Systems & Computational Biology
OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processesOrtSuite predicts synergistic species interactions using the genomic potential of microbial communities
Statistical guidelines for quality control of next-generation sequencing techniquesCondition-specific statistical guidelines and accurate classification trees for quality control of functional genomics NGS files (RNA-seq, ChIP-seq and DNase-seq) have been generated using thousands of reference files from the ENCODE project and made available to the community.
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19 and provide insights into viral entry inhibition, immune regulation, and drug optimisation strategies.
Incomplete antiviral treatment may induce longer durations of viral shedding during SARS-CoV-2 infectionTreatments initiated early, such as 0.5 d after virus inoculation, with intermediate to relatively high efficacy (30–70% inhibition of virus replication) yield a prolonged duration of viral shedding (by about 6.0 d) compared with no treatment.
Dynamic changes in RNA–protein interactions and RNA secondary structure in mammalian erythropoiesisAnalysis of PIP-seq data from a model of erythropoiesis reveals dynamics of RBP–RNA interaction and changes in RNA secondary structure throughout red blood cell development.
Hepatitis B virus compartmentalization and single-cell differentiation in hepatocellular carcinomaSingle-cell RNA-Seq unravels heterogeneity and compartmentalization of both hepatitis B virus and cancer identifying new candidate pathways for viral hepatocarcinogenesis.
Functional annotation of noncoding mutations in cancerRecurrent regulatory mutations affecting transcription factor binding sites in 2,500 cancer samples.
Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packingIt describes how hierarchical CpG distribution on the genomes of species change in the evolution and the correlation with the chromatin structure.
On the relation of gene essentiality to intron structure: a computational and deep learning approachA deep learning classifier predicts gene essentiality by intron sequence. A unique set of intron features of essential genes was found and its importance demonstrated by a high-performing classifier.
Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiationL929 cell supernatant is commonly used to differentiate murine macrophages from bone marrow. The supernatant and its effect on macrophage phenotype was characterised by proteomics and the authors identified novel immunoregulatory proteins.