Obtaining genetics insights from deep learning via explainable artificial intelligence
… nucleotides leads to a change in the model’s prediction. These changes are collected for all
… ’s predictions from the original sequence. c | Calculating the gradient of the model’s output …
… ’s predictions from the original sequence. c | Calculating the gradient of the model’s output …
Biological embedding of experience: A primer on epigenetics
…, A Goldenberg, S Mostafavi… - Proceedings of the …, 2020 - National Acad Sciences
Biological embedding occurs when life experience alters biological processes to affect later
life health and well-being. Although extensive correlative data exist supporting the notion …
life health and well-being. Although extensive correlative data exist supporting the notion …
[HTML][HTML] Multifunctional nanoparticle developments in cancer diagnosis and treatment
S Parvanian, SM Mostafavi, M Aghashiri - Sensing and Bio-Sensing …, 2017 - Elsevier
Nanotechnology, although still in the early stages, has the potential to revolutionize the early
diagnosis, treatment, and monitoring of disease progression. Technological application of …
diagnosis, treatment, and monitoring of disease progression. Technological application of …
[HTML][HTML] The genotype-tissue expression (GTEx) project
Genome-wide association studies have identified thousands of loci for common diseases,
but, for the majority of these, the mechanisms underlying disease susceptibility remain …
but, for the majority of these, the mechanisms underlying disease susceptibility remain …
The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans
Understanding the functional consequences of genetic variation, and how it affects complex
human disease and quantitative traits, remains a critical challenge for biomedicine. We …
human disease and quantitative traits, remains a critical challenge for biomedicine. We …
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
…, F Kazi, CT Lopes, A Maitland, S Mostafavi… - Nucleic acids …, 2010 - academic.oup.com
… GeneMANIA then extends the user’s list with genes that are functionally similar, or have …
with those in the query list based on GeneMANIA’s large and diverse data collection. …
with those in the query list based on GeneMANIA’s large and diverse data collection. …
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression
Major depressive disorder (MDD) is a common illness accompanied by considerable
morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide …
morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide …
The genetic landscape of a cell
A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene
pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles …
pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles …
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
…, L Byrnes, CM Lanata, RE Gate, S Mostafavi… - Nature …, 2018 - nature.com
… between samples s 1 , s 2 if and only if and the most likely mixing proportion is estimated to
be argmax α L c (s 1 , s 2 , α). We determine that the cell contains only a single individual s if, …
be argmax α L c (s 1 , s 2 , α). We determine that the cell contains only a single individual s if, …
[HTML][HTML] GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
… S by setting all its elements to zero, except for its diagonal elements, which we specify by
setting S … unregularized version of this problem, we simply set all of the elements of S to zero. …
setting S … unregularized version of this problem, we simply set all of the elements of S to zero. …