Mehdi Sadeghi

Mehdi Sadeghi

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Mehdi Sadeghi

Mehdi Sadeghi

Publications by authors named "Mehdi Sadeghi"

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Ambiguity in logic-based models of gene regulatory networks: An integrative multi-perturbation analysis.

PLoS One 2018 20;13(11):e0206976. Epub 2018 Nov 20.

National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206976PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245684PMC
April 2019

The effect of stochasticity on repair of DNA double strand breaks throughout non-homologous end joining pathway.

Math Med Biol 2018 12;35(4):517-539

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://dx.doi.org/10.1093/imammb/dqx017DOI Listing
December 2018

The effects of branch-chain amino acids on fatigue in the athletes.

Interv Med Appl Sci 2018 Dec;10(4):233-235

Shiraz Branch, Islamic Azad University, Shiraz, Iran.

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http://dx.doi.org/10.1556/1646.10.2018.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376352PMC
December 2018

Assessing the impact of exact reads on reducing the error rate of read mapping.

BMC Bioinformatics 2018 Nov 6;19(1):406. Epub 2018 Nov 6.

Department of Biotechnology and Molecular Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-018-2432-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220446PMC
November 2018

Modeling the probability distribution of the bacterial burst size via a game-theoretic approach.

J Bioinform Comput Biol 2018 08 3;16(4):1850012. Epub 2018 May 3.

∥ Department of Medical Biochemistry, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://dx.doi.org/10.1142/S0219720018500129DOI Listing
August 2018

A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression.

Methods Mol Biol 2018 ;1702:247-276

Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany.

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http://dx.doi.org/10.1007/978-1-4939-7456-6_12DOI Listing
July 2018

MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.

Sci Rep 2018 Mar 5;8(1):4009. Epub 2018 Mar 5.

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://www.nature.com/articles/s41598-018-22323-8
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http://dx.doi.org/10.1038/s41598-018-22323-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838159PMC
March 2018

HIV-1-infected T-cells dynamics and prognosis: An evolutionary game model.

Comput Methods Programs Biomed 2017 Dec 6;152:1-14. Epub 2017 Sep 6.

Computer Engineering Department, Amirkabir University of Technology and the Institute for Research in Fundamental Sciences, Tehran, Iran.

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http://dx.doi.org/10.1016/j.cmpb.2017.08.021DOI Listing
December 2017

Stochastic Cell Fate and Longevity of Offspring.

Cell J 2017 Oct 19;19(3):343-351. Epub 2017 Aug 19.

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://dx.doi.org/10.22074/cellj.2017.3919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570400PMC
October 2017

F-MAP: A Bayesian approach to infer the gene regulatory network using external hints.

PLoS One 2017 22;12(9):e0184795. Epub 2017 Sep 22.

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184795PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609748PMC
October 2017

Bayesian comparison of protein structures using partial Procrustes distance.

Stat Appl Genet Mol Biol 2017 09;16(4):243-257

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http://dx.doi.org/10.1515/sagmb-2016-0014DOI Listing
September 2017

Muscle Carnosine Concentration with the Co-Ingestion of Carbohydrate with β-alanine in Male Rats.

J Diet Suppl 2017 Jul 4;14(4):373-379. Epub 2016 Nov 4.

g Department of Sport and Exercise Sciences , University of Chichester , Chichester , UK.

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https://www.tandfonline.com/doi/full/10.1080/19390211.2016.1
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http://dx.doi.org/10.1080/19390211.2016.1244585DOI Listing
July 2017

Involvement of neuronal pathways in the protective effects of hindlimb perconditioning during renal ischemia.

Exp Ther Med 2017 May 2;13(5):1956-1960. Epub 2017 Mar 2.

Department of Physiology, Bushehr University of Medical Sciences, School of Medicine, Bushehr 7514633341, Iran.

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http://dx.doi.org/10.3892/etm.2017.4175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443195PMC
May 2017

Perspectives on the Prediction of the PLP's Epitopes involved in Multiple Sclerosis.

Iran J Biotechnol 2017 Mar;15(1):10-21

Department of medical biotechnology. Institute of Medical Genetic, National Institute of Genetics Engineering and Biotechnology (NIGEB), Tehran, 14965/161 Iran.

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http://dx.doi.org/10.15171/ijb.1356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582249PMC
March 2017

Does core stability exercise improve lumbopelvic stability (through endurance tests) more than general exercise in chronic low back pain? A quasi-randomized controlled trial.

