Author

Ryan S. Ziffra

University of California, San Francisco

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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Developmental Biology· 2 Genomics· 2

Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:statistical model· 4 Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Research Focus:GWAS / association mapping· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Tomasz Jan NowakowskiiD· 3 shared Chang N. KimiD· 2 shared Maximilian HaeussleriD· 2 shared Adib Adnan AblaiD· 1 shared Alex M. CasellaiD· 1 shared Amy B. WilfertiD· 1 shared Amy P MurthaiD· 1 shared Anat KreimeriD· 1 shared

Activity by Year

2019-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersDevelopmental Biology

Tomasz Jan NowakowskiORCID

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4 papers

Recent·Most cited

Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus

Matthew G. Heffel, Jingtian Zhou, Yi Zhang, Dong-Sung Lee, Kangcheng Hou, Oier Pastor-Alonso, Kevin Daniel Abuhanna, Anthony D. Schmitt, Terence Li, Maximilian Haeussler, Brittney D Wick, Martin Jinye Zhang, Fangming Xie, Ryan S. Ziffra, Eran A. Mukamel, , Chongyuan Luo

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

bioRxiv · Oct 7, 2022 · PreprintGenomics

Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth

Noboru J. Sakabe, Ivy Aneas, Nicholas Knoblauch, Débora R. Sobreira, Nicole Clark, Cristina Paz, Cynthia Horth, Ryan S. Ziffra, Harjot Kaur, Xiao Liu, Rebecca L. Anderson, Jean Morrison, Virginia Chu Cheung, Chad A. Grotegut, Timothy E. Reddy, , Marcelo A. Nóbrega

The paper integrates GWAS data with functional genomic annotations of decidual stromal cells to identify loci and target genes associated with gestational duration and preterm birth.

Science Advances · Dec 2, 2020Peer-reviewedGenomics

Human microglia upregulate cytokine signatures and accelerate maturation of neural networks

Galina Schmunk, Chang N. Kim, Sarah S. Soliman, Matthew G. Keefe, Derek Bogdanoff, Darío Tejera, Ryan S. Ziffra, David Shin, Denise E. Allen, Bryant B. Chhun, Christopher S. McGinnis, Ethan A. Winkler, Adib Adnan Abla, Edward F. Chang, Zev J. Gartner, , Tomasz Jan Nowakowski

This study maps human microglia development and identifies cytokine-associated subtypes and functional roles in neural network maturation.

bioRxiv · Mar 24, 2020 · PreprintDevelopmental Biology

Single cell epigenomic atlas of the developing human brain and organoids

Ryan S. Ziffra, Chang N. Kim, Amy B. Wilfert, Tychele N. Turner, Maximilian Haeussler, Alex M. Casella, Pawel F. Przytycki, Anat Kreimer, Katherine S. Pollard, Seth A. Ament, Evan E. Eichler, Nadav Ahituv, Tomasz Jan Nowakowski

The paper maps chromatin accessibility in developing human brain and organoids using scATAC-seq, revealing cell type-specific regulatory elements and their role in neurodevelopment.

bioRxiv · Dec 30, 2019 · PreprintDevelopmental Biology