ArticleBioinformatics (Oxford, England)2017
Planning bioinformatics workflows using an expert system.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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
26 citing papers in PubMed.
- Molecular Characterization and Prospective Evaluation of Pathologic Response and Outcomes with Neoadjuvant Therapy in Metaplastic Triple-Negative Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Trial
- Immune Phenotype and Response to Neoadjuvant Therapy in Triple-Negative Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Trial
- Regulation of mitochondrial ROS by C15ORF48 in a basal cell subpopulation contributes to chemotherapy resistance in TNBC.Science advances · 2026Article
- Divergent oncogenic signaling and immune microenvironment changes in low-grade serous ovarian cancer patients undergoing intraperitoneal chemotherapy.NPJ precision oncology · 2025Article
- System analysis links SMARCD3 regulons to growth signaling and MEK inhibitor response in everolimus-resistant ER+ breast cancer cells.Cell reports. Medicine · 2025Article
- Targeting neddylation and sumoylation in chemoresistant triple negative breast cancer.NPJ breast cancer · 2024Article
- The dual role of the DREAM/G2M pathway in non-tumorigenic immortalization of senescent cells.FEBS open bio · 2024Article
- Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer.Nature genetics · 2023Article
- Predictors of success in establishing orthotopic patient-derived xenograft models of triple negative breast cancer.NPJ breast cancer · 2023Article
- Identification of biomarkers of response to preoperative talazoparib monotherapy in treatment naïve gBRCA+ breast cancers.NPJ breast cancer · 2022Article
- ABCA1 Expression Is Upregulated in an EMT in Breast Cancer Cell Lines via MYC-Mediated De-Repression of Its Proximal Ebox Element.Biomedicines · 2022Article
- RAGE Inhibitors as Alternatives to Dexamethasone for Managing Cerebral Edema Following Brain Tumor Surgery.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2022Article
- Predicting clinical response to everolimus in ER+ breast cancers using machine-learning.Frontiers in molecular biosciences · 2022Article
- A machine learning framework for scRNA-seq UMI threshold optimization and accurate classification of cell types.Frontiers in genetics · 2022Article
- Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer.Nature communications · 2021Article
- Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.Briefings in bioinformatics · 2021Article
- Serial single-cell genomics reveals convergent subclonal evolution of resistance as early-stage breast cancer patients progress on endocrine plus CDK4/6 therapy.Nature cancer · 2021Article
- Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer.Nature communications · 2021Article
- High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types.Annals of oncology : official journal of the European Society for Medical Oncology · 2021Article
- A combinatorial oligogenic basis for the phenotypic plasticity between late-onset dilated and arrhythmogenic cardiomyopathy in a single family.The journal of cardiovascular aging · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab. Contact: jeffrey.t.chang@uth.tmc.edu.
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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.