Submitted – accepted – in press

Uthanumallian K., Del Cortona A., Coelho S. De Clerck O., Duchene S. & Verbruggen H.
Genome-wide patterns of selection-drift variation strongly associate with organismal traits across the green algae.
Hsieh Y.E., Tandon K., Verbruggen H. & Nikoloski Z.
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches.
npj Systems Biology and Applications: accepted
Preprint: bioRxiv
Bjornson S., Verbruggen H., Upham N., & Steenwyk J.
Reticulate evolution: Detection and utility in the phylogenomics era.
Preprint: 10.20944/preprints202309.0905.v2
Turnbull R., Steenwyk J., Mutch S.J., Scholten P., Salazar V.W., Birch J. & Verbruggen H.
OrthoFlow: phylogenomic analysis and diagnostics with one command.
Preprint: ResearchSquare
Terpis K., Salomaki E., Barcyte D., Panek T., Verbruggen H., Kolisko M., Bailey J.C., Elias M, & Lane C.
Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics.
Preprint: bioRxiv
Denoeud F., Godfroy O., Cruaud C., Heesch S., Nehr Z., Tadrent N., Couloux A., Brillet-Gueguen L., Delage L., Mckeown D., Motomura T., Sussfeld D., Fan X., Mazeas L., Terrapon N., Barrera-Redondo J., Petroll R., Reynes L., Choi S.W., Jo J., Uthanumallian K., Bogaert K., Duc C., Ratchinski P., Lipinska A., Noel B., Murphy E.A., Lohr M., Khatei A., Hamon-Giraud P., Vieira C., Akerfors S.S., Akita S., Avia K., Badis Y., Barbeyron T., Belcour A., Berrabah W., Blanquart S., Bouguerba-Collin A., Bringloe T., Cattolico R.A., Cormier A., Cruz de Carvalho H., Dallet R., De Clerck O., Debit A., Denis E., Destombe C., Dinatale E., Dittami S., Drula E., Faugeron S., Got J., Graf L., Groisillier A., Guillemin M.L., Harms L., Hatchett W.J., Henrissat B., Hoarau G., Jollivet C., Jueterbock A., Kayal E., Kogame K., Le Bars A., Leblanc C., Ley R., Liu X., Lopez P.J., Lopez P., Manirakiza E., Massau K., Mauger S., Mest L., Michel G., Monteiro C., Nagasato C., Negre D., Pelletier E., Phillips N., Potin P., Rensing S.A., Rousselot E., Rousvoal S., Schroeder D., Scornet D., Siegel A., Tirichine L., Tonon T., Valentin K., Verbruggen H., Weinberger F., Wheeler G., Kawai H., Peters A.F., Yoon H.S., Herve C., Ye N., Bapteste E., Valero M., Markov G.V., Corre E., Coelho S.M., Wincker P., Aury J.M. & Cock J.M.
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems.
Preprint: bioRxiv
Hossen R., Courtney M., Sim A., Khan M.A.A.K., Verbruggen H. & Bringloe T.
An optimized CTAB method for genomic DNA extraction from green algae.
Tandon K., Hu J., Pasella M.M., Pushpakumara B.L.D.U. & Verbruggen H.
Coral skeleton dwelling endolithic algae: Ostreobium and its biology.
Diaz-Tapia P., Bribiesca-Contreras G., Maggs C.A. & Verbruggen H.
Evolutionary radiation of the red algal family Rhodomelaceae after the Permian-Triassic mass extinction.


Assis J., Fernández Bejarano S.J., Salazar V.W., Schepers L., Gouvea L., Fragkopoulou E., Leclercq F., Vanhoorne B., Tyberghein L., Serrao E.A., Verbruggen H. & De Clerck O. (2024)
Bio-ORACLE v3.0. Pushing marine data layers to the CMIP6 Earth system models of climate change research
Global Ecology and Biogeography 33: e13813
DOI: 10.1111/geb.13813
Diaz-Tapia P. & Verbruggen H. (2024)
Resolving the taxonomy of the Polysiphonia scopulorum complex and the Bryocladia lineage (Rhodomelaceae, Rhodophyta).
Journal of Phycology 60: 49-72
DOI: 10.1111/jpy.13402
Wetherbee R., Bringloe T.T., Leliaert F. & Verbruggen H. (2024)
Molecular data and culture observations show that the microfilamentous marine alga Uronema marinum is a member of the genus Okellya (Cladophorales, Chlorophyta).
