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Integrating complex multi-omics data for individual patient decision making can be challenging. Here, the authors develop Knowledge Connector as a decision support system to generate and document Molecular Tumor Board recommendations and support medical decision-making.

Pathogenic variants in RBM20 cause an aggressive form of heart disease. van den Hoogenhof et al. show that overactivated CAMK2D drives this disease, and that pharmacological CAMK2D inhibition is a promising therapeutic approach in patients with RBM20 cardiomyopathy.

Broad anti-discrimination laws and practices could compensate for failing data protection and technology-linked loss of privacy, says Christoph Bock.

Bock and colleagues perform integrative analysis of JAK-STAT mutant mice and find JAK-STAT signaling regulates CD8⁺ T cell and macrophage homeostasis by contributing to a poised epigenetic and transcription-regulatory state, preparing cells to rapidly respond to stimuli.

CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.

CELLFIE, a CRISPR platform for optimizing cell-based immunotherapies, identifies gene knockouts that enhance CAR T cell efficacy using in vitro and in vivo screens.

All-optical coherent control schemes offer well-localized and ultrafast control of individual qubits in many-qubit systems. Here the authors report on all-optical resonant and Raman-based control of single silicon vacancies using picosecond pulses, much faster than the ground state coherence time.

Ibrutinib, a Bruton tyrosine kinase inhibitor, provides effective treatment for chronic lymphocytic leukemia (CLL). Here, the authors describe time-dependent molecular changes to malignant cells and to the immune system in patients undergoing ibrutinib therapy, with can be used for therapy monitoring.

Liquid biopsies enable minimally invasive applications for diagnosis and treatment monitoring. Here the authors analyse fragmentation patterns of circulating tumour DNA on multiple levels and develop a bioinformatic tool, LIQUORICE, to accurately detect and classify paediatric cancers with low mutational burden.

Wastewater surveillance of SARS-CoV-2 at the national scale tracks emerging variants.

The GLASS Consortium studies the evolutionary trajectories of 222 patients with a diffuse glioma to aid in our understanding of tumour progression and treatment failure

Here the authors use single-cell RNA sequencing data to identify genetic variants associated with gene expression (eQTLs) within the context of “trained immunity”, the immunological memory of innate immune cells. They establish a framework for understanding the genetic basis of complex traits by combining single-cell eQTLs with multi-omics data from patients and public databases.

Drug resistance is a common cause of treatment failure for HIV infection and cancer. Can HIV therapy provide a 'blueprint' for designing and validating patient-specific combination therapies in cancer?

Heralded entanglement between two independently trapped single rubidium atoms is generated over long telecom fibre links using quantum frequency conversion in an important step towards the realization of large-scale quantum network links.

Targeted sequencing of perturbation effects offers a sensitive approach to capture genes of interest in CRISPR-mediated screens, enabling genome-scale screens at higher scale and lower cost than whole-transcriptome Perturb-seq.

Comparison of the methylation patterns of cells in different developmental or disease states can help to elucidate both normal and pathological regulatory mechanisms. Bock et al. evaluate the ability of three sequencing-based methods and one microarray-based technology to detect differentially methylated regions on a genome-wide scale.

Epigenome profiling in combination with imaging-based chemosensitivity and integrative bioinformatic analysis establishes a method for detecting therapy-induced vulnerabilities, as shown here for ibrutinib-treated chronic lymphocytic leukemia.

Entanglement between photons and stationary quantum nodes is a fundamental resource for quantum communication, but typical transition wavelengths are far from the telecom band. Here, the authors deal with the problem using polarisation-independent, entanglement-preserving frequency conversion.

Pathogenic T helper type 2 cells (pTh2) are involved in allergic asthma and secrete high levels of IL-5 and IL-13. Here, using HDM challenged mice and developing an in vitro pTh2 culture system, the authors investigate the function of epigenetic modifications in pTh2 cells showing that HDAC1 limits the pathogenicity of pTh2 cells and scRNA analysis of these cells indicates two subsets in the lungs.

Bioinformatic imputation of epigenomic marks promises to supplement catalogs of experimental data.

The function of transient neuropeptides in developmental roles in the nervous system remains elusive. Here, authors demonstrate that galanin shapes synaptic wiring in the whisker pathway, a fundamental sensory modality for infant rodents before eye opening.

