Lee SW, Yon DK, James CC, Lee S, Koh HY, Sheen YH, et al. Short-term effects of multiple outdoor environmental factors on risk of asthma exacerbations: age-stratified time-series analysis. J Allergy Clin Immunol. 2019;144(6):1542–50. https://doi.org/10.1016/j.jaci.2019.08.037.

Article  CAS  PubMed  Google Scholar 

Kaufman JD, Adar SD, Barr RG, Budoff M, Burke GL, Curl CL, et al. 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. Lancet. 2016;388(10045):696–704. https://doi.org/10.1016/S0140-6736(16)00378-0.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang BY, Qian Z, Howard SW, Vaughn MG, Fan SJ, Liu KK, et al. Global association between ambient air pollution and blood pressure: a systematic review and meta-analysis. Environ Pollut. 2018;235:576–88. https://doi.org/10.1016/j.envpol.2018.01.001.

Article  CAS  PubMed  Google Scholar 

Zhu RX, Nie XH, Chen YH, Chen J, Wu SW, Zhao LH. Relationship between particulate matter (PM(2.5)) and hospitalizations and mortality of chronic obstructive pulmonary disease patients: a meta-analysis. Am J Med Sci. 2020;359(6):354–64. https://doi.org/10.1016/j.amjms.2020.03.016.

Article  PubMed  Google Scholar 

Wong CM, Tsang H, Lai HK, Thomas GN, Lam KB, Chan KP, et al. Cancer mortality risks from long-term exposure to ambient fine particle. Cancer Epidemiol Biomarkers Prev. 2016;25(5):839–45. https://doi.org/10.1158/1055-9965.EPI-15-0626.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gianicolo EA, Bruni A, Rosati E, Sabina S, Guarino R, Padolecchia G, et al. Congenital anomalies among live births in a polluted area. A ten-year retrospective study. BMC Pregnancy Childbirth. 2012;12:165. https://doi.org/10.1186/1471-2393-12-165.

Article  PubMed  PubMed Central  Google Scholar 

Mahalingaiah S, Hart JE, Laden F, Farland LV, Hewlett MM, Chavarro J, et al. Adult air pollution exposure and risk of infertility in the Nurses’ Health Study II. Hum Reprod. 2016;31(3):638–47. https://doi.org/10.1093/humrep/dev330.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bosc N, Atkinson F, Felix E, Gaulton A, Hersey A, Leach AR. Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery. J Cheminform. 2019;11(1):4. https://doi.org/10.1186/s13321-018-0325-4.

Article  PubMed  PubMed Central  Google Scholar 

Jacob L, Vert JP. Protein–ligand interaction prediction: an improved chemogenomics approach. Bioinformatics. 2008;24(19):2149–56. https://doi.org/10.1093/bioinformatics/btn409.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol. 2009;20(4):429–36. https://doi.org/10.1016/j.copbio.2009.08.003.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pham TH, Qiu Y, Liu J, Zimmer S, O’Neill E, Xie L, et al. Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. Patterns (N Y). 2022;3(4):100441. https://doi.org/10.1016/j.patter.2022.100441.

Article  CAS  PubMed  Google Scholar 

Pilarczyk M, Fazel-Najafabadi M, Kouril M, Shamsaei B, Vasiliauskas J, Niu W, et al. Connecting omics signatures and revealing biological mechanisms with iLINCS. Nat Commun. 2022;13(1):4678. https://doi.org/10.1038/s41467-022-32205-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee CW, Kim SM, Sa S, Hong M, Nam SM, Han HW. Relationship between drug targets and drug-signature networks: a network-based genome-wide landscape. BMC Med Genomics. 2023;16(1):17. https://doi.org/10.1186/s12920-023-01444-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

DALYs GBD, Collaborators H. 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. Lancet. 2018;392(10159):1859–922. https://doi.org/10.1016/S0140-6736(18)32335-3.

Article  Google Scholar 

Quenby S, Gallos ID, Dhillon-Smith RK, Podesek M, Stephenson MD, Fisher J, et al. Miscarriage matters: the epidemiological, physical, psychological, and economic costs of early pregnancy loss. Lancet. 2021;397(10285):1658–67. https://doi.org/10.1016/S0140-6736(21)00682-6.

