Author

Ali Ali

University of Maryland, College ParkORCID 0000-0002-7058-5150Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 4

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:bulk RNA-seq· 2 Research Focus:gene regulatory network inference· 2 Research Focus:GWAS / association mapping· 2 Assay:whole-genome sequencing· 2 Assay:ChIP-seq· 1 Approach:experimental assay· 1 Research Focus:genome assembly· 1

Frequent Co-Authors

Mohamed SalemiD· 4 shared Rafet Al-TobaseiiD· 2 shared Timothy D. LeedsiD· 2 shared Yniv PaltiiD· 2 shared Akash Raghu· 1 shared Brett Kenney· 1 shared Brian E. ScheffleriD· 1 shared Daniela A. L. LourencoiD· 1 shared

Activity by Year

2018-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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4 shared papersGenomics

Mohamed SalemORCID

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4 papers

Recent·Most cited

GenomicsMolecular Ecology ResourcesPeer-reviewedJun 17, 2026

De novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference

Ali Ali, Geoffrey C. Waldbieser, Ramey C. Youngblood…·Yniv Palti

The paper presents de novo genome assemblies of four rainbow trout lines to identify structural variants and build a pangenome reference for studying domestication and adaptation.

2 citations

whole-genome sequencingstatistical model

𝕏 PostBluesky

GenomicsbioRxivPreprintMay 27, 2026

QTL spanning the TGF-β2 locus is associated with muscle fiber hypertrophy in rainbow trout

Akash Raghu, Guglielmo Raymo, Ridwan Olawale Ahmed…·Mohamed Salem

The paper identifies a QTL spanning the TGF-β2 locus associated with muscle fiber hypertrophy in rainbow trout using GWAS and transcriptomic analysis.

DOI 10.64898/2026.05.24.727516

bulk RNA-seqstatistical model

𝕏 PostBluesky

GenomicsScientific ReportsPeer-reviewedMar 14, 2026

Splicing Retention and Enhancer Divergence Govern the Evolutionary Fate of Ohnologues Following Whole-Genome Duplication in Rainbow Trout

Ali Ali, Rafet Al-Tobasei, Huaijun Zhou, Mohamed Salem

This study examines the evolution of alternative splicing and enhancer divergence in rainbow trout ohnologues after a whole-genome duplication, showing that independent splicing and enhancer rewiring are key factors in their long-term evolutionary fate.

1 citation

ChIP-seqwhole-genome sequencing

𝕏 PostBluesky

GenomicsFrontiers in GeneticsPeer-reviewedSep 19, 2018

Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout

Mohamed Salem, Rafet Al-Tobasei, Ali Ali…·Timothy D. Leeds

The paper identifies QTL affecting muscle yield in rainbow trout using a 50K transcribed gene SNP-chip, finding larger genetic variance explained compared to previous studies.

55 citations

non-human primatebulk RNA-seq

𝕏 PostBluesky