ArticleBioData mining2016
SePIA: RNA and small RNA sequence processing, integration, and analysis.
Article in BioData mining, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 36 citations in OpenAlex.
- Multi-omics analysis reveals the attenuation of the interferon pathway as a driver of chemo-refractory ovarian cancer.Cell reports. Medicine · 2025Trial
- Multi-modal data integration reveals functionally credible predictive biomarkers in ovarian cancer.Genome medicine · 2026Article
- Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer.Cancer discovery · 2025Article
- Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer.Cancer cell · 2024Article
- Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer.bioRxiv : the preprint server for biology · 2024Article
- Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma.BMC cancer · 2024Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Article
- Co-evolution of matrisome and adaptive adhesion dynamics drives ovarian cancer chemoresistance.Nature communications · 2021Article
- Aggressive and recurrent ovarian cancers upregulate ephrinA5, a non-canonical effector of EphA2 signaling duality.Scientific reports · 2021Article
- A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.PLoS computational biology · 2021Article
- Multi-Omics Data Integration in Extracellular Vesicle Biology-Utopia or Future Reality?International journal of molecular sciences · 2020Review
- Functional Profiling of FSH and Estradiol in Ovarian Granulosa Cell Tumors.Journal of the Endocrine Society · 2020Article
- Article
- Defects in mtDNA replication challenge nuclear genome stability through nucleotide depletion and provide a unifying mechanism for mouse progerias.Nature metabolism · 2019Article
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- SEQdata-BEACON: a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500.BioData mining · 2019Article
- Article
- MicroRNAs regulate key cell survival pathways and mediate chemosensitivity during progression of diffuse large B-cell lymphoma.Blood cancer journal · 2017Article
- A survey of best practices for RNA-seq data analysis.Genome biology · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLarge-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types.
resultsWe developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow's extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance.
conclusionSePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA's modular design enables robust customization to a given experiment while maintaining overall workflow structure. It is available at http://anduril.org/sepia.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.