Author

Ghassan Filimban

University of California, IrvineORCID 0000-0002-2612-2554Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Bioinformatics· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 4 Organism:mouse· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Research Focus:gene regulatory network inference· 2 Research Focus:cell type annotation· 1 Approach:experimental assay· 1 Assay:long-read sequencing· 1

Frequent Co-Authors

Ali MortazaviiD· 4 shared Grant R. MacGregoriD· 4 shared Heidi Yahan LiangiD· 4 shared Shimako KawauchiiD· 4 shared Barbara J. WoldiD· 3 shared Brian A. WilliamsiD· 3 shared Diane E. TroutiD· 3 shared Elisabeth RebboahiD· 3 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersGenomics

Ali MortazaviORCID

Mutual co-authors in cluster

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4 papers

Recent·Most cited

GenomicsbioRxivPreprintJun 9, 2026

Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation

Ryan J. Weber, Maria Carilli, Elisabeth Rebboah…·Ali Mortazavi

The paper uses hybrid crosses to analyze regulatory variation in mouse tissues, finding cell-type-specific trans-acting effects and highlighting the limitations of bulk tissue analysis.

DOI 10.64898/2026.04.02.716195

mousebulk RNA-seq

𝕏 PostBluesky

GenomicsCell GenomicsPeer-reviewedDec 31, 2025

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation

Elisabeth Rebboah, Ryan Weber, Elnaz Abdollahzadeh…·Ali Mortazavi

The paper characterizes transcriptomes across 8 tissues in 8 mouse strains to identify expression variation linked to genetic differences and phenotypic traits.

6 citations

mousescRNA-seq

𝕏 PostBluesky

BioinformaticsPLoS Computational BiologyPeer-reviewedDec 1, 2025

Long-read sequencing transcriptome quantification with lr-kallisto

Rebekah K. Loving, Delaney K. Sullivan, Fairlie Reese…·Lior S. Pachter

The paper develops lr-kallisto, a tool for accurate long-read transcriptome quantification using ONT data, showing improved results with exome capture.

23 citationstop 2%

long-read sequencingstatistical model

𝕏 PostBluesky

NeuroscienceMolecular NeurodegenerationPeer-reviewedFeb 17, 2023

A Trem2*R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques

Kristine M. Tran, Shimako Kawauchi, Enikö A. Kramár…·Kim N. Green

50 citationstop 4%

mousebulk RNA-seq

𝕏 PostBluesky