Research graph
References from Nextcast: A software suite to analyse and model toxicogenomics data. Local targets link to admitted publications; unresolved targets remain external evidence.
Integrating toxicogenomics into human health risk assessment: lessons learned from the benzo [a] pyrene case study
10.3109/10408444.2014.973935 · 2015 · External reference
10.3390/nano10040750
10.3390/nano10040750 · External reference
Transcriptomics in toxicogenomics, part ii: preprocessing and differential expression analysis for high quality data
10.3390/nano10050903 · 2020 · External reference
10.3390/nano10040708
10.3390/nano10040708 · External reference
Toxicogenomics analysis of dynamic dose-response in macrophages highlights molecular alterations relevant for multi-walled carbon nanotube-induced lung fibrosis
10.1016/j.impact.2020.100274 · 2020 · External reference
INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterials
10.1038/s41598-018-37411-y · 2019 · External reference
10.1093/bib/bbaa417
10.1093/bib/bbaa417 · External reference
Integration of genome-wide mRNA and miRNA expression, and DNA methylation data of three cell lines exposed to ten carbon nanomaterials
10.1016/j.dib.2018.05.107 · 2018 · External reference
Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us
10.1016/j.nantod.2020.100945 · 2020 · External reference
Bmdx: a graphical shiny application to perform benchmark dose analysis for transcriptomics data
10.1093/bioinformatics/btaa030 · 2020 · External reference
BMDExpress 2: enhanced transcriptomic dose-response analysis workflow
10.1093/bioinformatics/bty878 · 2019 · External reference
Tindermix: Time-dose integrated modelling of toxicogenomics data
10.1093/gigascience/giaa055 · 2020 · External reference
10.1038/sdata.2016.18
10.1038/sdata.2016.18 · External reference
eutopia: solution for omics data preprocessing and analysis
10.1186/s13029-019-0071-7 · 2019 · External reference
Funmappone: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments
10.1186/s12859-019-2639-2 · 2019 · External reference
Inform: Inference of network response modules
10.1093/bioinformatics/bty063 · 2018 · External reference
Mvda: a multi-view genomic data integration methodology
10.1186/s12859-015-0680-3 · 2015 · External reference
A multi-view genomic data simulator
10.1186/s12859-015-0577-1 · 2015 · External reference
10.1371/journal.pone.0107801
10.1371/journal.pone.0107801 · External reference
Feature set optimization in biomarker discovery from genome-scale data
10.1093/bioinformatics/btaa144 · 2020 · External reference
10.1093/bioinformatics/btz521
10.1093/bioinformatics/btz521 · External reference
An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding
10.1186/s13321-019-0359-2 · 2019 · External reference
Computationally prioritized drugs inhibit sars-cov-2 infection and syncytia formation
10.1093/bib/bbab507 · 2022 · External reference
Molecular signature of asthma-enhanced sensitivity to cuo nanoparticle aerosols from 3d cell model
10.1021/acsnano.9b01823 · 2019 · External reference
Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials
10.1038/s41597-021-00808-y · 2021 · External reference
10.1111/all.14606
10.1111/all.14606 · External reference
Toxicogenomic profiling of 28 nanomaterials in mouse airways
10.1002/advs.202004588 · 2021 · External reference
Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
10.1038/s41597-020-00696-8 · 2020 · External reference
10.1111/all.14519
10.1111/all.14519 · External reference
Mechanistic similarities between 3d human bronchial epithelium and mice lung, exposed to copper oxide nanoparticles, support non-animal methods for hazard assessment
10.1002/smll.202000527 · 2020 · External reference
10.1016/j.csbj.2020.02.023 · Admitted local publication
10.1016/j.jaci.2020.06.012
10.1016/j.jaci.2020.06.012 · External reference
Toward rigorous materials production: new approach methodologies have extensive potential to improve current safety assessment practices
10.1002/smll.201904749 · 2020 · External reference
Transcriptomic profiling of adult-onset asthma related to damp and moldy buildings and idiopathic environmental intolerance
10.3390/ijms221910679 · 2021 · External reference
Bioinformatics-assisted, integrated omics studies on medicinal plants
10.1093/bib/bbz132 · 2020 · External reference
Volta: adVanced mOLecular neTwork analysis
10.1093/bioinformatics/btab642 · 2021 · External reference
Ageing-associated changes in the expression of lncrnas in human tissues reflect a transcriptional modulation in ageing pathways
10.1016/j.mad.2019.111177 · 2020 · External reference
Multiparametric profiling of engineered nanomaterials: Unmasking the surface coating effect
10.1002/advs.202002221 · 2020 · External reference
Changes in microbial communities and their predictive functionalities during fermentation of toddy, an alcoholic beverage of india
10.1016/j.micres.2021.126769 · 2021 · External reference
Multi-walled carbon nanotubes elicit concordant changes in dna methylation and gene expression following long-term pulmonary exposure in mice
10.1016/j.carbon.2021.03.045 · 2021 · External reference
Metataxonomic profiling of bacterial communities and their predictive functional profiles in traditionally preserved meat products of sikkim state in india
10.1016/j.foodres.2020.110002 · 2021 · External reference
10.1016/j.foodres.2020.110055
10.1016/j.foodres.2020.110055 · External reference
10.3390/biology9090295
10.3390/biology9090295 · External reference
Review of statistical learning methods in integrated omics studies (an integrated information science)
2018 · External reference
10.1007/978-3-319-24462-4_5
10.1007/978-3-319-24462-4_5 · External reference
10.1007/s00330-018-5984-z
10.1007/s00330-018-5984-z · External reference
