Hamid Pezeshk

Hamid Pezeshk

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Hamid Pezeshk

Hamid Pezeshk

Publications by authors named "Hamid Pezeshk"

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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

Task modulates functional connectivity networks in free viewing behavior.

Neuroimage 2017 10 3;159:289-301. Epub 2017 Aug 3.

Laboratory of Perceptual Dynamics, Brain & Cognition Research Unit, KU Leuven - University of Leuven, Tiensestraat 102, Leuven, 3000, Belgium; Department of Experimental Psychology II, TU Kaiserslautern, Postfach 3049, Kaiserslautern, 67653, Germany.

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http://dx.doi.org/10.1016/j.neuroimage.2017.07.066DOI Listing
October 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

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

Optimization of electrospinning parameters for polyacrylonitrile-MgO nanofibers applied in air filtration.

J Air Waste Manag Assoc 2016 09;66(9):912-21

f Department of Public Health and Preventive Medicine , University of Toledo College of Medicine , Toledo , OH , USA.

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http://dx.doi.org/10.1080/10962247.2016.1162228DOI Listing
September 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

Generalized Baum-Welch algorithm based on the similarity between sequences.

PLoS One 2013 20;8(12):e80565. Epub 2013 Dec 20.

Computer Science Department, Catholic University of Murcia (UCAM), Murcia, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080565PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869655PMC
March 2015

An optimization approach to calculating sample sizes with binary responses.

J Biopharm Stat 2014 ;24(4):715-31

a Department of Statistics and Actuarial Science , University of Waterloo , Waterloo , Ontario , Canada.

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http://dx.doi.org/10.1080/10543406.2014.902851DOI Listing
January 2015

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

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

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

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

School of Mathematics, Statistics and Computer Science, Shahid Beheshti University, G.C., Tehran, Iran.

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March 2014

Bayesian sample size calculation for estimation of the difference between two binomial proportions.

Stat Methods Med Res 2013 Dec 24;22(6):598-611. Epub 2011 Mar 24.

1School of Mathematics, Statistics and Computer Science and Center of Excellence in Biomathematics, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1177/0962280211399562DOI Listing
December 2013

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

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

Optimizing aeration rates for minimizing membrane fouling and its effect on sludge characteristics in a moving bed membrane bioreactor.

J Hazard Mater 2011 Feb 4;186(2-3):1097-102. Epub 2010 Dec 4.

Department of Civil & Environmental Engineering, Graduate Faculty of Environment, University of Tehran, No. 25 Qods St., Enghelab Ave., Tehran, Iran.

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https://linkinghub.elsevier.com/retrieve/pii/S03043894100154
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http://dx.doi.org/10.1016/j.jhazmat.2010.11.117DOI Listing
February 2011

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

The choice of sample size: a mixed Bayesian / frequentist approach.

Stat Methods Med Res 2009 Apr 29;18(2):183-94. Epub 2008 Apr 29.

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

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http://dx.doi.org/10.1177/0962280208089298DOI Listing
April 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

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

A Bayesian cost-benefit approach to the determination of sample size in clinical trials.

Stat Med 2008 Jan;27(1):68-82

Centre for Economics and Policy in Health, IMSCaR, University of Wales, Dean Street Building, Dean Street, Bangor, Gwynedd LL57 1UT, U.K.

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http://dx.doi.org/10.1002/sim.2965DOI Listing
January 2008

Beta-sheet capping: signals that initiate and terminate beta-sheet formation.

J Struct Biol 2008 Jan 11;161(1):101-10. Epub 2007 Oct 11.

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

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http://dx.doi.org/10.1016/j.jsb.2007.09.024DOI Listing
January 2008

The influence of deposit control additives on nitrogen oxides emissions from spark ignition engines (case study: Tehran).

Pak J Biol Sci 2007 Apr;10(8):1349-53

Faculty of Environment, University of Tehran, P.O. Box 14155-6135, Tehran, Iran.

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April 2007

Adaptation of proteins to different environments: a comparison of proteome structural properties in Bacillus subtilis and Escherichia coli.

J Theor Biol 2007 Jan 24;244(1):127-32. Epub 2006 Jul 24.

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

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http://dx.doi.org/10.1016/j.jtbi.2006.07.021DOI Listing
January 2007

Bayesian approach to determine the number of subsequent users of a new treatment.

Stat Methods Med Res 2006 Dec;15(6):585-92

Center of Excellence in Biomathematics and School of Mathematics, Statistics and Computer Science, University College of Science, University of Tehran 14155-6455, Iran.

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http://dx.doi.org/10.1177/0962280206070640DOI Listing
December 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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http://dx.doi.org/10.1016/j.compbiolchem.2005.10.009DOI Listing
February 2006

Bayesian techniques for sample size determination in clinical trials: a short review.

Authors:
Hamid Pezeshk

Stat Methods Med Res 2003 Dec;12(6):489-504

Department of Mathematics, Statistics and Computer Science, University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1191/0962280203sm345oaDOI Listing
December 2003