Afenteva et al. combine multi-omics, single-cell, and functional analyses to show that diminished type I interferon signaling in cancer cells underlies inherent platinum resistance in ovarian high-grade serous carcinoma. Exogenous interferon-alpha sensitizes cancer cells to cisplatin, nominating interferon pathway stimulation as a precision strategy for refractory disease.

Afenteva et al. combine multi-omics, single-cell, and functional analyses to show that diminished type I interferon signaling in cancer cells underlies inherent platinum resistance in ovarian high-gra...

Analysis of pre- and post-chemotherapy samples collected from 22 patients with high-risk neuroblastoma using single-nucleus RNA and ATAC sequencing and spatial omics characterizes therapy-related chan...

Comparison of paired primary and recurrent glioblastomas at the single-cell transcriptomic level describes molecular and cellular trajectories associated with tumor recurrence, highlighting extensive ...

Here the authors show that chromosomal instability signatures can predict resistance to anthracycline-, taxane- and platinum-based chemotherapeutics in breast, ovarian and prostate cancer and sarcoma....

Yates and Mathey-Andrews et al. dissect the cellular and spatial heterogeneity of esophageal adenocarcinoma across clinical stages. They identify five malignant cell programs with distinct transcriptomic and epigenetic profiles, linked to disease progression, prognosis, and immune response. These programs interact with the tumor microenvironment, highlighting potential therapeutic targets.

Seo et al. demonstrate that CXCL9+ macrophages interacting with CD8+ T cells improve survival outcome in patients with residual TNBC after neoadjuvant chemotherapy, while SPP1+ macrophages and basal-like features combined with HRD predict worse survival in HR+HER2− BCs, and ERBB2 structural variants predict worse survival outcomes in HER2+ BCs.

EpiTrace infers cell mitotic age and evolution from single-cell ATAC-seq data.

CRISPRai simultaneously activates and represses two genes in single cells.

AbstractMotivation. Multiplexed imaging and single-cell analysis are increasingly applied to investigate the tissue spatial ecosystems in cancer and other

Patient stratification is crucial for improving immunotherapy effectiveness. Acha-Sagredo et al. identified an interferon (IFN)-high immunophenotype and CD74 overexpression as predictors for immunotherapy response in colorectal cancer (CRC). This signature, involving cytotoxic T cells and antigen-presenting macrophages, was found in both mismatch repair-deficient and -proficient CRCs. CD74 overexpression could serve as a biomarker, enabling personalized CRC treatment.

Nature Biotechnology - The Protein Design Archive (PDA): insights from 40 years of protein design

Li et al. show through single-cell and functional data that tumor microenvironment remodeling promotes peritoneal metastasis of colorectal cancer through microbiome dysbiosis, neutrophil recruitment a...

Accuracy of gene regulatory network inference is increased by combining multiome single-cell and atlas-scale bulk data.

Chen et al. depict the comprehensive single-cell resolved spatial atlas of SCLC. Spatial analyses identify specific multi-positive tumor cell enriched neighborhood which correlates with aggressive pattern and transition trajectory. ColonyMap algorithm…

Version 1.11: 1.11.0 2025-02-14: Release candidates: rc2 2025-01-24, rc1 2024-12-20. Features: rc1 sample() supports both upsampling and downsampling of observations and variables. subsample() is n...

AbstractSummary. Spatial and temporal intra-tumor heterogeneity drives tumor evolution and therapy resistance. Existing visualization tools often fail to c

AbstractSummary. We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage

Install simpleaf 0.19.0 Install prebuilt binaries via shell script curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/simpleaf/releases/download/v0.19.0/simpleaf-installer.sh | sh...

single cell foundation model for Gene network inference and more - cantinilab/scPRINT