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1. Full Text Anaerobic naphthalene degradation by sulfatereducing Desulfobacteraceae from various anoxic aquifers
by Kümmel, Steffen and Herbst, Florian-Alexander and Bahr, Arne and Duarte, Márcia and Pieper, Dietmar H and Jehmlich, Nico and Seifert, Jana and Von Bergen, Martin and Bombach, Petra and Richnow, Hans H and Vogt, Carsten
FEMS Microbiology Ecology, ISSN 0168-6496, 02/2015, Volume 91, Issue 3
N47 | Metaproteomics | Illumina sequencing
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2. Full Text DNA methylation and exposure to ambient air pollution in two prospective cohorts
by Plusquin, Michelle and Guida, Florence and Polidoro, Silvia and Vermeulen, Roel and Raaschou-Nielsen, Ole and Campanella, Gianluca and Hoek, Gerard and Kyrtopoulos, Soterios A and Georgiadis, Panagiotis and Naccarati, Alessio and Sacerdote, Carlotta and Krogh, Vittorio and Bas Bueno-de-Mesquita, H and Monique Verschuren, W.M and Sayols-Baixeras, Sergi and Panni, Tommaso and Peters, Annette and Hebels, Dennie G.A.J and Kleinjans, Jos and Vineis, Paolo and Chadeau-Hyam, Marc
Environment International, ISSN 0160-4120, 11/2017, Volume 108, pp. 127 - 136
Long-term exposure to air pollution has been associated with several adverse health effects including cardiovascular, respiratory diseases and cancers.... 
Air pollution | EPIC | Particulate matter | NOx | Illumina 450 k human methylation array | Epigenome-wide DNA methylation | PROFILES | GENE-SPECIFIC METHYLATION | ASSOCIATIONS | POLLUTANTS | USE REGRESSION-MODELS | DIOXIDE | MARKERS | BIOMARKERS | LUNG-CANCER | ENVIRONMENTAL SCIENCES | EXPRESSION | Air Pollutants - analysis | Gene Expression | Genome-Wide Association Study | Epigenomics | Prospective Studies | Air Pollutants - pharmacology | Humans | Middle Aged | European Continental Ancestry Group | Male | Environmental Exposure - analysis | Particulate Matter - analysis | Soot - analysis | Female | Air Pollution - analysis | Cardiovascular Diseases - chemically induced | DNA Methylation - drug effects | Cohort Studies | Analysis | Genes | Genomics | DNA | Genetic research | Respiratory tract diseases | Genomes | Pollutants | Methylation | Gene expression | Environmental aspects | Index Medicus | Metilació | Aire | Contaminació | Illumina 450k human methylation array | Aspectes sanitaris | NO(x) | ADN | EpWAS, epigenome-wide association study | PMcoarse, particulate matter with a diameter smaller than 10 μm and bigger than 2.5 μm | Illumina 450 k human methylation array | LUMA, luminometric methylation assay | EPIC-NL, The Dutch part of the European Prospective Investigation into Cancer and Nutrition | PM2.5, particulate matter with a diameter smaller than 2.5 μm | NOx, nitrogen oxide | EPIC-Italy, The Italian part of the European Prospective Investigation into Cancer and Nutrition | LC-MS, liquid chromatography–mass spectrometry | ELISA, enzyme-linked immunosorbent assay | PM2.5abs, absorbance of the PM2.5 filter, a measure for soot | PM, particulate matter | HPLC, high-performance liquid chromatography | PM10, particulate matter with a diameter smaller than 10 μm | LINE1, long interspersed nuclear elements | CpG, 5′–C–phosphate–G–3′, a cytosine and guanine separated by one phosphate | ESCAPE, European Study of Cohorts for Air Pollution Effects | CPMA, cross-phenotype meta-analysis | NO2, nitrogen dioxide
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3. Full Text RELIC: A novel dye-bias correction method for Illumina Methylation BeadChip
by Xu, Zongli and Langie, Sabine A.S and De Boever, Patrick and Taylor, Jack A and Niu, Liang
BMC Genomics, ISSN 1471-2164, 01/2017, Volume 18, Issue 1, p. 4
Background: The Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in... 
