Collins RE. dānaSeq: containerized Nextflow pipelines for environmental metagenomics, metatranscriptomics and amplicon sequencing. Zenodo (preprint). (2026) preprint

Collins RE. dānaSeq nanopore_live: real-time processing of Oxford Nanopore metagenomic reads. Zenodo (preprint). (2026) preprint

Collins RE. dānaSeq nanopore_assembly and illumina_assembly: long- and short-read metagenome assembly. Zenodo (preprint). (2026) preprint

Collins RE. dānaSeq mag_analysis: recovery, annotation and exploration of metagenome-assembled genomes. Zenodo (preprint). (2026) preprint

Collins RE. dānaSeq illumina_amplicon: primer-aware amplicon denoising with a Python port of DADA2. Zenodo (preprint). (2026) preprint

Collins RE. MAG It Faster: Bioinformatics Pipeline Efficiencies Attained Through AI-Assisted Coding. Zenodo (preprint). (2026) preprint

Collins RE. fastsne: mapping millions of nanopore reads by tetranucleotide t-SNE. Zenodo (preprint). (2026) preprint

Collins RE. SampleTown: an open-source, MIxS-native laboratory information management system for environmental DNA, from field collection to sequence archive. Zenodo (preprint). (2026) preprint

Collins RE. microscape.app: dashboards for interactive exploration of ‘omics data. Zenodo (preprint). (2026) preprint

Collins RE, Kazmiruk Z. Microbial plankton in southern Hudson Bay and James Bay in late summer. bioRxiv. (2026) preprint

Shibue R, Collins RE. Marine Group II Archaea: A Review with a Focus on the Arctic Ocean. Submitted to EcoEvoRxiv. (2026) preprint

Shibue R, Collins RE. Prokaryotic Community Structures in the Bering and Chukchi Seas. bioRxiv. (2026) preprint

Shibue R, Collins RE. Particle-Associated Prokaryotic Community Structures in the Bering and Chukchi Seas. bioRxiv. (2026) preprint

Green K, Collins RE. Metagenome-assembled genomes reveal water-mass-associated distribution ecotypes of marine Archaea in the Western Arctic Ocean. bioRxiv. (2026) preprint

Green K, Collins RE. Proteomic signatures of cold adaptation and sponge host adaptation in marine Archaea. bioRxiv. (2026) preprint

Vidanage T, Collins RE. Marine oil snow formation in microcosm incubations of artificial seawater at 4 °C. bioRxiv. (2026) preprint

Vidanage T, Collins RE. Draft genome of Paraperlucidibaca sp. CMO1 isolated from marine oil snow in the Churchill Marine Observatory, MB, Canada. bioRxiv. (2026) preprint

Vidanage T, Desmond D, Isleifson D, Stern G, Collins RE. Oil biodegradation and marine oil snow formation in Arctic seawater microcosms at 4 °C. bioRxiv. (2026) preprint

Vidanage T, Desmond D, Collins RE. Putative biosurfactants from polar microbial consortia. bioRxiv. (2026) preprint

Vidanage T, Tataskweyak Environmental Monitoring Agency, Collins RE. Factors affecting microbial community composition in Split Lake, MB, Canada. bioRxiv. (2026) preprint

Rapp J, Eronen-Rasimus E, Deming JW, Collins RE. Phyloecology of Sea Ice Bacteria and Archaea. In Sea Ice, 4th Ed. (D. Thomas, Ed.). (in press) (2025)

Loutet SJT, Sanger A, Strong K, Collins RE, Mahmoudi N. Microbial communities in the Hudson Strait amidst rapid environmental change. Canadian Journal of Microbiology 71:1–9. (2025)

Saltymakova D, Desmond D, Smith AF, Bautista MA, Collins RE, Polcwiartek K, Snyder N, Wolfe T, Hubert C, Isleifson D, Stern G. Enhanced crude oil degradation observed in sea ice following bioaugmentation with arctic bacteria. Marine Environmental Research. (2025)

Gentilhomme A, Sweet C, Hennon GM, Collins RE. Genomic signatures of cold adaptation in the family Colwelliaceae. Extremophiles 28(3):39. (2024)

Tully BJ, Buongiorno J, Cohen AB, et al. (BVCN Instructor Consortium). The Bioinformatics Virtual Coordination Network: An Open-Source and Interactive Learning Environment. Frontiers in Education 6:711618. (2021)

Dilliplaine K, Oggier M, Collins RE, Eicken H, Gradinger R, Bluhm BA. Crude oil exposure reduces ice algal growth in a sea-ice mesocosm experiment. Polar Biology 44:525–537. (2021)

Mueter FJ, Iken K, Cooper LW, Grebmeier JM, Kuletz KJ, Hopcroft RR, Danielson SL, Collins RE, Cushing DA. Changes in diversity and species composition across multiple assemblages in the eastern Chukchi Sea during two contrasting years are consistent with borealization. Oceanography 34:38–51. (2021)

Eronen-Rasimus E, Hultman J, Hai T, Pessi IS, Collins E, Wright S, Laine P, Viitamäki S, Lyra C, Thomas DN, Golyshin PN, Luhtanen A, Kuosa H, Kaartokallio H. Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkanoic Acid (PHA) Storage Polymers at Low Temperature. Applied and Environmental Microbiology 87:e00929-21. (2021)

Bowman KL, Collins RE, Agather AM, Lamborg CH, Hammerschmidt CR, Kaul D, Dupont CL, Christensen GA, Elias DA. Distribution of mercury-cycling genes in the Arctic and equatorial Pacific Oceans and their relationship to mercury speciation. Limnology and Oceanography 65:S310–S320. (2019)

Kasanke C, Collins RE, Leigh MB. Identification and characterization of a dominant sulfolane-degrading Rhodoferax sp. via stable isotope probing combined with metagenomics. Scientific Reports 9:1–9. (2019)

Ducluzeau AL, Tyson JR, Collins RE, Snutch TP, Hassett BT. Genome Sequencing of Sub-Arctic Mesomycetozoean Sphaeroforma sirkka Strain B5, Performed with the Oxford Nanopore MinION and Illumina HiSeq Systems. Microbiology Resource Announcements 7:e00848-18. (2018)

Bluhm BA, Hop H, Melnikov IA, Poulin M, Vihtakari M, Collins RE, Gradinger R, Juul-Pedersen T, von Quillfeldt C. Chapter 3.1: Sea Ice Biota. In State of the Arctic Marine Biodiversity Report. Conservation of Arctic Flora and Fauna (CAFF). (2017)

Fuchsman CA, Collins RE, Rocap G, Brazelton WJ. Effect of the environment on horizontal gene transfer between bacteria and archaea. PeerJ 5:e3865. (2017)

Deming JW, Collins RE. Sea Ice as a Habitat for Bacteria, Archaea and Viruses. In Sea Ice, 3rd Edition (D. Thomas, Ed.). John Wiley & Sons, Ltd. (2017)

Moyer CL, Collins RE, Morita RY. Psychrophiles and Psychrotrophs. Encyclopedia of Life Sciences. (2017)

Hassett BT, Ducluzeau AL, Collins RE, Gradinger R. Spatial distribution of aquatic marine fungi across the western Arctic and sub-Arctic. Environmental Microbiology 19:475–484. (2017)

Firth E, Carpenter SD, Sørensen HL, Collins RE, Deming JW. Bacterial use of choline to tolerate salinity shifts in sea-ice brines. Elementa: Science of the Anthropocene 4. (2016)

Collins RE. Microbial Evolution in the Cryosphere. In Microbial Evolution Under Extreme Conditions (C. Bakermans, Ed.). De Gruyter, Berlin. (2016)

Kopf A, Bicak M, and 148 co-authors including Collins RE. The ocean sampling day consortium. GigaScience 4:1–5. (2015)

Eicken H, Bluhm BA, Collins RE, Gradinger RR, Haas C, Ingham M, Mahoney A, Nicolaus M, Perovich D. Field Techniques in Sea-Ice Research. In UNESCO Encyclopedia of Life Support Systems: Cold Regions Science and Marine Technology. (2015)

Miller LA, Fripiat F, Else BGT, Bowman JS, Brown KA, Collins RE, et al. Methods for biogeochemical studies of sea ice: The state of the art, caveats, and recommendations. Elementa 3:000038. (2015)

Collins RE, Deming JW. An inter-Order horizontal gene transfer event enables the catabolism of compatible solutes by Colwellia psychrerythraea 34H. Extremophiles 17:601–610. (2013)

Collins RE, Higgs PG. Testing the Infinitely Many Genes model for the evolution of the bacterial core genome and pangenome. Molecular Biology and Evolution 29:3413–3425. (2012)

Collins RE, Higgs PG. Origin and Evolution of Gene Families in Bacteria and Archaea. BMC Bioinformatics 12(Suppl 9):S14. (2011)

Collins RE, Deming JW. Abundant dissolved genetic material in Arctic sea ice, Part I: Extracellular DNA. Polar Biology 34:1819–1830. (2011)

Collins RE, Deming JW. Abundant dissolved genetic material in Arctic sea ice, Part II: Viral dynamics during autumn freeze-up. Polar Biology 34:1831–1841. (2011)

Miller LA, Papakyriakou TN, Collins RE, Deming JW, Ehn JK, Macdonald RW, Mucci A, Owens O, Raudsepp M, Sutherland N. Carbon dynamics in sea ice: A winter flux time series. Journal of Geophysical Research 116:C02028. (2011)

Collins RE, Rocap G, Deming JW. Persistence of bacterial and archaeal communities in sea ice through an Arctic winter. Environmental Microbiology 12:1828–1841. (2010)

Collins RE, Carpenter SD, Deming JW. Spatial heterogeneity and temporal dynamics of particles, bacteria, and pEPS in Arctic winter sea ice. Journal of Marine Systems 74:902–917. (2008)

Collins RE, Rocap G. REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. Nucleic Acids Research 35(Web Server issue):W58–W62. (2007)

Ehlmann BL, Chowdhury J, Marzullo TC, Collins RE, et al. Humans to Mars: a feasibility and cost-benefit analysis. Acta Astronautica 56:851. (2005)

Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG. An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof. Phytochemistry 64:1097–1112. (2003)