Functional interrogation of twenty type 2 diabetes-associated genes using isogenic human embryonic stem cell-derived β-like cells

The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits

(2023) Maria C. Costanzo et al.   Cell Metabolism

A multi-organoid platform identifies CIART as a key factor for SARS-CoV-2 infection

(2023) Xuming Tang et al.   NATURE CELL BIOLOGY

An effector index to predict target genes at GWAS loci

(2022) Vincenzo Forgetta et al.   HUMAN GENETICS

HNF1A Mutations and Beta Cell Dysfunction in Diabetes

(2022) Yasutaka Miyachi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation

(2022) Anubha Mahajan et al.   NATURE GENETICS

Molecular Functions of Ceruloplasmin in Metabolic Disease Pathology

(2022) Zhidong Liu et al.   Diabetes Metabolic Syndrome and Obesity-Targets and Therapy

ZnT8 loss-of-function accelerates functional maturation of hESC-derived β cells and resists metabolic stress in diabetes

(2022) Qing Ma et al.   Nature Communications

APOE4 drives inflammation in human astrocytes via TAGLN3 repression and NF-κB activation

(2022) Laurie Arnaud et al.   Cell Reports

3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk

(2022) Chun Su et al.   Cell Metabolism

DHRS2 inhibits cell growth and metastasis in ovarian cancer by downregulation of CHKα to disrupt choline metabolism

(2022) Zhenzhen Li et al.   Cell Death & Disease

Oxidative stress-mediated beta cell death and dysfunction as a target for diabetes management

(2022) Svetlana Dinić et al.   Frontiers in Endocrinology

The UCSC Genome Browser database: 2023 update

(2022) Luis R Nassar et al.   NUCLEIC ACIDS RESEARCH

SUR1-mutant iPS cell-derived islets recapitulate the pathophysiology of congenital hyperinsulinism

(2021) Väinö Lithovius et al.   DIABETOLOGIA

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

SARS-CoV-2 Infection Induces Beta Cell Transdifferentiation

(2021) Xuming Tang et al.   Cell Metabolism

Groucho co-repressor proteins regulate β cell development and proliferation by repressing Foxa1 in the developing mouse pancreas

(2021) Alexandra Theis et al.   DEVELOPMENT

Genetic effects on liver chromatin accessibility identify disease regulatory variants

(2021) Kevin W. Currin et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Targeting β-cell dedifferentiation and transdifferentiation: opportunities and challenges

(2021) Wenrui Wang et al.   Endocrine Connections

Gene-level analysis of rare variants in 379,066 whole exome sequences identifies an association of GIGYF1 loss of function with type 2 diabetes

(2021) Aimee M. Deaton et al.   Scientific Reports

TIGER: The gene expression regulatory variation landscape of human pancreatic islets

(2021) Lorena Alonso et al.   Cell Reports

From Genetic Association to Molecular Mechanisms for Islet-cell Dysfunction in Type 2 Diabetes

(2020) Katia K. Mattis et al.   JOURNAL OF MOLECULAR BIOLOGY

Insights into pancreatic islet cell dysfunction from type 2 diabetes mellitus genetics

(2020) Nicole A. J. Krentz et al.   Nature Reviews Endocrinology

High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation

(2020) Mateusz Legut et al.   Cell Reports

SIX2 Regulates Human β Cell Differentiation from Stem Cells and Functional Maturation In Vitro

(2020) Leonardo Velazco-Cruz et al.   Cell Reports

Glucose Response by Stem Cell-Derived β Cells In Vitro Is Inhibited by a Bottleneck in Glycolysis

(2020) Jeffrey C. Davis et al.   Cell Reports

Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis

(2020) Marijana Vujkovic et al.   NATURE GENETICS

Metabolic and functional specialisations of the pancreatic beta cell: gene disallowance, mitochondrial metabolism and intercellular connectivity

(2020) Guy A. Rutter et al.   DIABETOLOGIA

Pathophysiology of Type 2 Diabetes Mellitus

(2020) Unai Galicia-Garcia et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

(2020) Ana Viñuela et al.   Nature Communications

Genetic mapping of etiologic brain cell types for obesity

(2020) Pascal N Timshel et al.   eLife

Persistent or Transient Human β Cell Dysfunction Induced by Metabolic Stress: Specific Signatures and Shared Gene Expression with Type 2 Diabetes

(2020) Lorella Marselli et al.   Cell Reports

Point mutations in the PDX1 transactivation domain impair human β-cell development and function

(2019) Xianming Wang et al.   Molecular Metabolism

Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls

(2019) Jason Flannick et al.   NATURE

WITHDRAWN: Global and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045: results from the International Diabetes Federation Diabetes Atlas, 9th edition

