Author

Eric M. Kernfeld

Johns Hopkins UniversityORCID 0000-0002-2310-8191Unclaimed 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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Assay:bulk RNA-seq· 2 Organism:mouse· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Organism:E. coli· 1 Research Focus:gene regulatory network inference· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Alexis J. BattleiD· 2 shared Patrick CahaniD· 2 shared Aimée Bastidas-PonceiD· 1 shared Anna Fiedler· 1 shared David S. FischeriD· 1 shared Fabian Joachim TheisiD· 1 shared Heiko LickertiD· 1 shared Jan HasenaueriD· 1 shared

Activity by Year

2019-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersBioinformatics

Alexis J. BattleORCID

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3 papers

Recent·Most cited

Model-X knockoffs reveal data-dependent limits on regulatory network identification

Eric M. Kernfeld, Rebecca Keener, Patrick Cahan, Alexis J. Battle

The paper uses model-X knockoffs to assess false positives in regulatory network inference and identifies causal sufficiency as a major limitation.

Cell Systems · Aug 1, 2024Peer-reviewedBioinformatics

A systematic comparison of computational methods for expression forecasting

Eric M. Kernfeld, Yunxiao Yang, Joshua S. Weinstock, Alexis J. Battle, Patrick Cahan

This study benchmarks expression forecasting methods using 11 perturbation datasets, finding that simple baselines often outperform complex models using mean squared error.

bioRxiv · Jul 28, 2023 · PreprintBioinformatics

Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

David S. Fischer, Anna Fiedler, Eric M. Kernfeld, Ryan M. J. Genga, Aimée Bastidas-Ponce, Mostafa Bakhti, Heiko Lickert, Jan Hasenauer, René Maehr, Fabian Joachim Theis

The paper introduces pseudodynamics, a framework to model real-time cellular development using time-series and genetic knock-out data, applied to thymic T-cell maturation.

Nature Biotechnology · Apr 1, 2019Peer-reviewedBioinformatics