Systems Biology

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    Protocols in Current Issue
    Differential Analysis of N-glycopeptide Abundance and N-glycosylation Site Occupancy for Studying Protein N-glycosylation Dysregulation in Human Disease
    Authors:  Qi Zhang, Cheng Ma, Lian Li and Lih-Shen Chin, date: 06/20/2021, view: 201, Q&A: 0

    Protein N-glycosylation plays a vital role in diverse cellular processes, and dysregulated N-glycosylation is implicated in a variety of human diseases including neurodegenerative disorders and cancer. With recent advances in high-resolution mass

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    Differential Analysis of N-glycopeptide Abundance and N-glycosylation Site Occupancy for Studying Protein N-glycosylation Dysregulation in Human Disease
    Authors:  Qi Zhang, Cheng Ma, Lian Li and Lih-Shen Chin, date: 06/20/2021, view: 201, Q&A: 0
    [Abstract]

    Protein N-glycosylation plays a vital role in diverse cellular processes, and dysregulated N-glycosylation is implicated in a variety of human diseases including neurodegenerative disorders and cancer. With recent advances in high-resolution mass spectrometry-based glycoproteomics technologies enabling large-scale N-glycoproteome profiling of

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    Simplified Epigenome Profiling Using Antibody-tethered Tagmentation
    Authors:  Steven Henikoff, Jorja G. Henikoff and Kami Ahmad, date: 06/05/2021, view: 396, Q&A: 0
    [Abstract]

    We previously introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling method in which antibody tethering of the Tn5 transposase to a chromatin epitope of interest maps specific chromatin features in small samples and single cells. With CUT&Tag, intact cells or nuclei are permeabilized, followed by successive

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    Detecting Differentially Methylated Promoters in Genes Related to Disease Phenotypes Using R
    Authors:  Jordi Martorell Marugán and Pedro Carmona-Sáez, date: 06/05/2021, view: 265, Q&A: 0
    [Abstract]

    DNA methylation in gene promoters plays a major role in gene expression regulation, and alterations in methylation patterns have been associated with several diseases. In this context, different software suites and statistical methods have been proposed to analyze differentially methylated positions and regions. Among them, the novel statistical

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    Identification of R-loop-forming Sequences in Drosophila melanogaster Embryos and Tissue Culture Cells Using DRIP-seq
    Authors:  Célia Alecki and Nicole J. Francis, date: 05/05/2021, view: 726, Q&A: 0
    [Abstract]

    R-loops are non-canonical nucleic structures composed of an RNA–DNA hybrid and a displaced ssDNA. Originally identified as a source of genomic instability, R-loops have been shown over the last decade to be involved in the targeting of proteins and to be associated with different histone modifications, suggesting a regulatory function. In

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    Computational Analysis and Phylogenetic Clustering of SARS-CoV-2 Genomes
    Authors:  Bani Jolly and Vinod Scaria, date: 04/20/2021, view: 1400, Q&A: 0
    [Abstract]

    COVID-19, the disease caused by the novel SARS-CoV-2 coronavirus, originated as an isolated outbreak in the Hubei province of China but soon created a global pandemic and is now a major threat to healthcare systems worldwide. Following the rapid human-to-human transmission of the infection, institutes around the world have made efforts to generate

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    Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome
    [Abstract]

    Next generations sequencing (NGS) has become an important tool in biomedical research. The Primer ID approach combined with the MiSeq platform overcomes the limitation of PCR errors and reveals the true sampling depth of population sequencing, making it an ideal tool to study mutagenic effects of potential broad-spectrum antivirals on RNA viruses.

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    Trypanosomatid, fluorescence-based in vitro U-insertion/U-deletion RNA-editing (FIDE)
    Authors:  Wolf-Matthias Leeder, Elisabeth Kruse and H. Ulrich Göringer, date: 03/05/2021, view: 774, Q&A: 0
    [Abstract]

    Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. In the process exclusively uridine (U)-nucleotides are site-specifically inserted into and deleted from sequence-deficient primary transcripts to convert them into translatable mRNAs. The reaction is

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    EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error
    [Abstract]

    Transcription errors can substantially affect metabolic processes in organisms by altering the epigenome and causing misincorporations in mRNA, which is translated into aberrant mutant proteins. Moreover, within eukaryotic genomes there are specific Transcription Error-Enriched genomic Loci (TEELs) which are transcribed by RNA polymerases with

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    Low- and High-resolution Dynamic Analyses for Magnetic Resonance Spectroscopy Data
    Author:  Reuben Rideaux, date: 01/20/2021, view: 739, Q&A: 0
    [Abstract]

    Magnetic resonance spectroscopy (MRS) can be used to measure in vivo concentrations of neurometabolites. This information can be used to identify neurotransmitter involvement in healthy (e.g., perceptual and cognitive processes) and unhealthy brain function (e.g., neurological and psychiatric illnesses). The standard approach for analyzing MRS

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    Reference-free Association Mapping from Sequencing Reads Using k-mers
    Authors:  Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid, Lior Pachter and Atif Rahman, date: 11/05/2020, view: 1409, Q&A: 0
    [Abstract] Association mapping is the process of linking phenotypes with genotypes. In genome wide association studies (GWAS), individuals are first genotyped using microarrays or by aligning sequenced reads to reference genomes. However, both these approaches rely on reference genomes which limits their application to organisms with no or incomplete ...



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