Comprehensive Integration of Single-Cell Data

Cell, Journal Year: 2019, Volume and Issue: 177(7), P. 1888 - 1902.e21

Published: June 1, 2019

Language: Английский

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 46(W1), P. W537 - W544

Published: May 3, 2018

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started 2005, continues focus on three key challenges data-driven science: making analyses accessible all researchers, ensuring are completely reproducible, it simple communicate so that they can be reused extended. During last two years, team open-source community around have made substantial improvements Galaxy's core framework, user interface, tools, training materials. Framework interface now enable for analyzing datasets, >5500 tools available from ToolShed. The has led an effort create numerous high-quality tutorials focused common types genomic analyses. developer communities continue grow integral development. number servers, developers contributing framework its users server increased substantially.

Language: Английский

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UALCAN: An update to the integrated cancer data analysis platform

Neoplasia, Journal Year: 2022, Volume and Issue: 25, P. 18 - 27

Published: Jan. 22, 2022

Cancer genomic, transcriptomic, and proteomic profiling has generated extensive data that necessitate the development of tools for its analysis dissemination. We developed UALCAN to provide a portal easy exploring, analyzing, visualizing these data, allowing users integrate better understand gene, proteins, pathways perturbed in cancer make discoveries. web enables analyzing delivering transcriptome, proteomics, patient survival research community. With obtained from The Genome Atlas (TCGA) project, enabled evaluate protein-coding gene expression impact on across 33 types cancers. been used extensively since release received immense popularity, underlined by usage researchers more than 100 countries. present manuscript highlights task we have undertaken updates made 2017. Extensive user feedback motivated us expand resource including a) microRNAs (miRNAs), long non-coding RNAs (lncRNAs), promoter DNA methylation TCGA b) mass spectrometry-based proteomics Clinical Proteomic Tumor Analysis Consortium (CPTAC). provides access pre-computed, tumor subgroup-based gene/protein expression, status, Kaplan-Meier analyses. It also new visualization features comprehend observations aids generating hypotheses testing. is accessible at http://ualcan.path.uab.edu.

Language: Английский

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Impact of cytosine methylation on DNA binding specificities of human transcription factors

Science, Journal Year: 2017, Volume and Issue: 356(6337)

Published: May 4, 2017

Positives and negatives of methylated CpG When the DNA bases cytosine guanine are next to each other, a methyl group is generally added pyrimidine, generating mCpG dinucleotide. This modification alters structure but can also affect function by inhibiting transcription factor (TF) binding. Yin et al. systematically analyzed effect methylation on binding 542 human TFs (see Perspective Hughes Lambert). In addition some TFs, they found that mCpGs promote others, particularly involved in development, such as homeodomain proteins. Science , this issue p. eaaj2239 ; see 489

Language: Английский

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TOX is a critical regulator of tumour-specific T cell differentiation

Nature, Journal Year: 2019, Volume and Issue: 571(7764), P. 270 - 274

Published: June 17, 2019

Language: Английский

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The transcriptional landscape of polyploid wheat

Science, Journal Year: 2018, Volume and Issue: 361(6403)

Published: Aug. 17, 2018

The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes many world's major crops. Here we combine extensive gene datasets to produce a comprehensive, genome-wide analysis homoeolog patterns hexaploid bread wheat. Bias varies between tissues, with ~30% wheat homoeologs showing nonbalanced expression. We found asymmetries along chromosomes, largest inter-tissue, inter-cultivar, and coding sequence variation, most often located high-recombination distal ends chromosomes. These transcriptionally dynamic potentially represent first steps toward neo- or subfunctionalization homoeologs. Coexpression networks reveal coordination throughout development and, alongside detailed atlas, provide framework target candidate underpinning agronomic traits

Language: Английский

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High-resolution TADs reveal DNA sequences underlying genome organization in flies

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

Published: Jan. 9, 2018

Despite an abundance of new studies about topologically associating domains (TADs), the role genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) boundaries Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by M1BP protein, and two boundary motifs. In contrast mammals, CTCF only on small fraction flanking inactive chromatin while most active contain or Beaf-32 proteins. demonstrate that can be accurately predicted using sequences open sites. propose sequence guides genome architecture allocation proteins genome. Finally, present interactive online database access explore spatial organization fly, mouse human genomes, available http://chorogenome.ie-freiburg.mpg.de .

Language: Английский

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A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Cell, Journal Year: 2018, Volume and Issue: 174(5), P. 1309 - 1324.e18

Published: Aug. 1, 2018

Language: Английский

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CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

Science, Journal Year: 2016, Volume and Issue: 355(6320)

Published: Dec. 16, 2016

A very focused function for lncRNAs The human genome generates many thousands of long noncoding RNAs (lncRNAs). small number have been shown to be functional. Liu et al. carried out a large-scale CRISPR-based screen assess the ∼17,000 in seven different cell lines. considerable (∼500) tested influenced growth, suggesting biological function. In almost all cases, though, was highly type—specific, often limited just one type. Science , this issue p. 10.1126/science.aah7111

Language: Английский

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Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor

Nature, Journal Year: 2018, Volume and Issue: 555(7695), P. 251 - 255

Published: Feb. 28, 2018

Language: Английский

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