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Spatial multi-omic map of human myocardial infarction
A time-resolved high-resolution map of human cardiac remodelling after myocardial infarction, integrating single-cell transcriptomic, chromatin accessibility and spatial transcriptomic data, provides a valuable resource for the field.
- Christoph Kuppe
- , Ricardo O. Ramirez Flores
- & Rafael Kramann
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Environmental factors shaping the gut microbiome in a Dutch population
A study in which gut microbiomes of 8,208 individuals from 2,756 families were characterized and correlated to 241 host and environmental factors defines microbiome patterns shared across diverse diseases and shows that the microbiome is shaped largely by environment and cohabitation.
- R. Gacesa
- , A. Kurilshikov
- & R. K. Weersma
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Article
| Open AccessMulti-omic machine learning predictor of breast cancer therapy response
Integration of pre-treatment tumour features in predictive models using machine learning could inform on response to therapy.
- Stephen-John Sammut
- , Mireia Crispin-Ortuzar
- & Carlos Caldas
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A multi-scale map of cell structure fusing protein images and interactions
Protein immunofluorescence imaging and affinity purification–mass spectrometry are combined to create a unified map of human cell architecture across scales, which the authors call the multi-scale integrated cell (MuSIC).
- Yue Qin
- , Edward L. Huttlin
- & Trey Ideker
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Article
| Open AccessCell-type specialization is encoded by specific chromatin topologies
A new technique called immunoGAM, which combines genome architecture mapping (GAM) with immunoselection, enabled the discovery of specialized chromatin conformations linked to gene expression in specific cell populations from mouse brain tissues.
- Warren Winick-Ng
- , Alexander Kukalev
- & Ana Pombo
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Article
| Open AccessExpanded encyclopaedias of DNA elements in the human and mouse genomes
The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.
- Federico Abascal
- , Reyes Acosta
- & Zhiping Weng
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Article
| Open AccessIndex and biological spectrum of human DNase I hypersensitive sites
High-resolution maps of DNase I hypersensitive sites from 733 human biosamples are used to identify and index regulatory DNA within the human genome.
- Wouter Meuleman
- , Alexander Muratov
- & John Stamatoyannopoulos
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A reference map of the human binary protein interactome
A human binary protein interactome map that includes around 53,000 protein–protein interactions involving more than 8,000 proteins provides a reference for the study of human cellular function in health and disease.
- Katja Luck
- , Dae-Kyum Kim
- & Michael A. Calderwood
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Article
| Open AccessGenomic basis for RNA alterations in cancer
Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.
- Claudia Calabrese
- , Natalie R. Davidson
- & Christian von Mering
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Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia
The inactivation of tumour suppressor genes at the level of mRNA occurs by the generation of truncated proteins in leukaemia.
- Shih-Han Lee
- , Irtisha Singh
- & Christine Mayr
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Integrative structure and functional anatomy of a nuclear pore complex
The structure of the yeast nuclear pore complex, determined at sub-nanometre precision using an integrative approach that combines a wide range of data, reveals details of its architecture, transport mechanism and evolutionary origins.
- Seung Joong Kim
- , Javier Fernandez-Martinez
- & Michael P. Rout
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Letter
| Open AccessThe impact of rare variation on gene expression across tissues
The authors show that rare genetic variants contribute to large gene expression changes across diverse human tissues and provide an integrative method for interpretation of rare variants in individual genomes.
- Xin Li
- , Yungil Kim
- & Stephen B. Montgomery
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Letter |
Global circulation patterns of seasonal influenza viruses vary with antigenic drift
The analysis of more than 9,000 haemagglutinin sequences of human seasonal influenza viruses over a 12-year time period shows that the global circulation patterns of A/H1N1 and B viruses are different from those of the well characterised A/H3N2 viruses; in particular the A/H1N1 and B viruses are shown to persist locally across several seasons and do not display the same degree of global movement as the H3N2 viruses.
- Trevor Bedford
- , Steven Riley
- & Colin A. Russell
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| Open AccessIntegrative analysis of 111 reference human epigenomes
This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease.
- Anshul Kundaje
- , Wouter Meuleman
- & Manolis Kellis
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Letter
| Open AccessTopologically associating domains are stable units of replication-timing regulation
A study of DNA replication timing in mouse and human cells reveals that replication domains (domains of the genome which replicate at the same time) share a correlation with topologically associating domains; these results reconcile cell-type-specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large scale chromosome structure and function.
- Benjamin D. Pope
- , Tyrone Ryba
- & David M. Gilbert
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Article
| Open AccessDiversity and dynamics of the Drosophila transcriptome
A large-scale transcriptome analysis in Drosophila melanogaster, across tissues, cell types and conditions, provides insights into global patterns and diversity of transcription initiation, splicing, polyadenylation and non-coding RNA expression.
- James B. Brown
- , Nathan Boley
- & Susan E. Celniker
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Article
| Open AccessComprehensive molecular characterization of urothelial bladder carcinoma
This paper reports integrative molecular analyses of urothelial bladder carcinoma at the DNA, RNA, and protein levels performed as part of The Cancer Genome Atlas project; recurrent mutations were found in 32 genes, including those involved in cell-cycle regulation, chromatin regulation and kinase signalling pathways; chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any other common cancer studied so far.
- John N. Weinstein
- , Rehan Akbani
- & Greg Eley
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Article
| Open AccessComprehensive molecular characterization of clear cell renal cell carcinoma
The Cancer Genome Atlas Research Network reports an integrative analysis of more than 400 samples of clear cell renal cell carcinoma based on genomic, DNA methylation, RNA and proteomic characterisation; frequent mutations were identified in the PI(3)K/AKT pathway, suggesting this pathway might be a potential therapeutic target, among the findings is also a demonstration of metabolic remodelling which correlates with tumour stage and severity.
- Chad J. Creighton
- , Margaret Morgan
- & Heidi J. Sofia.