BACKGROUND: The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interac...
BACKGROUND: A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put...
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF b...
Forensic science international. Genetics
Nov 24, 2016
The deconvolution of DNA mixtures remains one of the most critical challenges in the field of forensic DNA analysis. In addition, of all the data features required to perform such deconvolution, the number of contributors in the sample is widely cons...
In our study, the development of amino functionalized carbon coated magnetic nanoparticles (NH-CC-MNPs) and their usage for electrochemical detection of hybridization of nucleic acids have been aimed. Firstly, NH-CC-MNPs were prepared by coating of p...
IEEE/ACM transactions on computational biology and bioinformatics
Sep 15, 2016
Through sequence-based classification, this paper tries to accurately predict the DNA binding sites of transcription factors (TFs) in an unannotated cellular context. Related methods in the literature fail to perform such predictions accurately, sinc...
DNA Fragment assembly - an NP-Hard problem - is one of the major steps in of DNA sequencing. Multiple strategies have been used for this problem, including greedy graph-based algorithms, deBruijn graphs, and the overlap-layout-consensus approach. Thi...
DNA-binding proteins are the functional proteins in cells, which play an important role in various essential biological activities. An effective and fast computational method gDNA-Prot is proposed to predict DNA-binding proteins in this paper, which ...
Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of fun...
Journal of chemical information and modeling
Apr 4, 2016
Dynamic force spectroscopy (DFS) measurements on biomolecules typically require classifying thousands of repeated force spectra prior to data analysis. Here, we study classification of atomic force microscope-based DFS measurements using machine-lear...