Author

Olga Pushkarev

SIB Swiss Institute of BioinformaticsORCID 0000-0002-4208-4498Unclaimed ORCID profile · follow to get notified of new preprints

Additional preprints under this name without ORCID

Olga Pushkarev1 paper · Stanford University;

Biology Disciplines

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Bioinformatics· 1 Genomics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 3 Assay:ChIP-seq· 2 Approach:statistical model· 2 Assay:ATAC-seq· 1 Research Focus:differential expression· 1 Organism:human· 1 Approach:machine learning (classical)· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Bart DeplanckeiD· 3 shared Guido van MierloiD· 2 shared Judith F. Kribelbauer-SwietekiD· 2 shared Vincent GardeuxiD· 2 shared Wouter SaelensiD· 2 shared Julie RusseiliD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

6 top collaborators · 14 mutual co-author links

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3 shared papersBioinformatics

Bart DeplanckeORCID

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3 papers

Recent·Most cited

BioinformaticsNature CommunicationsPeer-reviewedJan 2, 2025

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Wouter Saelens, Olga Pushkarev, Bart Deplancke

ChromatinHD uses raw ATAC-seq data to predict gene expression and detect differential accessibility, outperforming existing methods by capturing functional accessibility changes.

9 citations

ATAC-seqscRNA-seq

𝕏 PostBluesky

GenomicsbioRxivPreprintOct 11, 2023

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Olga Pushkarev, Guido van Mierlo, Judith F. Kribelbauer-Swietek…·Bart Deplancke

The paper evaluates CM mapping tools, shows cell type-specific CRE interactions, and demonstrates how non-coding variants affect CM activity in a cell type-specific manner.

DOI 10.1101/2023.10.11.561870

𝕏 PostBluesky

Molecular BiologybioRxivPreprintMay 5, 2023

Context transcription factors establish cooperative environments and mediate enhancer communication

Judith F. Kribelbauer-Swietek, Olga Pushkarev, Vincent Gardeux…·Bart Deplancke

The paper identifies 'context-only' transcription factors that contribute to enhancer communication by forming cooperative environments with pioneer factors.

4 citations

ChIP-seqstatistical model

𝕏 PostBluesky