<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36456?offset=500 https://bioinformaticsonline.com/researchlabs/view/39827/prof-dr-med-andreas-ramming Wed, 07 Aug 2019 03:25:48 -0500 <![CDATA[Prof. Dr. med. Andreas Ramming]]> In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of patients respond to these existing therapies on a permanent basis. In the remaining cases, these therapies miss their target from the beginning or later during the course of treatment failure. There are currently no causal therapies available for the treatment of fibrotic autoimmune diseases such as systemic sclerosis. Therefore, there is an urgent need to develop new therapeutic options for the treatment of fibrotic and synovitic autoimmune diseases. His group is therefore deal with the molecular mechanisms of these misdirected signaling pathways for the development of novel, targeted therapies

http://www.medizin3.uk-erlangen.de/forschung/arbeitsgruppen/matrixbiologie-entzuendliche-signalwege-in-arthritis-und-fibrose/

]]> https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing Sun, 16 Feb 2020 08:47:17 -0600 https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing <![CDATA[iSeqQC: a tool for expression-based quality control in RNA sequencing]]> iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers.

http://cancerwebpa.jefferson.edu/iSeqQC/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

Address of the bookmark: https://github.com/gkumar09/iSeqQC

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data Fri, 25 Feb 2022 04:42:09 -0600 https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data <![CDATA[Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data]]> This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

smudgeexample

Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

]]> Neel https://bioinformaticsonline.com/bookmarks/view/37416/gfinisher-a-new-strategy-to-refine-and-finish-bacterial-genome-assemblies Thu, 26 Jul 2018 09:31:55 -0500 https://bioinformaticsonline.com/bookmarks/view/37416/gfinisher-a-new-strategy-to-refine-and-finish-bacterial-genome-assemblies <![CDATA[GFinisher: a new strategy to refine and finish bacterial genome assemblies]]> GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references.

java -Xms2G -Xmx4G -jar GenomeFinisher.jar  \
    -i target_contigs.fasta  \
    -ds alternative_assemblies.fasta -ref reference.fasta  \
    -o outputDirectory

Address of the bookmark: http://gfinisher.sourceforge.net

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