Author

Castle Raley

Leidos Biomedical Research Inc. (United States)

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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Genetics· 2 Genomics· 2 Developmental Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Research Focus:gene regulatory network inference· 2 Assay:whole-genome sequencing· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Organism:fungi (other)· 1 Assay:long-read sequencing· 1

Frequent Co-Authors

Benjamin SchwessingeriD· 2 shared Cory D. HirschiD· 2 shared Jana SperschneideriD· 2 shared Marisa E. MilleriD· 2 shared Melania FigueroaiD· 2 shared Narayana M. UpadhyayaiD· 2 shared Peter N. DoddsiD· 2 shared Alejandro Aguilera-CastrejoniD· 1 shared

Activity by Year

2014-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersGenetics

Benjamin SchwessingerORCID

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Author profile →

5 papers

Recent·Most cited

Reconstituting Mouse Embryogenesis Ex Utero from Gastrulation to Fetal Development Reveals Maternally Independent Metabolic Programs

Dmitry Lokshtanov, Shihong Max Gao, Weizhi Xu, Avraham Kosman, Francesco Roncato, Nancy De La Cruz, Nawal A. Khan, Andrea Woods, Ian J. Campbell, Andrew Woehler, Christina P. Christoforou, Lang Ding, Amy Hu, Monique Copeland, Lihua Wang, , Alejandro Aguilera-Castrejon

This paper uses ex utero culture to study mouse embryogenesis from gastrulation to fetal development, revealing metabolically independent programs and environmental influences on metabolic transitions.

bioRxiv · Mar 18, 2026 · PreprintDevelopmental Biology

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation

Feng Li, Narayana M. Upadhyaya, Jana Sperschneider, Oadi Matny, Hoa Nguyen‐Phuc, Rohit Mago, Castle Raley, Marisa E. Miller, Kevin A.T. Silverstein, Eva C. Henningsen, Cory D. Hirsch, Botma Visser, Z. A. Pretorius, Brian Joel Steffenson, Benjamin Schwessinger, , Melania Figueroa

The paper shows that the Ug99 wheat stem rust pathogen emerged through somatic hybridisation and nuclear exchange between dikaryons, with one haploid nucleus genotype shared with an older African lineage.

Nature Communications · Nov 7, 2019Peer-reviewedGenetics

De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust

Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana P. Garnica, Narayana M. Upadhyaya, John Paul Rathjen, Jennifer M. Taylor, Robert Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa

This study presents haplotype-phased genome assemblies of two dikaryotic Puccinia coronata f. sp. avenae isolates, revealing structural variation and heterozygous SNPs, and identifies co-expressed effector candidates associated with virulence differences.

mBio · Feb 19, 2018Peer-reviewedGenomics

PacBio library preparation using blunt-end adapter ligation produces significant artefactual fusion DNA sequences

Paul Griffith, Castle Raley, David Sun, Yongmei Zhao, Zhonghe Sun, Monika Mehta, Bao Quoc Tran, Xiaolin Wu

The paper identifies artefactual fusion DNA sequences produced by blunt-end adapter ligation in PacBio library preparation and recommends an alternative A/T overhang method to reduce them.

bioRxiv · Jan 9, 2018 · PreprintGenetics

Preparation of next-generation DNA sequencing libraries from ultra-low amounts of input DNA: Application to single-molecule, real-time (SMRT) sequencing on the Pacific Biosciences RS II.

Castle Raley, David Munroe, Kristie Jones, Yu-Chih Tsai, Yan Guo, Bao Tran, Sujatha Gowda, Jennifer L. Troyer, Daniel R Soppet, Claudia Stewart, Robert Stephens, Jack Chen, TF Skelly, Cheryl Heiner, Jonas Korlach, Dwight Nissley

The paper develops an amplification-free method for preparing DNA sequencing libraries from very low DNA input for PacBio SMRT sequencing, achieving comparable yields with 1000-fold less starting material.

bioRxiv · Mar 25, 2014 · PreprintGenomics