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Results: 20

1.

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
2.

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

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

Proteins. 2014 Mar 5. doi: 10.1002/prot.24547. [Epub ahead of print]

PMID:
24596179
[PubMed - as supplied by publisher]
3.

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]
4.

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]
5.

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]
6.

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]
7.

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]
8.

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
9.

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
10.

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
11.

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
12.

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]
13.

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]
14.

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]
15.

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]
16.

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]
17.

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
18.

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]
19.

Impact of RNA structure on the prediction of donor and acceptor splice sites.

Marashi SA, Eslahchi C, Pezeshk H, Sadeghi M.

BMC Bioinformatics. 2006 Jun 13;7:297.

PMID:
16772025
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks.

Marashi SA, Goodarzi H, Sadeghi M, Eslahchi C, Pezeshk H.

Comput Biol Chem. 2006 Feb;30(1):50-7. Epub 2005 Dec 28.

PMID:
16386465
[PubMed - indexed for MEDLINE]

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