Publications

Population genetics/Protein evolution

Ogbunugafor CB. The mutation effect reaction norm (mu‐rn) highlights environmentally dependent mutation effects and epistatic interactions. Evolution. 2022 Jan 6. Available here:

Yoon J, Nekongo EE, Patrick JE, Hui T, Phillips AM, Ponomarenko AI, Hendel SJ, Sebastian RM, Zhang YM, Butty VL, Ogbunugafor CB. The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope. Plos Biology. 2022 Feb 18;20(2):e3001569. Available here

Pennings PS*, Ogbunugafor CB*, Hershberg R*. Reversion is most likely under high mutation supply, when compensatory mutations don’t fully restore fitness cost. bioRxiv 2020.12.28.424568;
*Equal contribution. Available here

Ogbunugafor CB. A Reflection on 50 Years of John Maynard Smith’s “Protein Space.” Genetics. April 1, 2020 vol. 214 no. 4. 749–754. Available here

Guerrero RF, Scarpino SV, Rodrigues JV, Hartl DL, Ogbunugafor CB. Proteostasis environment shapes higher-order epistasis operating on antibiotic resistance. 2019. Genetics. Jun 1;212(2):565–75. Available here. June 2019 highlighted article in Genetics. Faculty of 1000 Prime selection.

Rodrigues JV*, Ogbunugafor CB*, Hartl DL, Shakhnovich EI. Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity. 2019. Protein science. Jul;28(7):1359–67. Available here
*Co-lead author

Meszaros VA, Miller-Dickson MD, Ogbunugafor CB. Lexical Landscapes as large in silico data for examining advanced properties of fitness landscapes. 2019. PLoS ONE 14(8): e0220891. Available here

Ogbunugafor CB*, Eppstein MJ*. Genetic background modifies the topography of a fitness landscape, influencing the dynamics of adaptive evolution. 2019. IEEE Access;7:113675–83.
*Co-lead author. Available here

Ogbunugafor CB* and Eppstein MJ*. Competition along trajectories governs adaptation rates towards antimicrobial resistance. 2016. Nature Ecology and Evolution 1, Article Number: 0007. Available here
*Co-lead author.

Eppstein MJ and Ogbunugafor CB. Quantifying Deception: A case study in the evolution of antimicrobial resistance. 2016. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2016) (won award for Best Paper, Complex Systems track)

Ogbunugafor CB, Wylie CS, Diakite I, Weinreich DM, and Hartl DL. Adaptive landscape by environment interactions dictate evolutionary dynamics in models of drug resistance. 2016. PLoS Computational Biology. 12(1): e1004710

Ogbunugafor CB and Hartl DL (2016). A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax. 2016. Malaria Journal. Jan 25;15(1):40

Computational epidemiology

Balasubramanian D, López-Pérez M, Grant TA, Ogbunugafor CB, Almagro-Moreno S. Molecular mechanisms and drivers of pathogen emergence. Trends in Microbiology. 2022 Mar 2. Available here

Ayala, Andrea J., and C. Brandon Ogbunugafor. “When Vibrios Take Flight: A Meta-analysis of Pathogenic Vibrios Species in Wild and Domestic Birds.” bioRxiv (2022). Available here

Balasubramanian D, Murcia S, Ogbunugafor CB, Gavilan R, Almagro-Moreno S. J Cholera dynamics: lessons from an epidemic. Med Microbiol. 2021 Jan 8. Link here. (behind a paywall; contact me for more information)

Ogbunugafor CB, Meszaros VA, Miller-Dickson MD, Gomez LM, Murillo AL, and Scarpino SV. Variation in microparasite free-living survival and indirect transmission can modulate the intensity of emerging outbreaks. Scientific Reports 10, 20786 (2020). Available here

Gomez LM,Meszaros VA., Turner WC; Ogbunugafor CB. The Epidemiological Signature of Pathogen Populations That Vary in the Relationship between Free-Living Parasite Survival and Virulence. Viruses 2020, 12, 1055. Available here

Meszaros VA, Miller-Dickson MD, Junior FB-A, Almagro-Moreno S, Ogbunugafor CB. Direct transmission via households informs models of disease and intervention dynamics in cholera. 2020. PLOS ONE 15:e0229837.
Available here

Miller-Dickson Miles D., Meszaros Victor A., Almagro-Moreno Salvador, Ogbunugafor CB. Hepatitis C virus modelled as an indirectly transmitted infection highlights the centrality of injection drug equipment in disease dynamics. 2019. Journal of the Royal Society Interface. Sep 27; 16(158): 20190334. Available here. (Press coverage by Brown University & Science Daily)

Miller-Dickson, M., Meszaros, V.A., Baffour-Awuah Junior, F., Almagro-Moreno, S., and Ogbunugafor, CB. 2019. Waterborne, abiotic and other indirectly transmitted (W.A.I.T.) infections are defined by the dynamics of free-living pathogens and environmental reservoirs. BioRxiv 525089. Available here. Note: this preprint contains some data & methods that were later published in two peer-reviewed manuscripts (described above).

Ogbunugafor CB and Robinson SP. OFFl Models: Novel schema for dynamical modeling of biological systems. 2016. PLOS ONE 11(6): e01568

Theoretical ecology

Yitbarek S, Guittar JL, Knutie SA, Ogbunugafor CB. Deconstructing higher-order interactions in the microbiota: A theoretical examination. 2019. bioRxiv. Jan 1:647156. Available here

Virus evolution

Pham JY, Ogbunugafor CB, Ba AN, Hartl DL. Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes. 2019. MicrobiologyOpen. Available here

Wasik BR, Bhushan A, Ogbunugafor CB, and Turner PE. Prolonged transmission selects for Increased survival of vesicular stomatitis virus. 2014. Evolution. Oct 14.

Ogbunugafor CB, Alto, BW, Overton, TM, Bhushan, A, Morales, NM, and Turner PE. Evolution of increased survival in RNA viruses specialized on cancer-derived cells. 2013. American Naturalist. May;181(5):585–95

Ogbunugafor CB, Basu S, Morales NM, and Turner PE. Combining mathematics and empirical data to predict emergence of RNA viruses that differ in reservoir use. 2010. Philosophical Transactions of the Royal Society of London, Series B. Jun 27;365(1548):1919–30

Malaria vector biology & ecology

Ogbunugafor CB, and Sumba LA. Behavioral evidence for the existence of a region-specific oviposition cue in Anopheles gambiaes. 2008. Journal of Vector Ecology. Dec; Vol 33, №2

Sumba LA, Ogbunugafor CB, Deng AL, Hassanali A. Regulation of oviposition in Anopheles gambiae: Role of inter- and intra-specific signals. 2008. Journal of Chemical Ecology. Nov; 34(11): 1430–6

Omlin FX, Carlson JC, Ogbunugafor CB, Hassanali A. Anopheles gambiae exploits the treehole ecosystem in western Kenya: A new urban malaria Risk? 2007. American Journal of Tropical Medicine and Hygiene, 77(6_Suppl). pp. 264–269

Clinical infectious diseases

Maru DS, Ogbunugafor CB, and Basu S. “Treatment of latent tuberculosis infection.” 2009. Tuberculosis. : 776–82.

Pedagogy and learning tools

Ogbunugafor CB and Hartl DL. A new take on John Maynard Smith’s concept of protein space for understanding molecular evolution. 2016. PLoS Computational Biology 12(10): e1005046.

Health policy

Britto PR, Cerezo A, and Ogbunugafor CB. National ECD policy development: Case Study from the People’s Democratic Republic of Lao. 2009. International Journal of Early Childhood. 40(2)