Author

Il‐Youp Kwak

Chung-Ang UniversityORCID 0000-0002-7117-7669Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:DNA methylation· 2 Research Focus:gene regulatory network inference· 2 Assay:whole-genome sequencing· 2 Approach:deep learning· 1 Research Focus:imputation· 1 Assay:scRNA-seq· 1 Approach:statistical model· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Wuming GongiD· 3 shared Daniel J. GarryiD· 2 shared Juhyun LeeiD· 2 shared Taein Kang· 2 shared Aayush Prakash· 1 shared Abdul Muntakim RafiiD· 1 shared Andigoni MalousiiD· 1 shared Andreas Fønss MølleriD· 1 shared

Activity by Year

2018-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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3 shared papersBioinformatics

Wuming GongORCID

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Author profile →

3 papers

Recent·Most cited

Evaluation and optimization of sequence-based gene regulatory deep learning models

Abdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, Dohoon Lee, Danyeong Lee, N. S. KIM, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il‐Youp Kwak, Georgy Meshcheryakov, Andrey S. Lando, Arsenii O. Zinkevich, Byeongchan Kim, Juhyun Lee, , Carl G. de Boer

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

Nature Biotechnology · Oct 11, 2024Peer-reviewedGenomics

Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences

Il‐Youp Kwak, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Daniel J. Garry, Jianyi Jay Zhang, Wuming Gong

Proformer predicts gene expression from promoter sequences using a hybrid transformer model with improved performance over conventional designs.

BMC Bioinformatics · Feb 20, 2024Peer-reviewedBioinformatics

DrImpute: Imputing dropout events in single cell RNA sequencing data

Wuming Gong, Il‐Youp Kwak, Pruthvi Pota, Naoko Koyano‐Nakagawa, Daniel J. Garry

DrImpute imputes dropout events in scRNA-seq data, improving statistical tools that do not account for these events.

BMC Bioinformatics · Jun 8, 2018Peer-reviewedBioinformatics