Cryptogamie Algologie 45: 31-37
PDF: download
Verbruggen H. & Ballesteros E. (2024)
An Atlantic origin for the introduced species Halimeda incrassata.
Mediterranean Marine Science 25: 55-57
DOI: 10.12681/mms.35993
Huisman J.M., Verbruggen H., Hossen R., Rybalka N. & Entwisle T.J.
Morphological and molecular analyses of Vaucheria section Piloboloideae (Xanthophyceae: Vaucheriaceae) indicate alternative species identities for broadly distributed taxa.
Phycologia63: 170-178
DOI: 10.1080/00318884.2024.2306656


Salazar V.W., Shaban B., del Mar Quiroga M., Turnbull R., Tescari E., Marcelino V.R., Verbruggen H. & Le Cao K.A. (2023)
Metaphor - A workflow for streamlined assembly and binning of metagenomes.
GigaScience 12: giad055
DOI: 10.1093/gigascience/giad055 — Preprint: bioRxiv
Ricci F., Tandon K., Mosshammer M., Cho E.H.J., Blackall L.L., Kühl M. & Verbruggen H. (2023)
Fine-scale mapping of physicochemical and microbial landscapes of the coral skeleton.
Environmental Microbiology 25: 1505-1521
DOI: 10.1111/1462-2920.16369 — Preprint: ResearchSquare
Tandon K., Pasella M.M., Iha C., Ricci F., Hu J., O'Kelly C.J., Medina M., Kühl M. & Verbruggen H. (2023)
Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business.
Seminars in Cell & Developmental Biology 134: 27-36
DOI: 10.1016/j.semcdb.2022.03.010
Tandon K., Ricci F., Costa J., Medina M., Kühl M., Blackall L.L. & Verbruggen H. (2023)
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.
GigaScience 12: giac127
DOI: 10.1093/gigascience/giac127 — Preprint: ResearchSquare
Pushpakumara B.L.D.U., Tandon K., Willis A. & Verbruggen H. (2023)
Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks.
Scientific Reports 13: 2743
DOI: 10.1038/s41598-023-27816-9 — Preprint: bioRxiv
Wetherbee R., Bringloe T.T., van de Meene A., Andersen R.A. & Verbruggen H. (2023)
Structure and formation of the perforated theca defining the Pelagophyceae (Heterokonta), and three new genera that substantiate the diverse nature of the class.
Journal of Phycology 59: 126-151
DOI: 10.1111/jpy.13294
Diaz-Tapia P., Rodriguez-Bujan I. Maggs C.A. & Verbruggen H. (2023)
Phylogenomic analysis of pseudocryptic diversity reveals the new genus Deltalsia (Rhodomelaceae, Rhodophyta).
Journal of Phycology 59: 264-276
DOI: 10.1111/jpy.13311
Diaz-Tapia P., Nelson W.A. & Verbruggen H. (2023)
Molecular analysis of turf algae reveal a new species and an undetected introduction in the Pterosiphonieae (Rhodomelaceae, Rhodophyta).
Journal of Phycology 59: 603-618
DOI: 10.1111/jpy.13336
Pushpakumara B.L.D.U., Tandon K., Willis A. & Verbruggen H. (2023)
The bacterial microbiome of the coral skeleton algal symbiont Ostreobium shows preferential associations and signatures of phylosymbiosis.
Microbial Ecology 86: 2032-2046
DOI: 10.1007/s00248-023-02209-7 — Preprint: bioRxiv
Shaban B., del Mar Quiroga M., Turnbull R., Tescari E., Le Cao K.A. & Verbruggen H. (2023)
MetaGenePipe: an automated, portable pipeline for contig-based functional and taxonomic analysis.
Journal of Open Source Software 8: 4851
DOI: 10.21105/joss.04851 — Preprint: ResearchSquare
West J.A., Zuccarello G.C., Verbruggen H., Powling J., Miller J. & Loiseaux-de Goer S. (2023)
Amoenothamnion planktonicum (Heterothamnieae, Ceramiaceae, Rhodophyta), an annual drift event along sandy beaches of southern Australia and its affinities.
Notulae Algarum 271: 1-7
PDF download: Notulae Algarum
Preuss M., Diaz-Tapia P., Verbruggen H. & Zuccarello G.C. (2023)
Gene-rich plastid genomes of two parasitic red algal species, Laurencia australis and L. verruciformis (Rhodomelaceae, Ceramiales), and a taxonomic revision of Janczewskia.
Journal of Phycology 59: 950-962
DOI: 10.1111/jpy.13373
Huisman J.M. & Verbruggen H. (2023)
A morphological and molecular study supports the recognition of Rhipilia psammophila sp. nov. and Rhipilia baculifera comb. nov. (Halimedaceae, Chlorophyta) from southern Australia.
Australian Systematic Botany 36: 427-436
DOI: 10.1071/SB23016


Uthanumallian K., Iha C., Repetti S.I., Chan C.X., Bhattacharya D., Duchene S. & Verbruggen H. (2022)
Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis.
Molecular Biology and Evolution 39: msab295
DOI: 10.1093/molbev/msab295 — Preprint: bioRxiv
Repetti S.I., Iha C., Uthanumallian K., Jackson C.J., Chen Y., Chan C.X. & Verbruggen H. (2022)
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae.
New Phytologist 233: 2144-2154
DOI: 10.1111/nph.17926 — Preprint: bioRxiv
Bringloe T.T., Wilkinson D.P., Goldsmit J., Savoie A.M., Filbee-Dexter K., Macgregor K.A., Howland K.L., McKindsey C.W. & Verbruggen H. (2022)
Arctic marine forest distribution models showcase potentially severe habitat losses for cryophilic species under climate change.
Global Change Biology 28: 3711-3727
DOI: 10.1111/gcb.16142
Ricci F., Tandon K., Black J.R., Le Cao K.A., Blackall L.L. & Verbruggen H. (2022)
Host traits and phylogeny contribute to shaping coral-bacterial symbioses.
mSystems 7: e00044-22
DOI: 10.1128/msystems.00044-22 — Preprint: Research Square
Pasella M.M., Lee M.F.E., Marcelino V.R., Willis A. & Verbruggen H. (2022)
Ten Ostreobium strains from Great Barrier Reef corals as a resource for algal endolith biology and genomics.
Phycologia 61: 452-458
DOI: 10.1080/00318884.2022.2064132 — Preprint: bioRxiv
Bringloe T.T., Fort A., Inaba M., Sulpice R., Ghriofa C.N., Mols-Mortensen A., Filbee-Dexter K., Vieira C., Kawai H., Hanyuda T., Krause-Jensen D., Olesen B., Starko S. & Verbruggen H. (2022)
Whole genome population structure of North Atlantic kelp confirms high-latitude glacial refugia.
Molecular Ecology 31: 6473-6488
DOI: 10.1111/mec.16714


Iha C., Dougan K.E., Varela J.A., Avila V., Jackson C.J., Bogaert K.A., Chen Y., Judd L.M., Wick R., Holt K.E., Pasella M.M., Ricci F., Repetti S.I., Medina M., Marcelino V.R., Chan C.X. & Verbruggen H. (2021)
Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium.
Current Biology 31: 1393-1402
DOI: 10.1016/j.cub.2021.01.018 — Preprint: bioRxiv
Bringloe T.T., Sauermann R., Krause-Jensen D., Olesen B., Klimova A., Klochkova T.A. & Verbruggen H. (2021)
High-througput sequencing of the kelp Alaria (Phaeophyceae) reveals novel epi-endobiotic associations, including a likely phaeophycean parasite.
European Journal of Phycology 56: 494-504
DOI: 10.1080/09670262.2021.1882704
Ricci F., Fordyce A., Leggat W., Blackall L.L., Ainsworth T. & Verbruggen H. (2021)
Multiple techniques point to oxygenic phototrophs dominating the Isopora palifera skeletal microbiome.
Coral Reefs 40: 275-282
DOI: 10.1007/s00338-021-02068-z
Vieira C., Steen F., D'hondt S., Bafort Q., Tyberghein L., Fernandez-Garcia C., Wysor B., Tronholm A., Mattio L., Payri C., Kawai H., Saunders G., Leliaert F., Verbruggen H. & De Clerck O. (2021)
Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade-specific evolutionary processes.
Journal of Biogeography 48: 703-715
DOI: 10.1111/jbi.14047
Wetherbee R., Bringloe T.T., Costa J.F., van de Meene A., Andersen R.A. & Verbruggen H. (2021)
New pelagophytes show a novel mode of algal colony development and reveal a perforated theca that may define the class.
