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Probing the Relation Between Cell Function and Chromatin Interactions Using Community Detection Approaches
, M.Sc. Thesis Sharif University of Technology ; Rabiee, Hamid Reza (Supervisor) ; Jafari Siavoshani, Mahdi (Supervisor)
Abstract
Hi-C is a new technology invented to record the amount of interaction between all chromatin fragments. Chromatin interactions are manifestations of chromatin's 3D structure. It has been proved that different 3D structures of different cell types, despite having the same DNA, causes in different functionalities of cells. Therefore knowing chromatin structure, the factors affecting it and the way it affects cells' behaviors such as gene co-expression, sheds more light on the knowledge about cells and the methods that can change their fates. Finding the causes of diseases, designing more efficient drugs and progressing the conversion of different cell types into each other used for amending...
Use of second-order calibration for residue screening of some triazines in the presence of coeluting interferences by gas chromatography-selected ion mass spectrometry
, Article Analytica Chimica Acta ; Volume 537, Issue 1-2 , 2005 , Pages 89-100 ; 00032670 (ISSN) ; Vosough, M ; Sharif University of Technology
Elsevier
2005
Abstract
The quantities of residues of some triazines such as prometon, propazine, atrazine and simazine in complex matrices of apple samples were determined, using gas chromatography-selected ion mass (GC-SIM) spectrometry. Generalized rank annihilation method (GRAM) as a second-order calibration technique was used for screening, resolving and finally determining the amounts of the residues. Before the GRAM analysis, different steps of data preprocessing such as background correction, de-skewing and standardization for rank alignment was used for every target analyte. The de-skewing and rank alignment algorithms were used for bilinearity and trilinearity corrections, respectively. The two data...
MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
, Article PLoS Computational Biology ; Volume 18, Issue 6 , 2022 ; 1553734X (ISSN) ; Modegh, R. G ; Rabiee, H. R ; Sarbandi, E. R ; Rezaie, N ; Tam, K. T ; Forrest, A. R. R ; Sharif University of Technology
Public Library of Science
2022
Abstract
Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than transient background and artefactual interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly...