The paper identifies and characterizes a novel Crassvirales phage infecting Segatella copri from Egypt, showing amber stop codon reassignment and geographic diversity.

bioRxiv · Aug 26, 2026 · PreprintMicrobiology

A humanized mouse model system mimics prenatal Zika infection and reveals premature differentiation

Allison R. Horvath, Clara M. Abdelmalek, Eunbin Park, Aubrey P. Alexander, Sadhana A. Maheswaran, Anil Patel, Nandi G. Patel, Janet Ruan, Ademide T. Adeyemo, Erin C. Li, Katherine E. Helmicki, Stephen Lin, Paul C. Wang, Zhen Li, Li Wang, , Youssef A. Kousa

This paper develops a humanized mouse model of prenatal Zika infection and shows it mimics human phenotypes, including disrupted neural stem cells and brain injuries.

bioRxiv · Feb 21, 2025 · PreprintNeuroscience

The Great Genotyper: A Graph-Based Method for Population Genotyping of Small and Structural Variants

Moustafa Shokrof, Mohamed Abuelanin, C. Titus Brown, Tamer A. Mansour

The Great Genotyper efficiently genotypes structural variants in large populations using a graph-based method, improving precision and recall while reducing computational time.

GigaScience · Jan 1, 2025Peer-reviewedGenetic & Genomic Medicine

Transcriptomic Meta-analysis Identifies Long Non-Coding RNAs Mediating Zika's Oncolytic Impact in Glioblastoma Multiforme

Youssef A. Kousa, Shriya Singh, Allison R. Horvath, Federica Tomasso, Javad Nazarian, Lisa J. Henderson, Tamer A. Mansour

This study identifies long non-coding RNAs involved in Zika virus's oncolytic effect on glioblastoma multiforme through transcriptomic analysis and validation in cell lines.

bioRxiv · Aug 4, 2024 · PreprintCancer Biology

Building a growing genomic data repository for maternal and fetal health through the PING Consortium

Clara M. Abdelmalek, Shriya Singh, Blain Fasil, Allison R. Horvath, Sarah B. Mulkey, Carlos Curé, Maribel Campos, Denise P. Cavalcanti, Van T. Tong, Marcela Mercado, Marcela Daza, Mónica Marcela Benavides, Jacqueline Acosta, Suzanne M. Gilboa, Diana Valencia, , Youssef A. Kousa

The PING Consortium builds a genomic data repository to study genetic modifiers of prenatal viral infections' effects on brain development and neurodevelopmental outcomes.

medRxiv · May 24, 2024 · PreprintGenetic & Genomic Medicine

MQF and buffered MQF: Quotient filters for efficient storage of k-mers with their counts and metadata

Moustafa Shokrof, C. Titus Brown, Tamer A. Mansour

The paper introduces MQF and buffered MQF, efficient data structures for storing k-mers with counts and metadata, improving space efficiency and speed over existing methods.

BMC Bioinformatics · Feb 16, 2021Peer-reviewedBioinformatics

FGF4 Retrogene On CFA12 Is Responsible For Chondrodystrophy And Intervertebral Disc Disease In Dogs

Emily A. Brown, Peter J. Dickinson, Tamer A. Mansour, Beverly K. Sturges, Miriam Aguilar, Amy E Young, Courtney Korff, Jenna Lind, Cassandra L. Ettinger, Samuel Varon, Rachel E. Pollard, C. Titus Brown, Terje Raudsepp, Danika L. Bannasch

The paper identifies a FGF4 retrogene on CFA12 as the cause of chondrodystrophy and intervertebral disc disease in dogs, with a high odds ratio for IVDD.

Proceedings of the National Academy of Sciences · Oct 11, 2017Peer-reviewedGenetics

Tissue Resolved, Gene Structure Refined Equine Transcriptome

Tamer A. Mansour, Erica Y Scott, Carrie J Finno, Rebecca R Bellone, Michael J. Mienaltowski, M Cecilia Penedo, Pablo J Ross, Stephanie J. Valberg, James D Murray, C. Titus Brown

The paper constructs a refined equine transcriptome using RNA-seq data from multiple tissues, improving gene structure and isoform resolution.

bioRxiv · Sep 23, 2016Genomics