Systematic identification of safe harbor regions in the CHO genome through a comprehensive epigenome analysis

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Chromosome‐scale Scaffolds for the Chinese Hamster Reference Genome Assembly to Facilitate the Study of the CHO Epigenome

(2020) William Hilliard et al.   BIOTECHNOLOGY AND BIOENGINEERING

multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments

(2019) John C Stansfield et al.   BIOINFORMATICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

A reference genome of the Chinese hamster based on a hybrid assembly strategy

(2018) Oliver Rupp et al.   BIOTECHNOLOGY AND BIOENGINEERING

Changes in Chromosome Counts and Patterns in CHO Cell Lines upon Generation of Recombinant Cell Lines and Subcloning

(2018) Sabine Vcelar et al.   Biotechnology Journal

A multi-landing pad DNA integration platform for mammalian cell engineering

(2018) Leonid Gaidukov et al.   NUCLEIC ACIDS RESEARCH

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

Comprehensive characterization of glutamine synthetase-mediated selection for the establishment of recombinant CHO cells producing monoclonal antibodies

(2018) Soo Min Noh et al.   Scientific Reports

Changes in Chromosome Counts and Patterns in CHO Cell Lines upon Generation of Recombinant Cell Lines and Subcloning

(2018) Sabine Vcelar et al.   Biotechnology Journal

Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture

(2018) Inmaculada Hernandez et al.   BIOTECHNOLOGY AND BIOENGINEERING

Biopharmaceutical benchmarks 2018

(2018) Gary Walsh   NATURE BIOTECHNOLOGY

Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing

(2018) Jae Seong Lee et al.   ACS Synthetic Biology

Site-specific integration ushers in a new era of precise CHO cell line engineering

(2018) Nathaniel K Hamaker et al.   Current Opinion in Chemical Engineering

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

DNA methylation in CHO cells

(2017) Anna Wippermann et al.   JOURNAL OF BIOTECHNOLOGY

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

(2017) Houda Belaghzal et al.   METHODS

Cloning of CHO Cells, Productivity and Genetic Stability—A Discussion

(2017) Florian Wurm et al.   Processes

Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time

(2016) Julia Feichtinger et al.   BIOTECHNOLOGY AND BIOENGINEERING

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

(2016) Phillippa C. Taberlay et al.   GENOME RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Recombinase-mediated cassette exchange (RMCE) for monoclonal antibody expression in the commercially relevant CHOK1SV cell line

(2015) Lin Zhang et al.   BIOTECHNOLOGY PROGRESS

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

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

Fast identification of reliable hosts for targeted cell line development from a limited-genome screening using combined φC31 integrase and CRE-Lox technologies

(2013) Yongping Crawford et al.   BIOTECHNOLOGY PROGRESS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

CHO Quasispecies—Implications for Manufacturing Processes

(2013) Florian Wurm   Processes

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

Determination of Chinese hamster ovary cell line stability and recombinant antibody expression during long-term culture

(2012) Laura A Bailey et al.   BIOTECHNOLOGY AND BIOENGINEERING

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Genomics in mammalian cell culture bioprocessing

(2011) Diane M. Wuest et al.   BIOTECHNOLOGY ADVANCES

A mechanistic understanding of production instability in CHO cell lines expressing recombinant monoclonal antibodies

(2011) Minsoo Kim et al.   BIOTECHNOLOGY AND BIOENGINEERING

Promoter methylation and transgene copy numbers predict unstable protein production in recombinant chinese hamster ovary cell lines

(2011) Andrea Osterlehner et al.   BIOTECHNOLOGY AND BIOENGINEERING

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Generation of stable cell lines by site-specific integration of transgenes into engineered Chinese hamster ovary strains using an FLP-FRT system

(2010) Hong Zhou et al.   JOURNAL OF BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) E. Lieberman-Aiden et al.   SCIENCE