Eleven grand challenges in single-cell data science

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Feb. 7, 2020

Abstract The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell technology. Thousands—or even millions—of cells analyzed a single experiment amount to data revolution biology pose unique science problems. Here, we outline eleven challenges that will be central bringing this emerging field of forward. For each challenge, highlight motivating research questions, review prior work, formulate open This compendium is for established researchers, newcomers, students alike, highlighting interesting rewarding problems the coming years.

Language: Английский

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Multi-omics Data Integration, Interpretation, and Its Application

Bioinformatics and Biology Insights, Journal Year: 2020, Volume and Issue: 14, P. 117793221989905 - 117793221989905

Published: Jan. 1, 2020

To study complex biological processes holistically, it is imperative to take an integrative approach that combines multi-omics data highlight the interrelationships of involved biomolecules and their functions. With advent high-throughput techniques availability generated from a large set samples, several promising tools methods have been developed for integration interpretation. In this review, we collected adopt analyze multiple omics summarized ability address applications such as disease subtyping, biomarker prediction, deriving insights into data. We provide methodology, use-cases, limitations these tools; brief account repositories visualization portals; challenges associated with integration.

Language: Английский

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The vaginal microbiome and preterm birth

Nature Medicine, Journal Year: 2019, Volume and Issue: 25(6), P. 1012 - 1021

Published: May 29, 2019

Abstract The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency among populations within countries, and women African ancestry disproportionately bear burden risk United States. In present study, we report a community resource that includes ‘omics’ data from approximately 12,000 samples as part integrative Human Microbiome Project. Longitudinal analyses 16S ribosomal RNA, metagenomic, metatranscriptomic cytokine profiles 45 90 term controls identified harbingers this cohort predominantly ancestry. Women who delivered exhibited significantly lower vaginal levels Lactobacillus crispatus higher BVAB1, Sneathia amnii , TM7-H1, group Prevotella species nine additional taxa. first representative genomes BVAB1 TM7-H1 described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines fluid. These findings highlight new opportunities for assessment birth.

Language: Английский

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DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays

Bioinformatics, Journal Year: 2019, Volume and Issue: 35(17), P. 3055 - 3062

Published: Jan. 14, 2019

In the continuously expanding omics era, novel computational and statistical strategies are needed for data integration identification of biomarkers molecular signatures. We present Data Integration Analysis Biomarker discovery using Latent cOmponents (DIABLO), a multi-omics integrative method that seeks common information across different types through selection subset features, while discriminating between multiple phenotypic groups.Using simulations benchmark studies, we show DIABLO identifies features with superior biological relevance compared existing unsupervised methods, achieving predictive performance comparable to state-of-the-art supervised approaches. is versatile, allowing modular-based analyses cross-over study designs. two case identified both known consisting mRNAs, miRNAs, CpGs, proteins metabolites.DIABLO implemented in mixOmics R Bioconductor package functions parameters' choice visualization assist interpretation analyses, along tutorials on http://mixomics.org our vignette.Supplementary available at Bioinformatics online.

Language: Английский

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Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Metabolites, Journal Year: 2019, Volume and Issue: 9(4), P. 76 - 76

Published: April 18, 2019

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets life science. Omics provide a more holistic molecular perspective studied biological systems compared to traditional approaches. However, due their inherent data differences, integrating platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products interactions between genes, transcripts, proteins, metabolomics, tools approaches routinely used this field could assist with integration these complex multi-omics sets. question is, how? Here we some answers (in terms methods, software databases) along variety recommendations list continuing challenges as identified during peer session on that was held at recent ‘Australian New Zealand Metabolomics Conference’ (ANZMET 2018) Auckland, (Sept. 2018). We envisage document will serve guide metabolomics researchers other members community wishing perform studies. also believe ideas may allow full promise integrated research and, ultimately, biology be realized.

Language: Английский

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Maturation of the gut microbiome and risk of asthma in childhood

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Jan. 4, 2018

The composition of the human gut microbiome matures within first years life. It has been hypothesized that microbial compositions in this period can cause immune dysregulations and potentially asthma. Here we show, by associating from 16S rRNA gene amplicon sequencing during year life with subsequent risk asthma 690 participants, 1-year-old children an immature have increased at age 5 years. This association is only apparent among born to asthmatic mothers, suggesting lacking stimulation trigger their inherited risk. Conversely, adequate maturation may protect these pre-disposed children.

Language: Английский

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Integrated omics: tools, advances and future approaches

Journal of Molecular Endocrinology, Journal Year: 2018, Volume and Issue: 62(1), P. R21 - R45

Published: July 13, 2018

With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics and metabolomics, each analysis can generate tera- peta-byte sized data files on a daily basis. These file sizes, together with differences in nomenclature among these types, make integration multi-dimensional omics into biologically meaningful context challenging. Variously named integrated omics, multi-omics, poly-omics, trans-omics, pan-omics or shortened just ‘omics’, challenges include cleaning, normalization, biomolecule identification, dimensionality reduction, contextualization, statistical validation, storage handling, sharing archiving. The ultimate goal is toward holistic realization ‘systems biology’ understanding question. Commonly used are currently limited by 3 i’s – integration, interpretation insights. Post very large datasets aim yield unprecedented views cellular systems at exquisite resolution for transformative insights processes, events diseases through various computational informatics frameworks. continued reduction costs processing time sample analyses, increasing types generated glycomics, lipidomics, microbiomics phenomics, an number scientists this interdisciplinary domain bioinformatics face challenges. We discuss recent approaches, existing tools potential caveats development standardized analytical pipelines that could be adopted global research community.

Language: Английский

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Metformin Enhances Autophagy and Normalizes Mitochondrial Function to Alleviate Aging-Associated Inflammation

Cell Metabolism, Journal Year: 2020, Volume and Issue: 32(1), P. 44 - 55.e6

Published: May 12, 2020

Language: Английский

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Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Feb. 18, 2020

Abstract Cognitive decline is one of the complications type 2 diabetes (T2D). Intermittent fasting (IF) a promising dietary intervention for alleviating T2D symptoms, but its protective effect on diabetes-driven cognitive dysfunction remains elusive. Here, we find that 28-day IF regimen diabetic mice improves behavioral impairment via microbiota-metabolites-brain axis: enhances mitochondrial biogenesis and energy metabolism gene expression in hippocampus, re-structures gut microbiota, microbial metabolites are related to function. Moreover, strong connections observed between affected genes, microbiota metabolites, as assessed by integrative modelling. Removing with antibiotics partly abolishes neuroprotective effects IF. Administration 3-indolepropionic acid, serotonin, short chain fatty acids or tauroursodeoxycholic acid shows similar terms improving Together, our study purports axis mechanism can enable therapeutic strategies against metabolism-implicated pathophysiologies.

Language: Английский

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Multi-omic and multi-view clustering algorithms: review and cancer benchmark

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 46(20), P. 10546 - 10562

Published: Sept. 20, 2018

Recent high throughput experimental methods have been used to collect large biomedical omics datasets. Clustering of single omic datasets has proven invaluable for biological and medical research. The decreasing cost development additional now enable measurement multi-omic data. data the potential reveal further systems-level insights, but raises computational challenges. Here, we review algorithms multi-omics clustering, discuss key issues in applying these algorithms. Our covers developed specifically as well generic multi-view machine learning community joint clustering multiple types. In addition, using cancer from TCGA, perform an extensive benchmark spanning ten different types, providing first systematic comparison leading results highlight regarding use single- versus multi-omics, choice strategy, power approximated p-values gauging solution quality. Due growing data, expect be important future progress field.

Language: Английский

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