Article  CAS  PubMed  Google Scholar 

Go S, Kurita H, Matsumoto K, Hatano M, Inden M, Hozumi I. Methylmercury causes epigenetic suppression of the tyrosine hydroxylase gene in an in vitro neuronal differentiation model. Biochem Biophys Res Commun. 2018;502(4):435–41. https://doi.org/10.1016/j.bbrc.2018.05.162.

Article  CAS  PubMed  Google Scholar 

Huang D, Zhang Y, Qi Y, Chen C, Ji W. Global DNA hypomethylation, rather than reactive oxygen species (ROS), a potential facilitator of cadmium-stimulated K562 cell proliferation. Toxicol Lett. 2008;179(1):43–7. https://doi.org/10.1016/j.toxlet.2008.03.018.

Article  CAS  PubMed  Google Scholar 

van Tilburg CM, Milde T, Witt R, Ecker J, Hielscher T, Seitz A, et al. Phase I/II intra-patient dose escalation study of vorinostat in children with relapsed solid tumor, lymphoma, or leukemia. Clin Epigenet. 2019;11(1):188. https://doi.org/10.1186/s13148-019-0775-1.

Article  CAS  Google Scholar 

Bardia A, Kaklamani V, Wilks S, Weise A, Richards D, Harb W, et al. Phase I study of elacestrant (RAD1901), a novel selective estrogen receptor degrader, in ER-positive, HER2-negative advanced breast cancer. J Clin Oncol. 2021;39(12):1360–70. https://doi.org/10.1200/JCO.20.02272.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duttke SH, Chang MW, Heinz S, Benner C. Identification and dynamic quantification of regulatory elements using total RNA. Genome Res. 2019;29(11):1836–46. https://doi.org/10.1101/gr.253492.119.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43(W1):W39-49. https://doi.org/10.1093/nar/gkv416.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zou Z, Iwata M, Yamanishi Y, Oki S. Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. BMC Bioinform. 2022;23(1):51. https://doi.org/10.1186/s12859-022-04571-8.

Article  CAS  Google Scholar 

Zou Z, Ohta T, Miura F, Oki S. ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Res. 2022;50(W1):W175–82. https://doi.org/10.1093/nar/gkac199.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K, et al. DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucleic Acids Res. 2018;46(D1):D229–38. https://doi.org/10.1093/nar/gkx1001.

Article  CAS  PubMed  Google Scholar 

Wang T, Pehrsson EC, Purushotham D, Li D, Zhuo X, Zhang B, et al. The NIEHS TaRGET II Consortium and environmental epigenomics. Nat Biotechnol. 2018;36(3):225–7. https://doi.org/10.1038/nbt.4099.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database C. The sequence read archive. Nucleic Acids Res. 2011;39(Database issue):D19-21. https://doi.org/10.1093/nar/gkq1019.

Article  CAS  PubMed  Google Scholar 

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. https://doi.org/10.1186/GB-2008-9-9-R137.

Article  PubMed  PubMed Central  Google Scholar 

Pinero J, Ramirez-Anguita JM, Sauch-Pitarch J, Ronzano F, Centeno E, Sanz F, et al. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2020;48(D1):D845-855. https://doi.org/10.1093/nar/gkz1021.

Article  CAS  PubMed  Google Scholar 

Davis AP, Wiegers TC, Johnson RJ, Sciaky D, Wiegers J, Mattingly CJ. Comparative Toxicogenomics Database (CTD): update 2023. Nucleic Acids Res. 2023;51(D1):D1257–62. https://doi.org/10.1093/nar/gkac833.

Article  CAS  PubMed  Google Scholar 

SRA ToolKit v3.0.0. https://github.com/ncbi/sra-tools. Accessed 31 March 2022.

FASTX-Toolkit v0.0.13. http://hannonlab.cshl.edu/fastx_toolkit/. Accessed 31 March 2022.

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907–15. https://doi.org/10.1038/s41587-019-0201-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics.