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Results: 1 to 20 of 22

1.

TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets.

Poormohammadi H, Eslahchi C, Tusserkani R.

PLoS One. 2014 Sep 10;9(9):e106531. doi: 10.1371/journal.pone.0106531. eCollection 2014.

PMID:
25208028
[PubMed - in process]
Free PMC Article
2.

Do triplets have enough information to construct the multi-labeled phylogenetic tree?

Hassanzadeh R, Eslahchi C, Sung WK.

PLoS One. 2014 Jul 31;9(7):e103622. doi: 10.1371/journal.pone.0103622. eCollection 2014.

PMID:
25080217
[PubMed - in process]
Free PMC Article
3.

IPCA-CMI: an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score.

Aghdam R, Ganjali M, Eslahchi C.

PLoS One. 2014 Apr 11;9(4):e92600. doi: 10.1371/journal.pone.0092600. eCollection 2014.

PMID:
24728051
[PubMed - in process]
Free PMC Article
4.

ProDomAs, protein domain assignment algorithm using center-based clustering and independent dominating set.

Ansari ES, Eslahchi C, Pezeshk H, Sadeghi M.

Proteins. 2014 Sep;82(9):1937-46. doi: 10.1002/prot.24547. Epub 2014 Mar 24.

PMID:
24596179
[PubMed - in process]
5.

SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads.

Safikhani Z, Sadeghi M, Pezeshk H, Eslahchi C.

Genomics. 2013 Nov-Dec;102(5-6):507-14. doi: 10.1016/j.ygeno.2013.10.003. Epub 2013 Oct 23.

PMID:
24161398
[PubMed - indexed for MEDLINE]
6.

A clustering approach for estimating parameters of a profile hidden Markov model.

Aghdam R, Pezeshk H, Malekpour SA, Shemehsavar S, Eslahchi C.

Int J Data Min Bioinform. 2013;8(1):66-82.

PMID:
23865165
[PubMed - indexed for MEDLINE]
7.

Disruption of protein complexes.

Taheri G, Habibi M, Wong L, Eslahchi C.

J Bioinform Comput Biol. 2013 Jun;11(3):1341008. doi: 10.1142/S0219720013410084. Epub 2013 Mar 27.

PMID:
23796185
[PubMed - indexed for MEDLINE]
8.

Constructing phylogenetic supernetworks based on simulated annealing.

Hassanzadeh R, Eslahchi C, Sung WK.

Mol Phylogenet Evol. 2012 Jun;63(3):738-44. doi: 10.1016/j.ympev.2012.02.009. Epub 2012 Mar 3.

PMID:
22426435
[PubMed - indexed for MEDLINE]
9.

Constructing circular phylogenetic networks from weighted quartets using simulated annealing.

Eslahchi C, Hassanzadeh R, Mottaghi E, Habibi M, Pezeshk H, Sadeghi M.

Math Biosci. 2012 Feb;235(2):123-7. doi: 10.1016/j.mbs.2011.11.003. Epub 2011 Nov 13.

PMID:
22108294
[PubMed - indexed for MEDLINE]
10.

Protein complex prediction based on k-connected subgraphs in protein interaction network.

Habibi M, Eslahchi C, Wong L.

BMC Syst Biol. 2010 Sep 16;4:129. doi: 10.1186/1752-0509-4-129.

PMID:
20846398
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method.

Eslahchi C, Habibi M, Hassanzadeh R, Mottaghi E.

BMC Evol Biol. 2010 Aug 20;10:254. doi: 10.1186/1471-2148-10-254.

PMID:
20727135
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A pairwise residue contact area-based mean force potential for discrimination of native protein structure.

Arab S, Sadeghi M, Eslahchi C, Pezeshk H, Sheari A.

BMC Bioinformatics. 2010 Jan 9;11:16. doi: 10.1186/1471-2105-11-16.

PMID:
20064218
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Construction of random perfect phylogeny matrix.

Sadeghi M, Pezeshk H, Eslahchi C, Ahmadian S, Abadi SM.

Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16.

PMID:
21918630
[PubMed]
Free PMC Article
14.

A Segmental Semi Markov Model for protein secondary structure prediction.

Malekpour SA, Naghizadeh S, Pezeshk H, Sadeghi M, Eslahchi C.

Math Biosci. 2009 Oct;221(2):130-5. doi: 10.1016/j.mbs.2009.07.004. Epub 2009 Jul 29.

PMID:
19646454
[PubMed - indexed for MEDLINE]
15.

A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys.

Mirzaie M, Eslahchi C, Pezeshk H, Sadeghi M.

Proteins. 2009 Nov 1;77(2):454-63. doi: 10.1002/prot.22457.

PMID:
19452553
[PubMed - indexed for MEDLINE]
16.

STON: A novel method for protein three-dimensional structure comparison.

Eslahchi C, Pezeshk H, Sadeghi M, Massoud Rahimi A, Maboudi Afkham H, Arab S.

Comput Biol Med. 2009 Feb;39(2):166-72. doi: 10.1016/j.compbiomed.2008.12.004. Epub 2009 Jan 23.

PMID:
19167704
[PubMed - indexed for MEDLINE]
17.

Protein secondary structure prediction using three neural networks and a segmental semi Markov model.

Malekpour SA, Naghizadeh S, Pezeshk H, Sadeghi M, Eslahchi C.

Math Biosci. 2009 Feb;217(2):145-50. doi: 10.1016/j.mbs.2008.11.001. Epub 2008 Nov 18.

PMID:
19046975
[PubMed - indexed for MEDLINE]
18.

PROSIGN: a method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C(alpha) atoms.

Hosseini SR, Sadeghi M, Pezeshk H, Eslahchi C, Habibi M.

Comput Biol Chem. 2008 Dec;32(6):406-11. doi: 10.1016/j.compbiolchem.2008.07.027. Epub 2008 Aug 6.

PMID:
18789769
[PubMed - indexed for MEDLINE]
19.

A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins.

Sheari A, Kargar M, Katanforoush A, Arab S, Sadeghi M, Pezeshk H, Eslahchi C, Marashi SA.

BMC Bioinformatics. 2008 Jun 11;9:274. doi: 10.1186/1471-2105-9-274.

PMID:
18547401
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The performances of the chi-square test and complexity measures for signal recognition in biological sequences.

Pirhaji L, Kargar M, Sheari A, Poormohammadi H, Sadeghi M, Pezeshk H, Eslahchi C.

J Theor Biol. 2008 Mar 21;251(2):380-7. doi: 10.1016/j.jtbi.2007.11.021. Epub 2007 Nov 22.

PMID:
18177672
[PubMed - indexed for MEDLINE]

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