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Items: 48

1.

The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost.

Gorecki P, Eulenstein O, Tiuryn J.

IEEE/ACM Trans Comput Biol Bioinform. 2019 May 28. doi: 10.1109/TCBB.2019.2919617. [Epub ahead of print]

PMID:
31150345
2.

Tracing the ancestry of operons in bacteria.

Nguyen HN, Jain A, Eulenstein O, Friedberg I.

Bioinformatics. 2019 Sep 1;35(17):2998-3004. doi: 10.1093/bioinformatics/btz053.

PMID:
30689726
3.

Introduction to JBCB Special Issue on BICOB-2018.

Al-Mubaid H, Ding Q, Eulenstein O.

J Bioinform Comput Biol. 2018 Oct;16(5):1802004. doi: 10.1142/S0219720018020043. No abstract available.

PMID:
30419781
4.

Cophenetic Median Trees.

Markin A, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep 13. doi: 10.1109/TCBB.2018.2870173. [Epub ahead of print]

PMID:
30222583
5.

Foreword.

Eulenstein O, Ding Q, Al-Mubaid H.

J Bioinform Comput Biol. 2017 Dec;15(6):1702004. doi: 10.1142/S0219720017020048. Epub 2017 Dec 7. No abstract available.

PMID:
29216773
6.

Efficient Local Search for Euclidean Path-Difference Median Trees.

Markin A, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1374-1385. doi: 10.1109/TCBB.2017.2763137. Epub 2017 Oct 16.

PMID:
29035224
7.

Bijective Diameters of Gene Tree Parsimony Costs.

Gorecki P, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1723-1727. doi: 10.1109/TCBB.2017.2735968. Epub 2017 Aug 4.

PMID:
28792904
8.

Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach.

Markin A, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1063-1076. doi: 10.1109/TCBB.2017.2718507. Epub 2017 Jun 22.

PMID:
28650824
9.

Synthesizing large-scale species trees using the strict consensus approach.

Moon J, Eulenstein O.

J Bioinform Comput Biol. 2017 Jun;15(3):1740002. doi: 10.1142/S0219720017400029. Epub 2017 Apr 20.

PMID:
28513253
10.

Consensus properties and their large-scale applications for the gene duplication problem.

Moon J, Lin HT, Eulenstein O.

J Bioinform Comput Biol. 2016 Jun;14(3):1642005. doi: 10.1142/S0219720016420051. Epub 2016 Mar 6.

PMID:
27122201
11.

Unconstrained Diameters for Deep Coalescence.

Pawel Gorecki P, Paszek J, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1002-1012. doi: 10.1109/TCBB.2016.2520937. Epub 2016 Feb 11.

PMID:
26887001
12.

Gene Tree Diameter for Deep Coalescence.

Górecki P, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):155-65. doi: 10.1109/TCBB.2014.2351795.

PMID:
26357086
13.

Refining discordant gene trees.

Górecki P, Eulenstein O.

BMC Bioinformatics. 2014;15 Suppl 13:S3. doi: 10.1186/1471-2105-15-S13-S3. Epub 2014 Nov 13.

14.

Guest editors' introduction to the Proceedings of the 9th International Symposium on Biomedical Research and Applications.

Gibas CJ, Cai Z, Eulenstein O.

BMC Bioinformatics. 2014;15 Suppl 13:S1. doi: 10.1186/1471-2105-15-S13-S1. Epub 2014 Nov 13. No abstract available.

15.

Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications.

Cai Z, Eulenstein O, Gibas C.

IEEE/ACM Trans Comput Biol Bioinform. 2014 May-Jun;11(3):453-4. No abstract available.

PMID:
26605398
16.

Efficient algorithms for knowledge-enhanced supertree and supermatrix phylogenetic problems.

Wehe A, Burleigh JG, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1432-41. doi: 10.1109/TCBB.2012.162.

PMID:
24407302
17.

Maximizing Deep Coalescence Cost.

Górecki P, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):231-42. doi: 10.1109/TCBB.2013.144.

PMID:
26355521
18.

Algorithms for genome-scale phylogenetics using gene tree parsimony.

Bansal MS, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):939-56. doi: 10.1109/TCBB.2013.103.

PMID:
24334388
19.

Exact solutions for species tree inference from discordant gene trees.

Chang WC, Górecki P, Eulenstein O.

J Bioinform Comput Biol. 2013 Oct;11(5):1342005. doi: 10.1142/S0219720013420055. Epub 2013 Oct 2.

PMID:
24131054
20.

DrML: probabilistic modeling of gene duplications.

Górecki P, Eulenstein O.

J Comput Biol. 2014 Jan;21(1):89-98. doi: 10.1089/cmb.2013.0078. Epub 2013 Sep 27.

21.

Unrooted tree reconciliation: a unified approach.

Górecki P, Eulenstein O, Tiuryn J.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):522-36. doi: 10.1109/TCBB.2013.22.

PMID:
23929875
22.

Exploring biological interaction networks with tailored weighted quasi-bicliques.

Chang WC, Vakati S, Krause R, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S16. doi: 10.1186/1471-2105-13-S10-S16.

23.

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.

Górecki P, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S14. doi: 10.1186/1471-2105-13-S10-S14.

