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Jason Miller

Jason Rafe Miller

Associate Professor
Department of Computer Science, Mathematics, Engineering (CME)
College of Science, Technology, Engineering, Mathematics, Nursing (CSTEMN)
Shepherd University, Shepherdstown WV 25443 USA

office: 309 Byrd Science and Technology Center
office phone: 304-876-5070
maps: Google, Static, Interactive.



Courses Taught

CIS 104 – Introduction to CIS
CIS 211 – Computer Language Concepts
CIS 314 – Advanced Language Concepts
CIS 321 – Data Structures
CIS 431 – Algorithms
CIS 481 – Machine Learning

Education and Work History

West Virginia University: PhD
University of Pennsylvania: MS
New York University: BA

J. Craig Venter Institute, 2004-2017
Celera Genomics, 2000-2004
GlaxoSmithKline, 1996-2000

Campus Activities

Co-PI, NSF Campus Cyber Infrastructure planning grant, 2020-2021, to build campus research computing facilities. Also co-PI on Dept of Education implementation grant, 2022-2023.

PI, NASA WV SGC grant, 2021-2022, to build mechanical engineering facilities.

Mentor for grant-funded projects: NASA Fellows, SOARS Scholars, Seeding your Future. Mentor for off-campus events: West Virginia Academy of Sciences, BitCamp, Technica.

Live performance at Frank Hall (news) during the 2019 Appalachian Heritage Festival with the old time music string band, the Gravy Soppers.

Selected Publications

Miller JR & Adjeroh DA (2024) Machine Learning on Alignment Features for Parent-of-Origin Classification of Simulated Hybrid RNA-seq. BMC Bioinformatics.

Bramsiepe J et al. (2023) Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata. The Plant Journal.

van Ekelenburg YS et al. (2023) Spatial and Temporal Regulation of Parent-of-Origin Allelic Expression in the Endosperm. Plant Physiology.

Burnham AJ, Miller JR, et al. (2021) Novel isoforms of influenza virus PA-X and PB1-F2 indicated by automatic annotation. Virus Research.

Miller JR & Adjeroh DA (2020) Exploring Neural Network Models for LncRNA Sequence Identification. Proceedings of IEEE BIBM.

Hornslien KS, Miller JR, Grini PE (2019) Regulation of Parent-of-Origin Allelic Expression in the Endosperm. Plant Physiology.

Miller JR, et al. (2019) A host subtraction database for virus discovery in human cell line sequencing data. F1000Research.

Miller JR, et al.  (2018) A draft genome sequence for the Ixodes scapularis cell line, ISE6. F1000Research.

Miller JR, et al. (2018) Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation. GigaScience.

Koren S, et al. (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research.

Lien S, Koop BF, et al. (2016) The Atlantic salmon genome provides insights into rediploidization. Nature.

Prüfer K … Svante Pääbo. (2012) The bonobo genome compared with the chimpanzee and human genomes. Nature. Includes Miller J et al. (supplement #2) The Bonobo Shotgun Assembly.