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COVID19 is a heterogeneous medical condition involving diverse underlying pathophysiological processes including hyperinflammation, endothelial damage, thrombotic microangiopathy, and end-organ damage. Limited knowledge about the molecular mechanisms driving these processes and lack of staging biomarkers hamper the ability to stratify patients for targeted therapeutics. We report here the results of a cross-sectional multi-omics analysis of hospitalized COVID19 patients revealing that seroconversion status associates with distinct underlying pathophysiological states. Low antibody titers associate with hyperactive T cells and NK cells, high levels of IFN alpha, gamma and lambda ligands, markers of systemic complement activation, and depletion of lymphocytes, neutrophils, and platelets. Upon seroconversion, all of these processes are attenuated, observing instead increases in B cell subsets, emergency hematopoiesis, increased D-dimer, and hypoalbuminemia. We propose that seroconversion status could potentially be used as a biosignature to stratify patients for therapeutic intervention and to inform analysis of clinical trial results in heterogenous patient populations.
Pubmed ID: 33724185
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Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsScript distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data.
View all literature mentionsProvides bioinformatics services to research groups in Babraham Institute, United Kingdom and external commercial consultancy service. Provides assistance in genomics, proteomics, statistics, microarrays, and custom software development.
View all literature mentionsThis monoclonal targets CD123
View all literature mentionsThis monoclonal targets CD196
View all literature mentionsThis monoclonal targets CD45RA
View all literature mentionsThis monoclonal targets CD38
View all literature mentionsThis monoclonal targets FOXP3
View all literature mentionsThis monoclonal targets CD14
View all literature mentionsThis monoclonal targets HLA-DR
View all literature mentionsThis monoclonal targets CD197/CCR7
View all literature mentionsThis monoclonal targets CD95/Fas
View all literature mentionsThis monoclonal targets CD279
View all literature mentionsThis monoclonal targets CD1c (BDCA-1)
View all literature mentionsThis monoclonal targets CD185/CXCR5
View all literature mentionsThis unknown targets CD25
View all literature mentionsThis recombinant monoclonal targets CD56
View all literature mentionsThis monoclonal targets IgD
View all literature mentionsThis monoclonal targets TIGIT
View all literature mentionsThis monoclonal targets TIM-3
View all literature mentionsThis monoclonal targets CD183/CXCR3
View all literature mentionsThis monoclonal targets Ki-67
View all literature mentionsThis unknown targets CD274/PDL1
View all literature mentionsThis unknown targets CD127
View all literature mentionsThis unknown targets CD27
View all literature mentionsThis monoclonal targets IgM
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets CD16
View all literature mentionsThis monoclonal targets CD86 (B7-2)
View all literature mentionsThis monoclonal targets CD33
View all literature mentionsThis monoclonal targets CD3
View all literature mentionsThis monoclonal targets CD11b/Mac-1
View all literature mentionsThis monoclonal targets CD141
View all literature mentionsThis monoclonal targets EOMES
View all literature mentionsThis unknown targets CD45
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets CD278
View all literature mentionsThis monoclonal targets Tbet
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsConversion software that both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
View all literature mentionsOpen source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).
View all literature mentionsSoftware package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
View all literature mentionsHuman and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
View all literature mentionsSoftware environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.
View all literature mentionsSoftware tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses.
View all literature mentionsSoftware package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.
View all literature mentionsSoftware that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsGraph-based alignment of next generation sequencing reads to a population of genomes.
View all literature mentionsSoftware suite of bioinformatics tools for analysis of DNA and RNA sequence data. Used for file formats such as fastq, fasta, sam, scarf, fasta plus qual, compressed or raw, with autodetection of quality encoding and interleaving. Written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSoftware repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
View all literature mentionsOpen source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsCommand-line software tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
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