(2019) Pouya Saeedi et al.   DIABETES RESEARCH AND CLINICAL PRACTICE

CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing

(2019) Samuele Cancellieri et al.   BIOINFORMATICS

Loss of ZnT8 function protects against diabetes by enhanced insulin secretion

(2019) Om Prakash Dwivedi et al.   NATURE GENETICS

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

(2019) Vivek Rai et al.   Molecular Metabolism

Interactions between genetic variation and cellular environment in skeletal muscle gene expression

(2018) D. Leland Taylor et al.   PLoS One

Discovery of a drug candidate for GLIS3-associated diabetes

(2018) Sadaf Amin et al.   Nature Communications

The EndoC-βH1 cell line is a valid model of human beta cells and applicable for screenings to identify novel drug target candidates

(2018) Violeta Georgieva Tsonkova et al.   Molecular Metabolism

Fatty Acid-Induced Lipotoxicity in Pancreatic Beta-Cells During Development of Type 2 Diabetes

(2018) Yoon S. Oh et al.   Frontiers in Endocrinology

Type 2 diabetes genetic loci informed by multi-trait associations point to disease mechanisms and subtypes: A soft clustering analysis

(2018) Miriam S. Udler et al.   PLOS MEDICINE

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

Serum copper, zinc, and iron levels, and markers of carbohydrate metabolism in postmenopausal women with prediabetes and type 2 diabetes mellitus

(2017) Margarita G. Skalnaya et al.   JOURNAL OF TRACE ELEMENTS IN MEDICINE AND BIOLOGY

Allele-specific expression reveals interactions between genetic variation and environment

(2017) David A Knowles et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

DHRS2 inhibits cell growth and motility in esophageal squamous cell carcinoma

(2017) Y Zhou et al.   ONCOGENE

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

(2017) Arushi Varshney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using hESCs to Probe the Interaction of the Diabetes-Associated Genes CDKAL1 and MT1E

(2017) Min Guo et al.   Cell Reports

GATA6 Plays an Important Role in the Induction of Human Definitive Endoderm, Development of the Pancreas, and Functionality of Pancreatic β Cells

(2017) Amita Tiyaboonchai et al.   Stem Cell Reports

Analysis of Purified Pancreatic Islet Beta and Alpha Cell Transcriptomes Reveals 11β-Hydroxysteroid Dehydrogenase (Hsd11b1) as a Novel Disallowed Gene

(2017) Timothy J. Pullen et al.   Frontiers in Genetics

An Isogenic Human ESC Platform for Functional Evaluation of Genome-wide-Association-Study-Identified Diabetes Genes and Drug Discovery

(2016) Hui Zeng et al.   Cell Stem Cell

High-throughput allele-specific expression across 250 environmental conditions

(2016) Gregory A. Moyerbrailean et al.   GENOME RESEARCH

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

(2015) Stephen W. Hartley et al.   BMC BIOINFORMATICS

High-Throughput Luminescent Reporter of Insulin Secretion for Discovering Regulators of Pancreatic Beta-Cell Function

(2015) Sean M. Burns et al.   Cell Metabolism

The Basic Helix-Loop-Helix Transcription Factor NEUROG3 Is Required for Development of the Human Endocrine Pancreas

(2015) Patrick S. McGrath et al.   DIABETES

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

The Role of ARX in Human Pancreatic Endocrine Specification

(2015) Blair K. Gage et al.   PLoS One

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

ADCY5 Couples Glucose to Insulin Secretion in Human Islets

(2014) D. J. Hodson et al.   DIABETES

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells

(2014) Alireza Rezania et al.   NATURE BIOTECHNOLOGY

Zinc transporter 8 (ZnT8) and β cell function

(2014) Howard W. Davidson et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Overexpression of Monocarboxylate Transporter-1 (Slc16a1) in Mouse Pancreatic  -Cells Leads to Relative Hyperinsulinism During Exercise

(2012) T. J. Pullen et al.   DIABETES

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

(2012) T. E. Reddy et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells

(2011) A. DeLaForest et al.   DEVELOPMENT

INS GFP/w human embryonic stem cells facilitate isolation of in vitro derived insulin-producing cells

(2011) S. J. Micallef et al.   DIABETOLOGIA

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Epistasis of Transcriptomes Reveals Synergism between Transcriptional Activators Hnf1α and Hnf4α

(2010) Sylvia F. Boj et al.   PLoS Genetics

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

An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

(2009) Huanting Liu et al.   BMC BIOTECHNOLOGY

Update of mutations in the genes encoding the pancreatic beta-cell KATPchannel subunits Kir6.2 (KCNJ11) and sulfonylurea receptor 1 (ABCC8) in diabetes mellitus and hyperinsulinism

(2008) Sarah E. Flanagan et al.   HUMAN MUTATION

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY