Topology of mammalian developmental enhancers and their regulatory landscapes
How a complex animal can arise from a fertilized egg is one of the oldest and most
fascinating questions of biology, the answer to which is encoded in the genome. Body shape …
fascinating questions of biology, the answer to which is encoded in the genome. Body shape …
Decoding enhancer complexity with machine learning and high-throughput discovery
GD Smith, WH Ching, P Cornejo-Páramo, ES Wong - Genome biology, 2023 - Springer
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their
flexible organization and functional redundancies make deciphering their sequence-function …
flexible organization and functional redundancies make deciphering their sequence-function …
Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
Oligomers of length k, or k-mers, are convenient and widely used features for modeling the
properties and functions of DNA and protein sequences. However, k-mers suffer from the …
properties and functions of DNA and protein sequences. However, k-mers suffer from the …
A method to predict the impact of regulatory variants from DNA sequence
Most variants implicated in common human disease by genome-wide association studies
(GWAS) lie in noncoding sequence intervals. Despite the suggestion that regulatory element …
(GWAS) lie in noncoding sequence intervals. Despite the suggestion that regulatory element …
Candidate silencer elements for the human and mouse genomes
The study of gene regulation is dominated by a focus on the control of gene activation or
increase in the level of expression. Just as critical is the process of gene repression or …
increase in the level of expression. Just as critical is the process of gene repression or …
High-throughput functional testing of ENCODE segmentation predictions
JC Kwasnieski, C Fiore, HG Chaudhari… - Genome …, 2014 - genome.cshlp.org
The histone modification state of genomic regions is hypothesized to reflect the regulatory
activity of the underlying genomic DNA. Based on this hypothesis, the ENCODE Project …
activity of the underlying genomic DNA. Based on this hypothesis, the ENCODE Project …
Analysis of genomic sequence motifs for deciphering transcription factor binding and transcriptional regulation in eukaryotic cells
V Boeva - Frontiers in genetics, 2016 - frontiersin.org
Eukaryotic genomes contain a variety of structured patterns: repetitive elements, binding
sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured …
sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured …
A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway
C Praetorius, C Grill, SN Stacey, AM Metcalf, DU Gorkin… - Cell, 2013 - cell.com
Sequence polymorphisms linked to human diseases and phenotypes in genome-wide
association studies often affect noncoding regions. A SNP within an intron of the gene …
association studies often affect noncoding regions. A SNP within an intron of the gene …
gkmSVM: an R package for gapped-kmer SVM
We present a new R package for training gapped-kmer SVM classifiers for DNA and protein
sequences. We describe an improved algorithm for kernel matrix calculation that speeds run …
sequences. We describe an improved algorithm for kernel matrix calculation that speeds run …
Genetics of skin color variation in Europeans: genome-wide association studies with functional follow-up
Abstract In the International Visible Trait Genetics (VisiGen) Consortium, we investigated the
genetics of human skin color by combining a series of genome-wide association studies …
genetics of human skin color by combining a series of genome-wide association studies …