Physiother Theory Pract 2016 11;32(3):171-8. Epub 2016 Feb 11.

c School of Rehabilitation Sciences , Iran University of Medical Sciences , Tehran , Iran.

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http://dx.doi.org/10.3109/09593985.2015.1117550DOI Listing
January 2017

MMP-TIMP interactions in cancer invasion: An evolutionary game-theoretical framework.

J Theor Biol 2017 01 23;412:17-26. Epub 2016 Sep 23.

School of Biological Sciences, Institute for Research in Fundamental Sciences, Tehran, Iran; National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.09.019DOI Listing
January 2017

Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines.

BMC Bioinformatics 2017 Jan 25;18(1):67. Epub 2017 Jan 25.

School of Biology, College of Science, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1186/s12859-016-1418-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264486PMC
January 2017

Effect of Four Weeks of β-alanine Supplementation on Muscle Carnosine and Blood Serum Lactate during Exercise in Male Rats.

J Diet Suppl 2016 8;13(5):487-94. Epub 2016 Jan 8.

c Faculty of Dentistry, Shiraz Branch , Islamic Azad University , Shiraz , Iran.

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http://dx.doi.org/10.3109/19390211.2015.1113223DOI Listing
December 2016

PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.

BMC Bioinformatics 2016 Nov 3;18(1):30. Epub 2016 Nov 3.

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://dx.doi.org/10.1186/s12859-016-1296-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445519PMC
November 2016

Association of New Putative Epitopes of Myelin Proteolipid Protein (58-74) with Pathogenesis of Multiple Sclerosis.

Iran J Allergy Asthma Immunol 2016 Oct;15(5):394-402

Department of Medical Genetic, National Institute of Genetics Engineering and Biotechnology (NIGEB), Tehran, Iran.

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October 2016

MGP-HMM: Detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts.

Math Biosci 2016 09 16;279:53-62. Epub 2016 Jul 16.

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. Electronic address:

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http://dx.doi.org/10.1016/j.mbs.2016.07.006DOI Listing
September 2016

Preparatory brain activity and anticipatory postural adjustments accompanied by externally cued weighted-rapid arm rise task in non-specific chronic low back pain patients and healthy subjects.

Springerplus 2016 20;5(1):674. Epub 2016 May 20.

Department of Physical Therapy, School of Rehabilitation, Tehran University of Medical Sciences, P. O. Box 113635-1683, Tehran, 1148965141 Iran.

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http://dx.doi.org/10.1186/s40064-016-2342-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899386PMC
June 2016

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

J Mol Graph Model 2016 05 4;66:108-14. Epub 2016 Apr 4.

Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box 14115-134, Tehran, Iran.

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http://dx.doi.org/10.1016/j.jmgm.2016.04.001DOI Listing
May 2016

Efficient Cadmium Bioaccumulation by Displayed Hybrid CS3 Pili: Effect of Heavy Metal Binding Motif Insertion Site on Adsorption Capacity and Selectivity.

Appl Biochem Biotechnol 2015 Dec 5;177(8):1729-41. Epub 2015 Oct 5.

National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Karaj Highway, P.O. Box 14965/161, Tehran, Iran.

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http://dx.doi.org/10.1007/s12010-015-1849-yDOI Listing
December 2015

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms.

BMC Bioinformatics 2015 Oct 5;16:319. Epub 2015 Oct 5.

National Institute of Genetic Engineering and Biotechnology (NIGEB), Pajoohesh Blvd, 17 Km Tehran-Karaj Highway, PO Box 161-14965, Tehran, Iran.

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http://dx.doi.org/10.1186/s12859-015-0755-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595048PMC
October 2015

Conformational changes of a chemically modified HRP: formation of a molten globule like structure at pH 5.

EXCLI J 2014 27;13:611-22. Epub 2014 May 27.

Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463977PMC
September 2015

Efficient fast heuristic algorithms for minimum error correction haplotyping from SNP fragments.

Int J Comput Biol Drug Des 2014 25;7(4):358-68. Epub 2014 Dec 25.

National Institute of Genetic Engineering and Biotechnology, P.O. Box 14965/161, Tehran, Iran; School of Biological Sciences, Institute for Research in Fundamental Sciences, Tehran, Iran.

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http://dx.doi.org/10.1504/IJCBDD.2014.066543DOI Listing
September 2015

Erratum to: Inferring interaction type in gene regulatory networks using co-expression data.

Algorithms Mol Biol 2015 11;10:25. Epub 2015 Aug 11.

Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1186/s13015-015-0055-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532253PMC
August 2015

Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach.

