Barış Ekim, PhD
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Postdoctoral AssociateDownloadHi-Res Photo
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Postdoctoral Associate
Biography
Baris Ekim is a Postdoctoral Associate in the Department of Biomedical Informatics and Data Science (BIDS), supervised by Prof. Haoyu Cheng and Prof. Ira Hall. He received his PhD in Electrical Engineering and Computer Science from Massachusetts Institute of Technology (MIT) in 2025, advised by Prof. Bonnie Berger. Previously, he received his SM in Computer Science from MIT in 2022 and SB in Computer Science and Molecular Biology and SB in Mathematics from MIT in 2020. His research primarily focuses on designing scalable and efficient algorithms and data structures that allow researchers to work with large datasets and gaining biological insights from advances in analysis of sequencing data in order to answer fundamental questions. In particular, he is interested in designing scalable algorithms for downstream genomic data analysis tasks, such as genome assembly, read mapping, and sequence indexing and search.
Last Updated on June 16, 2025.
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Biomedical Informatics & Data Science
Postdoctoral AssociatePrimary
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Education & Training
- PhD
- Massachusetts Institute of Technology (MIT), Computer Science (2025)
- SM
- Massachusetts Institute of Technology (MIT), Computer Science (2022)
- SB
- Massachusetts Institute of Technology (MIT), Computer Science and Molecular Biology (2020)
- SB
- Massachusetts Institute of Technology (MIT), Mathematics (2020)
Research
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Overview
Medical Research Interests
Data Science; Genomics; Informatics; Information Theory; Metagenomics; Social Genomics
Public Health Interests
Bioinformatics; Cancer; Genetics, Genomics, Epigenetics
ORCID
0000-0002-4040-403XCheng Lab
Prof. Haoyu Cheng's group at Yale Biomedical Informatics and Data Science and Yale Center for Genomic Health.
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Research at a Glance
Publications Timeline
A big-picture view of Barış Ekim's research output by year.
Research Interests
Research topics Barış Ekim is interested in exploring.
9Publications
272Citations
Publications
2025
Graph-based deep reinforcement learning for haplotype assembly with Ralphi
Battistella E, Maheshwari A, Ekim B, Berger B, Popic V. Graph-based deep reinforcement learning for haplotype assembly with Ralphi. Genome Research 2025, 35: 2617-2625. PMID: 41238397, PMCID: PMC12667386, DOI: 10.1101/gr.280569.125.Peer-Reviewed Original ResearchCitationsAltmetricralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly
Battistella E, Maheshwari A, Ekim B, Berger B, Popic V. ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly. Lecture Notes In Computer Science 2025, 15647: 349-353. DOI: 10.1007/978-3-031-90252-9_37.ChaptersCitations
2024
Designing efficient randstrobes for sequence similarity analyses
Karami M, Mohammadi A, Martin M, Ekim B, Shen W, Guo L, Xu M, Pibiri G, Patro R, Sahlin K. Designing efficient randstrobes for sequence similarity analyses. Bioinformatics 2024, 40: btae187. PMID: 38579261, PMCID: PMC11034988, DOI: 10.1093/bioinformatics/btae187.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptssequence similarity analysisk-merssequence analysisbioinformatics applicationssimilarity analysisconstruction operationssequenceconstruction methodpublic GitHub repositorytree-based approachconstructionsampling biasevaluation benchmarktime complexityGitHub repositoryseedbioinformaticsdeletion
2023
Efficient minimizer orders for large values of k using minimum decycling sets
Pellow D, Pu L, Ekim B, Kotlar L, Berger B, Shamir R, Orenstein Y. Efficient minimizer orders for large values of k using minimum decycling sets. Genome Research 2023, 33: 1154-1161. PMID: 37558282, PMCID: PMC10538483, DOI: 10.1101/gr.277644.123.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsEfficient mapping of accurate long reads in minimizer space with mapquik
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R. Efficient mapping of accurate long reads in minimizer space with mapquik. Genome Research 2023, 33: 1188-1197. PMID: 37399256, PMCID: PMC10538364, DOI: 10.1101/gr.277679.123.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
2021
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
Ekim B, Berger B, Chikhi R. Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. Cell Systems 2021, 12: 958-968.e6. PMID: 34525345, PMCID: PMC8562525, DOI: 10.1016/j.cels.2021.08.009.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
2020
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets
Ekim B, Berger B, Orenstein Y. A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. Lecture Notes In Computer Science 2020, 12074: 37-53. PMID: 38835399, PMCID: PMC11148856, DOI: 10.1007/978-3-030-45257-5_3.ChaptersCitations
2017
The thermal modeling of deep-hole drilling process under MQL condition
Kuzu A, Berenji K, Ekim B, Bakkal M. The thermal modeling of deep-hole drilling process under MQL condition. Journal Of Manufacturing Processes 2017, 29: 194-203. DOI: 10.1016/j.jmapro.2017.07.020.Peer-Reviewed Original ResearchCitations
2016
The effect of chemical treatment methods on the outdoor performance of waste textile fiber-reinforced polymer composites
Bakkal M, Bodur M, Sonmez H, Ekim B. The effect of chemical treatment methods on the outdoor performance of waste textile fiber-reinforced polymer composites. Journal Of Composite Materials 2016, 51: 2009-2021. DOI: 10.1177/0021998316666335.Peer-Reviewed Original ResearchCitations
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Biomedical Informatics & Data Science
Academic Office
101 College Street, Fl 10, Ste 1021BB
New Haven, CT 06510