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Items: 1 to 50 of 74

1.

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data.

Zafar H, Navin N, Chen K, Nakhleh L.

Genome Res. 2019 Nov;29(11):1847-1859. doi: 10.1101/gr.243121.118. Epub 2019 Oct 18.

PMID:
31628257
2.

A divide-and-conquer method for scalable phylogenetic network inference from multilocus data.

Zhu J, Liu X, Ogilvie HA, Nakhleh LK.

Bioinformatics. 2019 Jul 15;35(14):i370-i378. doi: 10.1093/bioinformatics/btz359.

3.

Osteomalacia secondary to delayed diagnosis of a maxillary mesenchymal tumour.

Nakhleh L, Zink S, Raguin JM, Raguin T.

Eur Ann Otorhinolaryngol Head Neck Dis. 2019 Sep;136(4):335-336. doi: 10.1016/j.anorl.2019.02.007. Epub 2019 Aug 21. No abstract available.

PMID:
31445920
4.

Comments on the model parameters in "SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models".

Zafar H, Tzen A, Navin N, Chen K, Nakhleh L.

Genome Biol. 2019 May 16;20(1):95. doi: 10.1186/s13059-019-1692-5. No abstract available.

5.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics.

Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV.

PeerJ. 2019 Feb 14;7:e6399. doi: 10.7717/peerj.6399. eCollection 2019.

6.

Towards an accurate and efficient heuristic for species/gene tree co-estimation.

Wang Y, Nakhleh L.

Bioinformatics. 2018 Sep 1;34(17):i697-i705. doi: 10.1093/bioinformatics/bty599.

PMID:
30423064
7.

Inference of species phylogenies from bi-allelic markers using pseudo-likelihood.

Zhu J, Nakhleh L.

Bioinformatics. 2018 Jul 1;34(13):i376-i385. doi: 10.1093/bioinformatics/bty295.

8.

Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells.

Grindel BJ, Martinez JR, Tellman TV, Harrington DA, Zafar H, Nakhleh L, Chung LW, Farach-Carson MC.

Sci Rep. 2018 May 8;8(1):7262. doi: 10.1038/s41598-018-25435-3.

9.

ALPHA: a toolkit for Automated Local PHylogenomic Analyses.

Elworth RAL, Allen C, Benedict T, Dulworth P, Nakhleh L.

Bioinformatics. 2018 Aug 15;34(16):2848-2850. doi: 10.1093/bioinformatics/bty173.

PMID:
29562324
10.

Inferring Phylogenetic Networks Using PhyloNet.

Wen D, Yu Y, Zhu J, Nakhleh L.

Syst Biol. 2018 Jul 1;67(4):735-740. doi: 10.1093/sysbio/syy015.

11.

Bayesian inference of phylogenetic networks from bi-allelic genetic markers.

Zhu J, Wen D, Yu Y, Meudt HM, Nakhleh L.

PLoS Comput Biol. 2018 Jan 10;14(1):e1005932. doi: 10.1371/journal.pcbi.1005932. eCollection 2018 Jan.

12.

Stranger in a strange land: the experiences of immigrant researchers.

Kamoun S, Lozano-DurĂ¡n R, Nakhleh L.

Genome Biol. 2017 Dec 15;18(1):232. doi: 10.1186/s13059-017-1370-4.

13.

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data.

Wen D, Nakhleh L.

Syst Biol. 2018 May 1;67(3):439-457. doi: 10.1093/sysbio/syx085.

PMID:
29088409
14.

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models.

Zafar H, Tzen A, Navin N, Chen K, Nakhleh L.

Genome Biol. 2017 Sep 19;18(1):178. doi: 10.1186/s13059-017-1311-2.

15.

In the light of deep coalescence: revisiting trees within networks.

Zhu J, Yu Y, Nakhleh L.

BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):415. doi: 10.1186/s12859-016-1269-1.

16.

Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks.

Yu Y, Jermaine C, Nakhleh L.

BMC Genomics. 2016 Nov 11;17(Suppl 10):784. doi: 10.1186/s12864-016-3099-y.

17.

Correction: Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

Wen D, Yu Y, Nakhleh L.

PLoS Genet. 2017 Feb 8;13(2):e1006598. doi: 10.1371/journal.pgen.1006598. eCollection 2017 Feb.