J Bioinform Comput Biol 2015 Apr 19;13(2):1550002. Epub 2014 Nov 19.

Department of Mathematical Sciences, Sharif University of Technology, Tehran, Iran.

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http://dx.doi.org/10.1142/S021972001550002XDOI Listing
April 2015

Comparative Analysis of Prostate Cancer Gene Regulatory Networks via Hub Type Variation.

Avicenna J Med Biotechnol 2015 Jan-Mar;7(1):8-15

Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388891PMC
April 2015

Analysis of candidate genes has proposed the role of y chromosome in human prostate cancer.

Iran J Cancer Prev 2014 ;7(4):204-11

Dept. of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307103PMC
January 2015

Inferring gene correlation networks from transcription factor binding sites.

Genes Genet Syst 2013 ;88(5):301-9

Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran.

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November 2014

Network-based approach reveals Y chromosome influences prostate cancer susceptibility.

Comput Biol Med 2014 Nov 26;54:24-31. Epub 2014 Aug 26.

Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran. Electronic address:

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http://dx.doi.org/10.1016/j.compbiomed.2014.08.020DOI Listing
November 2014

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

Biosystems 2014 Oct 4;124:86-94. Epub 2014 Sep 4.

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://dx.doi.org/10.1016/j.biosystems.2014.09.002DOI Listing
October 2014

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

Proteins 2014 Sep 24;82(9):1937-46. Epub 2014 Mar 24.

Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1002/prot.24547DOI Listing
September 2014

In silico design and construction of metal-binding hybrid proteins for specific removal of cadmium based on CS3 pili display on the surface of Escherichia coli.

Biotechnol Appl Biochem 2013 Nov-Dec;60(6):564-72. Epub 2013 Oct 16.

National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran; Department of Biology, Faculty of Science, Zanjan University, Zanjan, Iran.

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http://dx.doi.org/10.1002/bab.1132DOI Listing
August 2014

Using data fusion for scoring reliability of protein-protein interactions.

J Bioinform Comput Biol 2014 Aug 2;12(4):1450014. Epub 2014 Jul 2.

School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1142/S0219720014500140DOI Listing
August 2014

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

Genomics 2013 Nov-Dec;102(5-6):507-14. Epub 2013 Oct 23.

Department of Computer Science, Shahid Beheshti University, GC., Tehran, Iran; School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.

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http://dx.doi.org/10.1016/j.ygeno.2013.10.003DOI Listing
July 2014

Delaunay-based nonlocal interactions are sufficient and accurate in protein fold recognition.

Proteins 2014 Mar 17;82(3):415-23. Epub 2013 Oct 17.

Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Bioinformatics, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.

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http://dx.doi.org/10.1002/prot.24407DOI Listing
March 2014

Inhibition of TGFβ signaling promotes ground state pluripotency.

Stem Cell Rev 2014 Feb;10(1):16-30

Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, PO Box 19395-4644, Tehran, Iran.

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http://dx.doi.org/10.1007/s12015-013-9473-0DOI Listing
February 2014

Dependency of codon usage on protein sequence patterns: a statistical study.

Theor Biol Med Model 2014 Jan 10;11. Epub 2014 Jan 10.

Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1186/1742-4682-11-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896713PMC
January 2014

Improving the chitinolytic activity of Bacillus pumilus SG2 by random mutagenesis.

J Microbiol Biotechnol 2013 Nov;23(11):1519-28

Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.

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November 2013

Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks.

Mitochondrion 2013 Nov 27;13(6):668-75. Epub 2013 Sep 27.

Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Electronic address:

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http://dx.doi.org/10.1016/j.mito.2013.09.006DOI Listing
November 2013

Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data.

Biochim Biophys Acta 2013 Jun 13;1834(6):1063-9. Epub 2013 Feb 13.

Shahid Beheshti University of Medical Sciences, Tehran, Iran.

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http://dx.doi.org/10.1016/j.bbapap.2013.02.003DOI Listing
June 2013

Evidence theoretic protein fold classification based on the concept of hyperfold.

Math Biosci 2012 Dec 20;240(2):148-60. Epub 2012 Jul 20.

Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1016/j.mbs.2012.07.001DOI Listing
December 2012

Post-injury repeated administrations of minocycline improve the antinociceptive effect of morphine in chronic constriction injury model of neuropathic pain in rat.

Pharmacol Biochem Behav 2012 Oct 10;102(4):520-5. Epub 2012 Jul 10.

Department of Physiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

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http://dx.doi.org/10.1016/j.pbb.2012.07.001DOI Listing
October 2012

Prediction of the pho regulon in Streptomyces clavuligerus DSM 738.

