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Items: 18

1.

Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes.

Bidkhori G, Benfeitas R, Klevstig M, Zhang C, Nielsen J, Uhlen M, Boren J, Mardinoglu A.

Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11874-E11883. doi: 10.1073/pnas.1807305115. Epub 2018 Nov 27.

PMID:
30482855
2.

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.

Zhang C, Bidkhori G, Benfeitas R, Lee S, Arif M, Uhlén M, Mardinoglu A.

Front Physiol. 2018 Sep 28;9:1355. doi: 10.3389/fphys.2018.01355. eCollection 2018.

3.

Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma.

Bidkhori G, Benfeitas R, Elmas E, Kararoudi MN, Arif M, Uhlen M, Nielsen J, Mardinoglu A.

Front Physiol. 2018 Jul 17;9:916. doi: 10.3389/fphys.2018.00916. eCollection 2018.

4.

Tamoxifen-Induced Apoptosis of MCF-7 Cells via GPR30/PI3K/MAPKs Interactions: Verification by ODE Modeling and RNA Sequencing.

Rouhimoghadam M, Safarian S, Carroll JS, Sheibani N, Bidkhori G.

Front Physiol. 2018 Jul 11;9:907. doi: 10.3389/fphys.2018.00907. eCollection 2018.

5.

Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling.

Rosario D, Benfeitas R, Bidkhori G, Zhang C, Uhlen M, Shoaie S, Mardinoglu A.

Front Physiol. 2018 Jun 25;9:775. doi: 10.3389/fphys.2018.00775. eCollection 2018.

6.

High Cell Density Perfusion Culture has a Maintained Exoproteome and Metabolome.

Zamani L, Lundqvist M, Zhang Y, Aberg M, Edfors F, Bidkhori G, Lindahl A, Mie A, Mardinoglu A, Field R, Turner R, Rockberg J, Chotteau V.

Biotechnol J. 2018 Oct;13(10):e1800036. doi: 10.1002/biot.201800036. Epub 2018 Jul 13.

PMID:
29957873
7.

TCSBN: a database of tissue and cancer specific biological networks.

Lee S, Zhang C, Arif M, Liu Z, Benfeitas R, Bidkhori G, Deshmukh S, Al Shobky M, Lovric A, Boren J, Nielsen J, Uhlen M, Mardinoglu A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D595-D600. doi: 10.1093/nar/gkx994.

8.

A pathology atlas of the human cancer transcriptome.

Uhlen M, Zhang C, Lee S, Sjöstedt E, Fagerberg L, Bidkhori G, Benfeitas R, Arif M, Liu Z, Edfors F, Sanli K, von Feilitzen K, Oksvold P, Lundberg E, Hober S, Nilsson P, Mattsson J, Schwenk JM, Brunnström H, Glimelius B, Sjöblom T, Edqvist PH, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F.

Science. 2017 Aug 18;357(6352). pii: eaan2507. doi: 10.1126/science.aan2507.

PMID:
28818916
9.

Molecular Mechanisms behind Free Radical Scavengers Function against Oxidative Stress.

Ahmadinejad F, Geir Møller S, Hashemzadeh-Chaleshtori M, Bidkhori G, Jami MS.

Antioxidants (Basel). 2017 Jul 10;6(3). pii: E51. doi: 10.3390/antiox6030051. Review.

10.

A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production.

Mohammadi R, Fallah-Mehrabadi J, Bidkhori G, Zahiri J, Javad Niroomand M, Masoudi-Nejad A.

Mol Biosyst. 2016 Jul 19;12(8):2552-61. doi: 10.1039/c6mb00119j.

PMID:
27265370
11.

FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction.

Khosraviani M, Saheb Zamani M, Bidkhori G.

Bioinformatics. 2016 Feb 1;32(3):398-408. doi: 10.1093/bioinformatics/btv578. Epub 2015 Oct 10.

PMID:
26454274
12.

Genome scale modeling in systems biology: algorithms and resources.

Najafi A, Bidkhori G, Bozorgmehr JH, Koch I, Masoudi-Nejad A.

Curr Genomics. 2014 Apr;15(2):130-59. doi: 10.2174/1389202915666140319002221.

13.

Cancer systems biology and modeling: microscopic scale and multiscale approaches.

Masoudi-Nejad A, Bidkhori G, Hosseini Ashtiani S, Najafi A, Bozorgmehr JH, Wang E.

Semin Cancer Biol. 2015 Feb;30:60-9. doi: 10.1016/j.semcancer.2014.03.003. Epub 2014 Mar 18. Review.

PMID:
24657638
14.

C-element: a new clustering algorithm to find high quality functional modules in PPI networks.

Ghasemi M, Rahgozar M, Bidkhori G, Masoudi-Nejad A.

PLoS One. 2013 Sep 5;8(9):e72366. doi: 10.1371/journal.pone.0072366. eCollection 2013.

15.

Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma.

Bidkhori G, Narimani Z, Hosseini Ashtiani S, Moeini A, Nowzari-Dalini A, Masoudi-Nejad A.

PLoS One. 2013 Jul 11;8(7):e67552. doi: 10.1371/journal.pone.0067552. Print 2013.

16.

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.

17.

Modeling of tumor progression in NSCLC and intrinsic resistance to TKI in loss of PTEN expression.

Bidkhori G, Moeini A, Masoudi-Nejad A.

PLoS One. 2012;7(10):e48004. doi: 10.1371/journal.pone.0048004. Epub 2012 Oct 24.

18.

Candidate gene prioritization.

Masoudi-Nejad A, Meshkin A, Haji-Eghrari B, Bidkhori G.

Mol Genet Genomics. 2012 Sep;287(9):679-98. doi: 10.1007/s00438-012-0710-z. Epub 2012 Aug 15. Review. Retraction in: Masoudi-Nejad A, Meshkin A, Haji-Eghrari B, Bidkhori G. Mol Genet Genomics. 2015 Dec;290(6):2357.

PMID:
22893106

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