Machine learning for profile prediction in genomics.

Current Opinion in Chemical Biology
Jacob Schreiber, Ritambhara Singh

Abstract

A recent deluge of publicly available multi-omics data has fueled the development of machine learning methods aimed at investigating important questions in genomics. Although the motivations for these methods vary, a task that is commonly adopted is that of profile prediction, where predictions are made for one or more forms of biochemical activity along the genome, for example, histone modification, chromatin accessibility, or protein binding. In this review, we give an overview of the research works performing profile prediction, define two broad categories of profile prediction tasks, and discuss the types of scientific questions that can be answered in each.

References

Oct 23, 2004·Science·UNKNOWN ENCODE Project Consortium
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Aug 23, 2008·Biochimica Et Biophysica Acta·Elena Fedorova, Daniele Zink
Nov 6, 2009·Nature·Melissa J FullwoodYijun Ruan
Mar 10, 2010·Cell·Timothy RavasiYoshihide Hayashizaki
Oct 15, 2010·Nature Biotechnology·Bradley E BernsteinJames A Thomson
Nov 8, 2011·Genes & Development·Kenneth S Zaret, Jason S Carroll
Jul 18, 2014·PLoS Computational Biology·Mahmoud GhandiMichael A Beer
Jul 28, 2015·Nature Biotechnology·Babak AlipanahiBrendan J Frey
Aug 25, 2015·Nature Methods·Jian Zhou, Olga G Troyanskaya
Sep 5, 2015·Nucleic Acids Research·Sushmita RoyRupa Sridharan
Feb 25, 2017·PLoS Computational Biology·Qian Qin, Jianxing Feng
Mar 24, 2017·Nucleic Acids Research·Rola Dali, Mathieu Blanchette
Sep 15, 2017·Nature·Job DekkerUNKNOWN 4D Nucleome Network
Oct 13, 2017·Nature·UNKNOWN GTEx ConsortiumStephen B Montgomery
Dec 6, 2017·ELife·Aviv RegevUNKNOWN Human Cell Atlas Meeting Participants
Mar 10, 2018·Nature Communications·Wei Vivian Li, Jingyi Jessica Li
Apr 13, 2018·Nature Communications·Timothy J DurhamWilliam Stafford Noble
Aug 10, 2018·Experimental & Molecular Medicine·Byungjin HwangDuhee Bang
Dec 21, 2018·Genome Research·Hongyang LiYuanfang Guan
Jan 12, 2019·Genome Biology·Jens KeilwagenJan Grau
Mar 27, 2019·F1000Research·Tallulah S Andrews, Martin Hemberg
Dec 8, 2019·Nature Communications·Shilu ZhangSushmita Roy
Jan 29, 2020·Nature Reviews. Genetics·Molly GasperiniJay Shendure
Mar 17, 2020·Bioinformatics·Valentine SvenssonLior Pachter

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