Systems Biology


    Protocols in Current Issue
    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: 7, Q&A: 0

    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

    Computational Analysis and Phylogenetic Clustering of SARS-CoV-2 Genomes
    Authors:  Bani Jolly and Vinod Scaria, date: 04/20/2021, view: 767, Q&A: 0

    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

    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: 1122, 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 ...
    Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria
    Authors:  Ramón Cervantes-Rivera and Andrea Puhar, date: 09/20/2020, view: 1450, Q&A: 0
    [Abstract] Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are involved in gene expression regulation. Taken into account the classical gene ...
    HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets
    Authors:  Gaston Rozadilla, Jorgelina Moreiras Clemente and Christina B. McCarthy, date: 07/20/2020, view: 1164, Q&A: 0
    [Abstract] Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy. When using taxonomy-dependent alignment-based methods to classify and label reads, the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are ...
    Delayed Alternation Task for the Study of Spatial Working and Long Term Memory in Rats
    Authors:  Megi Hoxha and Marta Sabariego, date: 03/05/2020, view: 2293, Q&A: 0
    [Abstract] Memory systems can hold previously presented information for several seconds, bridging gaps between discontinuous events. It has been previously demonstrated that the hippocampus and the medial entorhinal cortex (mEC) are necessary for memory retention over delay intervals in alternation tasks. Here we describe the delayed alternation task, a ...
    ChIP-Seq from Limited Starting Material of K562 Cells and Drosophila Neuroblasts Using Tagmentation Assisted Fragmentation Approach
    Authors:  Junaid Akhtar, Piyush More and Steffen Albrecht, date: 02/20/2020, view: 1700, Q&A: 0
    [Abstract] Chromatin immunoprecipitation is extensively used to investigate the epigenetic profile and transcription factor binding sites in the genome. However, when the starting material is limited, the conventional ChIP-Seq approach cannot be implemented. This protocol describes a method that can be used to generate the chromatin profiles from as low as ...
    Probabilistic Models for Predicting Mutational Routes to New Adaptive Phenotypes
    Authors:  Eric Libby and Peter A. Lind, date: 10/20/2019, view: 1890, Q&A: 0
    [Abstract] Understanding the translation of genetic variation to phenotypic variation is a fundamental problem in genetics and evolutionary biology. The introduction of new genetic variation through mutation can lead to new adaptive phenotypes, but the complexity of the genotype-to-phenotype map makes it challenging to predict the phenotypic effects of ...
    Genome-wide Estimation of Evolutionary Distance and Phylogenetic Analysis of Homologous Genes
    Authors:  Meixia Zhao, Biao Zhang, Jianxin Ma and Damon Lisch, date: 12/05/2018, view: 4273, Q&A: 0
    [Abstract] Homologous genes, including paralogs and orthologs, are genes that share sequence homologies within or between different species. Homologous genes originate from a common origin through speciation, genetic duplication or horizontal gene transfer. Estimation of the sequence divergence of homologous genes help us to understand divergence time, which ...
    Bacterial Microcolonies in Gel Beads for High-throughput Screening
    Author:  Yolanda Schaerli, date: 07/05/2018, view: 5618, Q&A: 0
    [Abstract] High-throughput screening of a DNA library expressed in a bacterial population for identifying potentially rare members displaying a property of interest is a crucial step for success in many experiments such as directed evolution of proteins and synthetic circuits and deep mutational scanning to identify gain- or loss-of-function mutants.

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