Author

Sierra S. Nishizaki

University of MichiganORCID 0000-0002-4288-4567Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Assay:ChIP-seq· 2 Approach:statistical model· 2 Research Focus:variant effect prediction· 2 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1

Frequent Co-Authors

Alan P. BoyleiD· 3 shared Jessica A. SwitzenbergiD· 2 shared Cody Morterud· 1 shared Colten Williams· 1 shared Courtney Asman· 1 shared G.A. FarnumiD· 1 shared Melissa L. DrexeliD· 1 shared Monica J. HolmesiD· 1 shared

Activity by Year

2019-2022 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 30 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Alan P. BoyleORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

SEMplMe: A tool for integrating DNA methylation effects in transcription factor binding affinity predictions

Sierra S. Nishizaki, Alan P. Boyle

SEMplMe predicts the effect of DNA methylation on transcription factor binding affinity across all positions in a motif, outperforming SELEX-based predictions for CTCF.

BMC Bioinformatics · Aug 4, 2022Peer-reviewedBioinformatics

The inducible lac operator-repressor system is functional in zebrafish cells

Sierra S. Nishizaki, Torrin L. McDonald, G.A. Farnum, Monica J. Holmes, Melissa L. Drexel, Jessica A. Switzenberg, Alan P. Boyle

The paper demonstrates that the lac operator-repressor system functions in zebrafish cells to modulate gene expression.

Frontiers in Genetics · Jun 18, 2021Peer-reviewedMolecular Biology

Predicting the effects of SNPs on transcription factor binding affinity

Sierra S. Nishizaki, Natalie Ng, Shengcheng Dong, Robert S. Porter, Cody Morterud, Colten Williams, Courtney Asman, Jessica A. Switzenberg, Alan P. Boyle

The paper develops SEMpl, a pipeline that predicts SNP effects on transcription factor binding affinity using ChIP-seq data to identify disease-causing regulatory loci.

Bioinformatics · Aug 1, 2019Peer-reviewedBioinformatics