VISION

ValIdated Systematic IntegratiON of hematopoietic epigenomes

Publications

Guanjue Xiang, Xi He, Belinda M. Giardine, Kathryn J. Isaac, Dylan J. Taylor, Rajiv C. McCoy et al. (2024) Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024. 34: 1089-1105 PMID: 38951027
Snapshot: clustering and visualizing epigenetic history during cell differentiation. Xiang et al. 2023. BMC Bioinformatics. PMID: 36941541
CLIMB: High-dimensional association detection in large scale genomic data. Koch H et al. Nat Commun. 2022 PMID: 36371401
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. Xiang et al. 2021. Bioinformatics. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab148/6157825
Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Luan J. et al. Cell Rep. 2021 PMID: 33626344
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Xiang, Keller et al. 2020. Genome Research. https://genome.cshlp.org/content/30/3/472
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells. Hardison et al. 2020. IUBMB Life. PMID: 31769130
S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data. Xiang et al. 2020. Nucleic Acids Research. PMID: 32086521
Chromatin Structure dynamics during the mitosis-to-G1 phase transition. Zhang et al., Philips-Cremins and Blobel. 2019. Nature. PMID: 31776509
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries. An et al. 2019. https://doi.org/10.1182/bloodadvances.2019032318
Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription. Behera et al. Blobel. 2019 Cell Reports: https://www.sciencedirect.com/science/article/pii/S2211124719303870?via%3Dihub
Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation. Bartman et al., Blobel and Raj. 2019 Molecular Cell: https://www.sciencedirect.com/science/article/pii/S1097276518309468?via%3Dihub
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Wang et al., Yue. 2018 Genome Biology: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1519-9
Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells. Grevet et al. Shi and Blobel. 2018 Science: https://science.sciencemag.org/content/361/6399/285.long
Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. Heuston et al. 2018 Epigenetics and Chromatin: https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-018-0195-z
Evolution of hemoglobin loci and their regulatory elements. Philipsen and Hardison. 2018. Blood Cells, Molecules, and Diseases: https://www.sciencedirect.com/science/article/pii/S1079979617301481?via%3Dihub
Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility. Behera et al. Blobel. 2018 Nature Communications: https://www.nature.com/articles/s41467-018-03082-6
Between form and function: the complexity of genome folding. Oudelaar et al. Higgs. 2017. Human Molecular Genetics: https://www.ncbi.nlm.nih.gov/pubmed/28977451
Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. Zhang and Hardison. 2017. Nucleic Acids Research: https://academic.oup.com/nar/article/45/17/9823/4056234
Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. Huang et al. Blobel. 2017. Genes and Development. http://genesdev.cshlp.org/content/31/16/1704.long
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Yang et al. Li. 2017. Genome Research: https://genome.cshlp.org/content/27/11/1939.long
The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Hsu et al. Blobel. 2017. Molecular Cell: https://www.sciencedirect.com/science/article/pii/S1097276517301648?via%3Dihub
A genome-editing strategy to treat beta-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition. Traxler, Yao et al. Weiss. 2016. Nature Medicine: https://www.nature.com/articles/nm.4170

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