We design and implement advanced computational methods for integrative analysis of cancer genomic, transcriptomic and epigenomic data, including high-throughput sequencing (WGS, WES, ChIP-seq, RNA-seq, scRNA-seq), chromatin profiling, transcriptional state characterization, and structural variation detection.
Software Developed by the Boeva Lab
Data Integration and Foundation Models
CancerFoundation – single-cell transcriptomics cancer foundation model.
Barkmann et al., NeurIPS Workshop 2024. Paper.
scTree – discover cellular hierarchies in scRNA-seq data.
Vandenhirtz et al., ICML Workshops 2024. Paper.
Spatial Data Analysis
DeepCMorph – classify histopathological images using cell morphology-aware DNNs.
Ignatov et al., CVPR Workshop 2024. Paper.
Survival Analysis
Sparsesurv – fit sparse survival models using knowledge distillation.
Wissel et al., Bioinformatics 2024. Paper.
SurvBoard – benchmark for multi-omics survival models.
Wissel et al., BioRxiv. Preprint.
ChIP-seq Analysis
CHIPIN – normalize ChIP-seq without spike-in using RNA-seq data. Polit et al., BMC Bioinformatics 2021. Paper.
LILY – detect super-enhancers. Boeva et al., Nature Genetics 2017. PMID.
HMCan / HMCan-diff – detect chromatin modifications and differences. Ashoor et al., Bioinformatics 2013, NAR 2017. HMCan, HMCan-diff.
MICSA, Nebula – TF binding site detection and ChIP-seq web server.
DNA Sequencing
FREEC, ONCOCNV – CNV detection from WGS and amplicon data.
QuantumClone – clonal reconstruction from WGS/WES. Deveau et al., Bioinformatics 2018.
SV-Bay, SVDetect – structural variant detection in cancer genomes.
Sequence Analysis
ChIPmunk – motif discovery. Kulakovskiy et al., Bioinformatics 2010.
AhoPro – motif over-representation. Boeva et al., Algorithms Mol Biol 2007.
TandemSwan – detect fuzzy tandem repeats.
Visualization
Feature Clock – visualize high-dimensional effects. Ovcharenko et al., IEEE VIS 2024. Paper
SegAnnDB – interactive genomic segmentation. Hocking et al., Bioinformatics 2014.
Simulation Tools
RNFtools – evaluate NGS read mappers. Brinda et al., Bioinformatics 2016.
ChIP-seq Simulator – cancer ChIP-seq simulator. Ashoor et al., Bioinformatics 2013.
TGSim – simulate cancer genomes with structural variants.
Explore all our tools at BoevaLab GitHub.