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The yin–yang codec transcoding algorithm is proposed to improve the practicality and robustness of DNA data storage.

Huanming Yang, Zhiming Cai, Jun Wang and colleagues report whole-exome sequencing of 10 clear cell renal cell carcinomas followed by a screen of ~1,100 genes in a total of 98 tumors. They found 12 new disease-associated genes and detected frequent alterations in the ubiquitin-mediated proteolysis pathway.

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.

Lampreys are jawless vertebrates that can offer unique insights into vertebrate evolution. Here they generate a comprehensive cell atlas of the lamprey, uncovering 70 distinct cell types across 14 tissues, and identify pancreas-like cells in the lamprey small intestine.

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.

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.

The PrimeGen framework is a multi-agent large language model system used to navigate intricate primer design workflows for amplicon sequencing.

Jun Wang and colleagues report the genome sequence of the cucumber. The cucumber genome is the seventh plant genome sequence to be reported and was assembled with a combination of traditional Sanger and next-generation sequencing methods.

Neovaginas are surgically constructed to correct uterovaginal agenesis in women with Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome. Here, in a longitudinal study, the authors characterize the dynamics of neovaginal microbiota assembly, showing resemblance to normal vaginal flora at 6-12 months post-surgery, albeit with a bacterial vaginosis-like structure, and further developed into a structure resembling that of the homeostatic pre-surgery dimple microbiota by 2-4 years post-surgery.

The rising incidence of young-onset sporadic colorectal cancer (yCRC) is global concern. Here, leveraging a substantial number of deep sequencing metagenomes, the authors show striking similarities in gut microbial patterns at both the taxonomic and selected gene marker levels between yCRC and old-onset CRC.

This study utilizes Stereo-seq to comprehensively map the geospatial architecture of breast cancer, revealing venular niches that promote immune infiltration and better clinical outcomes, offering new insights into tumor microenvironment regulation.

The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. The study closes an important gap in our understanding of genome structure and evolution in seed plants.

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.

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.

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.

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.

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

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.

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.

Single-cell datasets continue to grow in size and complexity, calling for computational tools to process and analyse data. Yang et al. present a contrastive learning framework to learn cell representations from single-cell multiomics datasets.

Adult zebrafish possess the ability to regenerate injured hearts through a complex orchestration of molecular and cellular activities. Here, the authors present a single cell and spatially-resolved atlas of the regenerating zebrafish heart, which serves as a valuable resource for research on heart regeneration.

Honeybee behavioral plasticity provides a model to study how brain gene networks regulate behavior. Here, authors show stripe activation in Kenyon cells links gene regulatory networks to behavioral maturation via spatial-cellular coordination.

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.

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.

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.

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.

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.

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.

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.

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.

Geckos are small, agile reptiles with nocturnal habits. Here, the authors sequence the genome of the Schlegel’s Japanese Gecko and reveal gene family expansions and reductions associated with formation of adhesive setae, nocturnal vision, tail regeneration, and diversification of olfactory sensation.

The genome sequence and its analysis of the diploid wild wheat Triticum urartu (progenitor of the wheat A genome) represent a tool for studying the complex, polyploid wheat genomes and should be a valuable resource for the genetic improvement of wheat.

Analysis of 43,191 genomes obtained from publicly available marine bacterial and archaeal metagenome data provides insights into marine bacterial evolution, CRISPR–Cas defence and antibiotic resistance genes, and demonstrates the potential of marine metagenomes for biotechnological applications.

The independently evolved extreme holoparasites Balanophora and Sapria display convergent characteristics of genome modifications, including gene loss in particular pathways, reduction of multigene families and relaxed selection pressures.

A large-scale single-cell transcriptomic atlas of the non-human primate Macaca fascicularis encompasses over 1 million cells from 45 adult tissues.

Data from two large longitudinal cohorts in China, in which the participants were clustered into five groups based on their metabolic characteristics, show that a signature of microbiome age modulates the risk of cardiovascular disease in metabolically unhealthy individuals.

Ginkgo is one of the living fossils from the plant kingdom. Here, authors conduct population genomics analyses to reveal its refugia and demographic history, and provide evidence of multiple anthropogenic introductions of ginkgo from eastern China into different continents.

Comparative genomics can provide valuable insights on adaptations to hostile environments. Here, the authors sequence the genomes and transcriptomes of the Bactrian camel, dromedary and alpaca, to reveal the demographic history of the group as well as metabolic adaptations to the desert environment.

The appearance of antibiotic resistance has been attributed to the misuse of antibiotics. By analysing the diversity of antibiotic resistance genes present in 162 human gut microbiota samples, the authors find that Chinese individuals harbour a larger pool of resistance genes than Spanish or Danish counterparts.

The sequencing and assembly of the highly polymorphic oyster genome through a combination of short reads and fosmid pooling, complemented with extensive transcriptome analysis of development and stress response and proteome analysis of the shell, provides new insight into oyster biology and adaptation to a highly changeable environment.

Whole-genome resequencing of 445 Lactuca accessions, including major lettuce crop types and wild relative species, provides a comprehensive map of lettuce genome variations and sheds light on the domestication history of cultivated lettuce.