Author

Ilyes Baali

Antalya Bilim ÜniversitesiORCID 0000-0002-8655-1721Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Approach:benchmark study· 1 Research Focus:differential expression· 1 Approach:graph neural network· 1 Assay:long-read sequencing· 1 Approach:optimal transport· 1

Frequent Co-Authors

Cesim ErteniD· 2 shared Hilal KazaniD· 2 shared Andrew Jung· 1 shared Bo WangiD· 1 shared Cyrus L. TamiD· 1 shared Defne Ceyhan· 1 shared Divya Koyyalagunta· 1 shared Evis Hoxha· 1 shared

Activity by Year

2019-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersBioinformatics

Cesim ErtenORCID

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3 papers

Recent·Most cited

GenomicsbioRxivPreprintJul 5, 2025

mRNABench: A curated benchmark for mature mRNA property and function prediction

Ruian Shi, Taykhoom Dalal, Philip Fradkin…·Quaid Morris

mRNABench evaluates self-supervised mRNA foundation models using 13 datasets and 81 tasks to assess their ability to predict mRNA properties.

3 citations

humanlong-read sequencing

𝕏 PostBluesky

BioinformaticsScientific ReportsPeer-reviewedDec 15, 2020

DriveWays: A Method for Identifying Possibly Overlapping Driver Pathways in Cancer

Ilyes Baali, Cesim Erten, Hilal Kazan

DriveWays identifies overlapping cancer driver pathways by solving an NP-hard optimization problem, outperforming existing methods on TCGA data.

7 citations

statistical modeloptimal transport

𝕏 PostBluesky

BioinformaticsBioinformaticsPeer-reviewedAug 19, 2019

MEXCOWalk: Mutual Exclusion and Coverage Based Random Walk to Identify Cancer Modules

Rafsan Ahmed, Ilyes Baali, Cesim Erten…·Hilal Kazan

MEXCOWalk identifies cancer driver modules using mutual exclusion and coverage in protein-protein interaction networks, outperforming existing methods on TCGA data.

33 citations

humanwhole-exome sequencing

𝕏 PostBluesky