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Scientific Reports|December 17, 2025
Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genesBatuhan Eralp, Emre SeferIEEE Transactions on Computational Biology and Bioinformatics|November 17, 2025
GAT-HiC: Efficient Reconstruction of 3D Chromosome Structure via Residual Graph Attention Neural NetworksBeyza Kaya, Emre SeferIEEE Transactions on Computational Biology and Bioinformatics|April 14, 2026
Optimal Reconstruction of Graph Evolution History Under Preferential Attachment ModelElena Kudret, Emre SeferComputational Biology and Chemistry|June 13, 2025
The significance of chromosome conformation capture in 3D genome architecture comprehensionSelinay Cetin, Emre SeferScientific Reports|October 29, 2025
Joint analysis of sQTL and Hi-C reveals spatial proximity between sQTLs and target genes in cancer tissuesBatuhan Eralp, Emre SeferBMC Cancer|May 20, 2024
Reference-free inferring of transcriptomic events in cancer cells on single-cell dataBatuhan Eralp, Emre SeferBMC Bioinformatics|March 28, 2026
A comparative analysis of topological domain callers over RNA-associated interactomeTuna Alaygut, Emre SeferPlos Computational Biology|May 3, 2011
Network archaeology: uncovering ancient networks from present-day interactionsSaket Navlakha, Carl KingsfordBioinformatics (Oxford, England)|April 26, 2015
Data-dependent bucketing improves reference-free compression of sequencing readsRob Patro, Carl KingsfordBioinformatics (Oxford, England)|February 27, 2010
The power of protein interaction networks for associating genes with diseasesSaket Navlakha, Carl KingsfordPageof 11