Deep learning in omics: a survey and guideline.


:Omics, such as genomics, transcriptome and proteomics, has been affected by the era of big data. A huge amount of high dimensional and complex structured data has made it no longer applicable for conventional machine learning algorithms. Fortunately, deep learning technology can contribute toward resolving these challenges. There is evidence that deep learning can handle omics data well and resolve omics problems. This survey aims to provide an entry-level guideline for researchers, to understand and use deep learning in order to solve omics problems. We first introduce several deep learning models and then discuss several research areas which have combined omics and deep learning in recent years. In addition, we summarize the general steps involved in using deep learning which have not yet been systematically discussed in the existent literature on this topic. Finally, we compare the features and performance of current mainstream open source deep learning frameworks and present the opportunities and challenges involved in deep learning. This survey will be a good starting point and guideline for omics researchers to understand deep learning.


Brief Funct Genomics


Zhang Z,Zhao Y,Liao X,Shi W,Li K,Zou Q,Peng S




Has Abstract


2019-02-14 00:00:00














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    abstract::Submitting sequences to the National Center for Biotechnology Information (NCBI) is an integral part of research and the publication process for many disciplines within the life sciences, and it will only become more important as sequencing technologies continue to improve. Here, I argue that the available infrastruct...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章


    authors: Smith DR

    更新日期:2020-12-04 00:00:00

  • Unravelling the biological secrets of microchimerism by single-cell analysis.

    abstract::The presence of microchimeric cells is known for >100 years and well documented since decades. Earlier, microchimeric cells were mainly used for cell-based non-invasive prenatal diagnostics during early pregnancy. Microchimeric cells are also present beyond delivery and are associated to various autoimmune diseases, t...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章


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  • The Human Cell Atlas: Technical approaches and challenges.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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    更新日期:2018-07-01 00:00:00

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    pub_type: 杂志文章


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  • Significance of whole-genome duplications on the emergence of evolutionary novelties.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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    更新日期:2018-09-27 00:00:00

  • Chromatin structure of pluripotent stem cells and induced pluripotent stem cells.

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    pub_type: 杂志文章,评审


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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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  • Three-dimensional chromosome organization in flowering plants.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章


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    更新日期:2020-03-23 00:00:00

  • Evolutionary genetics of insect innate immunity.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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  • Studying protein-protein interaction networks: a systems view on diseases.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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  • The structural variability of the influenza A hemagglutinin receptor-binding site.

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    pub_type: 杂志文章,评审


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    pub_type: 杂志文章,评审


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    pub_type: 杂志文章,评审


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  • Transcription attenuation in bacteria: theme and variations.

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    journal_title:Briefings in functional genomics

    pub_type: 更正并重新发布的文章,杂志文章,评审


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  • Proteomics in epigenetics: new perspectives for cancer research.

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    pub_type: 杂志文章,评审


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  • Germ line genome editing in clinics: the approaches, objectives and global society.

    abstract::Genome editing allows for the versatile genetic modification of somatic cells, germ cells and embryos. In particular, CRISPR/Cas9 is worldwide used in biomedical research. Although the first report on Cas9-mediated gene modification in human embryos focused on the prevention of a genetic disease in offspring, it raise...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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  • RNA regulatory networks in animals and plants: a long noncoding RNA perspective.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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    更新日期:2015-03-01 00:00:00

  • Gene-specific metrics to facilitate identification of disease genes for molecular diagnosis in patient genomes: a systematic review.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章


    authors: Alyousfi D,Baralle D,Collins A

    更新日期:2019-02-14 00:00:00

  • Barley genetic variation: implications for crop improvement.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章


    authors: Muñoz-Amatriaín M,Cuesta-Marcos A,Hayes PM,Muehlbauer GJ

    更新日期:2014-07-01 00:00:00

  • Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


    authors: Finotello F,Di Camillo B

    更新日期:2015-03-01 00:00:00

  • Systematic review of next-generation sequencing simulators: computational tools, features and perspectives.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


    authors: Zhao M,Liu D,Qu H

    更新日期:2017-05-01 00:00:00

  • Noncoding RNAs: modulators and modulatable players during infection-induced stress response.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章


    authors: Chattopadhyay P,Srinivasa Vasudevan J,Pandey R

    更新日期:2021-01-25 00:00:00

  • Catching RNAs on chromatin using hybridization capture methods.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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    更新日期:2018-03-01 00:00:00

  • Long noncoding RNAs in regulation of human breast cancer.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


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  • Gene set enrichment; a problem of pathways.

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    journal_title:Briefings in functional genomics

    pub_type: 杂志文章


    authors: Davies MN,Meaburn EL,Schalkwyk LC

    更新日期:2010-12-01 00:00:00

  • Using population isolates in genetic association studies.

    abstract::The use of genetically isolated populations can empower next-generation association studies. In this review, we discuss the advantages of this approach and review study design and analytical considerations of genetic association studies focusing on isolates. We cite successful examples of using population isolates in ...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


    authors: Hatzikotoulas K,Gilly A,Zeggini E

    更新日期:2014-09-01 00:00:00

  • Spec-seq: determining protein-DNA-binding specificity by sequencing.

    abstract::The specificity of protein-DNA interactions can be determined directly by sequencing the bound and unbound fractions in a standard binding reaction. The procedure is easy and inexpensive, and the accuracy can be high for thousands of sequences assayed in parallel. From the measurements, simple models of specificity, s...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


    authors: Stormo GD,Zuo Z,Chang YK

    更新日期:2015-01-01 00:00:00

  • Epigenetic memory in the context of nuclear reprogramming and cancer.

    abstract::Epigenetic memory represents a natural mechanism whereby the identity of a cell is maintained through successive cell cycles, allowing the specification and maintenance of differentiation during development and in adult cells. Cancer is a loss or reversal of the stable differentiated state of adult cells and may be me...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


    authors: Halley-Stott RP,Gurdon JB

    更新日期:2013-05-01 00:00:00

  • Heart genetics in a small package, exploiting the condensed genome of Ciona intestinalis.

    abstract::Defects in the initial establishment of cardiogenic cell fate are likely to contribute to pervasive human congenital cardiac abnormalities. However, the molecular underpinnings of nascent cardiac fate induction have proven difficult to decipher. In this review we explore the participation of extracellular, cellular an...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


    authors: Cota CD,Segade F,Davidson B

    更新日期:2014-01-01 00:00:00

  • Next-generation sequencing for understanding and accelerating crop domestication.

    abstract::Next generation Sequencing (NGS) provides a powerful tool for discovery of domestication genes in crop plants and their wild relatives. The accelerated domestication of new plant species as crops may be facilitated by this knowledge. Re-sequencing of domesticated genotypes can identify regions of low diversity associa...

    journal_title:Briefings in functional genomics

    pub_type: 杂志文章,评审


    authors: Henry RJ

    更新日期:2012-01-01 00:00:00