Sitemap
A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Future Blog Post
Published:
This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
posters
Integrative analysis identifies immune-related enhancers and lncRNAs perturbed by genetic variants associated with Alzheimer’s disease
Published:
Poster PDF. Received first place poster award in basic science category.
HIPPIE2: Hi-C-based landscape of physically interacting regions and interaction mechanisms
Published:
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
Published: