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Research Output 2012 2020

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Article
2020

NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis

Poncheewin, W., Hermes, G. D. A., Van Dam, J. C. J., Koehorst, J. J., Smidt, H. & Schaap, P. J., 23 Jan 2020, In : Frontiers in Genetics. 10, 1366.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Semantics
Galaxies
18S Ribosomal RNA
Databases
16S Ribosomal RNA

Organohalide-respiring Desulfoluna species isolated from marine environments

Peng, P., Goris, T., Lu, Y., Nijsse, B., Burrichter, A., Schleheck, D., Koehorst, J. J., Liu, J., Sipkema, D., Sinninghe Damste, J. S., Stams, A. J. M., Häggblom, M. M., Smidt, H. & Atashgahi, S., 2 Jan 2020, In : ISME Journal. 14, p. 815–827

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
marine environment
Sulfates
sulfates
sulfate
cell respiration
Open Access
Nannochloropsis
starvation
transcriptome
eicosapentaenoic acid
polyunsaturated fatty acids
2019

Diversity of tryptophan halogenases in sponges of the genus Aplysina

Gutleben, J., Koehorst, J. J., McPherson, K., Pomponi, S., Wijffels, R. H., Smidt, H. & Sipkema, D., 1 Aug 2019, In : FEMS microbiology ecology. 95, 8, fiz108.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Porifera
Chloroflexi
sponge
Actinobacteria
Psychrobacter
1 Citation (Scopus)
Open Access
Clostridium kluyveri
Carbon Monoxide
Ethanol
Coculture Techniques
Thermodynamics

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

van Dam, J. C. J., Koehorst, J. J., Vik, J. O., Martins dos Santos, V. A. P., Schaap, P. J. & Suarez-Diez, M., 4 Nov 2019, In : Scientific Data. 6, 1, 1 p., 254.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
ontology
Biology
Ontology
Annotation
biology
2018
7 Citations (Scopus)

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

Versluis, D., Nijsse, B., Naim, M. A., Koehorst, J. J., Wiese, J., Imhoff, J. F., Schaap, P. J., van Passel, M. W. J., Smidt, H. & Sipkema, D., 8 Jan 2018, In : Genome Biology and Evolution. 10, 1, p. 125-142

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Porifera
Genomics
genomics
sponge
Genome
8 Citations (Scopus)

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

Koehorst, J. J., van Dam, J. C. J., Saccenti, E., Martins Dos Santos, V. A. P., Suarez-Diez, M. & Schaap, P. J., 15 Apr 2018, In : Bioinformatics. 34, 8, p. 1401-1403

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Semantics
Annotation
Genome
Provenance
Genes
2017
4 Citations (Scopus)

Complete genome sequence of Akkermansia glycaniphila strain PytT, a mucin-degrading specialist of the reticulated python gut

Ouwerkerk, J. P., Koehorst, J. J., Schaap, P. J., Ritari, J., Paulin, L., Belzer, C. & de Vos, W. M., 5 Jan 2017, In : Genome Announcements. 5, 1, e01098-16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Boidae
Mucins
Genome
Intestines
Respiration
6 Citations (Scopus)

Concurrent haloalkanoate degradation and chlorate reduction by Pseudomonas chloritidismutans AW-1T

Peng, P., Zheng, Y., Koehorst, J. J., Schaap, P. J., Stams, F., Smidt, H. & Atashgahi, S., 2017, In : Applied and Environmental Microbiology. 83, 12, 11 p., e00325-17.

Research output: Contribution to journalArticleAcademicpeer-review

Chlorates
chlorates
Pseudomonas
electron
degradation
2 Citations (Scopus)

Persistence of functional protein domains in mycoplasma species and their role in host specificity and synthetic minimal life

Kamminga, T., Koehorst, J. J., Vermeij, P., Slagman, S. J., dos Santos, V. A. P. M., Bijlsma, J. J. E. & Schaap, P. J., 2017, In : Frontiers in Cellular and Infection Microbiology. 7, 31.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Mycoplasma
Host Specificity
Genome
Protein Domains
Host-Pathogen Interactions
1 Citation (Scopus)
Open Access
Genomics
Genes
Functional analysis
Proteins
Bacterial Genomes
79 Citations (Scopus)

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

Timmers, P. H. A., Welte, C. U., Koehorst, J. J., Plugge, C. M., Jetten, M. S. M. & Stams, A. J. M., 2017, In : Archaea : an international microbiological journal. 2017, 1654237.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Archaea
Methane
methanogenesis
methane production
methane
2016
14 Citations (Scopus)

Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

Koehorst, J. J., van Dam, J. C. J., van Heck, R. G. A., Saccenti, E., Martins dos Santos, V., Suarez-Diez, M. & Schaap, P. J., 2016, In : Scientific Reports. 6, 13 p., 38699.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Pseudomonas
genomics
bioengineering
genome
bioremediation
4 Citations (Scopus)

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T

Bosma, E. F., Koehorst, J. J., van Hijum, S. A. F. T., Renckens, B., Vriesendorp, B., van de Weijer, T., Schaap, P. J., de Vos, W. M., van der Oost, J. & van Kranenburg, R., 2016, In : Standards in Genomic Sciences. 11, 11 p., 52.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Nucleic Acid Databases
formate C-acetyltransferase
Bacillus
Acetates
Phosphate Acetyltransferase
9 Citations (Scopus)

Genome and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows on n-decane with chlorate or oxygen as electron acceptor

Mehboob, F., Oosterkamp, M. J., Koehorst, J. J., Farrakh, S., Veuskens, T., Plugge, C. M., Boeren, S., de Vos, W. M., Schraa, G., Stams, A. J. M. & Schaap, P. J., 2016, In : Environmental Microbiology. 18, 10, p. 3247-3257

Research output: Contribution to journalArticleAcademicpeer-review

Chlorates
decane
chlorates
Alkanes
Proteome
9 Citations (Scopus)
Open Access
Genomics
Genes
Proteins
Genome
Bacterial Genomes
2 Citations (Scopus)
Open Access
Genomics
Genes
Proteins
Genome
Bacterial Genomes
2015
5 Citations (Scopus)

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View

Saccenti, E., Nieuwenhuijse, D., Koehorst, J. J., Martins dos Santos, V. A. P. & Schaap, P. J., 2015, In : PLoS ONE. 10, 9, e0137908.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Streptococcus
Metabolic Networks and Pathways
biochemical pathways
Bacteria
Streptococcus suis
14 Citations (Scopus)

Comparative genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice

Fiebig, A., Loof, T. G., Babbar, A., Itzeg, A., Koehorst, J. J., Schaap, P. J. & Nitsche-Schmitz, D. P., 2015, In : International Journal of Medical Microbiology. 305, 6, p. 532-543

Research output: Contribution to journalArticleAcademicpeer-review

Streptococcus pyogenes
Genomics
Virulence
CRISPR-Cas Systems
Bacteriophages
18 Citations (Scopus)

Effects of Argonaute on Gene Expression in Thermus thermophilus

Swarts, D. C., Koehorst, J. J., Westra, E. R., Schaap, P. J. & van der Oost, J., 2015, In : PLoS ONE. 10, 4, 13 p., e0124880.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Thermus thermophilus
Gene expression
plasmids
Plasmids
Gene Expression
5 Citations (Scopus)

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource

van Dam, J. C. J., Koehorst, J. J., Schaap, P. J., Martins dos Santos, V. A. P. & Suarez Diez, M., 2015, In : Journal of Biomedical Semantics. 6, 12 p., 39.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Semantic Web
Semantics
Ontology
Technology
Structural integrity
2014
42 Citations (Scopus)

A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities

Worm, P., Koehorst, J. J., Visser, M., Sedano Nunez, V. T., Schaap, P. J., Plugge, C. M., Sousa, D. Z. & Stams, A. J. M., 2014, In : Biochimica et Biophysica Acta. B, Bioenergetics. 1837, 12, p. 2004-2016

Research output: Contribution to journalArticleAcademicpeer-review

Methanogens
Aptitude
Volatile Fatty Acids
Sulfates
Life Style
11 Citations (Scopus)

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

Visser, M., Parshina, S. N., Alves, J. I., Sousa, D. Z., Pereira, I. A. C., Muyzer, G., Kuever, J., Lebedinsky, A. V., Koehorst, J. J., Worm, P., Plugge, C. M., Schaap, P. J., Goodwin, L. A., Lapidus, A., Kyrpides, N. C., Detter, J. C., Woyke, T., Chain, P., Davenport, K. W., Spring, S. & 3 others, Rohde, M., Klenk, H. P. & Stams, A. J. M., 2014, In : Standards in Genomic Sciences. 9, 3, p. 655-675

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Desulfotomaculum
Carbon Monoxide
Sulfates
Genome
Fructose
130 Citations (Scopus)

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

Staals, R. H. J., Zhu, Y., Taylor, D. W., Kornfeld, J. E., Sharma, K., Barendregt, A., Koehorst, J. J., Vlot, M., Neupane, N., Varossieau, K., Sakamoto, K., Suzuki, T., Schaap, P. J., Urlaub, H., Heck, A. J. R., Nogales, E., Doudna, J. A., Shinkai, A. & van der Oost, J., 2014, In : Molecular Cell. 56, 4, p. 518-530

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Thermus thermophilus
RNA
CRISPR-Cas Systems
Complementary RNA
2013
36 Citations (Scopus)

Differential translation tunes uneven production of operon-encoded proteins

Quax, T. E. F., Wolf, Y. I., Koehorst, J. J., Wurtzel, O., van der Oost, R., Ran, W., Blombach, F., Makarova, K. S., Brouns, S. J. J., Forster, A. C., Wagner, E. G. H., Sorek, R., Koonin, E. V. & van der Oost, J., 2013, In : Cell Reports. 4, 5, p. 938-944

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Operon
Genes
Gene Expression
Proteins
Archaea
127 Citations (Scopus)

Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus

Staals, R. H. J., Agari, Y., Maki-Yonekura, S., Zhu, Y., Taylor, D. W., van Duijn, E., Barendregt, A., Vlot, M., Koehorst, J. J., Sakamoto, K., Masuda, A., Dohmae, N., Schaap, P. J., Doudna, J. A., Heck, A., Yonekura, K., van der Oost, J. & Shinkai, A., 2013, In : Molecular Cell. 52, 1, p. 135-145

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Thermus thermophilus
RNA
Protein Subunits
2012
48 Citations (Scopus)

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata

Kazakoff, S. H., Imelfort, M., Edwards, D., Koehorst, J., Biswas, B., Batley, J., Scott, P. T. & Gresshoff, P. M., 14 Dec 2012, In : PLoS ONE. 7, 12, e51687.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Millettia
Chloroplast Genome
Pongamia
Millettia pinnata
Wellheads