Nikolaus D. Schultz

Systemic iron sequestration restricts the intratumoral CD8+ T cell landscape in pancreas cancer

This study shows that systemic iron sequestration via hepcidin reduces CD8+ T cells in pancreas cancer, linking iron dysregulation to tumoral immunity.

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Loss of extracellular matrix-integrin signaling switches off YAP/TEAD and lets prostate adenocarcinoma organoids turn neuroendocrine; LATS inhibition reverses it, and combined YAP, NOTCH and AR inhibition fully reprograms them.

Integrated Clinicogenomic Risk Modeling for Metachronous Second Primary Cancers

The paper develops and validates a clinicogenomic risk model to predict second primary cancers in cancer survivors using genetic, clinical, and lifestyle factors.

Generalist large language models complement tailor-made predictors for tumor genomics interpretation

This paper evaluates generalist large language models (LLMs) in tumor genomic interpretation tasks, finding they can complement or outperform task-specific models in some cases.

MYC pathway reprogramming through a TIP60 coactivator switch in neuroendocrine lineage transition in prostate cancer

The paper identifies a TIP60 coactivator switch in neuroendocrine prostate cancer, revealing a therapeutic target for MYC-driven diseases.

Integrated histopathologic modeling of detailed tumor subtypes and actionable biomarkers

The paper develops Mosaic, a machine learning system that classifies tumors into detailed subtypes and identifies molecular phenotypes using histopathologic and genomic data from a large patient cohort.

MutationAssessor in cBioPortal

MutationAssessor version 4 provides updated functional impact scores for mutations using expanded data and improved analysis methods, now integrated into cBioPortal.

Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers

This study introduces tumor break load (TBL) as a measure of genomic instability across cancers, showing its association with gene expression changes and clinical outcomes.

BRCA2 reversion mutation-independent resistance to PARP inhibition in prostate cancer through loss of function perturbations in the DNA pre-replication complex

This study identifies loss of function mutations in the DNA pre-replication complex as a mechanism for PARP inhibitor resistance in BRCA-mutant prostate cancer, independent of reversion mutations.

Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement

The paper describes how the Human Tumor Atlas Network shares data through standards, infrastructure, and community engagement, making datasets accessible via multiple platforms.

Multimodal histopathologic models stratify hormone receptor-positive early breast cancer

This paper develops a multimodal transformer model using H&E images and text reports to predict recurrence scores in hormone receptor-positive breast cancer, achieving high accuracy and generalizability.

Paired primary-metastasis patient-derived organoids and mouse models identify phenotypic evolution and druggable dependencies of peritoneal metastasis from appendiceal cancer

The paper develops patient-derived organoids and mouse models of appendiceal cancer to identify phenotypic changes and drug targets in peritoneal metastasis.

Clinico-genomic features predict distinct metastatic phenotypes in cutaneous melanoma

This study identifies distinct metastatic phenotypes in cutaneous melanoma using clinico-genomic data and machine learning, linking specific mutations and clinical factors to organ-specific metastasis.

Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma

This study uses spatial profiling to show immune suppression and microenvironment changes in fallopian tube precursors of high-grade serous ovarian cancer.

Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers

The paper identifies a subset of mismatch repair proficient colorectal cancers with high immune infiltration that may benefit from immune checkpoint inhibitors, using spatial profiling and genomics.

Machine learning predictions improve identification of real-world cancer driver mutations

The paper uses machine learning to identify cancer driver mutations, finding that methods incorporating protein structure or functional genomic data outperform those using only evolutionary data, and validates their predictions using real-world patient cohorts.

Tumor suppressor heterozygosity and homologous recombination deficiency mediate resistance to front-line therapy in breast cancer

The paper identifies how germline and somatic mutations interact to cause resistance to CDK4/6 inhibitors in breast cancer and proposes a sequential treatment strategy using PARP inhibitors.

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

Enabling cross-study analysis of RNA-Sequencing data

This paper presents a pipeline to unify RNA-seq data from different studies by removing batch effects, enabling cross-study analysis.

A multi-method approach for proteomic network inference in 11 human cancers

This study evaluates 13 network inference methods on RPPA proteomic data from 11 cancers to identify common protein-protein interactions across tumor types.

Comparing cancer cell lines and tumor samples by genomic profiles

The paper develops a computational method to compare cancer cell lines and tumor samples using genomic profiles, identifying suitable and unsuitable models for six cancer types.

Protein Domain Hotspots Reveal Functional Mutations across Genes in Cancer

The paper identifies rare functional mutations in cancer by mapping them to protein domain hotspots across 22 tumor types, revealing both known and novel mutations with functional implications.

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

The paper identifies cancer driver pathways by detecting mutual exclusivity patterns in genomic alterations across TCGA datasets, revealing previously unreported driver events.

Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma

The paper analyzes RNA splicing patterns in kidney renal clear cell carcinoma patients to identify tumor-specific isoforms and splicing quantitative trait loci associated with disease.

Cancer-associated recurrent mutations in RNase III domains of DICER1

The paper identifies recurrent DICER1 mutations in cancer that disrupt miRNA processing and cause mRNA expression imbalances, contributing to oncogenesis.