Author

Alyssa A. Tran

Baylor College of Medicine

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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Genetic & Genomic Medicine· 3 Genetics· 2

Signature Assays, Organisms & Methods

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Organism:human· 5 Approach:statistical model· 3 Approach:experimental assay· 2 Research Focus:variant effect prediction· 2 Assay:whole-genome sequencing· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:clustering· 1

Frequent Co-Authors

Alan H. BeggsiD· 4 shared Ashok BalasubramanyamiD· 4 shared Brendan LeeiD· 4 shared Carlos A. BacinoiD· 4 shared Christine M. EngiD· 4 shared Daryl A. ScottiD· 4 shared Arjun TarakadiD· 3 shared Calum A. MacRaeiD· 3 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersGenetic & Genomic Medicine

Alan H. BeggsORCID

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Author profile →

5 papers

Recent·Most cited

Domain specific phenotypic expansion associated with variants in MACF1

Nikhita Gogate, Angad Jolly, Jill Anne Rosenfeld, Paulina Bahena Carbajal, Diana Carrasco, Jonathan A. Bernstein, Devon E. Bonner, Tiffany Busa, Ingrid Cristian, Precilla D’Souza, Jennifer Friedman, Svetlana Gorokhova, Thomas Haaf, Isabella Herman, Uğur Ufuk Işın, , Shamil R. Sunyaev

The paper identifies domain-specific phenotypic effects of MACF1 variants outside the GAR domain, revealing broader neurodevelopmental and craniofacial anomalies.

Genetics in Medicine · Oct 1, 2026Peer-reviewedGenetic & Genomic Medicine

Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing

Alexis Ferrasse, Rodrigo Mendez, John E. Gorzynski, Chloe M. Reuter, Jennefer N. Carter, Michael Blas, Undiagnosed Diseases Network, Alyssa A. Tran, Arjun Tarakad, Ashok Balasubramanyam, Brendan Lee, Carlos A. Bacino, Daryl A. Scott, Elaine Seto, Gary D. Clark, , Carlos A. Pardo-Villamizar

This paper demonstrates that ensilication preserves DNA integrity at ambient temperature, enabling diagnostic-quality long-read sequencing without cold-chain infrastructure.

Genome biology · Jun 15, 2026Peer-reviewedGenetic & Genomic Medicine

An optimized variant prioritization process for rare disease diagnostics: recommendations for Exomiser and Genomiser

Isabelle B. Cooperstein, Shruti Marwaha, Alistair N. Ward, Shilpa N. Kobren, Jennefer N. Carter, Undiagnosed Diseases Network, Aaron R. Quinlan, Abdul Aziz Elkadri, Adeline L. Vanderver, Adriana P. Rebelo, Alan H. Beggs, Albert R. La Spada, Alden Huang, Alex Paul, Alexander Miller, , Emily Glanton

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

Genome Medicine · Oct 21, 2025Peer-reviewedGenetic & Genomic Medicine

COPB2 haploinsufficiency causes a coatopathy with osteoporosis and developmental delay

Ronit Marom, Lindsay Catherine Burrage, Aurélie Clément, Bernardo Blanco‐Sánchez, Rossella Venditti, Mahim Jain, Ingo Grafe, Daryl A. Scott, Jill Anne Rosenfeld, Vernon Reid Sutton, Marwan S. Shinawi, Ghayda Mirzaa, Catherine J DeVile, Rowenna Roberts, Alistair Duncan Calder, , Brendan Lee

This study identifies COPB2 haploinsufficiency as a cause of a coatopathy with osteoporosis and developmental delay, showing disrupted collagen trafficking and potential treatment with ascorbic acid.

bioRxiv · Sep 14, 2020 · PreprintGenetics

De novo EIF2AK1 and EIF2AK2 variants are associated with developmental delay, leukoencephalopathy, and neurologic decompensation

Dongxue Mao, Chloe M. Reuter, Maura R. Z. Ruzhnikov, Anita E. Beck, Emily Farrow, Lisa Emrick, Jill Anne Rosenfeld, Katherine M. Mackenzie, Laurie A. Robak, Matthew Thomas Wheeler, Lindsay Catherine Burrage, Mahim Jain, Pengfei Liu, Daniel G. Calame, Sébastien Küry, , Christine M. Eng

The paper identifies de novo variants in EIF2AK1 and EIF2AK2 associated with neurodevelopmental disorders and leukoencephalopathy, showing similar pathogenic mechanisms to CACH/VWM.

The American Journal of Human Genetics · Mar 19, 2020Peer-reviewedGenetics