Journal of Phycology 57: 396-411
DOI: 10.1111/jpy.13074
Zou X., Verbruggen H., Li T., Zhu J., Chen Z., He W., Bao S. & Sun J. (2021)
Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data.
BMC Genomics 22: 298
DOI: 10.1186/s12864-021-07598-y
Preuss M., Verbruggen H., West J. & Zuccarello G.C. (2021)
Divergence times and plastid phylogenomics within the intron-rich order Erythropeltales (Compsopogonophyceae, Rhodophyta).
Journal of Phycology 57: 1035-1044
DOI: 10.1111/jpy.13159
Bringloe T.T., Zaparenkov D., Starko S., Grant W., Vieira C., Kawai H., Hanyuda T., Filbee-Dexter K., Klimova A., Klochkova T., Krause-Jensen D., Olesen B. & Verbruggen H. (2021)
Whole genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae).
Journal of Phycology 57: 1721-1738
DOI: 10.1111/jpy.13212
Fang J., Wang H., Chen Y., Liu G., Verbruggen H. & Zhu H. (2021)
Chloroplast genome traits correlate with organismal complexity and ecological traits in green algae.
Frontiers in Ecology and Evolution 9: 882
DOI: 10.3389/fevo.2021.791166
Fang J., Liu B., Wang H., Liu G., Verbruggen H. & Zhu H. (2021)
Six newly sequenced chloroplast genomes from Trentepohliales: inflated genomes, alternative genetic code and dynamic evolution.
Frontiers in Plant Science 12: 2865
DOI: 10.3389/fpls.2021.780054
Tonicelli G., Croce M.E., Diaz-Tapia P., Fredericq S., Freshwater D.W., Gauna M.C., Parodi E.R., Verbruggen H. & Hommersand M. (2021)
Meridionella gen. nov., a new genus of Cystocloniaceae (Gigartinales, Rhodophyta) from the southern hemisphere including M. obtusangula comb. nov. and M. antarctica sp. nov.
Journal of Phycology 57: 797-816
DOI: 10.1111/jpy.13127


del Cortona A., Jackson C.J., Bucchini F., Van Bel M., D'Hondt S., Skaloud P., Delwiche C.F., Knoll A.H., Raven J.A., Verbruggen H., Vandepoele K., De Clerck O. & Leliaert F. (2020)
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds.
Proceedings of the National Academy of Sciences of the USA 117: 2551-2559
DOI: 10.1073/pnas.1910060117 — preprint: 10.1101/668475
Bringloe T.T., Verbruggen H. & Saunders G.W. (2020)
Unique biodiversity in Arctic marine forests is shaped by diverse recolonization pathways and far northern glacial refugia.
Proceedings of the National Academy of Sciences of the USA 117: 22590-22596
DOI: 10.1073/pnas.2002753117 — preprint: bioRxiv
Bringloe T.T., Starko S., Wade R.M., Vieira C., Kawai H., De Clerck O., Cock J.M., Coelho S.M., Destombe C., Valero M., Neiva J., Pearson G.A., Faugeron S., Serrao E.A. & Verbruggen H. (2020)
Phylogeny and evolution of the brown algae.
Critical Reviews in Plant Sciences 39: 281-321
DOI: 10.1080/07352689.2020.1787679
Repetti S.I., Jackson C.J., Judd L.M., Wick R.R., Holt K.E. & Verbruggen H. (2020)
The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns.
PeerJ 8: e8273
DOI: 10.7717/peerj.8273
Goes-Neto A., Marcelino V.R., Verbruggen H., Ferreira da Silva F. & Badotti F. (2020)
Fungal diversity of coral skeletons in the southwestern Pacific using 18S rDNA metabarcoding.
Coral Reefs 39: 229-238
DOI: 10.1007/s00338-019-01880-y
Diaz-Tapia P., Ly M. & Verbruggen H. (2020)
Extensive cryptic diversity in the widely distributed Polysiphonia scopulorum (Rhodomelaceae, Rhodophyta): molecular species delimitation and morphometric analyses.
Molecular Phylogenetics and Evolution 152: 106909
DOI: 10.1016/j.ympev.2020.106909
Preuss M., Verbruggen H. & Zuccarello G.C. (2020)
The organelle genomes in the photosynthetic red algal parasite Pterocladiophila hemisphaerica have elevated substitution rates and extreme gene loss in the plastid genome.
Journal of Phycology 56: 1006-1018
DOI: 10.1111/jpy.12996
Charon J., Marcelino V.R., Wetherbee R., Verbruggen H. & Holmes E.C. (2020)
Metatranscriptomic identification of diverse and divergent RNA viruses associated with green and chlorarachniophyte algae.
Viruses 12: 1180
DOI: 10.3390/v12101180 — Preprint: bioRxiv
Graf L., Yang E.C., Han K.Y., Kupper F., Benes K.M., Oyadomari J., Herbert R.J.H., Verbruggen H., Wetherbee R., Andersen R.A. & Yoon H.S.
Multigene phylogeny, morphological observation and re-examination of the literature lead to the description of the Phaeosacciophyceae classis nova and four new species of the Heterokontophyta SI clade.
Protist 171: 125781
DOI: 10.1016/j.protis.2020.125781
Rindi F., Pasella M.M., Lee M-F.E. & Verbruggen H. (2020)
Phylogeography of the Mediterranean green seaweed Halimeda tuna.
Journal of Phycology 56: 1109-1113
DOI: 10.1111/jpy.13006
Pineiro-Corbeira C., Verbruggen H. & Diaz-Tapia P. (2020)
Molecular survey of the red algal family Rhodomelaceae (Ceramiales, Rhodophyta) in Australia reveals new introduced species.
Journal of Applied Phycology 32: 2535-2547
DOI: 10.1007/s10811-019-01932-4
Schneider C.W., Lam D.W. & Verbruggen H. (2020)
DNA sequencing and anatomy demonstrate that Pacific Codium simulans is a genetically variable species found in the floras of Bermuda and Florida.
Phycological Research 68: 98-102
DOI: 10.1111/pre.12396
Lagourgue L., Verbruggen H., Ampou E.E. & Payri C.E. (2020)
One hundred years later, resurrection of Tydemania gardineri (Udoteaceae, Chlorophyta) based on molecular and morphological data.
European Journal of Phycology 55: 89-99
DOI: 10.1080/09670262.2019.1654618
Diaz-Tapia P., Maggs C.A., Nelson W., Macaya E.C. & Verbruggen H. (2020)
Reassessment of the genus Lophurella (Rhodomelaceae, Rhodophyta) from Australia and New Zealand reveals four cryptic species.
European Journal of Phycology 55: 113-128
DOI: 10.1080/09670262.2019.1659419
Huisman J.M. & Verbruggen H. (2020)
Pseudoderbesia eckloniae, sp. nov. (Bryopsidaceae, Ulvophyceae) from Western Australia.
Cryptogamie Algologie 41: 19-23
DOI: 10.5252/cryptogamie-algologie2020v41a3
Dumilag R.V., Dumago F.S., Cabudoy R.K.R., Peralta M.C.E., Li C.C., Gamus G.C.V., Romero R.G.T., Yap S.L., Roleda M.Y., Geraldino P.J.L., Verbruggen H., Leliaert F., Draisma S.G.A., Liao L.M. & Kraft G.T. (2020)
The Ulvophyceae (Chlorophyta) of eastern Sorsogon, Philippines, including Halimeda magnicuneata sp. nov. (Bryopsidales).
Botanica Marina 63: 439-453
DOI: 10.1515/bot-2020-0017


Ricci F., Marcelino V.R., Blackall L.L., Kühl M., Medina M. & Verbruggen H. (2019)
Beneath the surface: community assembly and functions of the coral skeleton microbiome.
Microbiome 7: 159
DOI: 10.1186/s40168-019-0762-y
Wetherbee R., Jackson C.J., Repetti S.I., Clementson L.A., Costa J.F., van de Meene A., Crawford S. & Verbruggen H. (2019)
The golden paradox – a new heterokont lineage with chloroplasts surrounded by two membranes.
Journal of Phycology 55: 257-278
DOI: 10.1111/jpy.12822
Cremen M.C.M., Leliaert F., West J., Lam D.W., Shimada S., Lopez-Bautista J. & Verbruggen H. (2019)
Re-assessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses.
Molecular Phylogenetics and Evolution 130: 397-405
DOI: 10.1016/j.ympev.2018.09.009
Bribiesca-Contreras G., Pineda-Enriquez T., Marquez-Borras F., Solis-Marin F.A., Verbruggen H., Hugall A.F. & O'Hara T. (2019)
Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star.
