Jennifer Chang

Hello World!

Jennifer Chang grew up in northern Wisconsin and has been programming (in one language or another) since 2006. At Cornell College, she double majored in Biochemistry and Computer Science graduating in 2011. In 2017, Jennifer earned a PhD in Bioinformatics and Computational Biology from Iowa State University. During her PhD work with Dr. Hui-Hsien Chou, her research software "Mango Graph Studio" led to co-founding a software company (Complex Computation, LLC) and working on two Department of Defense SBIR contracts. To avoid conflict-of-interest due to co-managing a company with her PhD advisor, her major professor was switched to Dr. Pat Schnable. Later, she moved on from the company and was an ORISE USDA-ARS postdoc with Dr. Amy Vincent and automated the swine influenza reports from 2017-2020.

From June 2020 to November 2021, Jennifer shifted to an ORISE SCINet postdoc position with Drs. Andrew Severin and Brian Scheffler where she collaborated on the bioinformatic workbook and the geospatial workbook, submitted slurm jobs, and automated pipelines for different hardware architectures.

In Nov 2021, Jennifer Chang worked as a bioinformatic remote contractor with the Nextstrain project, and later, transitioned to a full time role as a Bioinformatic Analyst III. She aims to write flexible-general-purpose pipelines that reduce tedium and increase joy of discovery. Jennifer cares about collaboration, welcoming environments, and teaching.

Mango Software: Download | User Guide | Startup Experience: Complex Computation, LLC | Morloc, LLC

Some Projects

Publications or Research Outputs

----- 2024 -----

Zeller, M.A., Chang, J., Trevisan, G., Main, R., Gauger, P.C. and Zhang, J., Rapid PRRSV-2 ORF5-based lineage classification using Nextclade. Frontiers in Veterinary Science, 11, p.1419340.

Huddleston, J., Bedford, T., Chang. J., Lee, J., & Neher, R. A. Seasonal influenza circulation patterns and projections for February 2024 to February 2025. 2024 Zenodo.

----- 2023 -----

Chang, J., Stahlke, A.R., Chudalayandi, S., Rosen, B.D., Childers, A.K., Severin, A., polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies. 2023 Genome Biology and Evolution.

Stahlke, A.R., Chang, J., Chudalayandi, S., Heu, C.C., Geib, S.M., Scheffler, B.R., Childers, A.K., Fabrick, J.A., Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton. 2023 G3 Genes|Genomes|Genetics.

----- 2022 -----

Venkatesh D, Anderson TK, Kimble JB, Chang J, Lopes S, Souza CK, Pekosz A, Shaw-Saliba K, Rothman RE, Chen KF, Lewis NS., Baker ALV, Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine. Microbiology Spectrum. 2022 Nov 1:e01781-22.

Arendsee, Z.W., Chang, J., Wurtele, E.S., rmonad: pipelines you can compute on. 2022 The R Journal.

Stahlke, A.R., Chang, J., Tembrock, L.R., Sim, S.B., Chudalayandi, S., Geib, S.M., Scheffler, B.R., Perera, O.P., Gilligan, T.M., Childers, A.K. and Hackett, K.J., A chromosome-scale genome assembly of a Bacillus thuringiensis Cry1Ac insecticidal protein resistant strain of Helicoverpa zea. 2022 Genome Biology and Evolution.

Souza, C.K., Anderson, T.K., Chang, J., Venkatesh, D., Lewis, N.S., Pekosz, A., Shaw-Saliba, K., Rothman, R.E., Chen, K.F. and Vincent, A.L., Antigenic distance between North American swine and human seasonal H3N2 influenza A viruses as an indication of zoonotic risk to humans. 2022 Journal of Virology, pp.JVI-01374.

----- 2021 -----

Arendsee, Z.W., Chang, J., Hufnagel, D.E., Markin, A., Janas-Martindale, A., Vincent, A.L. and Anderson, T.K.. octoFLUshow: an Interactive Tool Describing Spatial and Temporal Trends in the Genetic Diversity of Influenza A Virus in US Swine. 2021 Microbiology Resource Announcements, 10(50), pp.e01081-21.

Kaplan, B.S., Anderson, T.K., Chang, J., Santos, J., Perez, D., Lewis, N. and Vincent, A.L., Evolution and antigenic advancement of N2 neuraminidase of swine influenza A viruses circulating in the United States following two separate introductions from human seasonal viruses. 2021 Journal of Virology, pp.JVI-00632.

Powell JD, Abente EJ, Chang J, Souza CK, Rajao DS, Anderson TK, Zeller MA, Gauger PG, Lewis NS, Vincent AL. Characterization of contemporary 2010.1 H3N2 swine influenza A viruses circulating in United States pigs. 2021 Virology.

Anderson TK, Chang J, Arendsee ZW, Venkatesh D, Souza CK, Kimble JB, Lewis NS, Davis CT, Vincent AL. Swine Influenza A Viruses and the Tangled Relationship with Humans . Cold Spring Harbor Perspectives in Medicine. 2021 Jan 27:a038737.

Zeller, M.A., Chang, J., Vincent, A.L., Gauger, P.C. and Anderson, T.K.,. Spatial and Temporal Coevolution of N2 Neuraminidase and H1 and H3 Hemagglutinin Genes of Influenza A Virus in United States Swine. 2021 Virus Evolution.

----- 2020 -----

Kaplan BS, Kimble JB, Chang J, Anderson TK, Gauger PC, Janas-Martindale A, Killian ML, Bowman AS, Vincent AL. Aerosol transmission from infected swine to ferrets of an H3N2 virus collected from an agricultural fair and associated with human variant infections. 2020 Journal of Virology, 94(16).

----- 2019 -----

Chang J, Anderson TK, Zeller MA, Gauger PC, Vincent AL. octoFLU: Automated Classification for the Evolutionary Origin of Influenza A Virus Gene Sequences Detected in US Swine. Microbiology resource announcements. 2019 Aug 8;8(32):e00673-19.

----- 2018 -----

Duwell MM, Blythe D, Radebaugh MW, Kough EM, Bachaus B, Crum DA, Perkins Jr KA, Blanton L, Davis CT, Jang Y, Vincent A, Chang J, Abney A, Gudmundson L, Brewster M, Polsky L, Rose D, Feldman K. Influenza A (H3N2) variant virus outbreak at three fairs—Maryland, 2017. Morbidity and Mortality Weekly Report. 2018 Oct 26;67(42):1169.

----- 2017 -----

Chang J, Chou HH. Cavatica: A pipeline for identifying author adoption trends among software or methods. In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2017 Nov 13 (pp. 2145-2150). IEEE.

----- 2016 -----

Chang J, Cho H, Chou HH. Mango: combining and analyzing heterogeneous biological networks. BioData mining. 2016 Dec;9(1):25.