Luay Nakhleh Vis

*	2009
38	EE	Troy A. Ruths, Derek A. Ruths, Luay Nakhleh: GS2: an efficiently computable measure of GO-based similarity of gene sets. Bioinformatics 25(9): 1178-1184 (2009)
37	EE	Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE/ACM Trans. Comput. Biology Bioinform. 6(3): 495-505 (2009)
	2008
36	EE	Cuong Than, Luay Nakhleh: SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. APBC 2008: 251-260
35	EE	Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh: Efficient inference of bacterial strain trees from genome-scale multilocus data. ISMB 2008: 123-131
34	EE	Cuong Than, Guohua Jin, Luay Nakhleh: Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. RECOMB-CG 2008: 113-127
33	EE	Iyad A. Kanj, Luay Nakhleh, Ge Xia: The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms. Algorithmica 51(2): 99-128 (2008)
32	EE	Cuong Than, Derek A. Ruths, Luay Nakhleh: PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9: (2008)
31	EE	Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia: Seeing the trees and their branches in the network is hard. Theor. Comput. Sci. 401(1-3): 153-164 (2008)
	2007
30		Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia: Seeing the Trees and Their Branches in the Forest is Hard. ICTCS 2007: 82-93
29	EE	Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. ISBRA 2007: 61-72
28	EE	Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23(2): 123-128 (2007)
27	EE	Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Maximum likelihood of phylogenetic networks. Bioinformatics 23(8): 1046-1047 (2007)
26	EE	Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh: Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. Journal of Computational Biology 14(4): 517-535 (2007)
	2006
25	EE	Derek A. Ruths, Luay Nakhleh: Techniques for Assessing Phylogenetic Branch Support: A Performance Study. APBC 2006: 187-196
24	EE	Derek A. Ruths, Luay Nakhleh: RECOMP: A Parsimony-Based Method for Detecting Recombination. APBC 2006: 59-68
23	EE	Iyad A. Kanj, Luay Nakhleh, Ge Xia: Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. COCOON 2006: 299-308
22	EE	Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh: Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. Comparative Genomics 2006: 215-229
21	EE	Derek A. Ruths, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram: De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis. Systems Biology and Computational Proteomics 2006: 108-118
20	EE	Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Maximum likelihood of phylogenetic networks. Bioinformatics 22(21): 2604-2611 (2006)
19	EE	Yuri Dotsenko, Cristian Coarfa, Luay Nakhleh, John M. Mellor-Crummey, Usman Roshan: PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. IJBRA 2(4): 407-419 (2006)
18	EE	Derek A. Ruths, Luay Nakhleh, M. Sriram Iyengar, Shrikanth A. G. Reddy, Prahlad T. Ram: Hypothesis Generation in Signaling Networks. Journal of Computational Biology 13(9): 1546-1557 (2006)
	2005
17	EE	Luay Nakhleh, Derek A. Ruths, Li-San Wang: RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. COCOON 2005: 84-93
16	EE	Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey: Reconstructing Phylogenetic Networks Using Maximum Parsimony. CSB 2005: 93-102
15	EE	Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh: Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. HPCC 2005: 776-785
14	EE	Cristian Coarfa, Yuri Dotsenko, John M. Mellor-Crummey, Luay Nakhleh, Usman Roshan: PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction. ICPADS (2) 2005: 346-350
13	EE	Luay Nakhleh, Li-San Wang: Phylogenetic Networks, Trees, and Clusters. International Conference on Computational Science (2) 2005: 919-926
12	EE	Derek A. Ruths, Luay Nakhleh: Recombination and phylogeny: effects and detection. IJBRA 1(2): 202-212 (2005)
11	EE	Luay Nakhleh, Tandy Warnow, C. Randal Linder, Katherine St. John: Reconstructing Reticulate Evolution in SpeciesTheory and Practice. Journal of Computational Biology 12(6): 796-811 (2005)
10	EE	Luay Nakhleh, Li-San Wang: Phylogenetic Networks: Properties and Relationship to Trees and Clusters. T. Comp. Sys. Biology 2: 82-99 (2005)
	2004
9	EE	Luay Nakhleh, Tandy Warnow, C. Randal Linder: Reconstructing reticulate evolution in species: theory and practice. RECOMB 2004: 337-346
8	EE	Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme: Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE/ACM Trans. Comput. Biology Bioinform. 1(1): 13-23 (2004)
	2003
7	EE	Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael J. Donoghue: Requirements of Phylogenetic Databases. BIBE 2003: 141-148
6	EE	Esra Erdem, Vladimir Lifschitz, Luay Nakhleh, Donald Ringe: Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming. PADL 2003: 160-176
5	EE	Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse: Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. Pacific Symposium on Biocomputing 2003: 315-326
	2002
4	EE	Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow: The Accuracy of Fast Phylogenetic Methods for Large Datasets. Pacific Symposium on Biocomputing 2002: 211-222
3	EE	Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy Warnow: Estimating the Deviation from a Molecular Clock. WABI 2002: 287-299
	2001
2		Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow: Designing fast converging phylogenetic methods. ISMB (Supplement of Bioinformatics) 2001: 190-198
1	EE	Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow: The Performance of Phylogenetic Methods on Trees of Bounded Diameter. WABI 2001: 214-226

Coauthor Index

1	François Barbançon	[7]
2	Cristian Coarfa	[14] [19]
3	Michael J. Donoghue	[7]
4	Yuri Dotsenko	[14] [19]
5	Z. Du	[15]
6	Esra Erdem	[6]
7	Hideki Innan	[22] [26] [35]
8	M. Sriram Iyengar	[18]
9	Guohua Jin	[16] [20] [27] [28] [29] [34] [37]
10	Katherine St. John	[1] [2] [4] [11]
11	Iyad A. Kanj	[23] [30] [31] [33]
12	Vladimir Lifschitz	[6]
13	F. Lin	[15]
14	C. Randal Linder	[5] [8] [9] [11]
15	John M. Mellor-Crummey	[14] [16] [19]
16	Daniel P. Miranker (Dan Miranker)	[7]
17	Bernard M. E. Moret	[4] [5] [8]
18	Anneke Padolina	[8]
19	William H. Piel	[7]
20	Prahlad T. Ram	[18] [21]
21	Shrikanth A. G. Reddy	[18]
22	Donald Ringe	[6]
23	Usman Roshan	[1] [2] [3] [4] [14] [15] [19]
24	Derek A. Ruths	[12] [17] [18] [21] [22] [24] [25] [26] [32] [38]
25	Troy A. Ruths	[38]
26	Sagi Snir	[20] [27] [28] [29] [37]
27	Alexandros Stamatakis	[15]
28	R. Sugino	[35]
29	Jerry Sun	[1] [2] [4] [5] [8]
30	Cuong Than	[22] [26] [30] [31] [32] [34] [35] [36]
31	Anna Tholse	[5] [8]
32	Ruth E. Timme	[8]
33	Jen-Te Tseng	[21]
34	Tamir Tuller	[20] [27] [28] [29] [37]
35	Lisa Vawter	[3]
36	Li-San Wang	[10] [13] [17]
37	Tandy Warnow	[1] [2] [3] [4] [5] [8] [9] [11]
38	Ge Xia	[23] [30] [31] [33]
39	Fengmei Zhao	[16]