Molecular Phylogenetics and Evolution 136: 151-163
DOI: 10.1016/j.ympev.2019.04.014
Diaz-Tapia P., Pasella M.M., Verbruggen H. & Maggs C.A. (2019)
Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics.
Molecular Phylogenetics and Evolution 137: 76-85
DOI: 10.1016/j.ympev.2019.04.022
Evans J.R., St. Amour N., Verbruggen H., Salomaki E.D. & Vis M.L. (2019)
Chloroplast and mitochondrial genomes of Balbiania investiens (Balbianiales, Nemaliophycidae).
Phycologia 58: 310-318
DOI: 10.1080/00318884.2019.1573349
Pasella M.M., Verbruggen H., Nelson W.A. & Diaz-Tapia P. (2019)
The phylogenetic position of the morphologically unusual Pleurostichidium falkenbergii (Rhodomelaceae, Rhodophyta) based on plastid phylogenomics.
Phycologia 58: 319-325
DOI: 10.1080/00318884.2019.1574462
Bribiesca-Contreras G., Verbruggen H., Hugall A.F. & O'Hara T. (2019)
Global biogeographic structuring of tropical shallow-water brittle stars.
Journal of Biogeography 46: 1287-1299
DOI: 10.1111/jbi.13620
Wetherbee R., Marcelino V.R., Costa J.F., Grant B., Crawford S., Waller R.F., Andersen R.A., Berry D., McFadden G.I. & Verbruggen H. (2019)
A new marine prasinophyte genus alternates between a flagellate and a dominant benthic stage with microrhizoids for adhesion.
Journal of Phycology 55: 1210-1225
DOI: 10.1111/jpy.12909


Diaz-Tapia P., Maggs C.A., Macaya E.C. & Verbruggen H. (2018)
Widely distributed red algae often represent hidden introductions, complexes of cryptic species or species with strong phylogeographic structure.
Journal of Phycology 54: 829-839
DOI: 10.1111/jpy.12778
Iha C., Grassa C.J., Lyra G.M., Davis C.C., Verbruggen H. & Oliveira M.C. (2018)
Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta).
Journal of Phycology 54: 775-787
DOI: 10.1111/jpy.12765
Croce M.E., Diaz-Tapia P. & Verbruggen H. (2018)
Molecular systematics of the siphonous green algal genus Codium in eastern Victoria, Australia.
Cryptogamie Algologie 39:391-407
DOI: 10.7872/crya/v39.iss4.2018.39
Leliaert F., Payo D.A., Gurgel C.F.D., Schils T., Draisma S.G.A., Saunders G.W., Kamiya M., Sherwood A.R., Lin S.M., Huisman J.M., Le Gall L., Anderson R.J., Bolton J.J., Mattio L., Zubia M., Payri C., Spokes T., Johnston E.T., Vieira C., Coppejans E., D'hondt S., Verbruggen H. & De Clerck O. (2018)
Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria.
Journal of Biogeography 10: 2299-2313
DOI: 10.1111/jbi.13410
Yates K.L., Bouchet P.J., Caley M.J., Mengersen K., Randin C.F., Parnell S., Fielding A.H., Bamford A.J., Ban S., Barbosa A.M., Dormann C.F., Elith J., Embling C.B., Ervin G.N., Fisher R., Gould S., Graf R.F., Gregr E.J., Halpin P.N., Heikkinen R.K., Heinanen S., Jones A.R., Krishnakumar P.K., Lauria V., Lozano-Montes H., Mannocci L., Mellin C., Mesgaran M.B., Moreno-Amat E., Mormede S. Novaczek E., Oppel S., Ortuno Crespo G., Peterson A.T., Rapacciuolo G., Roberts J.J., Ross R.E. Scales K.L., Schoeman D., Snelgrove P., Sundblad G., Thuiller W., Torres L.G., Verbruggen H., Wang L., Wenger S., Whittingham M.J., Zharikov Y., Zurell D. & Sequeira A.M.M. (2018)
Outstanding challenges in the transferability of ecological models.
Trends in Ecology & Evolution 33: 790-802
DOI: 10.1016/j.tree.2018.08.001
Diaz-Tapia P., Pasella M.M. & Verbruggen H. (2018)
Molecular analyses resolve the phylogenetic position of Polysiphonia adamsiae (Rhodomelaceae, Rhodophyta) and reveal a strong phylogeographic structure in Australia.