Integrating heterogeneous omics data via statistical inference and learning techniques
10.18547/gcb.2016.vol2.iss1.e32 · 2016 · External reference
10.1016/j.jbi.2016.09.004
10.1016/j.jbi.2016.09.004 · External reference
10.1016/j.jbi.2018.06.001
10.1016/j.jbi.2018.06.001 · External reference
Machine learning for bioinformatics and neuroimaging
10.1002/widm.1248 · 2018 · External reference
10.5772/intechopen.83470
10.5772/intechopen.83470 · External reference
10.1016/b978-0-12-815480-9.00013-x
10.1016/b978-0-12-815480-9.00013-x · External reference
10.1093/bib/bby120
10.1093/bib/bby120 · External reference
Mogonet integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification
2021 · External reference
Vertical integration methods for gene expression data analysis
10.1093/bib/bbaa169 · 2021 · External reference
Integrating multidimensional data for clustering analysis with applications to cancer patient data
10.1080/01621459.2020.1730853 · 2021 · External reference
Agro-ecological class stability decreases in response to climate change projections for the pacific northwest, usa
10.3389/fevo.2017.00074 · 2017 · External reference
Multi-class computational evolution: development, benchmark evaluation and application to rna-seq biomarker discovery
10.1186/s13040-017-0134-8 · 2017 · External reference
10.1016/j.taap.2015.12.014
10.1016/j.taap.2015.12.014 · External reference
Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling
2018 · External reference
10.3390/genes10020087
10.3390/genes10020087 · External reference
Knowledge generation with rule induction in cancer omics
10.3390/ijms21010018 · 2020 · External reference
10.1073/pnas.2009192117
10.1073/pnas.2009192117 · External reference
Oxidative stress and neuroinflammation potentiate each other to promote progression of dopamine neurodegeneration
2020 · External reference
Cobalt nanoparticles trigger ferroptosis-like cell death (oxytosis) in neuronal cells: Potential implications for neurodegenerative disease
10.1096/fj.201902191rr · 2020 · External reference
10.1080/17460441.2021.1867095
10.1080/17460441.2021.1867095 · External reference
10.1093/nar/gkm226
10.1093/nar/gkm226 · External reference
The reactome pathway knowledgebase
10.1093/nar/gkv1351 · 2016 · External reference
KEGG as a reference resource for gene and protein annotation
10.1093/nar/gkv1070 · 2016 · External reference
10.1038/75556
10.1038/75556 · External reference
Topklists: a comprehensive r package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists
10.1515/sagmb-2014-0093 · 2015 · External reference
Topklists: a comprehensive r package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists
2015 · External reference
Wisdom of crowds for robust gene network inference
10.1038/nmeth.2016 · 2012 · External reference
Map and model–moving from observation to prediction in toxicogenomics
10.1093/gigascience/giz057 · 2019 · External reference
10.1023/a:1010933404324
10.1023/a:1010933404324 · External reference
Multi-omics analysis of ten carbon nanomaterials effects highlights cell type specific patterns of molecular regulation and adaptation
10.1016/j.impact.2018.05.003 · 2018 · External reference
Fastbmd: an online tool for rapid benchmark dose–response analysis of transcriptomics data
10.1093/bioinformatics/btaa700 · 2021 · External reference
Data integration in genomics and systems biology
10.1109/cec.2016.7743934 · 2016 · External reference
10.1371/journal.pcbi.1007677
10.1371/journal.pcbi.1007677 · External reference
Grouping of nanomaterials to read-across hazard endpoints: a review
10.1080/17435390.2018.1506060 · 2019 · External reference
10.1038/ng1201-365
10.1038/ng1201-365 · External reference
Visualizing data using t-sne
2008 · External reference
10.32614/cran.package.uwot
10.32614/cran.package.uwot · External reference
10.1093/nar/gkz401
10.1093/nar/gkz401 · External reference
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
2013 · External reference
PathwAX: a web server for network crosstalk based pathway annotation
10.1093/nar/gkw356 · 2016 · External reference
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
10.1093/nar/gkaa1074 · 2020 · External reference
10.1101/gr.1239303
10.1101/gr.1239303 · External reference
10.1609/icwsm.v3i1.13937
10.1609/icwsm.v3i1.13937 · External reference
Towards FAIR nanosafety data
10.1038/s41565-021-00911-6 · 2021 · External reference
Prospects and challenges for FAIR toxicogenomics data
10.1038/s41565-021-01049-1 · 2021 · External reference
Reply to: Prospects and challenges for FAIR toxicogenomics data
10.1038/s41565-021-01050-8 · 2021 · External reference
A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure
10.1093/toxsci/kfm092 · 2007 · External reference
10.1007/978-1-0716-1839-4_11
10.1007/978-1-0716-1839-4_11 · External reference
Network analysis reveals similar transcriptomic responses to intrinsic properties of carbon nanomaterials in vitro and in vivo
10.1021/acsnano.6b08650 · 2017 · External reference
Multiwalled carbon nanotubes induce a fibrogenic response by stimulating reactive oxygen species production, activating nf-kb signaling, and promoting fibroblast-to-myofibroblast transformation
10.1021/tx200351d · 2011 · External reference
Basic biology and role of interleukin-17 in immunity and inflammation
10.1111/prd.12083 · 2015 · External reference
10.1021/la400561t
10.1021/la400561t · External reference
10.1021/nn2033055
10.1021/nn2033055 · External reference
10.1021/nn200595c
10.1021/nn200595c · External reference
10.1016/j.nano.2011.11.004
10.1016/j.nano.2011.11.004 · External reference
10.1021/nn305567s
10.1021/nn305567s · External reference
Open tg-gates: a large-scale toxicogenomics database
10.1093/nar/gku955 · 2015 · External reference
10.2217/14622416.7.7.1025
10.2217/14622416.7.7.1025 · External reference
