EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq

DNA Methylation of Imprinted Genes KCNQ1, KCNQ1OT1, and PHLDA2 in Peripheral Blood Is Associated with the Risk of Breast Cancer

(2022) Jinming Fu et al.   Cancers

Large-Scale Analysis of X Inactivation Variations between Primed and Naïve Human Embryonic Stem Cells

(2022) Roni Sarel-Gallily et al.   Cells

Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events

(2022) Jonathan M. Werner et al.   DEVELOPMENTAL CELL

Aberrations of Genomic Imprinting in Glioblastoma Formation

(2021) Anna Lozano-Ureña et al.   Frontiers in Oncology

Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis

(2021) Elyad Lezmi et al.   Nature Protocols

Two sides of the Dlk1-Dio3 story in imprinting

(2021) Yee Hoon Foong et al.   DEVELOPMENTAL CELL

Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells

(2021) Shihori Yokobayashi et al.   Cell Reports

Epigenetic imprinting alterations as effective diagnostic biomarkers for early-stage lung cancer and small pulmonary nodules

(2021) Jian Zhou et al.   Clinical Epigenetics

Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling

(2021) Gal Keshet et al.   Stem Cell Reports

Abnormal X chromosome inactivation and tumor development

(2020) Dan Wang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

X-linked diseases: susceptible females

(2020) Barbara R. Migeon   GENETICS IN MEDICINE

Transient inhibition of mTOR in human pluripotent stem cells enables robust formation of mouse-human chimeric embryos

(2020) Zhixing Hu et al.   Science Advances

Current progress in stem cell therapy for type 1 diabetes mellitus

(2020) Shuai Chen et al.   Stem Cell Research & Therapy

Acquired genetic changes in human pluripotent stem cells: origins and consequences

(2020) Jason Halliwell et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cancer-Related Mutations Identified in Primed Human Pluripotent Stem Cells

(2020) Yishai Avior et al.   Cell Stem Cell

Electrophysiological abnormalities in induced pluripotent stem cell-derived cardiomyocytes generated from Duchenne muscular dystrophy patients

(2019) Binyamin Eisen et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Genomic Imprinting and Physiological Processes in Mammals

(2019) Valter Tucci et al.   CELL

Epigenetic aberrations in human pluripotent stem cells

(2019) Shiran Bar et al.   EMBO JOURNAL

Global Characterization of X Chromosome Inactivation in Human Pluripotent Stem Cells

(2019) Shiran Bar et al.   Cell Reports

Defining Human Pluripotency

(2019) Atilgan Yilmaz et al.   Cell Stem Cell

Self-organization of stem cells into embryos: A window on early mammalian development

(2019) Marta N. Shahbazi et al.   SCIENCE

The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments

(2019) Jean-Simon Brouard et al.   Journal of Animal Science and Biotechnology

Distinct Imprinting Signatures and Biased Differentiation of Human Androgenetic and Parthenogenetic Embryonic Stem Cells

(2019) Ido Sagi et al.   Cell Stem Cell

Phase 1 clinical study of an embryonic stem cell–derived retinal pigment epithelium patch in age-related macular degeneration

(2018) Lyndon da Cruz et al.   NATURE BIOTECHNOLOGY

Pluripotent stem cell-based therapy for Parkinson’s disease: Current status and future prospects

(2018) Kai-C. Sonntag et al.   PROGRESS IN NEUROBIOLOGY

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

(2018) Roelof J. C. Kluin et al.   BMC BIOINFORMATICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Landscape of X chromosome inactivation across human tissues

(2017) Taru Tukiainen et al.   NATURE

Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells

(2017) Shiran Bar et al.   Cell Reports

Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation

(2017) Sanjeet Patel et al.   Cell Reports

Molecular Criteria for Defining the Naive Human Pluripotent State

(2016) Thorold W. Theunissen et al.   Cell Stem Cell

Stem cells: Aspiring to naivety

(2016) Ido Sagi et al.   NATURE

Dynamic stem cell states: naive to primed pluripotency in rodents and humans

(2016) Leehee Weinberger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pluripotent stem cells in disease modelling and drug discovery

(2016) Yishai Avior et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pluripotent stem cells progressing to the clinic

(2016) Alan Trounson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Profiling genome-wide DNA methylation

(2016) Wai-Shin Yong et al.   Epigenetics & Chromatin

New developments in Silver–Russell syndrome and implications for clinical practice

(2016) Miho Ishida   Epigenomics

Hallmarks of pluripotency

(2015) Alejandro De Los Angeles et al.   NATURE

Angelman Syndrome

(2015) Seth S. Margolis et al.   Neurotherapeutics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles

(2013) Uri Ben-David et al.   Nature Protocols

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Erosion of Dosage Compensation Impacts Human iPSC Disease Modeling

(2012) Shila Mekhoubad et al.   Cell Stem Cell

Prader-Willi syndrome

(2012) Suzanne B. Cassidy et al.   GENETICS IN MEDICINE

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Meta-analysis of the heterogeneity of X chromosome inactivation in human pluripotent stem cells

(2010) Tal Bruck et al.   Stem Cell Research

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

X Chromosome Inactivation: When Dosage Counts

(2009) Elphège P. Nora et al.   CELL

Lesch-Nyhan disease: from mechanism to model and back again

(2009) H. A. Jinnah   Disease Models & Mechanisms

Beckwith–Wiedemann syndrome

(2009) Rosanna Weksberg et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH

X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells

(2008) S. S. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations

(2008) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA