{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T23:58:42Z","timestamp":1776038322351,"version":"3.50.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":139,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Ribosome profiling is a useful technique for studying translational dynamics and quantifying protein synthesis. Applications of this technique have shown that ribosomes are not uniformly distributed along mRNA transcripts. Understanding how each transcript-specific distribution arises is important for unraveling the translation mechanism.<\/jats:p><jats:p>Results: Here, we apply kernel smoothing to construct predictive features and build a sparse model to predict the shape of ribosome footprint profiles from transcript sequences alone. Our results on Saccharomyces cerevisiae data show that the marginal ribosome densities can be predicted with high accuracy. The proposed novel method has a wide range of applications, including inferring isoform-specific ribosome footprints, designing transcripts with fast translation speeds and discovering unknown modulation during translation.<\/jats:p><jats:p>Availability and implementation: A software package called riboShape is freely available at https:\/\/sourceforge.net\/projects\/riboshape<\/jats:p><jats:p>Contact: \u00a0yss@berkeley.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw253","type":"journal-article","created":{"date-parts":[[2016,6,15]],"date-time":"2016-06-15T15:43:52Z","timestamp":1466005432000},"page":"i183-i191","source":"Crossref","is-referenced-by-count":22,"title":["Prediction of ribosome footprint profile shapes from transcript sequences"],"prefix":"10.1093","volume":"32","author":[{"given":"Tzu-Yu","family":"Liu","sequence":"first","affiliation":[{"name":"1 Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"2 Department of Electrical Engineering and Computer Sciences"}]},{"given":"Yun S.","family":"Song","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"2 Department of Electrical Engineering and Computer Sciences"},{"name":"3 Department of Statistics and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,6,11]]},"reference":[{"key":"2023020112321093400_btw253-B1","doi-asserted-by":"crossref","first-page":"e1004692.","DOI":"10.1371\/journal.pgen.1004692","article-title":"Genetic influences on translation in yeast","volume":"10","author":"Albert","year":"2014","journal-title":"PLoS Genet"},{"key":"2023020112321093400_btw253-B2","doi-asserted-by":"crossref","first-page":"2011","DOI":"10.1101\/gr.175893.114","article-title":"Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation","volume":"24","author":"Artieri","year":"2014","journal-title":"Genome Res"},{"key":"2023020112321093400_btw253-B3","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.pep.2008.01.008","article-title":"Codon optimization can improve expression of human genes in escherichia coli: a multi-gene study","volume":"59","author":"Burgess-Brown","year":"2008","journal-title":"Protein Expression Purif"},{"key":"2023020112321093400_btw253-B4","volume-title":"Introduction to Wavelets and Wavelet Transforms","author":"Burrus","year":"1998"},{"key":"2023020112321093400_btw253-B5","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1109\/83.661182","article-title":"Nonlinear wavelet image processing: variational problems, compression, and noise removal through wavelet shrinkage","volume":"7","author":"Chambolle","year":"1998","journal-title":"IEEE Trans. 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