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The identification of HLA epitopes is essential for vaccine and immunotherapy development. Here, authors develop ImmuneApp using deep learning on extensive immunopeptidomics data, advancing antigen presentation prediction, neoepitope prioritisation, and immunopeptidomics deconvolution.

The core circadian transcription factor BMAL1 regulates circadian-dependent myocardial injury.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

Development of the secondary palate is a complex process. Here, the authors profile mouse palatogenesis through single-cell multiome sequencing, revealing dynamic gene regulation across embryonic days (E) 12.5, E13.5, E14.0, and E14.5.

Single-cell RNA sequencing efforts have made large amounts of data available for transcriptomics research. Simon and colleagues develop a neural network embedding approach that avoids batch effects, such that it can rapidly and efficiently integrate large datasets from different studies.

Here, the authors fabricate hybrid van der Waals heterostructures based on 2D tessellations of DNA origami thin films, graphene and boron nitride, showing that the DNA films can induce periodic superlattices at the interface and modulate the electronic properties of the samples.

Better analytical methods are needed to extract biological meaning from genome-wide association studies (GWAS) of psychiatric disorders. Here the authors take GWAS data from over 60,000 subjects, including patients with schizophrenia, bipolar disorder and major depression, and identify common etiological pathways shared amongst them.

Drug response in cancer patients vary dramatically due to inter- and intra-tumor heterogeneity and transcriptome context plays a significant role in shaping the actual treatment outcome. Here, the authors develop a deep variational autoencoder model to compress gene signatures into latent vectors and accurately impute drug response.

The dysregulation of the m⁶A epitranscriptomic networks have been reported to contribute to the development of gliomas. Here, the authors utilize induced pluripotent stem cell-derived astrocytes with a p53 mutation and demonstrate that mutant p53 upregulates the m⁶A reader YTHDF2, resulting in the initiation of gliomas.

Xiao et al. report that adoptively transferred tumor-specific CD8⁺ interleukin-9-producing cytotoxic T cells promote the recruitment and activation of host effector CD4⁺ T cells to control the outgrowth of tumors with antigen loss.

Antiferromagnets have a variety of attractive features such as rapid operation, lack of stray fields, and insensitivity to external perturbations, that make an exciting prospect for memory and computing applications. Unfortunately, readout of the antiferromagnetic state is challenging. Here, Yan, Mao and coauthors demonstrate an antiferromagnet that can be switched between antiferromagnetic phases via piezoelectric strain with a large difference in the resistance between the two antiferromagnetic phases.

Feng, Luo and colleagues show that the combination of glucose and fructose, as found in sugar-sweetened beverages, promotes colorectal cancer metastasis through a mechanism involving sorbitol dehydrogenase (SORD).

Finding the process parameters in molecular beam epitaxy for a specific density of quantum dots is a multidimensional optimization challenge. Here, the authors demonstrate real-time feedback controlled self-assembled InAs/GaAs QDs growth based on machine learning (ML) outputs.

Yuzhalin et al. report that astrocyte-mediated upregulation of Cdk5 in metastatic breast cancer cells inhibits MHC-I expression on the cell surface, thereby enabling escape from killing by CD8⁺ T cells and facilitating brain metastasis.

Flexible electronic hydrogels that allow conformal tissue integration, online precision diagnosis, and simultaneous tissue regeneration are desired for advancing the treatment of myocardial infarction. Here, the authors report a chronological adhesive hydrogel patch integrating diagnostic and therapeutic functions through mechanophysiological monitoring and electrocoupling therapy.

Electric field controlled magnetism provides an energy efficient way for the operations in the spintronic devices. Here the authors show strain induced, reversible, nonvolatile electric field control of magnetization and magnetoresistance in a magnetic tunnel junction on a ferroelectric substrate at room temperature and zero magnetic field.

Here, the authors perform a whole-genome sequencing association analysis of genetic variants in ≤11,840 multi-ethnic participants with ≤1666 circulating metabolites, discovering 1985 novel variant-metabolite associations and insights into human disease.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

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.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

A ternary metallic alloy VS_2xSe_2(1–x) that has a tunable work function can be grown using chemical vapour deposition and used as contacts for two-dimensional semiconductors.

Glucose-sensing neurons are found in the ventromedial hypothalamic nucleus (VMH). Here the authors identify the role of estrogen receptor-α expressing neurons in the ventrolateral subdivision of the VMH in sensing hypoglycemia.

Clear cell renal cell carcinoma (ccRCC) is a urogenital cancer with a well-defined genetic landscape. Here, the authors analyse the clonal architecture of ccRCC patients from three populations, and find prognostic subtypes linked to immune infiltrates and clonal architecture.

Activation of the insulin-like growth factor 1 receptor may underlie clinical resistance to inhibition of the anaplastic lymphoma receptor kinase in lung cancer.

Chemical vapor deposition (CVD) is a versatile method to synthesize 2D materials, but usually requires high growth temperatures. Here, the authors report a BiOCl-assisted CVD approach to grow 2D nanosheets from 27 different layered and nonlayered materials at temperatures <500 °C, which are compatible with back-end-of-the-line industrial processes.

CrSe₂ nanosheets grown on WSe₂ show no apparent change in surface roughness or magnetic properties after months of exposure in air. Calculations suggest that charge transfer from the WSe₂ substrate and interlayer coupling within CrSe₂ play a critical role.

Though low-dimensional (LD) materials are attractive for polarization-type photodetectors, their low anisotropic photocurrent rate hinders widespread application. Here, the authors report an amplification system for enhanced photocurrent in polarization-sensitive LD material-based photodetectors.

The potential of organic phototransistors to surpass silicon-based devices is limited by the low carrier mobility of organic photoresponsive materials. Here, Ji et al. report high performance organic phototransistors featuring vacuum-deposited small-molecule films with band-like charge transport.