Author

Arif Harmanci

The University of Texas Health Science Center at Houston

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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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Research Focus:development & morphogenesis· 1 Assay:electronic health records· 1

Frequent Co-Authors

Alessandra BreschiiD· 1 shared Alex Dobin· 1 shared Andrea Tanzer· 1 shared Baikang Pei· 1 shared Carrie A Davis· 1 shared Cedric Notredame· 1 shared Chris Zaleski· 1 shared Dmitri Pervouchine· 1 shared

Activity by Year

2014-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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1 shared paperBioinformatics

Alessandra BreschiORCID

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2 papers

Recent·Most cited

RDEmbed: A Sentence-Embedding Framework for Rare Disease Phenotype Representation and Phenotypic Similarity Analysis

Xinghua Wang, Jianlian Wang, Zijian Zhang, Hongfang Liu, Arif Harmanci

RDEmbed uses sentence embeddings to analyze rare disease phenotypes from clinical text, outperforming ontology-based methods in similarity analysis and clustering.

bioRxiv · Oct 19, 2026 · PreprintBioinformatics

Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes

Dmitri Pervouchine, Sarah Djebali, Alessandra Breschi, Carrie A Davis, Pablo Prieto Barja, Alex Dobin, Andrea Tanzer, Julien Lagarde, Chris Zaleski, Lei-Hoon See, Meagan Fastuca, Jorg Drenkow, Huaien Wang, Giovanni Bussotti, Baikang Pei, , Thomas R Gingeras

The paper analyzes RNA-seq data from multiple mouse tissues to identify genes with conserved expression patterns across species and cell types, revealing evolutionary constraints in gene expression.

bioRxiv · Oct 30, 2014Bioinformatics