Phycologia 57: 593-600
DOI: 10.2216/18-36.1
Oliveira M.C., Repetti S.I., Iha C., Jackson C.J., Diaz-Tapia P., Magalhaes K., Cassano V., Costa J.F., Cremen M.C.M., Marcelino V.R. & Verbruggen H. (2018)
High-throughput sequencing for algal systematics.
European Journal of Phycology 53: 256-272
DOI: 10.1080/09670262.2018.1441446
Cremen M.C.M., Leliaert F., Marcelino V.R. & Verbruggen H. (2018)
Large diversity of nonstandard genes and dynamic evolution of chloroplast genomes in siphonous green algae (Bryopsidales, Chlorophyta).
Genome Biology and Evolution 10: 1048-1061
DOI: 10.1093/gbe/evy063
Paiano M.O., Del Cortona A., Costa J.F., Liu S.L., Verbruggen H., De Clerck O. & Necchi Jr O. (2018)
Complete mitochondrial genomes of six species of the freshwater red algal order Batrachospermales (Rhodophyta).
Mitochondrial DNA Part B - Resources 3: 607-610
DOI: 10.1080/23802359.2018.1473734
Assis J., Tyberghein L., Bosch S., Verbruggen H., Serrao E.A. & De Clerck O. (2018)
Bio-ORACLE v2.0: Extending marine data layers for bioclimatic modelling.
Global Ecology and Biogeography 27: 277-284.
DOI: 10.1111/geb.12693
Marcelino V.R., van Oppen M.J.H. & Verbruggen H. (2018)
Highly structured prokaryote communities exist within the skeleton of coral colonies.
ISME Journal 12: 300-303
DOI: 10.1038/ismej.2017.164
Jackson C., Knoll A.H., Chan C.X. & Verbruggen H. (2018)
Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids.
Scientific Reports 8: 1523
DOI: 10.1038/s41598-017-18805-w
Paiano M.O., Del Cortona A., Costa J.F., Liu S.L., Verbruggen H., De Clerck O. & Necchi O. (2018)
Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta).
Journal of Phycology 54: 25-33
DOI: 10.1111/jpy.12602
Hoffman R., Wynne M.J., Schils T., Lopez-Bautista J. & Verbruggen H. (2018)
Codium pulvinatum (Bryopsidales, Chlorophyta), a new species from the Arabian Sea, recently introduced into the Mediterranean Sea.
Phycologia 57: 79-89
DOI: 10.2216/17-74.1


del Cortona A., Leliaert F., Bogaert K.A., Turmel M., Boedeker C., Janouskovec J., Lopez-Bautista J.M., Verbruggen H., Vanepoele K., De Clerck O. (2017)
The plastid genome in Cladophorales green algae is encoded by hairpin plasmids.
Current Biology 27: 3771-3782
DOI: 10.1016/j.cub.2017.11.004 — preprint: 10.1101/145037
Marcelino V.R., Morrow K.M., van Oppen M.J.H., Bourne D.G. & Verbruggen H. (2017)
Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef.
Molecular Ecology 26: 5334-5357
DOI: 10.1111/mec.14268
Bribiesca-Contreras G., Verbruggen H., Hugall A.F. & O'Hara T.D. (2017)
The importance of offshore origination revealed through ophiuroid phylogenomics.
Proceedings of the Royal Society B: Biological Sciences 284: 20170160
DOI: 10.1098/rspb.2017.0160
Marcelino V.R. & Verbruggen H. (2017)
Reference datasets of tufA and UPA markers to identify algae in metabarcoding surveys.
Data Brief 11: 273-276
DOI: 10.1016/j.dib.2017.02.013
Diaz-Tapia P., Maggs C.A., West J.A. & Verbruggen H. (2017)
Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta).
Journal of Phycology 53: 920-937
DOI: 10.1111/jpy.12553
Diaz-Tapia P., Barbara I., Cremades J., Verbruggen H. & Maggs C.A. (2017)
Three new cryptogenic species in the tribe Polysiphonieae (Rhodomelaceae, Rhodophyta).
Phycologia 56: 605-623
DOI: 10.2216/17-17.1
Verbruggen H., Marcelino V.R., Guiry M.D., Cremen M.C.M. & Jackson C. (2017)
Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data.
