DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning
Motivation Alternative splicing generates multiple isoforms from a single gene, greatly
increasing the functional diversity of a genome. Although gene functions have been well …
increasing the functional diversity of a genome. Although gene functions have been well …
Isoform function prediction by Gene Ontology embedding
S Qiu, G Yu, X Lu, C Domeniconi, M Guo - Bioinformatics, 2022 - academic.oup.com
Motivation High-resolution annotation of gene functions is a central task in functional
genomics. Multiple proteoforms translated from alternatively spliced isoforms from a single …
genomics. Multiple proteoforms translated from alternatively spliced isoforms from a single …
Isoform function prediction based on bi-random walks on a heterogeneous network
Motivation Alternative splicing contributes to the functional diversity of protein species and
the proteoforms translated from alternatively spliced isoforms of a gene actually execute the …
the proteoforms translated from alternatively spliced isoforms of a gene actually execute the …
Differentiating isoform functions with collaborative matrix factorization
Motivation Isoforms are alternatively spliced mRNAs of genes. They can be translated into
different functional proteoforms, and thus greatly increase the functional diversity of protein …
different functional proteoforms, and thus greatly increase the functional diversity of protein …
Multiview multi-instance multilabel active learning
G Yu, Y Xing, J Wang, C Domeniconi… - IEEE Transactions on …, 2021 - ieeexplore.ieee.org
Multiview multi-instance multilabel learning (M3L) is a framework for modeling complex
objects. In this framework, each object (or bag) contains one or more instances, is …
objects. In this framework, each object (or bag) contains one or more instances, is …
DeepIsoFun: a deep domain adaptation approach to predict isoform functions
Motivation Isoforms are mRNAs produced from the same gene locus by alternative splicing
and may have different functions. Although gene functions have been studied extensively …
and may have different functions. Although gene functions have been studied extensively …
IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation
Motivation High resolution annotation of gene functions is a central goal in functional
genomics. A single gene may produce multiple isoforms with different functions through …
genomics. A single gene may produce multiple isoforms with different functions through …
Computational methods for predicting functions at the mRNA isoform level
Multiple mRNA isoforms of the same gene are produced via alternative splicing, a biological
mechanism that regulates protein diversity while maintaining genome size. Alternatively …
mechanism that regulates protein diversity while maintaining genome size. Alternatively …
DMIL-IsoFun: predicting isoform function using deep multi-instance learning
Motivation Alternative splicing creates the considerable proteomic diversity and complexity
on relatively limited genome. Proteoforms translated from alternatively spliced isoforms of a …
on relatively limited genome. Proteoforms translated from alternatively spliced isoforms of a …
Imbalance deep multi‐instance learning for predicting isoform–isoform interactions
Multi‐instance learning (MIL) can model complex bags (samples) that are further made of
diverse instances (subsamples). In typical MIL, the labels of bags are known while those of …
diverse instances (subsamples). In typical MIL, the labels of bags are known while those of …