M
Mikael Bodén
Researcher at University of Queensland
Publications - 143
Citations - 11000
Mikael Bodén is an academic researcher from University of Queensland. The author has contributed to research in topics: Gene & Recurrent neural network. The author has an hindex of 26, co-authored 132 publications receiving 8705 citations. Previous affiliations of Mikael Bodén include University of California, San Diego & Halmstad University.
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Journal ArticleDOI
Mapping the stabilome: a novel computational method for classifying metabolic protein stability
TL;DR: In this paper, the authors present five groups of features useful for predicting protein stability: (1) post-translational modifications, (2) domain types, (3) structural disorder, (4) identity of a protein's N-terminal residue and (5) amino acid sequence.
Proceedings ArticleDOI
Predicting nucleolar proteins using support-vector machines
TL;DR: A range of sequence-kernels are explored and it is found that while some success is achieved with a profile-based local alignment kernel, the problem is ill-suited to a standard compartment-classification approach.
Posted ContentDOI
ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates
TL;DR: It is demonstrated over a number of benchmarks that the adaptation “ChIP-R” (pronounced ‘chipper’) performs as well as or better than comparable approaches on recovering transcription factor binding sites in ChIP-seq peak data, and is extended to evaluate ATAC-seq peaks, finding reproducible peak sets even at low sequencing depth.
Posted ContentDOI
Conserved epigenetic regulatory logic infers genes governing cell identity
Woo Jun Shim,Enakshi Sinniah,Jun Xu,Burcu Vitrinel,Michael Alexanian,Gaia Andreoletti,Sophie Shen,Brad Balderson,Guangdun Peng,Naihe Jing,Yuliangzi Sun,Yash Chhabra,Yuliang Wang,Patrick P.L. Tam,Aaron G. Smith,Michael Piper,Lionel Christiaen,Quan Nguyen,Mikael Bodén,Nathan J. Palpant +19 more
TL;DR: A genome-wide metric based on the gene-repressive tri-methylation of histone 3 lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation is established.
Journal ArticleDOI
Statistical enrichment of epigenetic states around triplet repeats that can undergo expansions
Alexandra Essebier,Patricia Vera Wolf,Minh Duc Cao,Bernard J. Carroll,Sureshkumar Balasubramanian,Mikael Bodén +5 more
TL;DR: Using three complementary statistical tests, it is revealed that several epigenetic states are enriched around repeats that are associated with disease, even in cells that do not harbor expansion, relative to a carefully stratified background.