Journal of Phycology 53: 790-803
DOI: 10.1111/jpy.12540
Steen F., Aragay J., Zuljevic A., Verbruggen H., Mancuso F.P., Bunker F., Vitales D., Gomez Garreta A. & De Clerck O. (2017)
Tracing the introduction history of the brown seaweed Dictyota cyanoloma (Phaeophyceae, Dictyotales) in Europe.
European Journal of Phycology 52: 31-42
DOI: 10.1080/09670262.2016.1212998
Diaz-Tapia P., McIvor L., Freshwater D.W., Verbruggen H., Wynne M.J. & Maggs C.A (2017)
The genera Melanothamnus Bornet & Falkenberg and Vertebrata S.F. Gray constitute well-defined clades of the red algal tribe Polysiphonieae (Rhodomelaceae, Ceramiales).
European Journal of Phycology 52: 1-30
DOI: 10.1080/09670262.2016.1256436
Ximenes C.F., Cassano V., Oliveira-Carvalho M.F., Bandeira-Pedrosa M.E., Gurgel C.F.D., Verbruggen H. & Barreto-Pereira S.M. (2017)
Systematics of the genus Halimeda (Bryopsidales, Chlorophyta) in Brazil including the description of Halimeda jolyana sp. nov.
Phycologia 56: 369-381
DOI: 10.2216/16-77.1
Verbruggen H., Brookes M.J. & Costa J.F. (2017)
DNA barcodes and morphometric data indicate that Codium fragile may consist of two species (Bryopsidales, Chlorophyta).
Phycologia 56: 54-62
DOI: 10.2216/16-54.1


Rindi F. & Verbruggen H. (2016)
Taxonomic reshuffling of the Cladophoraceae.
Journal of Phycology 52: 901-904
DOI: 10.1111/jpy.12459
Costa J.F., Lin S.M., Macaya E.C., Fernandez-Garcia C. & Verbruggen H. (2016)
Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales.
BMC Evolutionary Biology 16: 205
DOI: 10.1186/s12862-016-0772-3
Alos J., Tomas F., Terrados J., Verbruggen H. & Ballesteros E. (2016)
Fast-spreading green beds of recently introduced Halimeda incrassata (Bryopsidales, Chlorophyta) invade Mallorca Island (NW Mediterranean Sea).
Molecular Ecology Progress Series 558: 153-158
DOI: 10.3354/meps11869
Marcelino V.R., Cremen M.C.M., Jackson C.J., Larkum A. & Verbruggen H. (2016)
Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green alga Ostreobium quekettii.
Genome Biology and Evolution 8: 2939-2951
DOI: 10.1093/gbe/evw206 — preprint: 10.1101/049833
Marcelino V.R. & Verbruggen H. (2016)
Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae.
Scientific Reports 6: 31508
DOI: 10.1038/srep31508
Wetherbee R. & Verbruggen H. (2016)
Kraftionema allantoideum, a new genus and family of Ulotrichales (Chlorophyta) adapted for survival in high intertidal pools.
Journal of Phycology 52: 704-715
DOI: 10.1111/jpy.12447
West J.A., Zuccarello G.C., Loiseaux de Goer S., Stavrias L.A. & Verbruggen H. (2016)
Rhodenigma contortum, an obscure new genus and species of Rhodogorgonales (Rhodophyta) from Western Australia.
Journal of Phycology 52: 397-403
DOI: 10.1111/jpy.12402
Cremen M.C.M., Huisman J.M., Marcelino V.R. & Verbruggen H. (2016)
Taxonomic revision of Halimeda in southwestern Australia.
Australian Systematic Botany 29: 41-54
DOI: 10.1071/SB15043
Fernandez-Garcia C., Wysor B., Riosmena-Rodriguez R., Pena-Salamanca E. & Verbruggen H. (2016)
DNA-assisted identification of Caulerpa (Caulerpaceae, Chlorophyta) reduces species richness estimates for the Eastern Tropical Pacific.
Phytotaxa 252: 185-204
DOI: 10.11646/phytotaxa.252.3.2
Lam D.W., Verbruggen H., Saunders G.W., Vis M.L. (2016)
Multigene phylogeny of the red algal subclass Nemaliophycidae.
Molecular Phylogenetics and Evolution 94: 730-736
DOI: 10.1016/j.ympev.2015.10.015

Older work

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