{"action":"created","issue":{"url":"https://api.github.com/repos/greenelab/deep-review/issues/74","repository_url":"https://api.github.com/repos/greenelab/deep-review","labels_url":"https://api.github.com/repos/greenelab/deep-review/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/greenelab/deep-review/issues/74/comments","events_url":"https://api.github.com/repos/greenelab/deep-review/issues/74/events","html_url":"https://github.com/greenelab/deep-review/issues/74","id":170271404,"number":74,"title":"Modeling translation elongation dynamics by deep learning reveals new insights into the landscape of ribosome stalling","user":{"login":"agitter","id":3532898,"avatar_url":"https://avatars.githubusercontent.com/u/3532898?v=3","gravatar_id":"","url":"https://api.github.com/users/agitter","html_url":"https://github.com/agitter","followers_url":"https://api.github.com/users/agitter/followers","following_url":"https://api.github.com/users/agitter/following{/other_user}","gists_url":"https://api.github.com/users/agitter/gists{/gist_id}","starred_url":"https://api.github.com/users/agitter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agitter/subscriptions","organizations_url":"https://api.github.com/users/agitter/orgs","repos_url":"https://api.github.com/users/agitter/repos","events_url":"https://api.github.com/users/agitter/events{/privacy}","received_events_url":"https://api.github.com/users/agitter/received_events","type":"User","site_admin":false},"labels":[{"id":443706109,"url":"https://api.github.com/repos/greenelab/deep-review/labels/study","name":"study","color":"0e8a16","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-08-09T21:09:07Z","updated_at":"2017-02-01T16:27:09Z","closed_at":null,"body":"http://doi.org/10.1101/067108\n"},"comment":{"url":"https://api.github.com/repos/greenelab/deep-review/issues/comments/276704809","html_url":"https://github.com/greenelab/deep-review/issues/74#issuecomment-276704809","issue_url":"https://api.github.com/repos/greenelab/deep-review/issues/74","id":276704809,"user":{"login":"gwaygenomics","id":7340421,"avatar_url":"https://avatars.githubusercontent.com/u/7340421?v=3","gravatar_id":"","url":"https://api.github.com/users/gwaygenomics","html_url":"https://github.com/gwaygenomics","followers_url":"https://api.github.com/users/gwaygenomics/followers","following_url":"https://api.github.com/users/gwaygenomics/following{/other_user}","gists_url":"https://api.github.com/users/gwaygenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/gwaygenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gwaygenomics/subscriptions","organizations_url":"https://api.github.com/users/gwaygenomics/orgs","repos_url":"https://api.github.com/users/gwaygenomics/repos","events_url":"https://api.github.com/users/gwaygenomics/events{/privacy}","received_events_url":"https://api.github.com/users/gwaygenomics/received_events","type":"User","site_admin":false},"created_at":"2017-02-01T16:27:08Z","updated_at":"2017-02-01T16:27:08Z","body":"Title is now: **ROSE: a deep learning based framework for predicting ribosome stalling**\r\n\r\nCNN applied to ribosome footprinting data predicts ribosome stalling and elongation efficiency. The name of the model stands for \"RibosOme Stalling Estimator\"\r\n\r\n# Why we should include it in the review\r\n\r\nAnother deep learning application that exceeds performance beyond more traditional ML approaches (with evidence). The goal of the paper is to use ribosome positioning data to study ribosome stalling dynamics and both how the sequence context regulates stalling, and how stalling impacts elongation efficiency.\r\n\r\n# Computational Aspects\r\n\r\nregularized CNN very similar to #214. Also applied as an ensemble model (64 CNNs with different initialized weights). Defined positive set as ribosome occupancy on a particular mRNA greater than 2 sd from background occupancy. Negative set was everything else. "}}
{"actor":{"display_login":"gwaygenomics"}}