Author

Leming Shi

Fudan University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:drug response / drug discovery· 1 Organism:human· 1 Approach:machine learning (classical)· 1 Research Focus:variant calling· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Anna GoldenbergiD· 2 shared Benjamin Haibe-Kains· 2 shared Christos Hatzis· 2 shared Hugo JWL Aerts· 2 shared John Quackenbush· 2 shared Nehme El-Hachem· 2 shared Nicolai Juul Birkbak· 2 shared Petr SmirnoviD· 2 shared

Activity by Year

2016-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Anna GoldenbergORCID

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3 papers

Recent·Most cited

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

Luyao Ren, Xiaoke Duan, Lianhua Dong, Rui Zhang, Jingcheng Yang, Yuechen Gao, Rongxue Peng, Wanwan Hou, Yaqing Liu, Jingjing Li, Ying Yu, Naixin Zhang, Jun Shang, Fan Liang, Depeng Wang, , Yuanting Zheng

This paper introduces Quartet DNA reference materials to comprehensively evaluate germline variant calling accuracy across the genome, including difficult regions and batch effects.

Genome biology · Nov 27, 2023Peer-reviewedBioinformatics

Revisiting inconsistency in large pharmacogenomic studies

Zhaleh Safikhani, Mark Freeman, Petr Smirnov, Nehme El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai Juul Birkbak, Christos Hatzis, Leming Shi, Andrew H Beck, Hugo JWL Aerts, John Quackenbush, Benjamin Haibe-Kains

This paper reanalyzes pharmacogenomic data from GDSC and CCLE, finding continued inconsistency in drug sensitivity measures despite improved statistical methods and expanded datasets.

F1000Research · Aug 11, 2017Peer-reviewedBioinformatics

Assessment of pharmacogenomic agreement

Zhaleh Safikhani, Nehme El-Hachem, Rene Quevedo, Petr Smirnov, Anna Goldenberg, Nicolai Juul Birkbak, Christopher E Mason, Christos Hatzis, Leming Shi, Hugo JWL Aerts, John Quackenbush, Benjamin Haibe-Kains

The paper reanalyzes pharmacogenomic data from GDSC and CCLE, finding continued inconsistency in drug response measures despite claims of agreement.

F1000Research · May 9, 2016Peer-reviewedBioinformatics