New Microbiol 2012 Oct 1;35(4):447-57. Epub 2012 Oct 1.

Department of Microbiology, College of Science, University of Tehran, Tehran, Iran.

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October 2012

Transcription factor binding sites detection by using alignment-based approach.

J Theor Biol 2012 Jul 6;304:96-102. Epub 2012 Apr 6.

Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1016/j.jtbi.2012.03.039DOI Listing
July 2012

Phloridzin reduces blood glucose levels and improves lipids metabolism in streptozotocin-induced diabetic rats.

Mol Biol Rep 2012 May 14;39(5):5299-306. Epub 2011 Dec 14.

Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom, Iran.

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http://dx.doi.org/10.1007/s11033-011-1328-7DOI Listing
May 2012

Distance-dependent atomic knowledge-based force in protein fold recognition.

Proteins 2012 Mar 9;80(3):683-90. Epub 2012 Jan 9.

Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

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http://dx.doi.org/10.1002/prot.24011DOI Listing
March 2012

Constructing circular phylogenetic networks from weighted quartets using simulated annealing.

Math Biosci 2012 Feb 13;235(2):123-7. Epub 2011 Nov 13.

Faculty of Mathematics, Shahid Beheshti University, G.C., Tehran, Iran.

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http://dx.doi.org/10.1016/j.mbs.2011.11.003DOI Listing
February 2012

Dynamical analysis of yeast protein interaction network during the sake brewing process.

J Microbiol 2011 Dec 28;49(6):965-73. Epub 2011 Dec 28.

Department of Computer Engineering, Islamic Azad University, Science and Research Branch, Tehran, Iran.

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http://dx.doi.org/10.1007/s12275-011-1194-yDOI Listing
December 2011

Construction of random perfect phylogeny matrix.

Adv Appl Bioinform Chem 2010 16;3:89-96. Epub 2010 Nov 16.

National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

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http://dx.doi.org/10.2147/AABC.S13397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170006PMC
November 2011

First report of a bifunctional chitinase/lysozyme produced by Bacillus pumilus SG2.

Enzyme Microb Technol 2011 Mar 12;48(3):225-31. Epub 2010 Nov 12.

Department of Molecular Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.

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http://dx.doi.org/10.1016/j.enzmictec.2010.11.001DOI Listing
March 2011

A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM.

Comput Biol Chem 2011 Feb 17;35(1):1-9. Epub 2010 Dec 17.

Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Iran.

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https://linkinghub.elsevier.com/retrieve/pii/S14769271100011
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http://dx.doi.org/10.1016/j.compbiolchem.2010.12.001DOI Listing
February 2011

Prediction of protein submitochondria locations based on data fusion of various features of sequences.

J Theor Biol 2011 Jan 30;269(1):208-16. Epub 2010 Oct 30.

Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan, Iran.

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http://dx.doi.org/10.1016/j.jtbi.2010.10.026DOI Listing
January 2011

Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae.

BMC Syst Biol 2010 Dec 19;4:172. Epub 2010 Dec 19.

Department of Computer Engineering, Islamic Azad University, Science and Research Branch, Tehran, Iran.

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http://dx.doi.org/10.1186/1752-0509-4-172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018396PMC
December 2010

Tag SNP selection via a genetic algorithm.

J Biomed Inform 2010 Oct 28;43(5):800-4. Epub 2010 May 28.

Department of Bioinformatics, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1016/j.jbi.2010.05.011DOI Listing
October 2010

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

BMC Bioinformatics 2010 Jan 9;11:16. Epub 2010 Jan 9.

Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1186/1471-2105-11-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821318PMC
January 2010

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

Proteins 2009 Nov;77(2):454-63

Department of Mathematical Sciences, Shahid Beheshti University, Post Code 1983963113, Tehran, Iran.

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http://dx.doi.org/10.1002/prot.22457DOI Listing
November 2009

A Segmental Semi Markov Model for protein secondary structure prediction.

Math Biosci 2009 Oct 29;221(2):130-5. Epub 2009 Jul 29.

School of Mathematics, Statistics and Computer Science and Center of Excellence in Biomathematics, College of Science, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1016/j.mbs.2009.07.004DOI Listing
October 2009

Global haplotype partitioning for maximal associated SNP pairs.

BMC Bioinformatics 2009 Aug 27;10:269. Epub 2009 Aug 27.

Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1186/1471-2105-10-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749056PMC
August 2009

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

Math Biosci 2009 Feb 18;217(2):145-50. Epub 2008 Nov 18.

