publications

Peer-reviewed publications and book chapters

by the Rinke Lab research team

An updated list including citations can be found on Google Scholar

TITLE	CITED BY	YEAR
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		2022
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		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	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 bioRxiv		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), 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		2021
Viruses of Asgard archaea S Medvedeva, J Sun, N Yutin, EV Koonin, T Nunoura, C Rinke, ... bioRxiv	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, ... FRONTIERS IN MICROBIOLOGY 9		2018
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 na	6	2002

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