24.

Consensus properties for the deep coalescence problem and their application for scalable tree search.

Lin HT, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S12. doi: 10.1186/1471-2105-13-S10-S12.

25.

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence.

Chaudhary R, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S11. doi: 10.1186/1471-2105-13-S10-S11.

26.

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

Górecki P, Burleigh GJ, Eulenstein O.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S15. doi: 10.1186/1471-2105-12-S1-S15.

27.

An ILP solution for the gene duplication problem.

Chang WC, Burleigh GJ, Fernández-Baca DF, Eulenstein O.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S14. doi: 10.1186/1471-2105-12-S1-S14.

28.

The plexus model for the inference of ancestral multidomain proteins.

Wiedenhoeft J, Krause R, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):890-901. doi: 10.1109/TCBB.2011.22.

PMID:
21282868
29.

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.

Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ.

Syst Biol. 2011 Mar;60(2):117-25. doi: 10.1093/sysbio/syq072. Epub 2010 Dec 24.

30.

iGTP: a software package for large-scale gene tree parsimony analysis.

Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O.

BMC Bioinformatics. 2010 Nov 23;11:574. doi: 10.1186/1471-2105-11-574.

31.

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.

Bansal MS, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S42. doi: 10.1186/1471-2105-11-S1-S42.

32.

Robinson-Foulds supertrees.

Bansal MS, Burleigh JG, Eulenstein O, Fernández-Baca D.

Algorithms Mol Biol. 2010 Feb 24;5:18. doi: 10.1186/1748-7188-5-18.

33.

Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants.

Burleigh JG, Bansal MS, Wehe A, Eulenstein O.

J Comput Biol. 2009 Aug;16(8):1071-83. doi: 10.1089/cmb.2009.0139.

PMID:
19689214
34.

The gene-duplication problem: near-linear time algorithms for NNI-based local searches.

Bansal MS, Eulenstein O, Wehe A.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):221-31. doi: 10.1109/TCBB.2009.7.

PMID:
19407347
35.

Triplet supertree heuristics for the tree of life.

Lin HT, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S8. doi: 10.1186/1471-2105-10-S1-S8.

36.

An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem.

Bansal MS, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec;5(4):514-24. doi: 10.1109/TCBB.2008.69.

PMID:
18989039
37.

The multiple gene duplication problem revisited.

Bansal MS, Eulenstein O.

Bioinformatics. 2008 Jul 1;24(13):i132-8. doi: 10.1093/bioinformatics/btn150.

38.

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

Wehe A, Bansal MS, Burleigh JG, Eulenstein O.

Bioinformatics. 2008 Jul 1;24(13):1540-1. doi: 10.1093/bioinformatics/btn230. Epub 2008 May 12.

PMID:
18474508
39.

Minimum-flip supertrees: complexity and algorithms.

Chen D, Eulenstein O, Fernandez-Baca D, Sanderson M.

IEEE/ACM Trans Comput Biol Bioinform. 2006 Apr-Jun;3(2):165-73.

PMID:
17048402
40.

Improved heuristics for minimum-flip supertree construction.

Chen D, Eulenstein O, Fernández-Baca D, Burleigh JG.

Evol Bioinform Online. 2007 Feb 28;2:347-56.

41.

The shape of supertrees to come: tree shape related properties of fourteen supertree methods.

Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR, Lapointe FJ, Levasseur C, McInerney JO, Pisani D, Thorley JL.

Syst Biol. 2005 Jun;54(3):419-31.

PMID:
16012108
42.

Identifying optimal incomplete phylogenetic data sets from sequence databases.

Yan C, Burleigh JG, Eulenstein O.

Mol Phylogenet Evol. 2005 Jun;35(3):528-35. Epub 2005 Mar 21.

PMID:
15878123
43.

Performance of flip supertree construction with a heuristic algorithm.

Eulenstein O, Chen D, Burleigh JG, Fernández-Baca D, Sanderson MJ.

Syst Biol. 2004 Apr;53(2):299-308.

PMID:
15205054
44.

Rainbow: a toolbox for phylogenetic supertree construction and analysis.

Chen D, Eulenstein O, Fernández-Baca D.

Bioinformatics. 2004 Nov 1;20(16):2872-3. Epub 2004 May 14.

PMID:
15145807
45.

Obtaining maximal concatenated phylogenetic data sets from large sequence databases.

Sanderson MJ, Driskell AC, Ree RH, Eulenstein O, Langley S.

Mol Biol Evol. 2003 Jul;20(7):1036-42. Epub 2003 May 30.

PMID:
12777519
46.

Investigating evolutionary lines of least resistance using the inverse protein-folding problem.

Schonfeld J, Eulenstein O, Velden KV, Naylor GJ.

Pac Symp Biocomput. 2002:613-24.

47.

Towards detection of orthologues in sequence databases.

Yuan YP, Eulenstein O, Vingron M, Bork P.

Bioinformatics. 1998;14(3):285-9.

PMID:
9614272
48.

Duplication-based measures of difference between gene and species trees.

Eulenstein O, Mirkin B, Vingron M.

J Comput Biol. 1998 Spring;5(1):135-48.

PMID:
9541877

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