Author

Ilya Soifer

Calico Life Sciences

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

Biology Disciplines

Click to filter author papers

Genomics· 3 Systems Biology· 2

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:experimental assay· 3 Organism:human· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Organism:yeast· 2

Frequent Co-Authors

David G. HendricksoniD· 2 shared Doron LipsoniD· 2 shared Aaron M. WengeriD· 1 shared Aaron W. AdamsoniD· 1 shared Adam FreundiD· 1 shared Alex R. HastieiD· 1 shared Alexander A Gooden· 1 shared Alison RojasiD· 1 shared

Activity by Year

2017-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 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

2 shared papersGenomics

David G. HendricksonORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Jennifer McDaniel, Vaidehi Patel, Nathan D. Olson, Hua‐Jun He, Zhiyong He, Kenneth D. Cole, Alexander A Gooden, Anthony D. Schmitt, Kristin L Sikkink, Fritz Joachim Sedlazeck, HarshaVardhan Doddapaneni, Shalini N. Jhangiani, Donna Marie Muzny, Marie‐Claude Gingras, Heer Hemant Mehta, , Justin M. Zook

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

Scientific Data · Jul 16, 2025Peer-reviewedGenomics

Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform

Gilad Almogy, Mark Pratt, Florian C. Oberstrass, Linda Lee, Dan Mazur, Nate Beckett, Omer Barad, Ilya Soifer, Eddie Perelman, Yoav Etzioni, Martin Sosa, April Jung, Tyson A. Clark, Eliane H. Trepagnier, Gila Lithwick‐Yanai, , Doron Lipson

Open flow cell on a circular wafer with mostly natural nucleotides and no reversible terminators: about 300 bp reads at $1/Gb, 99.6% SNP accuracy on reference human genomes.

bioRxiv · May 29, 2022 · PreprintGenomics

Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin

Michelle Chan, Han Yuan, Ilya Soifer, Tobias M. Maile, Rebecca Y. Wang, Andrea Ireland, Jonathon J. O’Brien, Jérôme Goudeau, Leanne Chan, Twaritha Vijay, Adam Freund, Cynthia J. Kenyon, Bryson D. Bennett, Fiona McAllister, David R. Kelley, , David G. Hendrickson

The paper analyzes replicative senescence in WI-38 cells using multi-omics data, finding early senescence markers, myofibroblast-like transitions, and YAP1/TEAD1 regulation.

eLife · Feb 4, 2022Peer-reviewedGenomics

The Miniature-chemostat Aging Device: A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of replicatively aging yeast

David G. Hendrickson, Ilya Soifer, Bernd J. Wranik, Griffin Kim, Michael C. Robles, Patrick A. Gibney, R. Scott McIsaac

The paper introduces a new platform to study aging yeast by purifying old cells and analyzing their transcriptional and chromatin changes.

eLife · Oct 18, 2018Peer-reviewedSystems Biology

Large-scale rewiring in a yeast hybrid

Rebecca H. Herbst, Dana Bar-Zvi, Sharon Reikhav, Ilya Soifer, Michal Breker, Ghil Jona, Eyal Shimoni, Maya Schuldiner, Avraham A. Levy, Naama Barkai

The paper describes a yeast hybrid with increased growth rate and biomass yield under various conditions, but identifies genetic perturbations and regulatory disruptions associated with heterosis.

BMC Biology · May 11, 2017Peer-reviewedSystems Biology