Academic Publications
Published academic work
Updated list can also be found here: https://ogbunulab.yale.edu/selected-publications
2023
Diaz-Colunga J, Sanchez A, Ogbunugafor CB*. Environmental modulation of global epistasis in a drug resistance fitness landscape. Nature Communications. 2023 Dec 5;14(1):8055.
Ogbunugafor, C. Brandon*. “The Dose Makes the Poison and the Lesson.” Evolution. (2023): 295.
Surasinghe S, Kabengele K, Turner PE, Ogbunugafor CB*. The context-specificity of virulence evolution revealed through evolutionary invasion analysis. arXiv preprint arXiv:2311.04369. 2023 Nov 7.
Ogbunugafor CB*, Guerrero RF, Miller-Dickson MD, Shakhnovich EI, Shoulders MD. Epistasis and pleiotropy shape biophysical protein subspaces associated with drug resistance. Physical Review E. 2023 Nov 14;108(5):054408.
Ogbunugafor, CB*. “Awakening innovations in biology and culture.” (2023): 1351–1352. Nature Ecology & Evolution.
Ogbunugafor CB*. Mutations that enhance evolvability may open doors to faster adaptation. Nature Communications. 2023 Oct 9;14(1):6310.
Yitbarek S, Guittar J, A Knutie S, Ogbunugafor CB. Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination. iScience. 2019 May 24.
Yoon J, Patrick JE, Ogbunugafor CB, Shoulders MD. Viral Evolution Shaped by Host Proteostasis Networks. Annual Review of Virology. 2023 Apr 18;10.
Segrè D, Mitri S, Shou W, Süel GM, Mizrahi I, Kelly L, Rebolleda-Gómez M, Ratzke C, Ogbunugafor CB, Schwartzman JA, Kryazhimskiy S. What do you most want to understand about how collective features emerge in microbial communities? Cell Systems. 2023 Feb 15;14(2):91–7.
Klein B, Ogbunugafor CB*, Schafer BJ, Bhadricha Z, Kori P, Sheldon J, Kaza N, Sharma A, Wang EA, Eliassi-Rad T, Scarpino SV. COVID-19 amplified racial disparities in the US criminal legal system. Nature. 2023 Apr 19:1–7.
Guerrero RF, Dorji T, Ra’Mal MH, Shoulders MD, Ogbunugafor CB*. Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications. bioRxiv. 2023 Apr 8.
Mwakibete L, Greening SS, Kalantar K, Ahyong V, Anis E, Miller EA, Needle DB, Oglesbee M, Thomas WK, Sevigny JL, Gordon LM. Metagenomics for pathogen detection during a wildlife mortality event in songbirds. bioRxiv. 2023:2023–06.
Bergstrom CT, Ogbunugafor CB. Undue publicity for flawed fraud detector. Science. 2023 Jul 14;381(6654):134-.
Ogbunugafor CB*, Jackson F. On evolutionary medicine and health disparities. Evolution, Medicine, and Public Health. 2023 Jan 1;11(1):126–8.
Ogbunugafor, CB*. “Awakening innovations in biology and culture.” Nature Ecology & Evolution(2023): 1351–1352.
Taylor LU, Ronconi RA, Spina HA, Jones ME, Ogbunugafor CB, Ayala AJ. Limited Outbreak of Highly Pathogenic Influenza A (H5N1) in Herring Gull Colony, Canada, 2022. Emerging Infectious Diseases. 2023 Oct;29(10):2150.
Surasinghe S, Rodriguez M, Meszaros V, Molofksy J, Almagro-Moreno S, Ogbunugafor CB*. Pathogen Emergence As Complex Biological Invasion: Lessons From Dynamical Systems Modeling. Northeast Journal of Complex Systems (NEJCS). 2023;5(1):4.
Ayala AJ, Munyenyembe K, Almagro-Moreno S, Ogbunugafor CB*. Meteorological associations of Vibrio vulnificus clinical infections in tropical settings: Correlations with air pressure, wind speed, and temperature. PLoS Neglected Tropical Diseases. 2023 Jul 6;17(7):e0011461.
Ayala AJ, Ogbunugafor CB*. When Vibrios Take Flight: A Meta-Analysis of Pathogenic Vibrio Species in Wild and Domestic Birds. InVibrio spp. Infections 2023 Feb 16 (pp. 295–336). Cham: Springer International Publishing.
2022
Van Nouhuijs F, Arakkal Antony M, Orcales F, Gozashti L, Roy SW, Ogbunugafor CB, Pennings PS. A phylogenetic approach to studying the roles of within-host evolution and between-host transmission of resistance for clinical Escherichia coli infections. bioRxiv. 2022:2022–12.
Ogbunugafor CB*, Edge MD*. Gattaca as a lens on contemporary genetics: marking 25 years into the film’s “not-too-distant” future. Genetics. 2022 Dec;222(4):iyac142. (Featured article, also on the cover of the December, 2022 issue)
*Co-lead author
Pennings PS*, Ogbunugafor CB*, Hershberg R* (2022). Reversion is most likely under high mutation supply, when compensatory
mutations don’t fully restore fitness cost. G3; https://doi.org/10.1093/g3journal/jkac190 *Co-lead author
Draghi JC and Ogbunugafor CB (2022). Exploring the expanse between theoretical questions and experimental approaches in the modern study of evolvability J Exp Zool B Mol Dev Evol. 2022;1–10. Available here.
Ogbunugafor C.B., Scarpino, S.V. (2022). Higher-Order Interactions in Biology: The Curious Case of Epistasis. In: Battiston, F., Petri, G. (eds) Higher-Order Systems. Understanding Complex Systems. Springer, Cham. https://doi.org/10.1007/978-3-030-91374-8_18
Ogbunugafor CB (2022). 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, Shoulders MD (2022). 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
Williams BJ, Ogbunugafor CB, Althouse BM, Hébert-Dufresne L. Immunity-induced criticality of the genotype network of influenza A (H3N2) hemagglutinin. PNAS nexus. 2022 Sep;1(4):pgac143.
Ayala AJ, Munyenyembe K, Almagro-Moreno S, Ogbunugafor CB. Patterns of air pressure, wind speed, and temperature are correlated with an increased risk of clinical infection from Vibrio vulnificus in endemic areas. medRxiv. 2022 Jan 1.
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
2021
Klein B*, Ogbunugafor CB*, Schafer BJ, Bhadricha Z, Kori P, Sheldon J, Kaza N, Wang EA, Eliassi-Rad T, Scarpino SV*, Hinton E*. The COVID-19 pandemic amplified long-standing racial disparities in the United States criminal justice system. medRxiv. 2021 Jan 1 (Now in press, Nature)
*Co-corresponding author
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)
2020
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
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.
2019
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
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
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
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).
Pre-2019
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. A new take on John Maynard Smith’s concept of protein space for understanding molecular evolution. 2016. PLoS Computational Biology 12(10): e1005046.
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
Ogbunugafor CB and Robinson SP. OFFl Models: Novel schema for dynamical modeling of biological systems. 2016. PLOS ONE 11(6): e01568
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
Maru DS, Ogbunugafor CB, and Basu S. “Treatment of latent tuberculosis infection.” 2009. Tuberculosis. : 776–82.
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)
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
