INFERNO – INFERring the molecular mechanisms of NOncoding genetic variants
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Posts by Collection
posters
Integrative analysis identifies immune-related enhancers and lncRNAs perturbed by genetic variants associated with Alzheimer’s disease
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Poster PDF. Received first place poster award in basic science category.
HIPPIE2: Hi-C-based landscape of physically interacting regions and interaction mechanisms
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publications
Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin Permalink
Published in PLoS ONE, 2015
Recommended citation: Amlie-Wolf A*, ..., Trojanowski JQ, Lee VM, Wang LS, Lee EB. Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin. PLoS ONE (2015). 10.1371/journal.pone.0141836
DASHR: database of small human noncoding RNAs Permalink
Published in Nucleic Acids Research, 2016
Recommended citation: Leung YY, Kuksa PP, Amlie-Wolf A, et al. DASHR: database of small human noncoding RNAs. Nucleic Acids Research (2016). 10.1093/nar/gkv1188
INFERNO: INFERring the molecular mechanisms of NOncoding genetic variants Permalink
Published in Nucleic Acids Research, 2018
Recommended citation: Amlie-Wolf A*, ..., Brown CD, Schellenberg GD, Wang LS. INFERNO: INFERring the molecular mechanisms of NOncoding genetic variants. Nucleic Acids Research (2018). 10.1093/nar/gky686
SPAR: small RNA-seq portal for analysis of sequencing experiments Permalink
Published in Nucleic Acids Research, 2018
Recommended citation: Kuksa PP, Amlie-Wolf A, et al., Leung YY. SPAR: small RNA-seq portal for analysis of sequencing experiments. Nucleic Acids Research (2018). 10.1093/nar/gky330
Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease Permalink
Published in Nature Neuroscience, 2018
Recommended citation: Nativio R, ..., Amlie-Wolf A, ..., Berger S. Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nature Neuroscience (2018). 10.1038/s41593-018-0101-9
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products Permalink
Published in Bioinformatics, 2018
Recommended citation: Kuksa PP, Amlie-Wolf A, et al., Wang LS. DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. Bioinformatics (2018). 10.1093/bioinformatics/bty709
Inferring the Molecular Mechanisms of Noncoding Alzheimer’s Disease-Associated Genetic Variants Permalink
Published in Journal of Alzheimer's Disease, 2019
Recommended citation: Amlie-Wolf A*, Tang M*, ..., Wang LS, Schellenberg GD. Inferring the Molecular Mechanisms of Noncoding Alzheimer's Disease-Associated Genetic Variants. Journal of Alzheimer's Disease (2019). 10.3233/jad-190568
Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing Permalink
Published in Nature Genetics, 2019
Recommended citation: Kunkle BW, ..., Amlie-Wolf A, ..., Schellenberg GD, Lambert JC, Pericak-Vance MA. Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. Nature Genetics (2019). 10.1038/s41588-019-0358-2
Activity of the poly(A) binding protein MSUT2 determines susceptibility to pathological tau in the mammalian brain Permalink
Published in Science Translational Medicine, 2019
Recommended citation: Wheeler JM, ..., Amlie-Wolf A, ..., Kraemer B. Activity of the poly(A) binding protein MSUT2 determines susceptibility to pathological tau in the mammalian brain. Science Translational Medicine (2019). 10.1126/scitranslmed.aao6545
Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons Permalink
Published in Cell Reports, 2019
Recommended citation: Liu EY, ..., Amlie-Wolf A, ..., Lee EB. Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons. Cell Reports (2019). 10.1016/j.celrep.2019.04.003
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions Permalink
Published in NAR Genomics and Bioinformatics, 2020
Recommended citation: Kuksa PP, Amlie-Wolf A*, Hwang YC*, ..., Wang LS. HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. NAR Genomics and Bioinformatics (2020). 10.1093/nargab/lqaa022
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease Permalink
Published in Nature Genetics, 2020
Recommended citation: Nativio R, ..., Amlie-Wolf A, ..., Berger S. An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. Nature Genetics (2020). 10.1038/s41588-020-0696-0
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants Permalink
Published in Bioinformatics, 2020
Recommended citation: Kuksa PP, Amlie-Wolf A, et al., Wang LS. SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants. Bioinformatics (2020). 10.1093/bioinformatics/btaa246
Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations Permalink
Published in Methods in Molecular Biology (Functional Analysis of Long Non-Coding RNAs), 2021
Recommended citation: Amlie-Wolf A*, et al. Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations. Methods in Molecular Biology: Functional Analysis of Long Non-Coding RNAs (2021). 10.1007/978-1-0716-1158-6_6
FILER: a framework for harmonizing and querying large-scale functional genomics knowledge Permalink
Published in NAR Genomics and Bioinformatics, 2022
Recommended citation: Kuksa PP, Leung YY, Gangadharan P, ..., Amlie-Wolf A, et al. FILER: a framework for harmonizing and querying large-scale functional genomics knowledge. NAR Genomics and Bioinformatics (2022). 10.1093/nargab/lqab123
talks
Inferring enhancer and noncoding RNA dysregulation underlying 2,419 UK Biobank Phenotypes
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