Author

Pinar Cakmak

Goethe University FrankfurtORCID 0009-0007-5229-9357Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1 Research Focus:deconvolution· 1

Frequent Co-Authors

Aakanksha SinghiD· 2 shared Jadranka MacasiD· 2 shared Jennifer H. LuniD· 2 shared Jonathan Schupp· 2 shared Karl Heinz Plate· 2 shared Katharina ImkelleriD· 2 shared Yvonne ReissiD· 2 shared Eike SteidliD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Aakanksha SinghORCID

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2 papers

Recent·Most cited

BioinformaticsGenome biologyPeer-reviewedAug 13, 2026

Benchmarking cell-type deconvolution in cross-platform transcriptomic data

Aakanksha Singh, Pinar Cakmak, Jennifer H. Lun…·Katharina Imkeller

This study benchmarks cell-type deconvolution methods across cross-platform transcriptomic data, finding that log-normal regression methods like SpatialDecon perform most reliably.

2 citations

bulk RNA-seqstatistical model

𝕏 PostBluesky

ImmunologyImmunityPeer-reviewedOct 21, 2025

Glioma-associated tertiary lymphoid structures are sites of lymphocyte clonal expansion and plasma cell formation

Pinar Cakmak, Jennifer H. Lun, Aakanksha Singh…·Katharina Imkeller

The paper identifies tertiary lymphoid structures in gliomas as sites of immune response, showing they correlate with better survival and involve T and B cell clonal expansion and plasma cell formation.

43 citationstop 1%

humanbulk RNA-seq

𝕏 PostBluesky