Combining whole-transcriptome preindexing with standard droplet microfluidics, scifi-RNA-seq enables single-cell RNA-seq with massive throughput and built-in sample multiplexing.

A region on chromosome 19p13 is associated with the risk of developing ovarian and breast cancer. Here, the authors genotyped SNPs in this region in thousands of breast and ovarian cancer patients and identified SNPs associated with three genes, which were analysed with functional studies.

Dopamine D2 receptor activity in the nucleus accumbens is associated with regulation of motivated responding. Here the authors show that overexpression of D2 receptors specifically in ventral striatal projection neurons leads to an increase in the willingness to work by reducing inhibitory transmission to ventral pallidal neurons.

The authors develop a nanomechanical straining technique to reveal previously inaccessible intervalley excitons in suspended WSe₂ and WS₂. They further unveil a mechanism that brightens the dark intervalley excitons through strain-controlled hybridization with intravalley excitons.

Fine-mapping of causal variants and integration of epigenetic and chromatin conformation data identify likely target genes for 150 breast cancer risk regions.

Structural cells implement a broad range of immune-regulatory functions beyond their roles as barriers and connective tissues, and they utilize an epigenetically encoded potential for immune gene activation in their rapid response to viral infection.

Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity. Here, the authors report the genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using ATAC-seq, and 10 matched RNA-seq datasets, providing a resource for studying epigenome deregulation in CLL.

Copy number alterations in stem cells impair neural crest differentiation and set the stage for neuroblastoma-like traits and tumours. This study hints at early tumourigenesis mechanisms and finds developmental gene signatures linked to prognosis.

ChIPmentation combines chromatin immunoprecipitation with on-bead tagmentation for rapid and highly robust ChIP-seq library preparation.

Reduced-representation bisulfite sequencing, optimized for DNA amounts as low as 30 nanograms and robust enough to process DNA extracted from formalin-fixed, paraffin-embedded tissue, allows genome-scale mapping of DNA methylation in many samples.

DNA methylation is involved in regulatory processes throughout the animal kingdom. Here, the authors map DNA methylation in 535 vertebrates and 45 invertebrates, establishing a reference dataset for cross-species analysis and exploring epigenetic variation across vertebrate evolution.

Deregulation of transcription factors is frequently observed in cancer. Here, the authors develop a blood-based approach to map transcription factor binding, revealing both patient-specific and tumour-specific aberrations

The bone marrow is a common site of metastasis for neuroblastoma patients. Here, the authors perform single cell RNA-seq and ATAC-seq of bone marrow aspirates from 16 subjects and show conservation of tumor cell plasticity in metastases and identify tumor-to-bone marrow cell signals that trigger tumor promoting monocytes.

SMNDC1 is a splicing factor that binds arginine methylation with its Tudor domain. Here, the authors study the protein’s phase-separating behavior and develop small-molecule Tudor domain inhibitors that perturb SMNDC1 function.

Mechanical strain is a powerful tuning knob for excitons in two-dimensional semiconductors. Here, the authors find that under the application of strain, dark and localized excitons in monolayer WSe₂ are brought into energetic resonance, forming a new hybrid state that inherits the properties of the constituent species.

Researchers demonstrate a laser-plasma accelerator-driven free-electron laser in a seeded configuration, where control over the radiation wavelength and longitudinal coherence are achieved.

The International Stem Cell Initiative tests methods in a multisite study to detect pluripotency and teratoma formation (PluriTest, Embryoid Body and Teratoma methods) in human pluripotent stem cells. Here, the authors provide guidelines for their application: only the teratoma assay offers evidence of malignant potential.

DNA methylation quantitative trait locus (mQTL) analyses on 32,851 participants identify genetic variants associated with DNA methylation at 420,509 sites in blood, resulting in a database of >270,000 independent mQTLs.

CROP-seq enables pooled CRISPR screens for complex transcriptome signatures by making gRNA expression detectable in single-cell RNA sequencing.

The hypothalamus is a brain region rich in functionally segregated neurons. Here Romanov and colleagues use single-cell RNA sequencing to distinguish 62 neuronal subtypes and define their neuropeptide and neurotransmitter makeup. They then show that onecut-3-containing dopamine neurons populate the periventricular area and are wired into the circadian circuitry.

In-depth methylation analysis of formalin-fixed paraffin-embedded glioblastoma samples demonstrates heterogeneity between primary and recurring tumors and enables prediction of composition of the tumor microenvironment and insights into progression.