Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
Published 2023 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
Authors
Keywords
-
Journal
NATURE BIOTECHNOLOGY
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2023-01-10
DOI
10.1038/s41587-022-01612-8
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters
- (2022) Havva Ortabozkoyun et al. NATURE GENETICS
- Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale
- (2022) Jian Zhou NATURE GENETICS
- Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation
- (2022) Sudarshan Pinglay et al. SCIENCE
- Base-resolution models of transcription-factor binding reveal soft motif syntax
- (2021) Žiga Avsec et al. NATURE GENETICS
- The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization
- (2021) Tiaojiang Xiao et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A versatile platform for locus-scale genome rewriting and verification
- (2021) Ran Brosh et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Understanding 3D genome organization by multidisciplinary methods
- (2021) Ivana Jerkovic´ et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes
- (2021) Xiaotao Wang et al. NATURE METHODS
- How subtle changes in 3D structure can create large changes in transcription
- (2021) Jordan Yupeng Xiao et al. eLife
- Effective gene expression prediction from sequence by integrating long-range interactions
- (2021) Žiga Avsec et al. NATURE METHODS
- ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
- (2021) Fayrouz Hammal et al. NUCLEIC ACIDS RESEARCH
- Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
- (2020) Arya Kaul et al. Nature Protocols
- Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
- (2020) Tsung-Han S. Hsieh et al. MOLECULAR CELL
- Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia
- (2020) Andreas Kloetgen et al. NATURE GENETICS
- DeepC: predicting 3D genome folding using megabase-scale transfer learning
- (2020) Ron Schwessinger et al. NATURE METHODS
- Predicting 3D genome folding from DNA sequence with Akita
- (2020) Geoff Fudenberg et al. NATURE METHODS
- Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia
- (2019) Eric Wang et al. CANCER CELL
- Deep learning: new computational modelling techniques for genomics
- (2019) Gökcen Eraslan et al. NATURE REVIEWS GENETICS
- Long-range enhancer–promoter contacts in gene expression control
- (2019) Stefan Schoenfelder et al. NATURE REVIEWS GENETICS
- Principles of genome folding into topologically associating domains
- (2019) Quentin Szabo et al. Science Advances
- Predicting three-dimensional genome organization with chromatin states
- (2019) Yifeng Qi et al. PLoS Computational Biology
- Developmentally regulated Shh expression is robust to TAD perturbations
- (2019) Iain Williamson et al. DEVELOPMENT
- Quantitative prediction of enhancer–promoter interactions
- (2019) Polina S. Belokopytova et al. GENOME RESEARCH
- In silico prediction of high-resolution Hi-C interaction matrices
- (2019) Shilu Zhang et al. Nature Communications
- The chromatin-remodeling factor CHD4 is required for maintenance of childhood acute myeloid leukemia
- (2018) Yaser Heshmati et al. HAEMATOLOGICA
- Polymer physics predicts the effects of structural variants on chromatin architecture
- (2018) Simona Bianco et al. NATURE GENETICS
- Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk
- (2018) Jian Zhou et al. NATURE GENETICS
- Structural variation in the 3D genome
- (2018) Malte Spielmann et al. NATURE REVIEWS GENETICS
- A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus
- (2018) A. Rasim Barutcu et al. Nature Communications
- The chromatin-remodeling factor CHD4 is required for maintenance of childhood acute myeloid leukemia
- (2018) Yaser Heshmati et al. HAEMATOLOGICA
- A primer on deep learning in genomics
- (2018) James Zou et al. NATURE GENETICS
- Organizational principles of 3D genome architecture
- (2018) M. Jordan Rowley et al. NATURE REVIEWS GENETICS
- De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture
- (2017) Michele Di Pierro et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Formation of new chromatin domains determines pathogenicity of genomic duplications
- (2016) Martin Franke et al. NATURE
- Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture
- (2016) Emily M. Darrow et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
- (2016) Anthony D. Schmitt et al. Cell Reports
- LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
- (2015) Nathan C. Sheffield et al. BIOINFORMATICS
- CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
- (2015) Zhonghui Tang et al. CELL
- Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
- (2015) Darío G. Lupiáñez et al. CELL
- Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics
- (2015) C. Kadoch et al. Science Advances
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
- (2014) Suhas S.P. Rao et al. CELL
- The 3D Genome in Transcriptional Regulation and Pluripotency
- (2014) David U. Gorkin et al. Cell Stem Cell
- Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
- (2014) F. Ay et al. GENOME RESEARCH
- Principles of regulatory information conservation between mouse and human
- (2014) Yong Cheng et al. NATURE
- Conservation of trans-acting circuitry during mammalian regulatory evolution
- (2014) Andrew B. Stergachis et al. NATURE
- Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
- (2013) Jennifer E. Phillips-Cremins et al. CELL
- Modification of Enhancer Chromatin: What, How, and Why?
- (2013) Eliezer Calo et al. MOLECULAR CELL
- The accessible chromatin landscape of the human genome
- (2012) Robert E. Thurman et al. NATURE
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Genomic approaches towards finding cis-regulatory modules in animals
- (2012) Ross C. Hardison et al. NATURE REVIEWS GENETICS
- Mediator and cohesin connect gene expression and chromatin architecture
- (2010) Michael H. Kagey et al. NATURE
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started