Olli Kallioniemi

Site-Dependent Decoupling of Drug-Biomarker Associations in Clear Cell Renal Cell Carcinoma Revealed by Functional Profiling of Patient-Derived Cell Models

The paper identifies site-dependent drug-biomarker associations in ccRCC using patient-derived models and multi-omic data, revealing discrepancies between genomic predictions and functional drug responses.

Transcriptionally defined AML cell states associate with treatment response and microenvironmental remodeling

This study defines AML cell states through single-cell transcriptomics and links them to drug response and microenvironmental interactions, identifying state-specific vulnerabilities and resistance mechanisms.

Pathway-centric multi-omics and functional precision medicine reveal shared drug vulnerabilities in heterogeneous adult Wilms tumor

This study identifies shared drug vulnerabilities in adult Wilms tumor through multi-omics and functional assays, showing pathway-level dependencies predict drug responses better than single-gene biomarkers.

Chromatin landscape and epigenetic heterogeneity of acute myeloid leukemia

This study identifies 16 AML subgroups based on chromatin accessibility profiles using ATAC-seq in 1,563 cases, revealing epigenetic heterogeneity and its clinical and therapeutic implications.

Pathway activation model for personalized prediction of drug synergy

This paper introduces DIPx, a model predicting drug synergy using pathway activation scores, showing better performance than existing methods on both known and novel drug combinations.

Phosphodiesterase 3A modulators sensitize tumor cells to Bcl-xL and Bcl-2/Bcl-xL inhibitors

This study identifies PDE3A modulators that synergize with Bcl-xL and Bcl-2/Bcl-xL inhibitors to induce tumor regression in sarcoma models.

Fibroblast Activation Protein Defines an Aggressive, Immunosuppressive EMT-associated Tumor Subtype in Highly Inflamed Localized Clear Cell Renal Cell Carcinoma

The paper identifies FAP-expressing EMT-associated cancer cells in highly inflamed localized ccRCC as an aggressive, immunosuppressive subtype linked to poor prognosis and metastasis.

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health

The paper integrates multiomics and digital health data from 96 individuals over 16 months to identify independent molecular factors linked to health outcomes and lifestyle changes.

FusionCatcher - a tool for finding somatic fusion genes in paired-end RNA-sequencing data

FusionCatcher identifies somatic fusion genes in RNA-sequencing data with high detection and validation rates.