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Publications

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Pre-prints

  • Solomon-Lane TK, Hofmann HA. A tagging method for very small fish. bioRxiv [Internet]. 437772. https://doi.org/10.1101/437772
  • Young RL, Weitekamp C, Triki Z, Su Y, Bshary R, Hofmann HA. Shared neural transcriptomic patterns underlie the repeated evolution of mutualistic cleaning behavior in Labridae wrasses. EcoEvoRxiv [Internet]. https://ecoevorxiv.org/4p638/
  • Nugent BM, Stiver KA, Han J, Kindsvater HK, Marsh-Rollo SE, Hofmann HA, Alonzo SH. Morpholino-mediated knockdown of the brain mineralocorticoid receptor affects glucocorticoid signaling and neuroplasticity in wild ocellated wrasse (Symphodus ocellatus). bioRxiv [Internet]. https://doi.org/10.1101/2021.11.17.468986
  • Harris RM, Kao HY, Alarcón JM, Fenton AA, Hofmann HA. Transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory. bioRxiv [Internet]. https://doi.org/10.1101/2020.02.05.935759
  • Miller-Crews IJ, Hofmann HA (2024). Single-nuclei transcriptomes in the hypothalamus and POA of a highly social cichlid. bioRxiv, 622449. https://doi.org/10.1101/2024.11.07.622449
  • Miller-Crews, I., & Hofmann, H. A. (2024). Social dominance reorganizes the transcriptomic neuropeptidome in a highly social cichlid fish. bioRxiv. https://doi.org/10.1101/2024.11.07.622449
  • Han, J., Grau-Perales, A., Harris, R. M., Kao, H.-Y., Pal, A., Alarcon, J. M., Sacktor, T. C., Martiniani, S., Hofmann, H. A., & Fenton, A. A. (2025). Persistently increased expression of PKMζ and unbiased gene expression profiles identify hippocampal molecular traces of a long-term active place avoidance memory and ‘shadow’ proteins. biorxiv. https://doi.org/10.1101/2025.04.28.651143

2025

  • Caro, S. M., Wu, K., & Hofmann, H. A. (2025b). Sex differences in parental response to offspring begging are associated with pair bond strength across birds. Behaviour, 162(9), 579–616. https://doi.org/10.1163/1568539X-bja10318
  • Caro, S. M., Villareal, R. M., Velasco, A. C., van Mastrigt, T., van Oers, K., Hinde, C. A., & Hofmann, H. A. (2025a). Decision-Making in the Wild: Urgency and Complexity Drive Feeding Decision Speed and the Likelihood of Revising a Choice in A Sex-Dependent Manner in Great Tit ( Parus major ) Parents. The American Naturalist. https://doi.org/10.1086/738498
  • Wylie, D., Hofmann, H. A., & Zemelman, B. V. (2025). Suffix Array Kernel Smoothing for de novo discovery of correlative sequence motifs and multi-motif domains: the sarks package.
  • Milewski, T. M., Lee, W., Young, R. L., Hofmann, H. A., & Curley, J. P. (2025). Rapid changes in plasma corticosterone and medial amygdala transcriptome profiles during social status change reveal molecular pathways associated with a major life history transition in mouse dominance hierarchies. PLoS genetics, 21(1), e1011548. https://doi.org/10.1371/journal.pgen.1011548

2024

  • Katona G, Vági B, Plagányi E, Végvári Z, Liker A, Hofmann HA, Freckleton RP, Székely T (2024). Evolution of parental care in ray-finned fishes. Evolution 78:1673–1684. https://doi.org/10.1093/evolut/qpae100
  • Zuniga A, Han J, Miller-Crews I, Agee LA, Hofmann HA, Drew MR (2024). Extinction training suppresses activity of fear memory ensembles across the hippocampus and alters transcriptomes of fear-encoding cells. Neuropsychopharmacology 49:1872–1882. https://doi.org/10.1038/s41386-024-01897-0
  • Keagy J, Hofmann HA, Boughman JW (2024). Mate choice in the brain: Species differ in how male traits ‘turn on’ gene expression in female brains. Proceedings of the Royal Society B 291:20240121. https://doi.org/10.1098/rspb.2024.0121

2023

  • Calvo R, Schluessel V, Hofmann HA, Hofmann MH (2023). Co-activation patterns of dopaminergic cells reflect instrumental and avoidance learning in a cichlid fish, Pseudotropheus zebra. Journal of Chemical Neuroanatomy 133:102342. https://doi.org/10.1016/j.jchemneu.2023.102342
  • Clites BL, Hofmann HA, Pierce JT. (2023). The promise of an evolutionary perspective of alcohol consumption. Neuroscience Insights 18:1-7. https://doi.org/10.1177/26331055231163589

2022

  • Calvo R, Schluessel V, Hofmann HA, Hofmann MH (2023). Co-activation patterns of dopaminergic cells reflect instrumental and avoidance learning in a cichlid fish, Pseudotropheus zebra. Journal of Chemical Neuroanatomy, 133:102342. https://doi.org/10.1016/j.jchemneu.2023.102342
  • Solomon-Lane TK, Butler RM, Hofmann HA (2023). Vasopressin mediates nonapeptide and glucocorticoid signaling and social dynamics in juvenile dominance hierarchies of a highly social cichlid fish. Hormones & Behavior, 145:105238. https://doi.org/10.1016/j.yhbeh.2022.105238
  • Rodriguez-Santiago M, Jordan AL, Hofmann HA (2023). Differential neural activity patterns mediate learning across contexts in a social cichlid fish. Proc R. Soc [Internet]. https://doi.org/10.1098/rspb.2022.0135
  • Wallace KJ, Choudhary KD, Kutty LA, Le DH, Lee MT, Wu K, Hofmann HA (2023). Social ascent changes cognition, behavior, and physiology in a highly social cichlid fish. Philosophical Transactions B. 377:20200448 [Internet]. https://doi.org/10.1098/rstb.2020.0448

2021

  • Weitekamp CA, Hofmann HA (2021). Human population density and reproductive health: a changing world needs endocrinology. Endocrinology [Internet]. 162:1–3. https://doi.org/10.1210/endocr/bqab198
  • Miller-Crews I, Matz MV, Hofmann HA (2021). A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples. Forensics Science International. Genetics [Internet]. 55:102590. https://doi.org/10.1016/j.fsigen.2021.102590
  • Chan ME, Bhamidipati PS, Goldsby HJ, Hintze A, Hofmann HA, Young RL (2021). Comparative transcriptomics reveal distinct patterns of gene expression conservation through vertebrate embryogenesis. Genome Biology and Evolution [Internet]. https://doi.org/10.1093/gbe/evab160
  • Weitekamp CA, Hofmann HA (2021). Effects of air pollution exposure on social behavior: a synthesis and call for research. Environmental Health [Internet]. 20:72. https://doi.org/10.1186/s12940-021-00761-8
  • Maguire SM, DeAngelis R, Dijkstra PD, Jordan A, Hofmann HA (2021). Social network dynamics predict hormone levels and behavior in a highly social cichlid fish. Hormones & Behavior [Internet]. 132:104994. https://doi.org/10.1016/j.yhbeh.2021.104994
  • Wallace KJ, Hofmann HA (2021). Decision-making in a social world: integrating cognitive ecology and social neuroscience. Current Opinion in Neurobiology [Internet]. 68:152-158. https://doi.org/10.1016/j.conb.2021.03.009
  • Wallace KJ, Hofmann HA (2021). Equal performance but distinct behaviors: sex differences in a novel object recognition task and spatial maze in a highly social cichlid fish. Animal Cognition [Internet]. https://doi.org/10.1007/s10071-021-01498-0
  • Hernandez Scudder ME, Young RL, Thompson LM, Kore P, Crews D, Hofmann HA, Gore AC. (2021). Prenatal exposure to EDCs dis-integrates and reconstitutes neuromolecular-behavioral relationships in adult rats. Journal of the Endocrine Society [Internet]. https://doi.org/10.1210/jendso/bvab021
  • Arasappan D, Eickhoff SB, Nemeroff CB, Hofmann HA, Jabbi M (2021). Transcription factor motifs associated with anterior insula gene-expression underlying mood disorder phenotypes. Molecular Neurobiology [Internet]. https://doi.org/10.1007/s12035-020-02195-8
  • Whitaker KW, Alvarez M, Preuss T, Cummings ME, Hofmann HA (2021). Courting danger: Socially dominant cichlid fish adjust their startle-escape behavior to compensate for increased visual conspicuousness to avian predators. Hydrobiologia [Internet]. https://doi.org/10.1007/s10750-020-04475-9

2020

  • DeAngelis R, Hofmann HA (2020). Neural and molecular mechanisms underlying female mate choice decisions in vertebrates. Journal of Experimental Biology [Internet]. 223:jeb207324. https://doi.org/10.1242/jeb.207324
  • Rodriguez-Santiago M, Nührenberg P, Derry J, Deussen O, Francisco FA, Garrison LK, Garza SF, Hofmann HA, Jordan A (2020). Behavioral traits that define social dominance are the same that reduce social influence in a consensus task. Proceedings of the National Academy of Sciences USA [Internet]. https://doi.org/10.1073/pnas.2000158117
  • Sinha S, Jones BM, Traniello IM, Bukhari SA, Halfon MS, Hofmann HA, Huang S, Katz PS, Keagy J, Lynch VJ, et al. (2020). Behavior-related gene regulatory networks: A new level of organization in the brain. Proceedings of the National Academy of Sciences USA [Internet]. https://doi.org/10.1073/pnas.1921625117
  • Eastman G, Valiño G, Radío S, Young RL, Quintana L, Zakon HH, Hofmann HA, Sotelo-Silveira J, Silva A (2020). Brain transcriptomics of agonistic behaviour in the weakly electric fish Gymnotus omarorum, a wild teleost model of non-breeding aggression. Scientific Reports [Internet]. 10(9496). https://doi.org/10.1038/s41598-020-66494-9
  • Jabbi M, Arasappan D, Eickhoff SB, Strakowski M, Nemeroff CB, Hofmann HA (2020). Neuro-transcriptomic signatures for mood disorder morbidity and suicide mortality. Journal of Psychiatric Research [Internet]. 127:62-74. https://doi.org/10.1016/j.jpsychires.2020.05.013
  • Harris RM, Kao H-Y, Alarcón JM, Fenton AA, Hofmann HA (2020). Transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory. Hippocampus [Internet]. https://doi.org/10.1101/2020.02.05.935759

2019

  • Yin W, Borniger JC, Wang X, Maguire SM, Munselle ML, Bezner KS, Tesfamariam HM, Liang J, Garcia AN, Hofmann HA, Gore AC, et al. (2019). Estradiol treatment improves biological rhythms in a preclinical rat model of menopause. Neurobiology of Aging, 83, 1-10. https://doi.org/10.1016/j.neurobiolaging.2019.08.029
  • Rubenstein DR, Agren JA, Carbone L, Hoekstra HE, Kapheim KM, Keller L, Moreau CS, Toth AL, Yeaman S, Hofmann HA (2019). Coevolution of genome architecture and social behavior. Trends in Ecology and Evolution [Internet]. 34(9):844-855. https://doi.org/10.1016/j.tree.2019.04.011
  • Still MB, Lea AM, Hofmann HA, Ryan MJ (2019). Multimodal stimuli regulate reproductive behavior and physiology in male túngara frogs. Hormones and Behavior [Internet]. https://doi.org/10.1016/j.yhbeh.2019.06.010
  • Solomon-Lane TK, Hofmann HA (2019). Early-life social environment alters juvenile behavior and neuroendocrine function in a highly social cichlid fish. Hormones and Behavior [Internet]. 115. https://doi.org/10.1016/j.yhbeh.2019.06.016
  • Northcutt AJ, Kick DR, Otopalik AG, Goetz BM, Harris RM, Santin JM, Hofmann HA, Marder E, Schulz DJ (2019). Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proceedings of the National Academy of Sciences USA [Internet]. https://doi.org/10.1101/690388
  • Harris RM, Kao H-Y, Alarcon JM, Hofmann HA, Fenton AA (2019). Hippocampal transcriptomic responses to enzyme-mediated cellular dissociation. Hippocampus [Internet];29:876–882. https://doi.org/10.1002/hipo.23095
  • Wylie DC, Hofmann HA, BV Z (2019). SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing. Bioinformatics [Internet]. btz198. https://doi.org/10.1093/bioinformatics/btz198
  • Friesen CN, Hofmann HA (2019). Molecular origins and outcomes of status and stress in primates. Proceedings of the National Academy of Sciences USA [Internet]. 116(4):1081-1083.
  • Young RL, Ferkin MH, Ockendon NF, Orr VN, Phelps SM, Pogány Á, Richards-Zawacki CL, Summers K, Székely T, Trainor BC, et al. (2019). Conserved transcriptomic profiles underpin monogamy across vertebrates. Proceedings of the National Academy of Sciences USA [Internet]. 116(4):1331-1336. https://doi.org/10.1073/pnas.1813775116
  • Nugent BM, Stiver KA, Hofmann HA, Alonzo SH (2019). Experimentally‐induced variation in neuroendocrine processes affects male reproductive behavior, sperm characteristics, and social interactions. Molecular Ecology [Internet]. 28:3464–3481. https://doi.org/10.1111/mec.14999

2018

  • Kabelik D, Hofmann HA (2018). Comparative neuroendocrinology: A call for more study of reptiles!. Hormones and Behavior [Internet]. 106:189-192. https://doi.org/10.1016/j.yhbeh.2018.10.005
  • Kabelik D, Weitekamp CA, Choudhury SC, Hartline JT, Smith AN, Hofmann HA (2018). Neural activity in the social decision-making network of the brown anole during reproductive and agonistic encounters. Hormones and Behavior [Internet]. 106:178-188. https://doi.org/10.1016/j.yhbeh.2018.06.013
  • Li CY, Hofmann HA, Harris ML, Earley RL (2018). Real or fake? Natural and artificial social stimuli elicit divergent behavioral and neural responses in the mangrove rivulus fish, Kryptolebias marmoratus. Proc. R. Soc. B. [Internet]. 285(20181610). http://dx.doi.org/10.1098/rspb.2018.1610
  • Solomon-Lane TK, Hofmann HA (2018). A tagging method for very small fish. bioRxiv.
  • Goldsby HJ, Young RL, Hofmann HA, Hintze A (2018). Serendipitous Scaffolding to improve a Genetic Algorithm’s Speed and Quality, in Genetic and Evolutionary Computation Conference (GECCO). Kyoto (Japan):959-966. https://doi.org/10.1145/3205455.3205617
  • Renn SCP, Machado HE, Duftner N, Sessa AK, Harris RM, Hofmann HA (2018). Gene expression signatures of mating system evolution. Genome [Internet]. https://doi.org/10.1139/gen-2017-0075

2017

  • Baker MR, Hofmann HA, Wong RY (2017). Neurogenomics of behavioural plasticity in socioecological contexts. In: Encyclopedia of Life Sciences. Chichester: John Wiley & Sons, Ltd. https://doi.org/10.1002/9780470015902.a0026839
  • Weitekamp CA, Nguyen J, Hofmann HA (2017). Neuromolecular Regulation of Aggression Differs by Social Role during Joint Territory Defense. Integrative and Comparative Biology:1-9.
  • Liebeskind BJ, Hofmann HA, Hillis DA, Zakon HH (2017). Evolution of Animal Neural Systems. Annual Review of Ecology, Evolution, and Systematics. 48:377-398.
  • Rodriguez-Santiago M, Nguyen J, Winton LS, Weitekamp CA, Hofmann HA (2017). Arginine vasotocin preprohormone is expressed in surprising regions of the teleost forebrain. Frontiers in Endocrinology [Internet]. 8. https://doi.org/10.3389/fendo.2017.00195
  • Goldsby HJ, Young RL, Hofmann HA, Hintze A (2017). Increasing the complexity of solutions produced by an evolutionary developmental system., in Genetic and Evolutionary Computation Conference (GECCO). Berlin (Germany):57-58.
  • Weitekamp CA, Solomon-Lane TK, Del Valle P, Triki Z, Nugent BM, Hofmann HA (2017). A role for oxytocin-like receptor in social habituation in a teleost. Brain, Behavior, and Evolution. 89:153-161.
  • Weitekamp CA, Nguyen J, Hofmann HA (2017). Social context affects behavior, preoptic area gene expression, and response to D2 receptor manipulationduring territorial defense in a cichlid fish. Genes, Brain and Behavior. 16:601-611.
  • Dijkstra PD, Maguire SM, Harris RM, Rodriguez AA, DeAngelis RS, Flores SA, Hofmann HA (2017). The melanocortin system regulates body pigmentation and social behaviour in the cichlid fish Astatotilapia burtoni. Proc R Soc B. (doi: 10.1098/rspb.2016.2838)
  • Weitekamp CA, Hofmann HA (2017). Neuromolecular correlates of cooperation and conflict during territory defense in a cichlid fish. Hormones and Behavior [Internet]. 89:145-156. https://doi.org/10.1016/j.yhbeh.2017.01.001
  • Harris RM, O’Connell LA, Hofmann HA (2017). Chapter 15: Brain Evolution, Development, and Plasticity. In: Shepherd SV The Wiley Handbook of Evolutionary Neuroscience. 1st ed. John Wiley & Sons, Ltd; pp. 422-443.
  • Weitekamp CA, Hofmann HA (2017). Brain Systems Underlying Social Behavior. In: Kaas J Evolution of Nervous Systems. Vol. 1. 2nd ed. Oxford: Elsevier; pp. 327-334.

2016

  • Renn SCP, O’Rourke CF, Aubin-Horth N, Fraser EJ, Hofmann HA (2016). Dissecting the transcriptional patterns of social dominance across teleosts. Integrative and Comparative Biology [Internet]. 56:1250-1265. https://doi.org/10.1093/icb/icw118
  • Nishi R, Castaneda E, Davis GW, Fenton AA, Hofmann HA, King J, Ryan TA, Trujillo KA (2016). The Global Challenge in Neuroscience Education and Training: The MBL Perspective. Neuron [Internet]. 92:632-636. http://dx.doi.org/10.1016/j.neuron.2016.10.026
  • Hofmann HA, Renn SCP, Rubenstein DR (2016). New Frontiers in the Integrative Study of Animal Behavior: Nothing in Neuroscience Makes Sense Except in the Light of Behavior. Integrative and Comparative Biology [Internet]:icw127–icw127. https://doi.org/10.1093/icb/icw127
  • Nugent BM, Stiver KA, Alonzo SH, Hofmann HA (2016). Neuroendocrine profiles associated with discrete behavioural variation in Symphodus ocellatus, a species with male alternative reproductive tactics. Molecular Ecology [Internet]. 25(20):5212-5227. https://doi.org/10.1111/mec.13828
  • Göppert C, Harris RM, Theis A, Boila A, Hohl S, Ruegg A, Hofmann HA, Salzburger W, Bohne A (2016). Inhibition of Aromatase Induces Partial Sex Change in a Cichlid Fish: Distinct Functions for Sex Steroids in Brains and Gonads. Sexual Development [Internet]. 10:97-110. https://doi.org/10.1159/000445463
  • Jordan LA, Maguire SM, Hofmann HA, Kohda M (2016). The social and ecological costs of an “over-extended” phenotype. Proceedings of the Royal Society B [Internet]. 283:20152359. https://doi.org/10.1098/rspb.2015.2359
  • Liebeskind BJ, Hillis DM, Zakon HH, Hofmann HA (2016). Complex Homology and the Evolution of Nervous Systems. Trends in Ecology and Evolution [Internet]. 31(2):127–135. https://doi.org/10.1016/j.tree.2015.12.005
  • Ockendon NF, O’Connell LA, Bush, Stephen J, Monzonsandoval J, Barnes H, Szekely T, Hofmann HA, Dorus S, Urrutia AO (2016). Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes. Molecular Ecology Resources [Internet]. 16:446-458. https://doi.org/10.1111/1755-0998.12465

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