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Author Details

Galip G??rkan Yard??mc??
University of Washington
2012
20
16
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36945371Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types.bioRxiv2023
37918402Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility.Cell Rep Methods2023
35788238GoPeaks: histone modification peak calling for CUT&Tag.Genome Biol2022
34226710High-content single-cell combinatorial indexing.Nat Biotechnol2021
32946435Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.PLoS Comput Biol2020
30890172Measuring the reproducibility and quality of Hi-C data.Genome Biol2019
30022617Computational methods for analyzing and modeling genome structure and organization.Wiley Interdiscip Rev Syst Biol Med2019
30948719Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.Nat Commun2019
29554289GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs.Bioinformatics2018
30202056Integrative detection and analysis of structural variation in cancer genomes.Nat Genet2018
29950005Unsupervised embedding of single-cell Hi-C data.Bioinformatics2018
28855260HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.Genome Res2017
28159004Software tools for visualizing Hi-C data.Genome Biol2017
28369339HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.Bioinformatics2017
26494755Transcriptional control of tissue formation throughout root development.Science2015
26567152Predictive model of 3D domain formation via CTCF-mediated extrusion.Proc Natl Acad Sci U S A2015
25294828Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.Nucleic Acids Res2014
23576570Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases.Mol Biol Evol2013
22955983Predicting cell-type-specific gene expression from regions of open chromatin.Genome Res2012
23034120Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.Genome Biol2012
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Collaborators

William Stafford Noble
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Humboldt University
Co-authored papers 4
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Altius Institute for Biomedical Sciences
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Vikram Agarwal
University of Washington
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David M Gilbert
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Anirudh Natarajan
University of California at Berkeley
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Yoichiro Shibata
Center for Genomic and Computational Biology, Duke University.
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Julia E Maxson
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Barry S Taylor
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Morgan Diegel
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Release 1.2