Peer-reviewed publications and book chapters

 by the Rinke Lab research team


An updated list including citations can be found on Google Scholar

Chemotaxis shapes the microscale organization of the ocean’s microbiome
JB Raina, BS Lambert, DH Parks, C Rinke, N Siboni, A Bramucci, ...
Nature 605 (7908), 132-138
1 2022
Jinlong Dai, Qi Ye*, Ying Wu*, Miao Zhang and Jing Zhang
C Rinke, Y Liu, RM Ceballos, Q Ye, Y Wu
Proceedings of the International Workshop on Geo-Omics of Archaea
Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota
J Sun, PN Evans, EJ Gagen, BJ Woodcroft, BP Hedlund, T Woyke, ...
ISME Communications 2 (1), 1-1
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
DH Parks, M Chuvochina, C Rinke, AJ Mussig, PA Chaumeil, ...
Nucleic acids research 50 (D1), D785-D794
60 2022
Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials
J Sun, A Prabhu, S Aroney, C Rinke
Microvolume DNA extraction methods for microscale amplicon and metagenomic studies
AR Bramucci, A Focardi, C Rinke, P Hugenholtz, GW Tyson, JR Seymour, ...
ISME Communications 1 (1), 1-5
2 2021
A standardized archaeal taxonomy for the Genome Taxonomy Database
C Rinke, M Chuvochina, AJ Mussig, PA Chaumeil, AA Davín, DW Waite, ...
Nature Microbiology 6 (7), 946-959
72* 2021
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages
J Sun, PN Evans, EJ Gagen, BJ Woodcroft, BP Hedlund, T Woyke, ...
ISME Communications 1 (1), 1-14
7 2021
A genomic catalog of Earth’s microbiomes
S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ...
Nature biotechnology 39 (4), 499-509
207 2021
Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea
BP Hedlund, C Zhang, F Wang, C Rinke, WF Martin
Frontiers in Microbiology 12
Viruses of Asgard archaea
S Medvedeva, J Sun, N Yutin, EV Koonin, T Nunoura, C Rinke, ...
3 2021
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
519 2020
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
35 2020
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
63 2019
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
86 2019
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
61 2019
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
1710 2018
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)(vol 8, 682, 2017)
DW Waite, I Vanwonterghem, C Rinke, DH Parks, Y Zhang, K Takai, ...
Single-cell genomics of microbial dark matter
C Rinke
Microbiome Analysis, 99-111
3 2018
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
84 2017
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
1016 2017
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
47 2017
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
846 2017
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
252* 2017
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
29 2017
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
22 2016
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
55 2016
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
154 2016
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
65 2016
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
279 2015
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
88 2015
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
69 2015
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
58 2015
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
115 2014
Stop codon reassignments in the wild
NN Ivanova, P Schwientek, HJ Tripp, C Rinke, A Pati, M Huntemann, ...
Science 344 (6186), 909-913
108 2014
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
240 2014
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
538 2014
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
73 2014
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
111 2013
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
1905 2013
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
156 2011
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
7 2009
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
11 2009
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
48 2009
Cell proliferation and growth inZoothamnium niveum (Oligohymenophora, Peritrichida)—Thiotrophic bacteria symbiosis
U Kloiber, B Pflugfelder, C Rinke, M Bright
Symbiosis 47 (1), 43-50
5 2009
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
22 2009
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
25 2007
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), 2014-2021
69 2006
Carbonfixation,-incorporation and-transfer in the chemoautotrophic Zoothamnium niveum symbioses with 14 C bicarbonat autoradiography
C Rinke
6 2002


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