,
"PRec-I-DCM3: A Parallel Framework for Fast and
Accurate Large Scale Phylogeny Reconstruction."
International Journal on Bioinformatics Research and Applications
(IJBRA), 2(4): 407-419, 2006. |
|
| 23 |
D. Ruths and L. Nakhleh,
"Techniques for Assessing Phylogenetic Branch Support: A
Performance Study."
Proceedings of the Fourth Asia-Pacific Bioinformatics Conference,
(APBC2006), 187-196, 2006. |
|
| 22 |
D. Ruths and L. Nakhleh,
"RECOMP: A Parsimony-based Method for Detecting Recombination."
Proceedings of the Fourth Asia-Pacific Bioinformatics Conference,
(APBC2006), 59-68, 2006. |
|
| 21 |
Z. Du, A. Stamatakis, F. Lin, U. Roshan, and L. Nakhleh,
"Parallel
divide-and-conquer phylogeny reconstruction by maximum likelihood."
Proceedings of the 2005 International Conference on High Performance
Computing and Communications (HPCC 05), 2:346-350, 2005. |
|
| 20 |
L. Nakhleh, D. Ruths, and H. Innan,
"Gene trees, species trees, and species networks."
In "Meta-analysis and Combining Information in Genetics", R. Guerra
and D. Allison, editors, 2005. |
|
| 19 |
L. Nakhleh, G. Jin, F. Zhao, and J. Mellor-Crummey,
"Reconstructing Phylogenetic Networks Using Maximum Parsimony."
Proceedings of the 2005 IEEE Computational Systems Bioinformatics
Conference (CSB2005), 93-102, 2005. |
|
| 18 |
L. Nakhleh and L.S. Wang,
"Phylogenetic Networks: Properties and Relationship to Trees and Clusters."
LNCS Transactions on Computational Systems Biology, II, LNBI 3680, 82-99,
2005. |
|
| 17 |
L. Nakhleh, D. Ruths, and L.S. Wang,
"RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing
Horizontal Gene Transfer."
Proceedings of the Eleventh International Computing and
Combinatorics Conference (COCOON
05). LNCS #3595 (L. Wang, editor), 84-93, 2005. |
|
| 16 |
C. Coarfa, Y. Dotsenko, J. Mellor-Crummey, L. Nakhleh, and U. Roshan,
"PRec-I-DCM3: A Parallel Framework for Fast and
Accurate Large Scale Phylogeny Reconstruction."
Proceedigns of the First IEEE Workshop on High Performance Computing in
Medicine and Biology
(HiPCoMP 2005), 2:346-350, 2005. (Best paper
award.) |
|
| 15 |
D. Ruths and L. Nakhleh,
"Recombination and Phylogeny: Effects and Detection."
The International Journal of Bioinformatics
Research and Applications (IJBRA), 1(2): 202-212, 2005. |
|
| 14 |
L. Nakhleh, T. Warnow, D. Ringe, and S.N. Evans,
"A Comparison of Phylogenetic Reconstruction Methods on an IE
Dataset."
Transactions of the Philological Society, 3(2): 171-192, 2005. |
|
| 13 |
L. Nakhleh and L.S. Wang,
"Phylogenetic Networks, Trees, and Clusters."
Proceedings of the 2005 International Workshop on Bioinformatics
Research and Applications (IWBRA 05).
Lecture Notes in Computer Science,
LNCS
#3515, pp. 919-926,
2005. |
|
| 12 |
L. Nakhleh, T. Warnow, C.R. Linder, and K. St. John, "Reconstructing
Reticulate
Evolution
in Species -- Theory and Practice."
Journal of Computational Biology, 12(6-7), 796-811, 2005. |
|
| 11 |
L. Nakhleh, D. Ringe, and T. Warnow, "Perfect
Phylogenetic
Networks: A New Methodology for Reconstructing the
Evolutionary History of Natural Languages." LANGUAGE, Journal of the
Linguistic Society of America. 81(2):382-420, 2005. |
|
| 10 |
B.M.E. Moret, L. Nakhleh, T. Warnow, C.R.
Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme, "Phylogenetic
networks: modeling, reconstructibility, and accuracy." The IEEE/ACM
Transactions on Computational Biology and
Bioinformatics, 1(1):13-23, 2004. [Lemma 1 is incorrect
(and hence Theorem 3). m^{tri} is a dissimilarity measure, but
not a metric on the space of reduced networks.] |
|
| 9 |
T. Warnow, S.N. Evans, D. Ringe, and L. Nakhleh,
"A Stochastic model of language evolution that
incorporates homoplasy and borrowing." In Phylogenetic
Methods and the Prehistory
of Languages, P. Forster and C. Renfrew, Editors, 75-87.
McDonald Institute Monographs, Cambridge, UK, 2004. |
|
| 8 |
L. Nakhleh, T. Warnow, and C.R. Linder, "Reconstructing
Reticulate
Evolution
in Species -- Theory and Practice." Proceedings of the Eighth Annual
International Conference on Research in
Computational Molecular Biology (RECOMB 2004), 337-346. |
|
| 7 |
L. Nakhleh, D. Miranker, F. Barbancon, W.H. Piel, and M.J.
Donoghue,
"Requirements of Phylogenetic Databases." Proceedings of the
Third
IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2003), IEEE
Press, 2003, 141-148. (For online proceedings of the conference,
press
here. Full technical report version of the paper: PDF.) |
|
| 6 |
E. Erdem, V. Lifschitz, L. Nakhleh, and D. Ringe,
"Reconstructing the
Evolutionary History of Indo-European Languages using Answer Set
Programming." Proceedings of the Fifth International Symposium
on
Practical Aspects of Declarative Languages
(PADL
2003). Lecture Notes in Computer Science
(LNCS
#2562). |
|
| 5 |
L. Nakhleh, J. Sun, T. Warnow, C.R. Linder, B.M.E. Moret,
and Anna Tholse, "Towards the
Development of Computational Tools for Evaluating Phylogenetic Network
Reconstruction Methods." Proceedings of the Eighth Pacific
Symposium
on Biocomputing (PSB 03), January
2003. |
|
| 4 |
L. Nakhleh, U. Roshan, L. Vawter, and T. Warnow, "Estimating
the
Deviation from a Molecular Clock."
Proceedings of the Second International Workshop on Algorithms in
Bioinformatics (WABI
02),
Rome,
Italy, Lecture Notes in Computer Science
(LNCS #2452). |
|
| 3 |
L. Nakhleh, B.M.E. Moret, U. Roshan, K. St. John, J. Sun, and
T.
Warnow, "The Accuracy of Phylogenetic Methods for Large Datasets."
Proceedings of the Seventh Pacific Symposium on Biocomputing (PSB 02), 7:211-222, January 2002. |
|
| 2 |
L. Nakhleh, U. Roshan, K. St. John, J. Sun, and T. Warnow,
"The Performance of Phylogenetic Methods on Trees of Bounded
Diameter." Proceedings of the First International Workshop on
Algorithms in
Bioinformatics (WABI 01),
Aarhus, Denmark, Lecture Notes in Computer Science
(
LNCS #2149). Pages 214-226. |
|
| 1 |
L. Nakhleh, U. Roshan, K. St. John, J. Sun, and T. Warnow,
"Designing Fast Converging Phylogenetic Methods."
Bioinformatics, 17(90001), pp S190-S198, 2001. Proceedings of the
Ninth
International Conference on Intelligent Systems for Molecular Biology
(ISMB 01), Copenhagen, Denmark. |
|
|