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Items: 17

1.

A systematic survey of centrality measures for protein-protein interaction networks.

Ashtiani M, Salehzadeh-Yazdi A, Razaghi-Moghadam Z, Hennig H, Wolkenhauer O, Mirzaie M, Jafari M.

BMC Syst Biol. 2018 Jul 31;12(1):80. doi: 10.1186/s12918-018-0598-2.

2.

Evolution of computational models in BioModels Database and the Physiome Model Repository.

Scharm M, Gebhardt T, Touré V, Bagnacani A, Salehzadeh-Yazdi A, Wolkenhauer O, Waltemath D.

BMC Syst Biol. 2018 Apr 12;12(1):53. doi: 10.1186/s12918-018-0553-2.

3.

Unveiling network-based functional features through integration of gene expression into protein networks.

Jalili M, Gebhardt T, Wolkenhauer O, Salehzadeh-Yazdi A.

Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2349-2359. doi: 10.1016/j.bbadis.2018.02.010. Epub 2018 Feb 18. Review.

4.

Comprehensive functional enrichment analysis of male infertility.

Razavi SM, Sabbaghian M, Jalili M, Divsalar A, Wolkenhauer O, Salehzadeh-Yazdi A.

Sci Rep. 2017 Nov 17;7(1):15778. doi: 10.1038/s41598-017-16005-0.

5.

Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways.

Jalili M, Salehzadeh-Yazdi A, Mohammadi S, Yaghmaie M, Ghavamzadeh A, Alimoghaddam K.

Int J Hematol Oncol Stem Cell Res. 2017 Jan 1;11(1):1-12.

6.

Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological Networks.

Jalili M, Salehzadeh-Yazdi A, Gupta S, Wolkenhauer O, Yaghmaie M, Resendis-Antonio O, Alimoghaddam K.

Front Physiol. 2016 Aug 26;7:375. doi: 10.3389/fphys.2016.00375. eCollection 2016. No abstract available.

7.

Cancerome: A hidden informative subnetwork of the diseasome.

Jalili M, Salehzadeh-Yazdi A, Yaghmaie M, Ghavamzadeh A, Alimoghaddam K.

Comput Biol Med. 2016 Sep 1;76:173-7. doi: 10.1016/j.compbiomed.2016.07.010. Epub 2016 Jul 20.

PMID:
27468170
8.

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells.

von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG.

Mol Cell. 2016 Jun 16;62(6):983. doi: 10.1016/j.molcel.2016.06.005. Epub 2016 Jun 16. No abstract available.

9.

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells.

von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG.

Mol Cell. 2016 Jun 16;62(6):848-861. doi: 10.1016/j.molcel.2016.04.025. Epub 2016 May 26. Erratum in: Mol Cell. 2016 Jun 16;62(6):983.

10.

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis.

Jalili M, Salehzadeh-Yazdi A, Asgari Y, Arab SS, Yaghmaie M, Ghavamzadeh A, Alimoghaddam K.

PLoS One. 2015 Nov 16;10(11):e0143111. doi: 10.1371/journal.pone.0143111. eCollection 2015.

11.

Alterations in cancer cell metabolism: the Warburg effect and metabolic adaptation.

Asgari Y, Zabihinpour Z, Salehzadeh-Yazdi A, Schreiber F, Masoudi-Nejad A.

Genomics. 2015 May;105(5-6):275-81. doi: 10.1016/j.ygeno.2015.03.001. Epub 2015 Mar 13.

12.

Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.

Salehzadeh-Yazdi A, Asgari Y, Saboury AA, Masoudi-Nejad A.

PLoS One. 2014 Nov 3;9(11):e111686. doi: 10.1371/journal.pone.0111686. eCollection 2014.

13.

Controllability in cancer metabolic networks according to drug targets as driver nodes.

Asgari Y, Salehzadeh-Yazdi A, Schreiber F, Masoudi-Nejad A.

PLoS One. 2013 Nov 25;8(11):e79397. doi: 10.1371/journal.pone.0079397. eCollection 2013.

14.

Computational structure analysis of biomacromolecule complexes by interface geometry.

Mahdavi S, Salehzadeh-Yazdi A, Mohades A, Masoudi-Nejad A.

Comput Biol Chem. 2013 Dec;47:16-23. doi: 10.1016/j.compbiolchem.2013.06.003. Epub 2013 Jun 25.

PMID:
23850846
15.

HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens.

Ahmadi H, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, Masoudi-Nejad A.

Genomics. 2013 Feb;101(2):94-100. doi: 10.1016/j.ygeno.2012.11.005. Epub 2012 Nov 19.

16.

CytoKavosh: a cytoscape plug-in for finding network motifs in large biological networks.

Masoudi-Nejad A, Ansariola M, Kashani ZR, Salehzadeh-Yazdi A, Khakabimamaghani S.

PLoS One. 2012;7(8):e43287. doi: 10.1371/journal.pone.0043287. Epub 2012 Aug 29.

17.

Computational analysis of RNA-protein interaction interfaces via the Voronoi diagram.

Mahdavi S, Mohades A, Salehzadeh Yazdi A, Jahandideh S, Masoudi-Nejad A.

J Theor Biol. 2012 Jan 21;293:55-64. doi: 10.1016/j.jtbi.2011.09.033. Epub 2011 Oct 10.

PMID:
22004995

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