University of Tehran, Enghelab Square, Tehran, Iran.

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http://dx.doi.org/10.1016/j.mbs.2008.11.001DOI Listing
February 2009

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

Comput Biol Med 2009 Feb 23;39(2):166-72. Epub 2009 Jan 23.

Department of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran.

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http://dx.doi.org/10.1016/j.compbiomed.2008.12.004DOI Listing
February 2009

Genetic algorithm for dyad pattern finding in DNA sequences.

Genes Genet Syst 2009 Feb;84(1):81-93

Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

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February 2009

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

Comput Biol Chem 2008 Dec 6;32(6):406-11. Epub 2008 Aug 6.

Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.

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https://linkinghub.elsevier.com/retrieve/pii/S14769271080010
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http://dx.doi.org/10.1016/j.compbiolchem.2008.07.027DOI Listing
December 2008

Impact of residue accessible surface area on the prediction of protein secondary structures.

BMC Bioinformatics 2008 Aug 31;9:357. Epub 2008 Aug 31.

Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1186/1471-2105-9-357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553345PMC
August 2008

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

BMC Bioinformatics 2008 Jun 11;9:274. Epub 2008 Jun 11.

Bioinformatics Group, School of Computer Science, Institute for Studies in Theoretical Physics and Mathematics, Tehran, Iran.

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http://dx.doi.org/10.1186/1471-2105-9-274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474621PMC
June 2008

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

J Theor Biol 2008 Mar 22;251(2):380-7. Epub 2007 Nov 22.

Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1016/j.jtbi.2007.11.021DOI Listing
March 2008

Evolution of 'ligand-diffusion chreodes' on protein-surface models: a genetic-algorithm study.

Chem Biodivers 2007 Dec;4(12):2766-71

Department of Biotechnology, University College of Science, University of Tehran, Enghelab Avenue, Tehran, Iran.

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http://dx.doi.org/10.1002/cbdv.200790225DOI Listing
December 2007

A method for protein accessibility prediction based on residue types and conformational states.

Comput Biol Chem 2007 Oct 19;31(5-6):384-8. Epub 2007 Aug 19.

Khatam University, Tehran, Iran.

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http://dx.doi.org/10.1016/j.compbiolchem.2007.08.006DOI Listing
October 2007

The influence of insertion of a critical residue (Arg356) in structure and bioluminescence spectra of firefly luciferase.

J Biol Chem 2007 Mar 30;282(12):8641-7. Epub 2006 Dec 30.

Department of Genetics, Faculty of Basic Sciences, Tarbiat Modares University, Tehran 14115-175, Iran.

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http://dx.doi.org/10.1074/jbc.M609271200DOI Listing
March 2007

Comparison of the molten globule states of thermophilic and mesophilic alpha-amylases.

Biophys Chem 2006 Jun 3;122(1):58-65. Epub 2006 Mar 3.

Department of Biochemistry, Faculty of Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.

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http://dx.doi.org/10.1016/j.bpc.2005.12.014DOI Listing
June 2006

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

BMC Bioinformatics 2006 Jun 13;7:297. Epub 2006 Jun 13.

Department of Biotechnology, University College of Science, University of Tehran, Tehran, Iran.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526458PMC
June 2006

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

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

Department of Biotechnology, Faculty of Science, University of Tehran, Tehran, Iran.

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February 2006

Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

FEBS Lett 2005 Jun;579(16):3397-400

Department of Biophysics, National Institute of Genetic Engineering and Biotechnology, P.O.Box 14155-6343, Tehran, Iran.

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http://doi.wiley.com/10.1016/j.febslet.2005.04.082
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June 2005

Audiological and vestibular features in affected subjects with USH3: a genotype/phenotype correlation.

Int J Audiol 2005 May;44(5):307-16

The Sahlgrenska Academy, Institute of Selected Clinical Sciences, Dept. of Audiology, Box 452, SE-405 30 Gothenburg, Sweden.

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May 2005

Modification of substrate inhibition of synaptosomal acetylcholinesterase by cardiotoxins.

J Biochem Mol Biol 2004 May;37(3):330-8

Institute of Biotechnology and Biophysics, University of Tehran, Tehran, Iran.

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May 2004

Audiological findings in Usher syndrome types IIa and II (non-IIa).

Int J Audiol 2004 Mar;43(3):136-43

Department of Audiology, The Sahlgrenska Academy, Institute of Selected Clinical Sciences, Gothenburg, Sweden.

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March 2004