Author

Siqi Shen

University of Wisconsin–MadisonORCID 0000-0003-1661-1247Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:dimensionality reduction· 2 Assay:Hi-C· 2 Research Focus:benchmarking· 1 Assay:ChIP-seq· 1 Approach:contrastive learning· 1 Research Focus:database / resource· 1 Research Focus:deconvolution· 1

Frequent Co-Authors

Sündüz KeleşiD· 3 shared Ye ZhengiD· 2 shared Chenyang DongiD· 1 shared

Activity by Year

2021-2023 · peak 1/yr

Co-Author Collaboration Network

3 top collaborators · 2 mutual co-author links

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3 shared papersBioinformatics

Sündüz KeleşORCID

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3 papers

Recent·Most cited

BioinformaticsBioinformaticsPeer-reviewedMar 30, 2023

AdaLiftOver: High-resolution identification of orthologous regulatory elements with adaptive liftOver

Chenyang Dong, Siqi Shen, Sündüz Keleş

AdaLiftOver identifies orthologous regulatory elements across species by improving upon sequence conservation methods with epigenomic and sequence grammar features.

6 citations

humanmouse

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BioinformaticsBioinformaticsPeer-reviewedJun 2, 2022

scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data

Siqi Shen, Ye Zheng, Sündüz Keleş

scGAD provides a dimension reduction tool for scHi-C data to explore gene-level chromatin interactions and integrate with other single-cell modalities.

11 citations

Hi-Cstatistical model

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BioinformaticsbioRxivPreprintMar 10, 2021

Normalization and De-noising of Single-cell Hi-C Data with BandNorm and 3DVI

Ye Zheng, Siqi Shen, Sündüz Keleş

This paper introduces BandNorm and 3DVI to normalize and de-noise scHi-C data, improving performance in cell type separation and 3D genomic structure recovery.

7 citations

Hi-Cdeep learning

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