4.8 Article

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Cell Biology

Hi-C as a molecular rangefinder to examine genomic rearrangements

Kyukwang Kim et al.

Summary: Hi-C technology plays a crucial role in genome analysis, particularly in the detection of large-scale structural variations. Recent studies have also explored the potential of Hi-C at the single-cell level for investigating genomic rearrangements.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2022)

Article Biotechnology & Applied Microbiology

Accurate and efficient detection of gene fusions from RNA sequencing data

Sebastian Uhrig et al.

GENOME RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

Ruli Gao et al.

Summary: CopyKAT is a method for estimating genomic copy number profiles from high-throughput single-cell RNA sequencing data, which can accurately distinguish cancer cells from normal cell types in tumors and resolve clonal subpopulations within tumors.

NATURE BIOTECHNOLOGY (2021)

Review Biotechnology & Applied Microbiology

Nanopore sequencing technology, bioinformatics and applications

Yunhao Wang et al.

Summary: Advancements in nanopore technologies for sequencing long DNA and RNA molecules have greatly improved accuracy, read length, and throughput. The field of nanopore sequencing continues to offer opportunities for enhancing data quality and analytical approaches through the development of new technologies tailored to specific applications.

NATURE BIOTECHNOLOGY (2021)

Article Biochemical Research Methods

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

Xiaotao Wang et al.

Summary: This work presents NeoLoopFinder, a computational method for identifying chromatin interactions of structurally rearranged genomes. It was applied in 50 cancer datasets and identified genes associated with enhancer-hijacking events. Experimental validation showed that NeoLoopFinder can potentially reveal therapeutic targets by identifying critical oncogenic regulatory elements.

NATURE METHODS (2021)

Article Biochemical Research Methods

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

Nezar Abdennur et al.

BIOINFORMATICS (2020)

Article Genetics & Heredity

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Kadir C. Akdemir et al.

NATURE GENETICS (2020)

Review Genetics & Heredity

Long-read human genome sequencing and its applications

Glennis A. Logsdon et al.

NATURE REVIEWS GENETICS (2020)

Article Multidisciplinary Sciences

A map of cis-regulatory elements and 3D genome structures in zebrafish

Hongbo Yang et al.

NATURE (2020)

Review Biotechnology & Applied Microbiology

Methods for copy number aberration detection from single-cell DNA-sequencing data

Xian F. Mallory et al.

GENOME BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Pleiotropic tumor suppressor functions of WWOX antagonize metastasis

Saleh Khawaled et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2020)

Article Biotechnology & Applied Microbiology

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

Su Wang et al.

GENOME BIOLOGY (2020)

Article Multidisciplinary Sciences

Next-generation characterization of the Cancer Cell Line Encyclopedia

Mahmoud Ghandi et al.

NATURE (2019)

Review Biochemistry & Molecular Biology

Mechanisms of Genomic Instability in Breast Cancer

Pascal H. G. Duijf et al.

TRENDS IN MOLECULAR MEDICINE (2019)

Article Biochemical Research Methods

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

Dong-Sung Lee et al.

NATURE METHODS (2019)

Article Biochemical Research Methods

SVIM: structural variant identification using mapped long reads

David Heller et al.

BIOINFORMATICS (2019)

Article Biotechnology & Applied Microbiology

Evaluating nanopore sequencing data processing pipelines for structural variation identification

Anbo Zhou et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Review Oncology

The biology and role of CD44 in cancer progression: therapeutic implications

Chen Chen et al.

JOURNAL OF HEMATOLOGY & ONCOLOGY (2018)

Article Biochemical Research Methods

Picky comprehensively detects high-resolution structural variants in nanopore long reads

Liang Gong et al.

NATURE METHODS (2018)

Article Biochemical Research Methods

Accurate detection of complex structural variations using single-molecule sequencing

Fritz J. Sedlazeck et al.

NATURE METHODS (2018)

Article Genetics & Heredity

Integrative detection and analysis of structural variation in cancer genomes

Jesse R. Dixon et al.

NATURE GENETICS (2018)

Article Genetics & Heredity

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

Bjort K. Kragesteen et al.

NATURE GENETICS (2018)

Article Multidisciplinary Sciences

Three-dimensional genome structures of single diploid human cells

Longzhi Tan et al.

SCIENCE (2018)

Review Biochemistry & Molecular Biology

Targeting oncogenic Myc as a strategy for cancer treatment

Hui Chen et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2018)

Article Biochemical Research Methods

Identification of copy number variations and translocations in cancer cells from Hi-C data

Abhijit Chakraborty et al.

BIOINFORMATICS (2018)

Article Genetics & Heredity

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

Joachim Weischenfeldt et al.

NATURE GENETICS (2017)

Article Biochemical Research Methods

Massively multiplex single-cell Hi-C

Vijay Ramani et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

Genome Organization Drives Chromosome Fragility

Andres Canela et al.

Article Multidisciplinary Sciences

Formation of new chromatin domains determines pathogenicity of genomic duplications

Martin Franke et al.

NATURE (2016)

Article Multidisciplinary Sciences

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

Serena Nik-Zainal et al.

NATURE (2016)

Article Biochemical Research Methods

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

Maxwell R. Mumbach et al.

NATURE METHODS (2016)

Article Biochemistry & Molecular Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Genetics & Heredity

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

Borbala Mifsud et al.

NATURE GENETICS (2015)

Article Biochemistry & Molecular Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S. P. Rao et al.

Article Biochemistry & Molecular Biology

Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

Patrick Essletzbichler et al.

GENOME RESEARCH (2014)

Review Medical Laboratory Technology

Cancer Cytogenetics: Methodology Revisited

Thomas S. K. Wan

ANNALS OF LABORATORY MEDICINE (2014)

Article Biotechnology & Applied Microbiology

LUMPY: a probabilistic framework for structural variant discovery

Ryan M. Layer et al.

GENOME BIOLOGY (2014)

Review Oncology

Chromosomal rearrangements in cancer Detection and potential causal mechanisms

Paul Hasty et al.

MOLECULAR & CELLULAR ONCOLOGY (2014)

Article Biochemical Research Methods

The UCSC genome browser and associated tools

Robert M. Kuhn et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Genetics & Heredity

Pan-cancer patterns of somatic copy number alteration

Travis I. Zack et al.

NATURE GENETICS (2013)

Article Biochemical Research Methods

DELLY: structural variant discovery by integrated paired-end and split-read analysis

Tobias Rausch et al.

BIOINFORMATICS (2012)

Article Multidisciplinary Sciences

The landscape of somatic copy-number alteration across human cancers

Rameen Beroukhim et al.

NATURE (2010)

Article Genetics & Heredity

Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET

Yoshiyuki Shibata et al.

GENOME MEDICINE (2010)

Review Biochemistry & Molecular Biology

Cancer genome sequencing: a review

Elaine R. Mardis et al.

HUMAN MOLECULAR GENETICS (2009)

Article Multidisciplinary Sciences

An oestrogen-receptor-α-bound human chromatin interactome

Melissa J. Fullwood et al.

NATURE (2009)

Article Multidisciplinary Sciences

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Erez Lieberman-Aiden et al.

SCIENCE (2009)

Review Oncology

The impact of translocations and gene fusions on cancer causation

Felix Mitelman et al.

NATURE REVIEWS CANCER (2007)

Article Biochemistry & Molecular Biology

Association of p53 and MSH2 with recombinative repair complexes during S phase

D Zink et al.

ONCOGENE (2002)