Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data

Relationship between drug targets and drug-signature networks: a network-based genome-wide landscape

(2023) Chae Won Lee et al.   BMC Medical Genomics

PPARα activation partially drives NAFLD development in liver-specific Hnf4a-null mice

(2023) Carlos Ichiro Kasano-Camones et al.   JOURNAL OF BIOCHEMISTRY

Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses

(2022) Zhaonan Zou et al.   BMC BIOINFORMATICS

Chronic lead exposure induces fatty liver disease associated with the variations of gut microbiota

(2022) Heng Wan et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

(2022) Zhaonan Zou et al.   NUCLEIC ACIDS RESEARCH

Connecting omics signatures and revealing biological mechanisms with iLINCS

(2022) Marcin Pilarczyk et al.   Nature Communications

Comparative Toxicogenomics Database (CTD): update 2023

(2022) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Roles of Ambient Temperature and PM2.5 on Childhood Acute Bronchitis and Bronchiolitis from Viral Infection

(2022) Pei-Chun Chen et al.   Viruses-Basel

Acute Impact of Fine Particulate Air Pollution on Cardiac Arrhythmias in a Population‐Based Sample of Adolescents: The Penn State Child Cohort

(2022) Fan He et al.   Journal of the American Heart Association

The Role of Fine Particles (PM 2.5) in the Genesis of Atherosclerosis and Myocardial Damage: Emphasis on Clinical and Epidemiological Data, and Pathophysiological Mechanisms

(2022) Aleksey Michailovich Chaulin et al.   Cardiology Research

Childhood lead exposure is associated with lower cognitive functioning at older ages

(2022) Haena Lee et al.   Science Advances

Phase I Study of Elacestrant (RAD1901), a Novel Selective Estrogen Receptor Degrader, in ER-Positive, HER2-Negative Advanced Breast Cancer

(2021) Aditya Bardia et al.   JOURNAL OF CLINICAL ONCOLOGY

Circadian Mechanisms in Medicine

(2021) Ravi Allada et al.   NEW ENGLAND JOURNAL OF MEDICINE

Miscarriage matters: the epidemiological, physical, psychological, and economic costs of early pregnancy loss

(2021) Siobhan Quenby et al.   LANCET

Respiratory function declines in children with asthma associated with chemical species of fine particulate matter (PM2.5) in Nagasaki, Japan

(2021) Yoonhee Kim et al.   Environmental Health

Evaluation of the effects produced by subacute tributyltin administration on vascular reactivity of male wistar rats

(2021) Ana Beatriz Araújo Mendes et al.   TOXICOLOGY

Relationship between particulate matter (PM2.5) and hospitalizations and mortality of chronic obstruective pulmlonary disease patients: A meta-analysis

(2020) Rui-Xia Zhu et al.   AMERICAN JOURNAL OF THE MEDICAL SCIENCES

PM2.5 impairs macrophage functions to exacerbate pneumococcus-induced pulmonary pathogenesis

(2020) Yu-Wen Chen et al.   Particle and Fibre Toxicology

Ambient PM2.5 and its chemical constituents on lifetime-ever pneumonia in Chinese children: A multi-center study

(2020) Wenming Shi et al.   ENVIRONMENT INTERNATIONAL

Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology

(2020) Judith A Blake et al.   NUCLEIC ACIDS RESEARCH

Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery

(2019) Nicolas Bosc et al.   Journal of Cheminformatics

Short-term effects of multiple outdoor environmental factors on risk of asthma exacerbations: age-stratified time-series analysis

(2019) Seung Won Lee et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Tributyltin exposure disturbs hepatic glucose metabolism in male mice

(2019) Jing Xu et al.   TOXICOLOGY

Identification and dynamic quantification of regulatory elements using total RNA

(2019) Sascha H. Duttke et al.   GENOME RESEARCH

The DisGeNET knowledge platform for disease genomics: 2019 update

(2019) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

Phase I/II intra-patient dose escalation study of vorinostat in children with relapsed solid tumor, lymphoma, or leukemia

