Peer-reviewed publications and book chapters

     Microbial Dark Matter (MDM) research team (Rinke lab)


    An updated list including citations can be found on Google Scholar

    Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy
    C Rinke, M Chuvochina, AJ Mussig, PA Chaumeil, AA Davin, DW Waite, ...
    bioRxiv, 2020.03. 01.972265
    Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages
    J Sun, PN Evans, EJ Gagen, BJ Woodcroft, BP Hedlund, T Woyke, ...
    A complete domain-to-species taxonomy for Bacteria and Archaea
    DH Parks, M Chuvochina, PA Chaumeil, C Rinke, AJ Mussig, ...
    Nature biotechnology 38 (9), 1079-1086
    Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution
    N Dombrowski, TA Williams, J Sun, BJ Woodcroft, JH Lee, BQ Minh, ...
    Nature communications 11 (1), 1-15
    A rank-normalized archaeal taxonomy based on genome phylogeny resolves widespread incomplete and uneven classifications
    C Rinke, M Chuvochina, AJ Mussig, PA Chaumeil, DW Waite, ...
    Defining the human gut host–phage network through single-cell viral tagging
    M Džunková, SJ Low, JN Daly, L Deng, C Rinke, P Hugenholtz
    Nature microbiology 4 (12), 2192-2203
    A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)
    C Rinke, F Rubino, LF Messer, N Youssef, DH Parks, M Chuvochina, ...
    The ISME journal 13 (3), 663-675
    The importance of designating type material for uncultured taxa
    M Chuvochina, C Rinke, DH Parks, MS Rappé, GW Tyson, P Yilmaz, ...
    Systematic and applied microbiology 42 (1), 15-21
    A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
    DH Parks, M Chuvochina, DW Waite, C Rinke, A Skarshewski, ...
    Nature biotechnology 36 (10), 996-1004
    Single-cell genomics of microbial dark matter
    C Rinke
    Microbiome Analysis, 99-111
    Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients
    AK Hawley, MK Nobu, JJ Wright, WE Durno, C Morgan-Lang, B Sage, ...
    Nature communications 8 (1), 1-10
    Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
    DH Parks, C Rinke, M Chuvochina, PA Chaumeil, BJ Woodcroft, ...
    Nature microbiology 2 (11), 1533-1542
    A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities
    BS Lambert, JB Raina, VI Fernandez, C Rinke, N Siboni, F Rubino, ...
    Nature microbiology 2 (10), 1344-1349
    Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
    RM Bowers, NC Kyrpides, R Stepanauskas, M Harmon-Smith, D Doud, ...
    Nature biotechnology 35 (8), 725-731
    Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)
    DW Waite, I Vanwonterghem, C Rinke, DH Parks, Y Zhang, K Takai, ...
    Frontiers in microbiology 8, 682
    Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota
    IV Kublanov, OM Sigalova, SN Gavrilov, AV Lebedinsky, C Rinke, ...
    Frontiers in microbiology 8, 195
    acdc–Automated Contamination Detection and Confidence estimation for single-cell genome data
    M Lux, J Krüger, C Rinke, I Maus, A Schlüter, T Woyke, A Sczyrba, ...
    BMC bioinformatics 17 (1), 1-11
    Validation of picogram-and femtogram-input DNA libraries for microscale metagenomics
    C Rinke, S Low, BJ Woodcroft, JB Raina, A Skarshewski, XH Le, ...
    PeerJ 4, e2486
    Phylogeny and physiology of candidate phylum ‘Atribacteria’(OP9/JS1) inferred from cultivation-independent genomics
    MK Nobu, JA Dodsworth, SK Murugapiran, C Rinke, EA Gies, G Webster, ...
    The ISME journal 10 (2), 273-286
    ProDeGe: a computational protocol for fully automated decontamination of genomes
    K Tennessen, E Andersen, S Clingenpeel, C Rinke, DS Lundberg, J Han, ...
    The ISME journal 10 (1), 269-272
    Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor
    MK Nobu, T Narihiro, C Rinke, Y Kamagata, SG Tringe, T Woyke, WT Liu
    The ISME journal 9 (8), 1710-1722
    In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)
    NH Youssef, IF Farag, C Rinke, SJ Hallam, T Woyke, MS Elshahed
    PloS one 10 (6), e0127499
    Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’
    NH Youssef, C Rinke, R Stepanauskas, I Farag, T Woyke, MS Elshahed
    The ISME journal 9 (2), 447-460
    Reconstructing each cell's genome within complex microbial communities—dream or reality?
    S Clingenpeel, A Clum, P Schwientek, C Rinke, T Woyke
    Frontiers in microbiology 5, 771
    Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”
    BP Hedlund, JA Dodsworth, SK Murugapiran, C Rinke, T Woyke
    Extremophiles 18 (5), 865-875
    Stop codon reassignments in the wild
    NN Ivanova, P Schwientek, HJ Tripp, C Rinke, A Pati, M Huntemann, ...
    Science 344 (6186), 909-913
    Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics
    C Rinke, J Lee, N Nath, D Goudeau, B Thompson, N Poulton, E Dmitrieff, ...
    Nature protocols 9 (5), 1038-1048
    An environmental bacterial taxon with a large and distinct metabolic repertoire
    MC Wilson, T Mori, C Rückert, AR Uria, MJ Helf, K Takada, C Gernert, ...
    Nature 506 (7486), 58-62
    The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features
    J Kamke, C Rinke, P Schwientek, K Mavromatis, N Ivanova, A Sczyrba, ...
    PloS one 9 (1), e87353
    Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges
    J Kamke, A Sczyrba, N Ivanova, P Schwientek, C Rinke, K Mavromatis, ...
    The ISME journal 7 (12), 2287-2300
    Insights into the phylogeny and coding potential of microbial dark matter
    C Rinke, P Schwientek, A Sczyrba, NN Ivanova, IJ Anderson, JF Cheng, ...
    Nature 499 (7459), 431-437
    S. Malfa i, BK Swan, EA Gies, JA Dodsworth, BP Hedlund, G. Tsiamis, SM Sievert, W
    C Rinke, P Schwientek, A Sczyrba, NN Ivanova, IJ Anderson, JF Cheng, ...
    T. Liu, JA Eisen, SJ Hallam, NC Kyrpides, R. Stepanauskas, EM Rubin, P …
    Decontamination of MDA reagents for single cell whole genome amplification
    T Woyke, A Sczyrba, J Lee, C Rinke, D Tighe, S Clingenpeel, ...
    PloS one 6 (10), e26161
    Macro camera temperature logger array for deep‐sea hydrothermal vent and benthic studies
    C Rinke, RW Lee
    Limnology and Oceanography: Methods 7 (7), 527-534
    Pathways, activities and thermal stability of anaerobic and aerobic enzymes in thermophilic vent paralvinellid worms
    C Rinke, RW Lee
    Marine Ecology Progress Series 382, 99-112
    Molecular characterization of the symbionts associated with marine nematodes of the genus Robbea
    C Bayer, NR Heindl, C Rinke, S Lücker, JA Ott, S Bulgheresi
    Environmental Microbiology Reports 1 (2), 136-144
    Cell proliferation and growth in Zoothamnium niveum (Oligohymenophora, Peritrichida)—Thiotrophic bacteria symbiosis
    U Kloiber, B Pflugfelder, C Rinke, M Bright
    Symbiosis 47 (1), 43-50
    High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont ‘Candidatus Thiobios zoothamnicoli’
    C Rinke, S Schmitz-Esser, A Loy, M Horn, M Wagner, M Bright
    FEMS microbiology ecology 67 (2), 229-241
    The effects of sulphide on growth and behaviour of the thiotrophic Zoothamnium niveum symbiosis
    C Rinke, R Lee, S Katz, M Bright
    Proceedings of the Royal Society B: Biological Sciences 274 (1623), 2259-2269
    “Candidatus Thiobios zoothamnicoli,” an ectosymbiotic bacterium covering the giant marine ciliate Zoothamnium niveum
    C Rinke, S Schmitz-Esser, K Stoecker, AD Nussbaumer, DA Molnár, ...
    Applied and environmental microbiology 72 (3), 2014


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