18.

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies.

Fan X, Chaisson M, Nakhleh L, Chen K.

Genome Res. 2017 May;27(5):793-800. doi: 10.1101/gr.214767.116. Epub 2017 Jan 19.

19.

Inferring Local Genealogies on Closely Related Genomes.

Elworth RAL, Nakhleh L.

Comp Genom. 2017;10562:213-231. doi: 10.1007/978-3-319-67979-2_12. Epub 2017 Sep 15.

20.

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

Wen D, Yu Y, Nakhleh L.

PLoS Genet. 2016 May 4;12(5):e1006006. doi: 10.1371/journal.pgen.1006006. eCollection 2016 May. Erratum in: PLoS Genet. 2017 Feb 8;13(2):e1006598.

21.

Monovar: single-nucleotide variant detection in single cells.

Zafar H, Wang Y, Nakhleh L, Navin N, Chen K.

Nat Methods. 2016 Jun;13(6):505-7. doi: 10.1038/nmeth.3835. Epub 2016 Apr 18.

22.

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.

Wen D, Yu Y, Hahn MW, Nakhleh L.

Mol Ecol. 2016 Jun;25(11):2361-72. doi: 10.1111/mec.13544. Epub 2016 Mar 10.

23.

Irrational exuberance for resolved species trees.

Hahn MW, Nakhleh L.

Evolution. 2016 Jan;70(1):7-17. doi: 10.1111/evo.12832. Epub 2015 Dec 17.

PMID:
26639662
24.

A maximum pseudo-likelihood approach for phylogenetic networks.

Yu Y, Nakhleh L.

BMC Genomics. 2015;16 Suppl 10:S10. doi: 10.1186/1471-2164-16-S10-S10. Epub 2015 Oct 2.

25.

Interspecific introgressive origin of genomic diversity in the house mouse.

Liu KJ, Steinberg E, Yozzo A, Song Y, Kohn MH, Nakhleh L.

Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):196-201. doi: 10.1073/pnas.1406298111. Epub 2014 Dec 15.

26.

Mutations in global regulators lead to metabolic selection during adaptation to complex environments.

Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kaiser BL, Valovska MT, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nakhleh L, Gibbons HS, Kreuzer HW, Shamoo Y.

PLoS Genet. 2014 Dec 11;10(12):e1004872. doi: 10.1371/journal.pgen.1004872. eCollection 2014 Dec.

27.

Maximum likelihood inference of reticulate evolutionary histories.

Yu Y, Dong J, Liu KJ, Nakhleh L.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16448-53. doi: 10.1073/pnas.1407950111. Epub 2014 Nov 3.

28.

Towards accurate characterization of clonal heterogeneity based on structural variation.

Fan X, Zhou W, Chong Z, Nakhleh L, Chen K.

BMC Bioinformatics. 2014 Sep 8;15:299. doi: 10.1186/1471-2105-15-299.

29.

An HMM-based comparative genomic framework for detecting introgression in eukaryotes.

Liu KJ, Dai J, Truong K, Song Y, Kohn MH, Nakhleh L.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003649. doi: 10.1371/journal.pcbi.1003649. eCollection 2014 Jun.

30.

Mapping network motif tunability and robustness in the design of synthetic signaling circuits.

Iadevaia S, Nakhleh LK, Azencott R, Ram PT.

PLoS One. 2014 Mar 18;9(3):e91743. doi: 10.1371/journal.pone.0091743. eCollection 2014.

31.

Fast algorithms and heuristics for phylogenomics under ILS and hybridization.

Yu Y, Ristic N, Nakhleh L.

BMC Bioinformatics. 2013;14 Suppl 15:S6. doi: 10.1186/1471-2105-14-S15-S6. Epub 2013 Oct 15.

32.

Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

Berestovsky N, Zhou W, Nagrath D, Nakhleh L.

PLoS Comput Biol. 2013;9(11):e1003306. doi: 10.1371/journal.pcbi.1003306. Epub 2013 Nov 7.

33.

Computational approaches to species phylogeny inference and gene tree reconciliation.

Nakhleh L.

Trends Ecol Evol. 2013 Dec;28(12):719-28. doi: 10.1016/j.tree.2013.09.004. Epub 2013 Oct 1. Review.

34.

Evolution after whole-genome duplication: a network perspective.

Zhu Y, Lin Z, Nakhleh L.

G3 (Bethesda). 2013 Nov 6;3(11):2049-57. doi: 10.1534/g3.113.008458.

35.

An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data.

Berestovsky N, Nakhleh L.

PLoS One. 2013 Jun 21;8(6):e66031. doi: 10.1371/journal.pone.0066031. Print 2013.

36.

Networks: expanding evolutionary thinking.

Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitfield J.

Trends Genet. 2013 Aug;29(8):439-41. doi: 10.1016/j.tig.2013.05.007. Epub 2013 Jun 11.

PMID:
23764187
37.

Boosting forward-time population genetic simulators through genotype compression.

Ruths T, Nakhleh L.

BMC Bioinformatics. 2013 Jun 14;14:192. doi: 10.1186/1471-2105-14-192.

38.

Parsimonious inference of hybridization in the presence of incomplete lineage sorting.

Yu Y, Barnett RM, Nakhleh L.

Syst Biol. 2013 Sep;62(5):738-51. doi: 10.1093/sysbio/syt037. Epub 2013 Jun 4.

39.

Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology.

Ruths T, Nakhleh L.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7754-9. doi: 10.1073/pnas.1217630110. Epub 2013 Apr 22.

40.

Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria.

Park HJ, Nakhleh L.

BMC Bioinformatics. 2012;13 Suppl 19:S12. doi: 10.1186/1471-2105-13-S19-S12. Epub 2012 Dec 19.

41.

Quantifying and assessing the effect of chemical symmetry in metabolic pathways.

Zhou W, Nakhleh L.

J Chem Inf Model. 2012 Oct 22;52(10):2684-96. doi: 10.1021/ci300259u. Epub 2012 Sep 28.

PMID:
22985501
42.

Gene duplicability-connectivity-complexity across organisms and a neutral evolutionary explanation.

Zhu Y, Du P, Nakhleh L.

PLoS One. 2012;7(9):e44491. doi: 10.1371/journal.pone.0044491. Epub 2012 Sep 11.

43.

Convergent evolution of modularity in metabolic networks through different community structures.

Zhou W, Nakhleh L.

BMC Evol Biol. 2012 Sep 14;12:181. doi: 10.1186/1471-2148-12-181.

44.

ncDNA and drift drive binding site accumulation.

Ruths T, Nakhleh L.

BMC Evol Biol. 2012 Aug 30;12:159. doi: 10.1186/1471-2148-12-159.

45.

The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection.

Yu Y, Degnan JH, Nakhleh L.

PLoS Genet. 2012;8(4):e1002660. doi: 10.1371/journal.pgen.1002660. Epub 2012 Apr 19.

46.

Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles.

Yu Y, Warnow T, Nakhleh L.

J Comput Biol. 2011 Nov;18(11):1543-59. doi: 10.1089/cmb.2011.0174. Epub 2011 Oct 28.

47.

Population genomics in bacteria: a case study of Staphylococcus aureus.

Takuno S, Kado T, Sugino RP, Nakhleh L, Innan H.

Mol Biol Evol. 2012 Feb;29(2):797-809. doi: 10.1093/molbev/msr249. Epub 2011 Oct 17.

48.

Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling.

Lu Y, Muller M, Smith D, Dutta B, Komurov K, Iadevaia S, Ruths D, Tseng JT, Yu S, Yu Q, Nakhleh L, Balazsi G, Donnelly J, Schurdak M, Morgan-Lappe S, Fesik S, Ram PT, Mills GB.

Oncogene. 2011 Nov 10;30(45):4567-77. doi: 10.1038/onc.2011.164. Epub 2011 Jun 13.

49.

The strength of chemical linkage as a criterion for pruning metabolic graphs.

Zhou W, Nakhleh L.

Bioinformatics. 2011 Jul 15;27(14):1957-63. doi: 10.1093/bioinformatics/btr271. Epub 2011 May 5.

50.

Properties of metabolic graphs: biological organization or representation artifacts?

Zhou W, Nakhleh L.

BMC Bioinformatics. 2011 May 4;12:132. doi: 10.1186/1471-2105-12-132.

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