Open Access

In biomedical research, managing computational workflows across numerous projects-with varying parameters, tools, and environments-creates major challenges in scalability, reproducibility, and collaboration. Here we present WESkit, an implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) interface, designed to streamline the execution, monitoring, and documentation of data processing workflows. [...]

To assess the level of awareness, attitudes, and implementation of sustainability practices among gynecologists in Germany, and to identify barriers to sustainable behavior within the field.Climate change increasingly affects gynecological and obstetric care. The world health organization (WHO) and the International federation of gynecology and obstetrics (FIGO) have emphasized the need for stronger climate action in healthcare. [...]

Tumor-associated macrophages (TAMs) and monocytes that accumulate in colorectal cancer (CRC) play a crucial role in shaping the tumor microenvironment (TME) and anti-tumor immune responses. Although TAMs have been linked to both pro- and anti-tumor functions, our understanding of the cues instructing their heterogeneous phenotypes and function in cancer patients remains limited. [...]

Leveraging ferroptosis as a cancer therapy has faced challenges due to the limited bioavailability and systemic toxicities of small-molecule ferroptosis modulators. Small molecule inhibitors such as RSL3 and ML210 trigger ferroptosis by targeting glutathione peroxidase 4 (GPX4), a key enzyme that neutralizes lipid peroxides. [...]

The oncologic value of lymphadenectomy (LND) in biliary tract cancers (BTC) remains controversial. While guidelines recommend retrieval of ≥ 6 lymph nodes to ensure accurate staging, evidence for a therapeutic survival benefit is limited.We retrospectively analyzed 253 consecutive resections for intrahepatic cholangiocarcinoma (iCCA), perihilar cholangiocarcinoma (pCCA), and gallbladder carcinoma (GBC) at a high‑volume hepatobiliary center from a prospectively maintained database (2013-2023). [...]

Microsatellite instability (MSI) is associated with high immunogenicity in tumors due to the abundance of neoantigens, making MSI cancers particularly responsive to immune checkpoint blockade (ICB) therapy. However, a substantial proportion of patients with MSI gastrointestinal (GI) adenocarcinomas do not benefit from ICB, and non-invasive biomarkers for monitoring treatment response are lacking. [...]

Single-cell spatial omics data provides unprecedented insights into disease states. Comprehensive analysis of such data requires frameworks that integrate diverse modalities and enable joint processing of multiple datasets and corresponding metadata.To address these challenges, we introduce InSituPy, a versatile and scalable framework for analyzing spatial omics data from the multi-sample level down to the cellular and subcellular level. [...]

Commercial solutions like 10X cellranger provide robust UMI quantification for their proprietary single-cell protocols, but open methods such as Smart-seq3 lack comparable support.Here, we introduce umite, a Smart-seq3 UMI counting pipeline with a focus on speed and a light memory footprint. Unlike existing tools, umite offers efficient mismatch-tolerant UMI detection, boosting UMI retrieval by 5-15% in benchmarks. [...]

Surgical re-resection for recurrent IDH–wildtype glioblastoma remains controversial, and no molecular biomarkers currently inform on tailoring the extent of cytoreduction and hence onco-functional balance at recurrence. On the other hand, while the prognostic relevance of O6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation is established in glioblastoma. [...]