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Items: 9


Uncovering tissue-specific binding features from differential deep learning.

Phuycharoen M, Zarrineh P, Bridoux L, Amin S, Losa M, Chen K, Bobola N, Rattray M.

Nucleic Acids Res. 2020 Jan 24. pii: gkaa009. doi: 10.1093/nar/gkaa009. [Epub ahead of print]


A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree.

Losa M, Latorre V, Andrabi M, Ladam F, Sagerström C, Novoa A, Zarrineh P, Bridoux L, Hanley NA, Mallo M, Bobola N.

Elife. 2017 Sep 27;6. pii: e31362. doi: 10.7554/eLife.31362.


Predicting brain network changes in Alzheimer's disease with link prediction algorithms.

Sulaimany S, Khansari M, Zarrineh P, Daianu M, Jahanshad N, Thompson PM, Masoudi-Nejad A.

Mol Biosyst. 2017 Mar 28;13(4):725-735. doi: 10.1039/c6mb00815a.


Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources.

Taghipour S, Zarrineh P, Ganjtabesh M, Nowzari-Dalini A.

BMC Bioinformatics. 2017 Jan 3;18(1):10. doi: 10.1186/s12859-016-1422-x.


Co-expressional conservation in virulence and stress related genes of three Gammaproteobacterial species: Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa.

Hosseinkhan N, Zarrineh P, Rokni-Zadeh H, Ashouri MR, Masoudi-Nejad A.

Mol Biosyst. 2015 Nov;11(11):3137-48. doi: 10.1039/c5mb00353a.


Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung.

Hosseinkhan N, Zarrineh P, Masoudi-Nejad A.

Curr Genomics. 2014 Oct;15(5):408-18. doi: 10.2174/1389202915666140818205444.


Genome-scale co-expression network comparison across Escherichia coli and Salmonella enterica serovar Typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles.

Zarrineh P, Sánchez-Rodríguez A, Hosseinkhan N, Narimani Z, Marchal K, Masoudi-Nejad A.

PLoS One. 2014 Aug 7;9(8):e102871. doi: 10.1371/journal.pone.0102871. eCollection 2014.


Draft Genome Sequence of Pseudomonas fluorescens LMG 5329, a White Line-Inducing Principle-Producing Bioindicator for the Mushroom Pathogen Pseudomonas tolaasii.

Ghequire MG, Rokni-Zadeh H, Zarrineh P, De Mot R.

Genome Announc. 2013 Jul 25;1(4). pii: e00383-13. doi: 10.1128/genomeA.00383-13.


COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms.

Zarrineh P, Fierro AC, Sánchez-Rodríguez A, De Moor B, Engelen K, Marchal K.

Nucleic Acids Res. 2011 Apr;39(7):e41. doi: 10.1093/nar/gkq1275. Epub 2010 Dec 10.

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