Author

Alper Gokden

New York Genome CenterORCID 0000-0002-9659-7352Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 4 Assay:bulk RNA-seq· 3 Approach:experimental assay· 3 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:variant effect prediction· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Tuuli LappalaineniD· 4 shared Marcello ZiosiiD· 2 shared Margot K. BrandtiD· 2 shared Aaron Wolman· 1 shared Beryl B. CummingsiD· 1 shared Dafni A. GlinosiD· 1 shared Daniel G. MacArthuriD· 1 shared Eoghan Donal HarringtoniD· 1 shared

Activity by Year

2020-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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4 shared papersGenomics

Tuuli LappalainenORCID

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4 papers

Recent·Most cited

Evaluation of noninvasive biospecimens for transcriptome studies

Molly Martorella, Silva Kasela, Renee Garcia-Flores, Alper Gokden, Stephane E. Castel, Tuuli Lappalainen

This study evaluates noninvasive biospecimens for transcriptome studies, finding hair follicles and urine cell pellets to be most promising for disease-relevant applications.

BMC Genomics · Dec 19, 2023Peer-reviewedGenomics

Transcriptome variation in human tissues revealed by long-read sequencing

Dafni A. Glinos, Garrett Garborcauskas, Paul Hoffman, Nava Ehsan, Lihua Jiang, Alper Gokden, Xiaoguang Dai, François Aguet, Kathleen L. Brown, Kiran V. Garimella, Tera Bowers, Maura Costello, Kristin Ardlie, Ruiqi Jian, Nathan R. Tucker, , Beryl B. Cummings

The paper uses long-read RNA-seq data to identify new transcripts and develop a tool to analyze genetic effects on transcript structure, revealing insights into splicing regulation and variant interpretation.

Nature · Aug 3, 2022Peer-reviewedGenomics

An autoimmune disease risk variant has a trans master regulatory effect mediated by IRF1 under immune stimulation

Margot K. Brandt, Sarah Kim-Hellmuth, Marcello Ziosi, Alper Gokden, Aaron Wolman, Nora Lam, Yocelyn Recinos, Zharko Daniloski, John A. Morris, Veit Hornung, Johannes Schumacher, Tuuli Lappalainen

This study identifies a risk variant for autoimmune disease that acts as a trans-eQTL regulating IRF1 under immune stimulation, demonstrating its causal role and mechanism.

PLoS Genetics · Jul 27, 2021Peer-reviewedGenomics

A polyclonal allelic expression assay for detecting regulatory effects of transcript variants

Margot K. Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen

The paper introduces a CRISPR/Cas9-based assay to test regulatory effects of genetic variants and applies it to detect effects in eQTLs and nonsense-mediated decay.

Genome Medicine · Sep 10, 2020Peer-reviewedGenetics