DNA methylation | Dye-bias correction | Illumina MethylationEPIC | Data preprocessing | Illumina HumanMethylation450 | RELIC | QUANTILE | ARRAY | PROBE DESIGN BIAS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | NORMALIZATION | Computational Biology - methods | DNA Methylation | Reproducibility of Results | Datasets as Topic | Oligonucleotide Array Sequence Analysis - standards | Oligonucleotide Array Sequence Analysis - methods | Humans | Software | Computational Biology - standards | High-Throughput Nucleotide Sequencing - methods | Web Browser | High-Throughput Nucleotide Sequencing - standards | Methylation | DNA microarrays | Research
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4. Full Text Nitrogen inputs are more important than denitrifier abundances in controlling denitrification-derived N 2 O emission from both urban and agricultural soils
by Xu, Hui-Juan and Yang, Xiao-Ru and Li, Shun and Xue, Xi-Mei and Chang, Shuai and Li, Hu and Singh, Brajesh K and Su, Jian-Qiang and Zhu, Yong-Guan
Science of the Total Environment, ISSN 0048-9697, 02/2019, Volume 650, Issue Pt 2, pp. 2807 - 2817
Cities are increasingly being recognized as important contributors in global warming, for example by increasing atmospheric nitrous oxide (N O). However, urban... 
Denitrifier | Denitrification | Urbanization | Nitrous oxide | Illumina sequencing
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5. Full Text Access mats partially mitigate direct traffic impacts on soil microbial communities in temperate grasslands
by Thompson, K.A and Bent, E and James, K and Carlyle, C.N and Quideau, S and Bork, E.W
Applied Soil Ecology, ISSN 0929-1393, 09/2019
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6. Full Text Comparison of Illumina 450K and EPIC arrays in placental DNA methylation
by Fernandez-Jimenez, Nora and Allard, Catherine and Bouchard, Luigi and Perron, Patrice and Bustamante, Mariona and Bilbao, Jose Ramon and Hivert, Marie-France
Epigenetics, ISSN 1559-2294, 12/2019, Volume 14, Issue 12, pp. 1177 - 1182
Illumina HumanMethylation450 BeadChip (450K) has been commonly used to investigate DNA methylation in human tissues. Recently, it has been replaced by Illumina... 
DNA methylation | placenta | Illumina 450K | EPIC
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7. Full Text Acinetobacter sp. as the key player in diesel oil degrading community exposed to PAHs and heavy metals
by Czarny, J and Staninska-Pięta, J and Piotrowska-Cyplik, A and Juzwa, W and Wolniewicz, A and Marecik, R and Ławniczak, Ł and Chrzanowski, Ł
Journal of Hazardous Materials, ISSN 0304-3894, 02/2020, Volume 383, p. 121168
The aim of this study was to verify the hypothesis that a hydrocarbon degrading community isolated from a site heavily polluted with polycyclic aromatic... 
Hydrocarbons | Flow cytometry | MiSeq illumina | Bioremediation | Gammaproteobacteria
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8. Full Text Diversity of bacterial microbiota of coastal halophyte Limonium sinense and amelioration of salinity stress damage by symbiotic plant growthpromoting actinobacterium Glutamicibacter halophytocola KLBMP 5180
by Qin, Sheng and Feng, Wei-Wei and Zhang, Yue-Ji and Wang, Tian-Tian and Xiong, You-Wei and Xing, Ke
Applied and Environmental Microbiology, ISSN 0099-2240, 10/2018, Volume 84, Issue 19
Halophyte | Glutamicibacter | Rhizobacteria | Illumina MiSeq | Diversity | Transcriptome | Endophytes
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9. Full Text Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome–Picea glauca system at an arctic treeline ecotone
by Eusemann, Pascal and Schnittler, Martin and Nilsson, R. Henrik and Jumpponen, Ari and Dahl, Mathilde B and Würth, David G and Buras, Allan and Wilmking, Martin and Unterseher, Martin and Naturvetenskapliga fakulteten and Faculty of Sciences and Department of Biological and Environmental Sciences and Göteborgs universitet and Institutionen för biologi och miljövetenskap and Gothenburg University
New Phytologist, ISSN 0028-646X, 09/2016, Volume 211, Issue 4, pp. 1221 - 1231
Plant‐associated mycobiomes in extreme habitats are understudied and poorly understood. We analysed Illumina‐generated ITS1 sequences from the needle mycobiome... 
