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Johns Hopkins HealthCare string tie software
String Tie Software, supplied by Johns Hopkins HealthCare, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/transcriptome+assembly+software+trinity/stringtie+software/pmc12066608-82-5-8
Average 90 stars, based on 1 article reviews
string tie software - by Bioz Stars, 2026-09
90/100 stars

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Article Title: Microcarrier stiffness controls human amniotic epithelial cells (hAECs) proliferation and epithelial-mesenchymal transition (EMT) via remodeling ECM and Wnt/β-catenin pathway
Article Snippet: Human amniotic epithelial cells (hAECs) are ideal candidates for use in regenerative medicine because of their low immunogenicities and levels of tumorigenic potential.. However, the in vitro cultivation of hAECs is challenged by their limited proliferative capacities and ambiguous cellular characteristics.. Microcarrier stiffness is crucial in the immediate epithelial-mesenchymal transition (EMT) of hAECs upon in vitro cultivation.

Article Title: STAT3 signaling enhances tissue expansion during postimplantation mouse development.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER StringTie (v2.1.4) Johns Hopkins University, Center for Computational Biology https://ccb.jhu.edu/software/stringtie/ ComplexHeatmap (version 2.1.0) N/A https://doi.org/10.18129/ B9.bioc.ComplexHeatmap biomaRt (version2.50.3) N/A https://doi.org/10.18129/B9.bioc.biomaRt DESeq2 (v1.30.1) Love et al.50 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html CellRanger (v6.0.1) 10x Genomics Inc. N/A R (v4.2.2) N/A https://www.R-project.org/ scran (1.26) Bioconductor https://bioconductor.org/packages/ release/bioc/html/scran.html scuttle (1.8) Bioconductor https://bioconductor.org/packages/ release/bioc/html/scuttle.html scds (v1.14) Bioconductor https://www.bioconductor.org/packages/ release/bioc/html/scds.html batchelor (v1.14) Bioconductor https://bioconductor.org/packages/ release/bioc/html/batchelor.html BiocNeighbors (v1.8.2) Bioconductor https://www.bioconductor.org/packages/ release/bioc/html/BiocNeighbors.html irlba (v2.3.5.1) Cran https://cran.r-project.org/web/ packages/irlba/index.html miloR (1.6) Bioconductor https://www.bioconductor.org/packages/ release/bioc/html/miloR.html edgeR (v3.40) Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html destiny (3.12) Bioconductor https://www.bioconductor.org/packages/ release/bioc/html/destiny.html slingshot (v2.6) Bioconductor https://www.bioconductor.org/packages/ release/bioc/html/slingshot.html tradeSeq (v1.12) Bioconductor https://www.bioconductor.org/packages/ release/bioc/html/tradeSeq.html Metascape Zhou et al.51 https://metascape.org/gp/ index.html#/main/step1 Fiji (2.16.0) Fiji community, ImageJ https://fiji.sc/ CellProfiler (4.2.1) Broad Institute https://cellprofiler.org/ FlowJo (10.10.0) BD Biosciences https://www.flowjo.com/ Code https://github.com/BartTheeuwes/ Stat3_code Other Accession code Gene Expression Omnibus data GSE260590

Article Title: Allelopathic Molecular Mechanisms of the Two Main Allelochemicals in Sweet Potato
Article Snippet: StringTie 2.1.4 software (Johns Hopkins University, Baltimore, MD, USA) was used to conduct new transcript assembly and calculate the level of gene expression for FPKM.

Software:

Article Title: Feedback loop centered on MAF1 reduces blood-brain barrier damage in sepsis-associated encephalopathy.
Article Snippet: .. We used Stringtie software (Johns Hopkins University Center) to count the fragments within each gene segment and then normalized them using the trimmed mean of M values algorithm and converted them into gene expression levels using fragments per kilobase of transcript per million. ..

Article Title: Metallothionein 1B attenuates inflammation and hepatic steatosis in MASH by inhibiting the AKT/PI3K pathway
Article Snippet: The cleaned high-quality reads were aligned to the reference genome (e.g., human reference genome GRCh38) using HISAT2 (Johns Hopkins University, Baltimore, MD). .. Alignment results were used for transcript assembly and quantification analysis with StringTie software (Johns Hopkins University, Baltimore, MD). ..

Article Title: Elucidating the Pathogenic Mechanism of Spinal Muscular Atrophy Through the Investigation of UTS2
Article Snippet: These high-quality reads were subsequently aligned to a reference genome via HISAT2 software 2.1.0 (Center for Computational Biology at Johns Hopkins University, Baltimore, MD, USA). .. For gene expression analysis, String Tie software 2.1.5 (Center for Computational Biology at Johns Hopkins University, Baltimore, MD, USA) was used to quantify gene expression levels, which were normalized to fragments per kilobase of transcript per million mapped reads (FPKM). ..

Article Title: Metallothionein 1B attenuates inflammation and hepatic steatosis in MASH by inhibiting the AKT/PI3K pathway.
Article Snippet: The cleaned high-quality reads were aligned to the reference genome (e.g., human reference genome GRCh38) using HISAT2 (Johns Hopkins University, Baltimore, MD, USA). .. Alignment results were used for transcript assembly and quantification analysis with StringTie software (Johns Hopkins University, Baltimore, MD, USA). ..

Article Title: Characterization of temporal expression of immune genes in female locust challenged by fungal pathogen, Aspergillus sp.
Article Snippet: Hisat2 v2.0.5 software (Johns Hopkins University, U.S.A.) was used to quickly and accurately compare clean reads with the reference genome to obtain the reference genome’s location information. .. Novel transcripts were assembled using String Tie software (Johns Hopkins University, U.S.A.) and annotated using the Pfam database (European Bioinformatics Institute, U.K.). ..

Gene Expression:

Article Title: Feedback loop centered on MAF1 reduces blood-brain barrier damage in sepsis-associated encephalopathy.
Article Snippet: .. We used Stringtie software (Johns Hopkins University Center) to count the fragments within each gene segment and then normalized them using the trimmed mean of M values algorithm and converted them into gene expression levels using fragments per kilobase of transcript per million. ..

Article Title: Elucidating the Pathogenic Mechanism of Spinal Muscular Atrophy Through the Investigation of UTS2
Article Snippet: These high-quality reads were subsequently aligned to a reference genome via HISAT2 software 2.1.0 (Center for Computational Biology at Johns Hopkins University, Baltimore, MD, USA). .. For gene expression analysis, String Tie software 2.1.5 (Center for Computational Biology at Johns Hopkins University, Baltimore, MD, USA) was used to quantify gene expression levels, which were normalized to fragments per kilobase of transcript per million mapped reads (FPKM). ..



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