Collecting cod eggs. Photo credit: Espen Bierud
THEMES and tools
adaptation | plasticity | behaviour
gene flow | structural variation | mating systems | reproductive barriers
common garden experiments | mating experiments
genomics | transcriptomics | bioacoustics | telemetry
bioinformatics | modelling | artificial intelligence | network science
gene flow | structural variation | mating systems | reproductive barriers
common garden experiments | mating experiments
genomics | transcriptomics | bioacoustics | telemetry
bioinformatics | modelling | artificial intelligence | network science
Atlantic cod; Photo credit: Emilie Reuchlin-Hugenholtz
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Gene expression network of the larval stress response
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Spectrogram of a cod mating call and a female spawner
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Publications**
23 articles published/accepted; 2 preprints/manuscripts in review/revision; h-index = 12
PREPRINTS/MANUSCRIPTS IN REVIEW/REVISION
25) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings [2022; revision requested]. Comparison of de novo and reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data. bioRxiv. preprint
24) Oomen, RA, E Juliussen, EM Olsen, H Knutsen, S Jentoft, & JA Hutchings [2021; second revision requested]. Cryptic microgeographic variation in responses of larval Atlantic cod to warmer temperatures. bioRxiv. preprint
PEER-REVIEWED
23) Kao, AB, AK Hund, FP Santos, J-G Young, D Bhat, J Garland, RA Oomen, & HF McCreery [in press]. Opposing responses to scarcity emerge from functionally unique sociality drivers. The American Naturalist. preprint / twitter thread
22) Theissinger K, G Formenti, C Fernandes, ..., RA Oomen*, ..., J Höglund (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2023. How genomics can help biodiversity conservation. Trends in Genetics. *middle 21 authors contributed equally LINK
21) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings. 2022. Warming accelerates the onset of the molecular stress response and increases mortality of larval Atlantic cod. Integrative & Comparative Biology. doi:10.1093/icb/icac145 LINK
20) Oomen, RA & JA Hutchings. 2022. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. Journal of Animal Ecology, 91:1073-1087. doi:10.1111/1365-2656.13707 Invited LINK / twitter thread / podcast
19) Rasmussen JH, M Moyano, L Fuiman, & RA Oomen. 2022. FishSizer: Software solution for efficiently measuring larval fish size. Ecology & Evolution, 12:e8672. doi:10.1002/ece3.8672 LINK / twitter thread
18) Goodwin M*, KT Halvorsen*, L Jiao*, KM Knausgård*, AH Martin*, M Moyano*, RA Oomen*^, JH Rasmussen*, TK Sørdalen*, & SH Thorbjørnsen*. 2022. Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook. ICES Journal of Marine Science, 79:319–336. doi:10.1093/icesjms/fsab255 *all authors contributed equally ^corresponding author LINK / twitter thread
17) Formenti, G, K Theissinger, C Fernandes, ..., RA Oomen*, ..., M Bálint (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2022. The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, 37:197-202. doi:10.1016/j.tree.2021.11.008 *middle 21 authors contributed equally LINK
16) Wolf, JF, L MacKay*, SE Haworth*, ML Cossette*, MN Dedato*, KB Young*, CI Elliott*, & RA Oomen. 2021. Preprinting is positively associated with early career researcher status in ecology and evolution. Ecology & Evolution, 11:13624-13632. doi:10.1002/ece3.8106 *contributed equally LINK / twitter thread / podcast
15) Raatikainen, KJ, J Purhonen, T Pohjanmies, M Peura, …, RA Oomen*, …, J Ziemacki* (31 authors). 2021. Pathways towards a sustainable future envisioned by early-career conservation researchers. Conservation Science & Practice, 3:e493. doi:10.1111/csp2.493 *last 24 authors contributed equally LINK
14) Deininger, A, AH Martin, JC Pardo, PR Berg*, J Bhardwaj*, D Catarino*, A Fernandez-Chacon*, K Martinez-Swatson*, K Ono*, RA Oomen*, M Sodeland*, TK Sørdalen*, A-E Synnes*, SH Thorbjørnsen*, & J Thormar*. 2021. Coastal research seen through an early career lens – a perspective on barriers to interdisciplinarity in Norway. Frontiers in Marine Science, 8:634999. doi:10.3389/fmars.2021.634999 *contributed equally LINK
13) Oomen, RA & JA Hutchings. “Evolution of Reaction Norms.” In Oxford Bibliographies in Evolutionary Biology. Ed. D Futuyma. New York: Oxford University Press, October 28, 2020. doi:10.1093/OBO/9780199941728-0130 Commission LINK / twitter thread
12) Oomen, RA, A Kuparinen, & JA Hutchings. 2020. Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change. Journal of Heredity, 111:319-332. doi:10.1093/jhered/esaa020 Invited & Editor's Choice PDF / twitter thread / presentation / podcast
11) Mérot, C*, RA Oomen*, A Tigano*, & M Wellenreuther*. 2020. A roadmap for understanding the evolutionary significance of structural genomic variation. Trends in Ecology and Evolution, 35:561-572. doi:10.1016/j.tree.2020.03.002 *all authors contributed equally Featured article PDF / twitter thread
10) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2018. Fine-scale population differences in Atlantic cod reproductive success: a potential mechanism for ecological speciation in a marine fish. Ecology & Evolution, 8:11634-11644. doi:10.1002/ece3.4615 PDF
9) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2017. Temporal variability in offspring quality and individual reproductive output in a broadcast-spawning marine fish. ICES Journal of Marine Science, 75:1353-1361. doi:10.1093/icesjms/fsx232 PDF
8) Oomen, RA & JA Hutchings. 2017. Transcriptomic responses to environmental change in fishes: insights from RNA-seq. FACETS, 2:610–641. doi:10.1139/facets-2017-0015 PDF / popular science article
7) Oomen, RA & JA Hutchings. 2016. Genetic variation in plasticity of life-history traits between Atlantic cod (Gadus morhua) populations exposed to contrasting thermal regimes. Canadian Journal of Zoology, 94:257-264. doi:10.1139/cjz-2015-0186 PDF
6) Kuparinen, A, NE Roney, RA Oomen, JA Hutchings, & EM Olsen. 2015. Small-scale life history variability suggests potential for spatial mismatches in Atlantic cod management units. ICES Journal of Marine Science, 73:286-292. doi:10.1093/icesjms/fsv181 PDF
5) Oomen, RA & JA Hutchings. 2015. Genetic variability in reaction norms in fishes. Environmental Reviews, 23:353-366. doi:10.1139/er-2014-0077 PDF
4) Oomen, RA & JA Hutchings. 2015. Variation in spawning time promotes genetic variability in population responses to environmental change in a marine fish. Conservation Physiology, 3:1-12. doi:10.1093/conphys/cov027 PDF
PREPRINTS/MANUSCRIPTS IN REVIEW/REVISION
25) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings [2022; revision requested]. Comparison of de novo and reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data. bioRxiv. preprint
24) Oomen, RA, E Juliussen, EM Olsen, H Knutsen, S Jentoft, & JA Hutchings [2021; second revision requested]. Cryptic microgeographic variation in responses of larval Atlantic cod to warmer temperatures. bioRxiv. preprint
PEER-REVIEWED
23) Kao, AB, AK Hund, FP Santos, J-G Young, D Bhat, J Garland, RA Oomen, & HF McCreery [in press]. Opposing responses to scarcity emerge from functionally unique sociality drivers. The American Naturalist. preprint / twitter thread
22) Theissinger K, G Formenti, C Fernandes, ..., RA Oomen*, ..., J Höglund (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2023. How genomics can help biodiversity conservation. Trends in Genetics. *middle 21 authors contributed equally LINK
21) Oomen, RA, H Knutsen, EM Olsen, S Jentoft, NC Stenseth, & JA Hutchings. 2022. Warming accelerates the onset of the molecular stress response and increases mortality of larval Atlantic cod. Integrative & Comparative Biology. doi:10.1093/icb/icac145 LINK
20) Oomen, RA & JA Hutchings. 2022. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. Journal of Animal Ecology, 91:1073-1087. doi:10.1111/1365-2656.13707 Invited LINK / twitter thread / podcast
19) Rasmussen JH, M Moyano, L Fuiman, & RA Oomen. 2022. FishSizer: Software solution for efficiently measuring larval fish size. Ecology & Evolution, 12:e8672. doi:10.1002/ece3.8672 LINK / twitter thread
18) Goodwin M*, KT Halvorsen*, L Jiao*, KM Knausgård*, AH Martin*, M Moyano*, RA Oomen*^, JH Rasmussen*, TK Sørdalen*, & SH Thorbjørnsen*. 2022. Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook. ICES Journal of Marine Science, 79:319–336. doi:10.1093/icesjms/fsab255 *all authors contributed equally ^corresponding author LINK / twitter thread
17) Formenti, G, K Theissinger, C Fernandes, ..., RA Oomen*, ..., M Bálint (25 authors + European Reference Genome Atlas [ERGA] Consortium). 2022. The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, 37:197-202. doi:10.1016/j.tree.2021.11.008 *middle 21 authors contributed equally LINK
16) Wolf, JF, L MacKay*, SE Haworth*, ML Cossette*, MN Dedato*, KB Young*, CI Elliott*, & RA Oomen. 2021. Preprinting is positively associated with early career researcher status in ecology and evolution. Ecology & Evolution, 11:13624-13632. doi:10.1002/ece3.8106 *contributed equally LINK / twitter thread / podcast
15) Raatikainen, KJ, J Purhonen, T Pohjanmies, M Peura, …, RA Oomen*, …, J Ziemacki* (31 authors). 2021. Pathways towards a sustainable future envisioned by early-career conservation researchers. Conservation Science & Practice, 3:e493. doi:10.1111/csp2.493 *last 24 authors contributed equally LINK
14) Deininger, A, AH Martin, JC Pardo, PR Berg*, J Bhardwaj*, D Catarino*, A Fernandez-Chacon*, K Martinez-Swatson*, K Ono*, RA Oomen*, M Sodeland*, TK Sørdalen*, A-E Synnes*, SH Thorbjørnsen*, & J Thormar*. 2021. Coastal research seen through an early career lens – a perspective on barriers to interdisciplinarity in Norway. Frontiers in Marine Science, 8:634999. doi:10.3389/fmars.2021.634999 *contributed equally LINK
13) Oomen, RA & JA Hutchings. “Evolution of Reaction Norms.” In Oxford Bibliographies in Evolutionary Biology. Ed. D Futuyma. New York: Oxford University Press, October 28, 2020. doi:10.1093/OBO/9780199941728-0130 Commission LINK / twitter thread
12) Oomen, RA, A Kuparinen, & JA Hutchings. 2020. Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change. Journal of Heredity, 111:319-332. doi:10.1093/jhered/esaa020 Invited & Editor's Choice PDF / twitter thread / presentation / podcast
11) Mérot, C*, RA Oomen*, A Tigano*, & M Wellenreuther*. 2020. A roadmap for understanding the evolutionary significance of structural genomic variation. Trends in Ecology and Evolution, 35:561-572. doi:10.1016/j.tree.2020.03.002 *all authors contributed equally Featured article PDF / twitter thread
10) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2018. Fine-scale population differences in Atlantic cod reproductive success: a potential mechanism for ecological speciation in a marine fish. Ecology & Evolution, 8:11634-11644. doi:10.1002/ece3.4615 PDF
9) Roney, NE, RA Oomen, H Knutsen, EM Olsen, & JA Hutchings. 2017. Temporal variability in offspring quality and individual reproductive output in a broadcast-spawning marine fish. ICES Journal of Marine Science, 75:1353-1361. doi:10.1093/icesjms/fsx232 PDF
8) Oomen, RA & JA Hutchings. 2017. Transcriptomic responses to environmental change in fishes: insights from RNA-seq. FACETS, 2:610–641. doi:10.1139/facets-2017-0015 PDF / popular science article
7) Oomen, RA & JA Hutchings. 2016. Genetic variation in plasticity of life-history traits between Atlantic cod (Gadus morhua) populations exposed to contrasting thermal regimes. Canadian Journal of Zoology, 94:257-264. doi:10.1139/cjz-2015-0186 PDF
6) Kuparinen, A, NE Roney, RA Oomen, JA Hutchings, & EM Olsen. 2015. Small-scale life history variability suggests potential for spatial mismatches in Atlantic cod management units. ICES Journal of Marine Science, 73:286-292. doi:10.1093/icesjms/fsv181 PDF
5) Oomen, RA & JA Hutchings. 2015. Genetic variability in reaction norms in fishes. Environmental Reviews, 23:353-366. doi:10.1139/er-2014-0077 PDF
4) Oomen, RA & JA Hutchings. 2015. Variation in spawning time promotes genetic variability in population responses to environmental change in a marine fish. Conservation Physiology, 3:1-12. doi:10.1093/conphys/cov027 PDF
3) Oomen, RA, RM Gillett, & CJ Kyle. 2013. Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage. Molecular Ecology Resources, 13:103-116. doi:10.1111/1755-0998.12027 PDF
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2) Oomen, RA, MW Reudink, JJ Nocera, CM Somers, MC Green, & CJ Kyle. 2011. Mitochondrial evidence for panmixia despite perceived barriers to gene flow in a widely distributed waterbird. Journal of Heredity, 102:584-592. doi:10.1093/jhered/esr055 Journal cover image PDF
1) Reudink, MW, CJ Kyle, JJ Nocera, RA Oomen, MC Green, & CM Somers. 2011. Panmixia on a continental scale in a widely distributed colonial waterbird. Biological Journal of the Linnean Society, 102:583-592. doi:10.1111/j.1095-8312.2010.01608.x PDF |
Journal of Heredity cover image; Photo credit: Scott Butner
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