Rinke Lab
The Rinke Lab: Environmental OMICS Group (E-OMICS)
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Peer-reviewed publications and book chapters

 by the Rinke Lab research team

   
       
       
Title
 
Cited by
Year
Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov
Z Dutkiewicz, CM Singleton, M Sereika, JC Villada, AJ Mussig, ...
ISME Communications, ycae147
1 2024
Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode
D Tamarit, S Köstlbacher, KE Appler, K Panagiotou, V de Anda, C Rinke, ...
Systematic and Applied Microbiology, 126525
5 2024
Putative genome contamination has minimal impact on the GTDB taxonomy
AJ Mussig, PA Chaumeil, M Chuvochina, C Rinke, DH Parks, ...
Microbial Genomics 10 (5), 001256
1 2024
Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary
A Prabhu, S Tule, M Chuvochina, M Bodén, SJ McIlroy, J Zaugg, C Rinke
ISME Communications, ycae067
  2024
Rendering the metabolic wiring powering wetland soil methane production
AM Oliverio, AB Narrowe, JA Villa, C Rinke, DW Hoyt, P Liu, BB McGivern, ...
 
  2024
Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth
L Fan, B Xu, S Chen, Y Liu, F Li, W Xie, A Prabhu, D Zou, R Wan, H Li, ...
PNAS nexus 3 (2), pgae057
4* 2024
Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes
MC Thomas, G Waugh, I Vanwonterghem, NS Webster, C Rinke, R Fisher, ...
Science of the Total Environment 904, 166658
2 2023
Diversity, ecology and evolution of archaeal viruses
L Fan, J Liu, C Rinke, BJ Baker, C Zhang
Frontiers in Microbiology 14, 1333790
  2023
Genome Taxonomy Database and SeqCode: microbial taxonomy and nomenclature in the age of big sequence data
M Chuvochina, C Rinke, A Mussig, PA Chaumeil, D Parks, P Hugenholtz
Biodiversity Information Science and Standards 7, e111135
3 2023
Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes
M Chuvochina, AJ Mussig, PA Chaumeil, A Skarshewski, C Rinke, ...
FEMS Microbiology Letters 370, fnad071
28 2023
Mystery find of microbial DNA elements called Borgs
C Rinke
Nature 610 (7933), 635-637
1 2022
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes
S Medvedeva, J Sun, N Yutin, EV Koonin, T Nunoura, C Rinke, ...
Nature microbiology 7 (7), 962-973
31* 2022
Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials
J Sun, A Prabhu, STN Aroney, C Rinke
Microbial genomics 8 (6), 000842
63 2022
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
75 2022
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, 827229
3 2022
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
1189 2022
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), 79
18 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), 30
38 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
326* 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
694 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
1192 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), 3939
91 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
111 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
167 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
105 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
3026 2018
Single-cell genomics of microbial dark matter
C Rinke
Microbiome Analysis: Methods and Protocols, 99-111
8 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), 1507
133 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
1697 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
68 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
1787 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
416* 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
46 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, 1-11
30 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
87 2016
Genomic analysis of
IV Kublanov, OM Sigalova, SN Gavrilov, AV Lebedinsky, C Rinke, ...
Frontiers in microbiology 8
3 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
179 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
78 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
391 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
119 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
90 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
73 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, 865-875
152 2014
Stop codon reassignments in the wild
NN Ivanova, P Schwientek, HJ Tripp, C Rinke, A Pati, M Huntemann, ...
Science 344 (6186), 909-913
153 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
319 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
644 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
83 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
144 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
2466 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
184 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
14 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
55 2009
Cell proliferation and growth inZoothamnium niveum (Oligohymenophora, Peritrichida) — Thiotrophic bacteria symbiosis
U Kloiber, B Pflugfelder, C Rinke, M Bright
Symbiosis 47, 43-50
8 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
26 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
31 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
85 2006
Carbonfixation,-incorporation and-transfer in the chemoautotrophic Zoothamnium niveum symbioses with 14 C bicarbonat autoradiography
C Rinke
na
6 2002

 

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