Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
Network propagation: a universal amplifier of genetic associations
Biological networks are powerful resources for the discovery of genes and genetic modules
that drive disease. Fundamental to network analysis is the concept that genes underlying the …
that drive disease. Fundamental to network analysis is the concept that genes underlying the …
Structure-based protein function prediction using graph convolutional networks
The rapid increase in the number of proteins in sequence databases and the diversity of
their functions challenge computational approaches for automated function prediction. Here …
their functions challenge computational approaches for automated function prediction. Here …
GeneMANIA update 2018
M Franz, H Rodriguez, C Lopes, K Zuberi… - Nucleic acids …, 2018 - academic.oup.com
Abstract GeneMANIA (http://genemania. org) is a flexible user-friendly web site for
generating hypotheses about gene function, analyzing gene lists and prioritizing genes for …
generating hypotheses about gene function, analyzing gene lists and prioritizing genes for …
Predicting multicellular function through multi-layer tissue networks
M Zitnik, J Leskovec - Bioinformatics, 2017 - academic.oup.com
Motivation Understanding functions of proteins in specific human tissues is essential for
insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular …
insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular …
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh… - Genome biology, 2019 - Springer
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an
ongoing, global, community-driven effort to evaluate and improve the computational …
ongoing, global, community-driven effort to evaluate and improve the computational …
Understanding multicellular function and disease with human tissue-specific networks
Tissue and cell-type identity lie at the core of human physiology and disease. Understanding
the genetic underpinnings of complex tissues and individual cell lineages is crucial for …
the genetic underpinnings of complex tissues and individual cell lineages is crucial for …
Integrated multi-omics analyses in oncology: a review of machine learning methods and tools
In recent years, high-throughput sequencing technologies provide unprecedented
opportunity to depict cancer samples at multiple molecular levels. The integration and …
opportunity to depict cancer samples at multiple molecular levels. The integration and …
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
It is well established that autism spectrum disorders (ASD) have a strong genetic
component; however, for at least 70% of cases, the underlying genetic cause is unknown …
component; however, for at least 70% of cases, the underlying genetic cause is unknown …
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
D Warde-Farley, SL Donaldson, O Comes… - Nucleic acids …, 2010 - academic.oup.com
Abstract GeneMANIA (http://www. genemania. org) is a flexible, user-friendly web interface
for generating hypotheses about gene function, analyzing gene lists and prioritizing genes …
for generating hypotheses about gene function, analyzing gene lists and prioritizing genes …