(2019) Cornelis M. van Tilburg et al.   Clinical Epigenetics

Methylmercury causes epigenetic suppression of the tyrosine hydroxylase gene in an in vitro neuronal differentiation model

(2018) Suzuna Go et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Global association between ambient air pollution and blood pressure: A systematic review and meta-analysis

(2018) Bo-Yi Yang et al.   ENVIRONMENTAL POLLUTION

The NIEHS TaRGET II Consortium and environmental epigenomics

(2018) Ting Wang et al.   NATURE BIOTECHNOLOGY

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

(2018) Shinya Oki et al.   EMBO REPORTS

Global, regional, and national disability-adjusted life-years (DALYs) for 359 diseases and injuries and healthy life expectancy (HALE) for 195 countries and territories, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017

(2018) Hmwe Hmwe Kyu et al.   LANCET

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

DBTSS/DBKERO for integrated analysis of transcriptional regulation

(2017) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice

(2017) Raquel Chamorro-Garcia et al.   Nature Communications

Relationship between exposure to PM2.5 and lung cancer incidence and mortality: A meta-analysis

(2017) Feifei Huang et al.   Oncotarget

Cancer Mortality Risks from Long-term Exposure to Ambient Fine Particle

(2016) C. M. Wong et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Adult air pollution exposure and risk of infertility in the Nurses' Health Study II

(2016) S. Mahalingaiah et al.   HUMAN REPRODUCTION

Association between air pollution and coronary artery calcification within six metropolitan areas in the USA (the Multi-Ethnic Study of Atherosclerosis and Air Pollution): a longitudinal cohort study

(2016) Joel D Kaufman et al.   LANCET

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Open TG-GATEs: a large-scale toxicogenomics database

(2014) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

QSAR and QSPR Model Interpretation Using Partial Least Squares (PLS) Analysis

(2012) David T. Stanton   Current Computer-Aided Drug Design

The Transcription Factor T-bet Is Induced by Multiple Pathways and Prevents an Endogenous Th2 Cell Program during Th1 Cell Responses

(2012) Jinfang Zhu et al.   IMMUNITY

Molecular and cellular effects of oncogene cooperation in a genetically accurate AML mouse model

(2012) K Reckzeh et al.   LEUKEMIA

Congenital anomalies among live births in a polluted area. A ten-year retrospective study

(2012) Emilio Antonio Luca Gianicolo et al.   BMC Pregnancy and Childbirth

Inhibition of PP2A and the consequent activation of JNK/c-Jun are involved in tributyltin-induced apoptosis in human amnionic cells

(2011) Yali Zhang et al.   ENVIRONMENTAL TOXICOLOGY

The environmental obesogen tributyltin chloride acts via peroxisome proliferator activated receptor gamma to induce adipogenesis in murine 3T3-L1 preadipocytes

(2011) Xia Li et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

An Essential Developmental Checkpoint for Production of the T Cell Lineage

(2010) T. Ikawa et al.   SCIENCE

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

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

Docking and chemoinformatic screens for new ligands and targets

(2009) Peter Kolb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Tributyltin causes obesity and hepatic steatosis in male mice

(2009) Zhenghong Zuo et al.   ENVIRONMENTAL TOXICOLOGY

Reduction in Peripheral Lymphocytes and Thymus Atrophy Induced by Organotin Compounds In Vivo

(2009) Shunji UENO et al.   JOURNAL OF VETERINARY MEDICAL SCIENCE

Protein-ligand interaction prediction: an improved chemogenomics approach

(2008) Laurent Jacob et al.   BIOINFORMATICS

Global DNA hypomethylation, rather than reactive oxygen species (ROS), a potential facilitator of cadmium-stimulated K562 cell proliferation

(2008) Dejun Huang et al.   TOXICOLOGY LETTERS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY