John Colbourne

2025

A web-based histology atlas for the freshwater sentinel species Daphnia magna

Ngu, M. S., Vanselow, D. J., Zaino, C. R., Lin, A. Y., Copper, J. E., Beaton, M. J., Orsini, L., Colbourne, J., Cheng, K. C. & Ang, K. C., 1 Jan 2025, In: Science of the Total Environment. 958, 14 p., 177930.

Research output: Contribution to journal › Article › peer-review

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2024

A molecular mechanism for environmental sex determination

Li, X. & Colbourne, J. K., 29 Jul 2024, (E-pub ahead of print) In: Trends in Genetics.

Research output: Contribution to journal › Article › peer-review

Open Access

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An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

Perry, W. B., Seymour, M., Orsini, L., Jâms, I. B., Milner, N., Edwards, F., Harvey, R., de Bruyn, M., Bista, I., Walsh, K., Emmett, B., Blackman, R., Altermatt, F., Lawson Handley, L., Mächler, E., Deiner, K., Bik, H. M., Carvalho, G., Colbourne, J. & Cosby, B. J. & 2 others, Durance, I. & Creer, S., 23 May 2024, In: Nature Communications. 15, 1, 13 p., 4372.

Research output: Contribution to journal › Article › peer-review

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A novel method to derive a human safety limit for PFOA by gene expression profiling and modelling

Silva, A. C., Loizou, G. D., McNally, K., Osborne, O., Potter, C., Gott, D., Colbourne, J. K. & Viant, M. R., 21 Mar 2024, In: Frontiers in toxicology. 6, 11 p., 1368320.

Research output: Contribution to journal › Article › peer-review

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Author Correction: Mixtures of organic micropollutants exacerbated in vitro neurotoxicity of prymnesins and contributed to aquatic toxicity during a toxic algal bloom

Escher, B. I., Ahlheim, J., Böhme, A., Borchardt, D., Brack, W., Braun, G., Colbourne, J. K., Dann, J. P., Gessner, J., Jahnke, A., König, M., Klüver, N., Krauss, M., Lee, J., Li, X., Lips, S., Orsini, L., Rinke, K., Schmitt-Jansen, M. & Scholz, S. & 5 others, Schulze, T., Spahr, S., Ulrich, N., Weitere, M. & Varga, E., Oct 2024, In: Nature Water. 2, 10, 1 p., 1039.

Research output: Contribution to journal › Comment/debate

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Bioactivity Profiling of Chemical Mixtures for Hazard Characterisation

Li, X., Zhou, J., Bai, Y., Qiao, M., Xiong, W., Schulze, T., Krauss, M., Williams, T., Brown, B. J., Orsini, L., Guo, L.-H. & Colbourne, J., 20 Dec 2024, (E-pub ahead of print) In: Environmental Science and Technology. 11 p.

Research output: Contribution to journal › Article › peer-review

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Evaluating Toxicity of Chemicals using a Zebrafish Vibration Startle Response Screening System

Hayot, G., Marcato, D., Cramer von clausbruch, C. A., Pace, G., Strähle, U., Colbourne, J. K., Pylatiuk, C., Peravali, R., Weiss, C., Scholz, S. & Dickmeis, T., 12 Jan 2024, In: Journal of visualized experiments : JoVE. 203, e66153.

Research output: Contribution to journal › Article › peer-review

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Metabolomics Simultaneously Derives Benchmark Dose Estimates and Discovers Metabolic Biotransformations in a Rat Bioassay

Sostare, E., Bowen, T. J., Lawson, T. N., Freier, A., Li, X., Lloyd, G. R., Najdekr, L., Jankevics, A., Smith, T., Varshavi, D., Ludwig, C., Colbourne, J. K., Weber, R. J. M., Crizer, D. M., Auerbach, S. S., Bucher, J. R. & Viant, M. R., 17 Jun 2024, In: Chemical Research in Toxicology. 37, 6, p. 923–934

Research output: Contribution to journal › Article › peer-review

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Mixtures of organic micropollutants exacerbated in vitro neurotoxicity of prymnesins and contributed to aquatic toxicity during a toxic algal bloom

Escher, B. I., Ahlheim, J., Böhme, A., Borchardt, D., Brack, W., Braun, G., Colbourne, J. K., Dann, J. P., Gessner, J., Jahnke, A., König, M., Klüver, N., Krauss, M., Lee, J., Li, X., Lips, S., Orsini, L., Rinke, K., Schmitt-Jansen, M. & Scholz, S. & 5 others, Schulze, T., Spahr, S., Ulrich, N., Weitere, M. & Varga, E., 6 Sept 2024, In: Nature Water. 2, 9, p. 889-898 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Multi-omics bioactivity profile-based chemical grouping and read-across: a case study with Daphnia magna and azo dyes

Gruszczynska, H., Barnett, R. E., Lloyd, G. R., Weber, R. J. M., Lawson, T. N., Zhou, J., Sostare, E., Colbourne, J. K. & Viant, M. R., 2 May 2024, (E-pub ahead of print) In: Archives of toxicology.

Research output: Contribution to journal › Article › peer-review

Open Access

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New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project

Tal, T., Myhre, O., Fritsche, E., Rüegg, J., Craenen, K., Aiello-Holden, K., Agrillo, C., Babin, P. J., Escher, B. I., Dirven, H., Hellsten, K., Dolva, K., Hessel, E., Heusinkveld, H. J., Hadzhiev, Y., Hurem, S., Jagiello, K., Judzinska, B., Klüver, N. & Knoll-Gellida, A. & 14 others, Kühne, B. A., Leist, M., Lislien, M., Lyche, J. L., Müller, F., Colbourne, J. K., Neuhaus, W., Pallocca, G., Seeger, B., Scharkin, I., Scholz, S., Spjuth, O., Torres-Ruiz, M. & Bartmann, K., 26 Apr 2024, In: Frontiers in toxicology. 6, 1359507.

Research output: Contribution to journal › Article › peer-review

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Precision toxicology: new approach methodologies for chemical safety

Cavoski, A., Colbourne, J., Holden, L. & Lee, R., 31 Jan 2024, In: Bio-Science Law Review. 19, 3, p. 101-107 7 p.

Research output: Contribution to journal › Article › peer-review

Recommendations for the Adoption of New Approach Methodologies (NAMs) in UK Chemical Regulation

Colbourne, J. (Contributor), Margiotta-Casaluci, L. (Contributor), Chilton, S. M. (Contributor), Jones, K. A. (Contributor), Lynch, I. (Contributor), Owen, S. (Contributor), Holden, L. (Contributor), Andrews, E. (Contributor), Cavoski, A. (Contributor) & Lee, R. (Contributor), Nov 2024, 20 p. Defra.

Research output: Other contribution

Open Access

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Utilizing Omics Data for Chemical Grouping

Viant, M. R., Barnett, R. E., Campos, B., Colbourne, J. K., Barnard, M., Biales, A. D., Cronin, M. T. D., Fay, K. A., Koehrn, K., McGarry, H. F., Sachana, M. & Hodges, G., 8 Aug 2024, (E-pub ahead of print) In: Environmental Toxicology and Chemistry. p. 1-11 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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2023

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Eastwood, N., Zhou, J., Derelle, R., Abdallah, M.A.-E., Stubbings, W. A., Jia, Y., Crawford, S. E., Davidson, T. A., Colbourne, J. K., Creer, S., Bik, H., Hollert, H., Orsini, L. & Weigel, D., 7 Nov 2023, In: eLife. 12, 28 p., RP86576.

Research output: Contribution to journal › Article › peer-review

Open Access

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Assessment of Chemical Toxicity in Adult Drosophila Melanogaster

Holsopple, J. M., Smoot, S. R., Popodi, E. M., Colbourne, J. K., Shaw, J. R., Oliver, B., Kaufman, T. C. & Tennessen, J. M., 24 Mar 2023, In: Journal of visualized experiments : JoVE. 193, 16 p., e65029.

Research output: Contribution to journal › Article › peer-review

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Modernizing persistence–bioaccumulation–toxicity (PBT) assessment with high throughput animal-free methods

Escher, B. I., Altenburger, R., Blüher, M., Colbourne, J. K., Ebinghaus, R., Fantke, P., Hein, M., Köck, W., Kümmerer, K., Leipold, S., Li, X., Scheringer, M., Scholz, S., Schloter, M., Schweizer, P.-J., Tal, T., Tetko, I., Traidl-Hoffmann, C., Wick, L. Y. & Fenner, K., May 2023, In: Archives of toxicology. 97, 5, p. 1267-1283 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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110 Downloads (Pure)

The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome

Chaturvedi, A., Li, X., Dhandapani, V., Marshall, H., Kissane, S., Cuenca Cambronero, M., Adesole, G., Ferriol, C., Ruiz-Romero, M., Marangio, P., Guigó, R., Rago, D., Mirbahai, L., Eastwood, N., Colbourne, J., Zhou, J., Mallon, E. & Orsini, L., 28 Aug 2023, (E-pub ahead of print) In: Nucleic Acids Research. gkad685.

Research output: Contribution to journal › Article › peer-review

Open Access

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The Precision Toxicology Initiative

PrecisionTox, 19 May 2023, (E-pub ahead of print) In: Toxicology Letters.

Research output: Contribution to journal › Article › peer-review

2022

Combined exome and transcriptome sequencing of non-muscle-invasive bladder cancer: associations between genomic changes, expression subtypes, and clinical outcomes

Goel, A., Ward, D. G., Noyvert, B., Yu, M., Gordon, N. S., Abbotts, B., Colbourne, J. K., Kissane, S., James, N. D., Zeegers, M. P., Cheng, K. K., Cazier, J.-B., Whalley, C. M., Beggs, A. D., Palles, C., Arnold, R. & Bryan, R. T., Dec 2022, In: Genome medicine. 14, 1, 16 p., 59 .

Research output: Contribution to journal › Article › peer-review

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Daphnia as a Sentinel Species for Environmental Health Protection: A Perspective on Biomonitoring and Bioremediation of Chemical Pollution

Abdullahi, M., Li, X., Abdallah, M.A.-E., Stubbings, W., Yan, N., Barnard, M., Guo, L.-H., Colbourne, J. K. & Orsini, L., 18 Oct 2022, In: Environmental Science and Technology. 56, 20, p. 14237-14248 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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2 Citations (Scopus)

211 Downloads (Pure)

Knowledge-driven approaches to create the MTox700+ metabolite panel for predicting toxicity

Sostare, E., Lawson, T. N., Saunders, L. R., Colbourne, J. K., Weber, R. J. M., Sobanski, T. & Viant, M. R., Apr 2022, In: Toxicological Sciences. 186, 2, p. 208-220 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Toxicity by descent: A comparative approach for chemical hazard assessment

Colbourne, J. K., Shaw, J. R., Sostare, E., Rivetti, C., Derelle, R., Barnett, R., Campos, B., LaLone, C., Viant, M. R. & Hodges, G., 15 Sept 2022, In: Environmental Advances. 9, 100287.

Research output: Contribution to journal › Article › peer-review

Open Access

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188 Downloads (Pure)

Web-based histology reference atlas for the freshwater crustacean Daphnia magna

Ngu, M. S., Vanselow, D. J., Zaino, C. R., Lin, A. Y., Copper, J. E., Beaton, M. J., Colbourne, J. K., Cheng, K. C. & Ang, K. C., 12 Mar 2022, bioRxiv.

Research output: Working paper/Preprint › Preprint

2021

Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia

Chaturvedi, A., Zhou, J., Raeymaekers, J. A. M., Orsini, L., Czypionka, T., Jackson, C. E., Spanier, K. I., Shaw, J. R., Colbourne, J. & De Meester, L., 14 Jul 2021, In: Nature Communications. 12, 1, 1 p., 4306 .

Research output: Contribution to journal › Article › peer-review

Open Access

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Multigenerational exposure to nano‐TiO₂ induces ageing as a stress response mitigated by environmental interactions

Bradford, L., Kissane, S., Hoffman, E., Valsami-Jones, E., Brown, J. B., Colbourne, J. K. & Lynch, I., 19 Jun 2021, In: Advanced NanoBiomed Research. 1, 6, 15 p., 2000083.

Research output: Contribution to journal › Article › peer-review

Open Access

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Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology

Harrill, J. A., Viant, M. R., Yauk, C. L., Sachana, M., Gant, T. W., Auerbach, S. S., Beger, R. D., Bouhifd, M., O'Brien, J., Burgoon, L., Caiment, F., Carpi, D., Chen, T., Chorley, B. N., Colbourne, J., Corvi, R., Debrauwer, L., O'Donovan, C., Ebbels, T. M. D. & Ekman, D. R. & 22 others, Faulhammer, F., Gribaldo, L., Hilton, G. M., Jones, S. P., Kende, A., Lawson, T. N., Leite, S. B., Leonards, P. E. G., Luijten, M., Martin, A., Moussa, L., Rudaz, S., Schmitz, O., Sobanski, T., Strauss, V., Vaccari, M., Vijay, V., Weber, R. J. M., Williams, A. J., Williams, A., Thomas, R. S. & Whelan, M., Oct 2021, In: Regulatory Toxicology and Pharmacology. 125, 6 p., 105020.

Research output: Contribution to journal › Comment/debate › peer-review

Open Access

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Refining the evolutionary time machine: an assessment of whole genome amplification using single historical Daphnia eggs

O’Grady, C. J., Dhandapani, V., Colbourne, J. K. & Frisch, D., 20 Oct 2021, In: Molecular ecology resources. 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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S09-02: Strengthening a grouping/read-across case using omics-derived molecular mechanistic evidence from an invertebrate model

Gruszczynska, H., Barnett, R., Hirmann, D., Weber, R., Zhou, J., Sostare, E., Versonnen, B., Colbourne, J., Sobanski, T. & Viant, M., Sept 2021, In: Toxicology Letters. 350 Supplement, 1 p., S27.

Research output: Contribution to journal › Abstract

2020

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male daphnia pulex

Kvist, J., Gonçalves Athanásio, C., Pfrender, M. E., Brown, J., Colbourne, J. & Mirbahai, L., 6 Jan 2020, In: BMC Genomics. 21, 1, 17 p., 17.

Research output: Contribution to journal › Article › peer-review

Open Access

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6 Citations (Scopus)

186 Downloads (Pure)

Broccoli: Combining Phylogenetic and Network Analyses for Orthology Assignment

Derelle, R., Philippe, H. & Colbourne, J. K., 1 Nov 2020, In: Molecular biology and evolution. 37, 11, p. 3389-3396 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Citations (Scopus)

Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability

Dane, M., Anderson, N. J., Osburn, C. L., Colbourne, J. K. & Frisch, D., 29 Dec 2020, In: Ecology and Evolution. 10, 24, p. 14178-14188

Research output: Contribution to journal › Article › peer-review

Open Access

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Multigenerational exposures of Daphnia magna to pristine and aged silver nanoparticles: epigenetic changes and phenotypical ageing related effects

Ellis, L., Kissane, S., Hoffman, E., Brown, J., Valsami-Jones, E., Colbourne, J. & Lynch, I., 27 Apr 2020, (E-pub ahead of print) In: Small. 16, 21, 2000301.

Research output: Contribution to journal › Article › peer-review

Open Access

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8 Citations (Scopus)

197 Downloads (Pure)

Perfluoroalkyl substances stimulate insulin secretion by islet β cells via G protein-coupled receptor 40

Qin, W.-P., Cao, L.-Y., Li, C.-H., Guo, L.-H., Colbourne, J. & Ren, X.-M., 17 Mar 2020, In: Environmental Science and Technology. 54, 6, p. 3428-3436 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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5 Citations (Scopus)

347 Downloads (Pure)

Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis

Rago, A., Werren, J. H. & Colbourne, J., 27 Jan 2020, In: PLoS Genetics. 16, 1, 32 p., e1008518.

Research output: Contribution to journal › Article › peer-review

Open Access

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3 Citations (Scopus)

184 Downloads (Pure)

Spatio-temporal processes drive fine-scale genetic structure in an otherwise panmictic seabird population

Garrett, L. J. H., Myatt, J. P., Sadler, J. P., Dawson, D. A., Hipperson, H., Colbourne, J. K., Dickey, R. C., Weber, S. B. & Reynolds, S. J., 26 Nov 2020, In: Scientific Reports. 10, 1, 20725.

Research output: Contribution to journal › Article › peer-review

Open Access

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150 Downloads (Pure)

Vision of a near future: bridging the human health–environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment

Rivetti, C., Allen, T. E. H., Brown, J. B., Butler, E., Carmichael, P. L., Colbourne, J. K., Dent, M., Falciani, F., Gunnarsson, L., Gutsell, S., Harrill, J. A., Hodges, G., Jennings, P., Judson, R., Kienzler, A., Margiotta-Casaluci, L., Muller, I., Owen, S. F., Rendal, C. & Russell, P. J. & 8 others, Scott, S., Sewell, F., Shah, I., Sorrel, I., Viant, M. R., Westmoreland, C., White, A. & Campos, B., Feb 2020, In: Toxicology in Vitro. 62, 9 p., 104692.

Research output: Contribution to journal › Article › peer-review

9 Citations (Scopus)

2019

Dynamics of cadmium acclimation in Daphnia pulex: linking fitness costs, cross-tolerance, and hyper-induction of metallothionein

Shaw, J., Colbourne, J., Glaholt, S. P., Turner, E., Folt, C. L. & Chen, C. Y., 17 Dec 2019, In: Environmental Science and Technology. 53, 24, p. 14670-14678

Research output: Contribution to journal › Article › peer-review

Open Access

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4 Citations (Scopus)

193 Downloads (Pure)

Improved algal toxicity test system for robust omics-driven mode-of-action discovery in Chlamydomonas reinhardtii

Schade, S., Butler, E., Gutsell, S., Hodges, G., Colbourne, J. & Viant, M., 10 May 2019, In: Metabolites. 9, 5, 22 p., E94.

Research output: Contribution to journal › Article › peer-review

Open Access

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1 Citation (Scopus)

200 Downloads (Pure)

Mixtures of aluminum and indium induce more than additive phenotypic and toxicogenomic responses in daphnia magna

Brun, N. R., Fields, P. D., Horsfield, S., Mirbahai, L., Ebert, D., Colbourne, J. K. & Fent, K., 5 Feb 2019, In: Environmental Science and Technology. 53, 3, p. 1639-1649 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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8 Citations (Scopus)

337 Downloads (Pure)

Review of and recommendations for monitoring contaminants and their effects in the San Francisco Bay−Delta

Connon, R. E., Hasenbein, S., Brander, S. M., Poynton, H. C., Holland, E. B., Schlenk, D., Orlando, J. L., Brown, J., Todgham, A. E., Whitehead, A., Cherr, G., Colbourne, J., Young, T. M., Hajibabaei, M., Breuer, R. S. & Fong, S., 9 Dec 2019, In: San Francisco Estuary and Watershed Science. 17, 4, 42 p., 2.

Research output: Contribution to journal › Article › peer-review

Open Access

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3 Citations (Scopus)

169 Downloads (Pure)

Transgenerational response to early spring warming in Daphnia

Toyota, K., Cuenca Cambronero, M., Dhandapani, V., Suppa, A., Rossi, V., Colbourne, J. & Orsini, L., 14 Mar 2019, In: Scientific Reports. 9, 1, 4449.

Research output: Contribution to journal › Article › peer-review

Open Access

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8 Citations (Scopus)

215 Downloads (Pure)

2018

Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms

Seymour, M., Colbourne, J., Durance, I., Cosby, B. J., Ransom-Jones, E., Deiner, K., Ormerod, S. J., Wilgar, G., Carvalho, G. R., de Bruyn, M., Edwards, F., Emmett, B. A., Bik, H. M. & Creer, S., 22 Jan 2018, In: Communications Biology. 1, 4.

Research output: Contribution to journal › Article › peer-review

Open Access

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85 Citations (Scopus)

187 Downloads (Pure)

Arsenic reduces gene expression response to changing salinity in killifish

Hampton, T., Jackson, C., Jung, D., Chen, C. Y., Glaholt, S. P., Stanton, B. A., Colbourne, J. & Shaw, J., 7 Aug 2018, In: Environmental Science and Technology. 52, 15, p. 8811-8821 11 p.

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes

Orsini, L., Brown, J., Shams Solari, O., Li, D., He, S., Podicheti, R., Stoiber, M., Spanier, K. I., Gilbert, D., Jansen, M., Rusch, D., Pfrender, M. E., Colbourne, J., Frilander, M. J., Kvist, J., Decaestecker, E., De Schamphelaere, K. A. C. & De Meester, L., 1 Feb 2018, In: Molecular Ecology. 27, 4, p. 886-897 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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16 Citations (Scopus)

272 Downloads (Pure)

Evolutionary transition from blood feeding to obligate nonbiting in a mosquito

Bradshaw, W., Burkhart, J., Colbourne, J., Borowczak, R., Lopez, J., Denlinger, D., Reynolds, J., Pfrender, M. & Holzapfel, C., 30 Jan 2018, In: National Academy of Sciences. Proceedings. 115, 5, p. 1009-1014

Research output: Contribution to journal › Article › peer-review

Open Access

9 Citations (Scopus)

How omics technologies can enhance chemical safety regulation: perspectives from academia, government, and industry

Campos, B., Colbourne, J. K., Viant, M., Brown, J. B., Biales, A., Gallagher, K., Henry, T. R., Sappington, K. G., Marshall, S. & Whale, G., May 2018, In: Environmental Toxicology and Chemistry. 37, 5, p. 1252-1259 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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8 Citations (Scopus)

268 Downloads (Pure)

Invertebrate model species in AOP development

Hodges, G., Taylor, N., Colbourne, J., Gutsell, S., Brockmeier, E., Butler, E. & Rendal, C., 24 Feb 2018, A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment. Springer, p. 75-106 32 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

2 Citations (Scopus)

Mitotic activity patterns and cytoskeletal changes throughout the progression of diapause developmental program in Daphnia

Chen, L., Barnett, R. E., Horstmann, M., Bamberger, V., Heberle, L., Krebs, N., Colbourne, J. K., Gómez, R. & Weiss, L. C., 29 Dec 2018, In: BMC Cell Biology. 19, 1, 30.

Research output: Contribution to journal › Article › peer-review

Open Access

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4 Citations (Scopus)

189 Downloads (Pure)

Pattern of DNA methylation in Daphnia: evolutionary perspective

Kvist, J., Athanàsio, C. G., Solari, O. S., Brown, J., Colbourne, J., Pfrender, M. E. & Mirbahai, L., 1 Aug 2018, In: Genome Biology and Evolution. 10, 8, p. 1988-2007

Research output: Contribution to journal › Article › peer-review

Open Access

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15 Citations (Scopus)

261 Downloads (Pure)

John Colbourne

Research output

Search results