ArticleGenome biology2014
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers, 2 of them syntheses that pooled it.
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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
217 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies.Nature communications · 2022Pooled it
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- NCBoost v2: a classifier for non-coding single-nucleotide variants in Mendelian diseases.Bioinformatics (Oxford, England) · 2026Article
- Article
- JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models.Nucleic acids research · 2026Article
- Functional characterization of a multi-cancer risk locus on chromosome band 2q33.1 nearbioRxiv : the preprint server for biology · 2026Article
- A bioinformatics pipeline for identifying clinically relevant immune and adhesion biomarkers in thyroid risk stratification.Frontiers in molecular biosciences · 2026Article
- Evolving computational paradigms for noncoding variant pathogenicity prediction.Frontiers in molecular biosciences · 2026Review
- DRP-PSM: Multi-Level Feature Integration Reveals Hierarchical Contributions to Pathogenic Synonymous Mutation Prediction.ACS omega · 2025Article
- Impact of 5' Near Gene Variants of Mannose Binding Lectin (MBL2) on Breast Cancer Risk.Biochemical genetics · 2025Article
- Disruption of TAD hierarchy promotes LTR co-option in cancer.Nature genetics · 2025Article
- Enhancer RNA-mediated transcriptional regulatory programs reveal the malignant progression of glioma.Science advances · 2025Article
- AI-powered precision medicine: utilizing genetic risk factor optimization to revolutionize healthcare.NAR genomics and bioinformatics · 2025Review
- The Germline and Somatic Origins of Prostate Cancer Heterogeneity.Cancer discovery · 2025Article
- A 3D Genome Atlas of Genetic Variants and Their Pathological Effects in Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Practical microenvironment classification in diffuse large B cell lymphoma using digital pathology.Cell reports. Medicine · 2025Article
- The genetic landscape of early-onset Alzheimer's disease in China.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Ensemble learning-based predictor for driver synonymous mutation with sequence representation.PLoS computational biology · 2025Article
- Quantifying the regulatory potential of genetic variants via a hybrid sequence-oriented model with SVEN.Nature communications · 2024Article
157 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Identification of noncoding drivers from thousands of somatic alterations in a typical tumor is a difficult and unsolved problem. We report a computational framework, FunSeq2, to annotate and prioritize these mutations. The framework combines an adjustable data context integrating large-scale genomics and cancer resources with a streamlined variant-prioritization pipeline. The pipeline has a weighted scoring system combining: inter- and intra-species conservation;loss- and gain-of-function events for transcription-factor binding; enhancer-gene linkages and network centrality; and per-element recurrence across samples. We further highlight putative drivers with information specific to a particular sample, such as differential expression. FunSeq2 is available from funseq2.gersteinlab.org.
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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.