Author

Joanna E. Handzlik

University of North DakotaORCID 0000-0001-8679-7046Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 2 Bioinformatics· 1 Developmental Biology· 1

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Research Focus:gene regulatory network inference· 4 Approach:statistical model· 4 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Organism:mouse· 2 Research Focus:database / resource· 1 Organism:Drosophila· 1 Assay:long-read sequencing· 1

Frequent Co-Authors

ManuiD· 3 shared Yen Lee LohiD· 2 shared Andrea Repele· 1 shared Artemis G. HatzigeorgiouiD· 1 shared David A. Fehr· 1 shared Ioannis S. VlachosiD· 1 shared Nimasha Samarawickrama· 1 shared Spyros TastsoglouiD· 1 shared

Activity by Year

2019-2026 · peak 1/yr

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10 top collaborators · 20 mutual co-author links

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3 shared papersSystems Biology

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4 papers

Recent·Most cited

Developmental BiologyPLoS Computational BiologyPeer-reviewedMay 12, 2026

The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence

Andrea Repele, Joanna E. Handzlik, Nimasha Samarawickrama…·Manu

The paper profiles gene expression during myeloid differentiation at high temporal resolution, revealing cascading waves of gene regulation that remodel cellular physiology in a characteristic sequence.

DOI 10.1371/journal.pcbi.1014276

mousebulk RNA-seq

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Systems BiologyPLoS Computational BiologyPeer-reviewedJan 14, 2022

Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential progenitors

Joanna E. Handzlik, Manu

The paper uses data-driven dynamical modeling to predict gene regulatory network dynamics during hematopoietic differentiation, finding that neutrophil differentiation is driven by C/EBP and Gfi1 rather than the Gata1-PU.1 switch.

8 citations

mousescRNA-seq

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BioinformaticsScientific ReportsPeer-reviewedJan 20, 2020

Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data

Joanna E. Handzlik, Spyros Tastsoglou, Ioannis S. Vlachos, Artemis G. Hatzigeorgiou

Manatee quantifies small non-coding RNA classes and detects uncharacterized loci from sRNA-Seq data with high accuracy.

29 citations

long-read sequencingstatistical model

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Systems BiologyG3 Genes Genomes GeneticsPeer-reviewedOct 17, 2019

Classification-based Inference of Dynamical Models of Gene Regulatory Networks

David A. Fehr, Joanna E. Handzlik, Manu, Yen Lee Loh

This paper introduces FIGR, a classification-based method for inferring gene regulatory networks, showing it is significantly faster than traditional optimization methods.

5 citations

Drosophilabulk RNA-seq

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