microsatellites | metabarcoding | biodiversity | needle‐inhabiting fungal phytobiome | tree phenotypic plasticity | plant–fungus interactions | Illumina high‐throughput sequencing | internal transcribed spacer (ITS) rDNA | Plant-fungus interactions | Tree phenotypic plasticity | Metabarcoding | Internal transcribed spacer (ITS) rDNA | Microsatellites | Needle-inhabiting fungal phytobiome | Illumina high-throughput sequencing | Biodiversity | plant-fungus interactions | needle-inhabiting fungal phytobiome | PHENOTYPIC PLASTICITY | ABIES CLONES | WHITE SPRUCE | ENDOPHYTE COMMUNITIES | PLANT SCIENCES | NORWAY SPRUCE | RANGE SHIFTS | SOIL MICROBIAL COMMUNITIES | PHYLLOSPHERE FUNGAL ASSEMBLAGES | WARMING ALTERS | SPECIES ABUNDANCE DISTRIBUTIONS | Picea - microbiology | Mycobiome | Quantitative Trait, Heritable | Arctic Regions | Ecosystem | Trees - microbiology | Genotype | Principal Component Analysis | Sequence Analysis, DNA | Trees - genetics | Analysis | Genetic aspects | Biological diversity | Botanik | Microbiology | Mikrobiologi | Ecology | Bioinformatik och systembiologi | Bioinformatics and Systems Biology | Biological Systematics | Geovetenskap och miljövetenskap | Climate Research | Biologisk systematik | Skogsvetenskap | Klimatforskning | Botany | Forest Science | biodiversity; Illumina high-throughput sequencing; internal transcribed spacer (ITS) rDNA; metabarcoding; microsatellites; needle-inhabiting fungal phytobiome; plant–fungus interactions; tree phenotypic plasticity | Ekologi | Earth and Related Environmental Sciences
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10. Full Text Assisted phytoremediation of a co-contaminated soil with biochar amendment: Contaminant removals and bacterial community properties
by Zhang, Yaling and Zhang, Manyun and Wang, Jun and Bai, Shahla Hosseini and Teng, Ying and Xu, Zhihong
Geoderma, ISSN 0016-7061, 08/2019, Volume 348, pp. 115 - 123
There are growing trends of combined contaminations in agricultural soils, and therefore it is urgently needed to remediate contaminated soils with... 
Illumina-MiSeq sequencing | Bacterial biomass | Biochar | Bacterial community structure | Phytoremediation
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11. Full Text Error filtering, pair assembly and error correction for next-generation sequencing reads
by Edgar, Robert C and Flyvbjerg, Henrik
Bioinformatics, ISSN 1367-4803, 12/2014, Volume 31, Issue 21, pp. 3476 - 3482
Motivation: Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage... 
AMPLICON READS | ILLUMINA | DIVERSITY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | High-Throughput Nucleotide Sequencing - methods | Software | Algorithms | Filtration | Filtering | Mathematical analysis | Packages | Error correction | Sequencing | Bioinformatics | Assembly
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12. Full Text An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
by Blanc-Mathieu, Romain and Verhelst, Bram and Derelle, Evelyne and Rombauts, Stephane and Bouget, François-Yves and Carré, Isabelle and Château, Annie and Eyre-Walker, Adam and Grimsley, Nigel and Moreau, Hervé and Piégu, Benoit and Rivals, Eric and Schackwitz, Wendy and Van de Peer, Yves and Piganeau, Gwenaël
BMC Genomics, ISSN 1471-2164, 12/2014, Volume 15, Issue 1, pp. 1103 - 1103
Background: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes,... 
Domestication of microalgae | Correctness of short reads assembly | Plant glutamate receptor | Illumina re-sequencing | Ostreococcus tauri | Genome evolution | Picoeukaryote | BIAS | TRANSCRIPTION | SACCHAROMYCES | PICOEUKARYOTE OSTREOCOCCUS | ALGORITHMS | GREEN LINEAGE | CHLOROPHYTA | EUKARYOTE | EVOLUTION | Ostreococcus touri | PRASINOPHYCEAE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | Genetic Variation | Chlorophyta - genetics | Genomics | Molecular Sequence Annotation | Computational Biology | Molecular Sequence Data | High-Throughput Nucleotide Sequencing | Genome, Plant | Evolution, Molecular | Physiological aspects | Nucleotide sequencing | Photosynthesis | Analysis | Membrane proteins | DNA sequencing | RNA sequencing | Genes | Models | Research | Glutamate | Biological diversity | Life Sciences | Biotechnology | Other
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13. Full Text Archaeorhizomycetes Spatial Distribution in Soils Along Wide Elevational and Environmental Gradients Reveal Co-abundance Patterns With Other Fungal Saprobes and Potential Weathering Capacities
by Pinto-Figueroa, EA and Seddon, E and Yashiro, E and Buri, A and Niculita-Hirzel, H and van der Meer, JR and Guisan, A
FRONTIERS IN MICROBIOLOGY, ISSN 1664-302X, 04/2019, Volume 10, p. 656
Archaeorhizomycetes, a widespread fungal class with a dominant presence in many soil environments, contains cryptic filamentous species forming plant-root... 
BIODIVERSITY | MICROBIOLOGY | Swiss Alps | NICHE CONSERVATISM | phyllosilicates | SPECIES DISTRIBUTION MODELS | MYCORRHIZAL | COMMUNITY STRUCTURE | MICROBES | Archaeorhizomyces | correlation analyses | fungi | ECTOMYCORRHIZAL FUNGI | network analysis | SP-NOV | DIVERSITY | SCALE | abiotic and biotic requirements | Illumina sequencing | Environmental aspects | Soils
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14. Full Text Influence of elevated CO2 on arbuscular mycorrhizal fungal community elucidated using Illumina MiSeq platform in sub-humid tropical paddy soil
by Panneerselvam, Periyasamy and Kumar, Upendra and Senapati, Ansuman and Parameswaran, Chidambaranathan and Anandan, Annamalai and Kumar, Anjani and Jahan, Afrin and Padhy, Soumya Ranjan and Nayak, Amaresh Kumar
Applied Soil Ecology, ISSN 0929-1393, 08/2019
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15. Full Text Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing 06 Biological Sciences 0604 Genetics 06 Biological Sciences 0601 Biochemistry and Cell Biology
by Luo, Mingkun and Wang, Lanmei and Zhu, Wenbin and Fu, Jianjun and Song, Feibiao and Fang, Min and Dong, Juanjuan and Dong, Zaijie
BMC Genomics, 10/2018, Volume 19, Issue 1
Characterization | miRNAs | Skin color | Koi carp | Illumina sequencing
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16. Full Text Fungal diversity of “Tomme d'Orchies” cheese during the ripening process as revealed by a metagenomic study
by Ceugniez, Alexandre and Taminiau, Bernard and Coucheney, Françoise and Jacques, Philippe and Delcenserie, Véronique and Daube, Georges and Drider, Djamel
International Journal of Food Microbiology, ISSN 0168-1605, 10/2017, Volume 258, pp. 89 - 93
Tomme d'Orchies is an artisanal pressed and uncooked cheese produced and marketed in the north of France. This study aimed at showing the fungal microbiota... 
5.8S-ITS2 rDNA | Illumina | Artisanal cheese | Fungal microbiota
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17. Full Text Transcriptome profiling of the meristem tissue of Saccharina japonica (Phaeophyceae, Laminariales) under severe stress of copper
by Zhang, Yurong and Wang, Xuemei and Shan, Tifeng and Pang, Shaojun and Xu, Nianjun
Marine Genomics, ISSN 1874-7787, 10/2019, Volume 47, p. 100671
Copper (Cu) is an essential metal involved in many physiological processes of living organisms. However, beyond a certain threshold, Cu can become highly... 
Seaweed | Toxicity | Kelp | Illumina sequencing | Heavy metal
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