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science & technology (11) 11
microbiology (6) 6
multidisciplinary sciences (6) 6
science & technology - other topics (6) 6
microorganisms (5) 5
genomes (4) 4
life sciences & biomedicine (4) 4
phylogenetics (4) 4
algorithms (3) 3
computer science (3) 3
microbiome (3) 3
phylogeny (3) 3
physical sciences (3) 3
research (3) 3
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[info.info-ds]computer science [cs]/data structures and algorithms [cs.ds] (2) 2
amplicon sequencing (2) 2
analysis (2) 2
archaea - genetics (2) 2
bacteria (2) 2
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basic biological sciences (2) 2
biological diversity (2) 2
data structures and algorithms (2) 2
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evolution (2) 2
gene sequencing (2) 2
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life sciences (2) 2
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operational taxonomic units (2) 2
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sequence clustering (2) 2
string algorithms (2) 2
studies (2) 2
technology (2) 2
16s rrna phylogenetic analysis (1) 1
[info.info-bi]computer science [cs]/bioinformatics [q-bio.qm] (1) 1
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[sdv:bibs] sciences du vivant/bio-informatique, biologie systémique (1) 1
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adenocarcinoma (1) 1
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1. Full Text Deblur rapidly resolves single-nucleotide community sequence patterns
by Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob
mSystems, ISSN 2379-5077, 03/2017, Volume 2, Issue 2, p. e00191-16
DNA sequencing | Microbiome | Next-generation sequencing
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2. Full Text SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
by Kopylova, Evguenia and Noé, Laurent and Touzet, Hélène
Bioinformatics, ISSN 1367-4803, 12/2012, Volume 28, Issue 24, pp. 3211 - 3217
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | General aspects | Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) | RNA, Ribosomal - classification | RNA, Ribosomal, 16S - chemistry | Algorithms | Sequence Analysis, RNA | Ecosystem | RNA, Ribosomal - chemistry | RNA, Messenger - chemistry | RNA, Ribosomal - biosynthesis | Gene Expression Profiling | Software | Phylogeny | Index Medicus | Life Sciences | Quantitative Methods | Bioinformatics | Data Structures and Algorithms
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3. Full Text A communal catalogue reveals Earth's multiscale microbial diversity
by Thompson, Luke R and Sanders, Jon G and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J and Prill, Robert J and Tripathi, Anupriya and Gibbons, Sean M and Ackermann, Gail and Navas-Molina, Jose A and Janssen, Stefan and Kopylova, Evguenia and Vazquez-Baeza, Yoshiki and Gonzalez, Antonio and Morton, James T and Mirarab, Siavash and Xu, Zhenjiang Zech and Jiang, Lingjing and Haroon, Mohamed F and Kanbar, Jad and Zhu, Qiyun and Song, Se Jin and Kosciolek, Tomasz and Bokulich, Nicholas A and Lefler, Joshua and Brislawn, Colin J and Humphrey, Gregory and Owens, Sarah M and Hampton-Marcell, Jarrad and Berg-Lyons, Donna and McKenzie, Valerie and Fierer, Noah and Fuhrman, Jed A and Clauset, Aaron and Stevens, Rick L and Shade, Ashley and Pollard, Katherine S and Goodwin, Kelly D and Jansson, Janet K and Gilbert, Jack A and Knight, Rob and Earth Microbiome Project Consortiu and Earth Microbiome Project Consortium and The Earth Microbiome Project Consortium and Argonne National Lab. (ANL), Argonne, IL (United States) and Pacific Northwest National Lab. (PNNL), Richland, WA (United States) and Naturvetenskapliga fakulteten and Faculty of Sciences and Göteborgs universitet and Gothenburg University and Institutionen för marina vetenskaper and Department of marine sciences
Nature (London), ISSN 0028-0836, 11/2017, Volume 551, Issue 7681, pp. 457 - +
CONSISTENT | ARCHAEAL | EVOLUTION | MARINE BACTERIAL | GLOBAL PATTERNS | BACTERIAL DIVERSITY | OPERON COPY NUMBER | ONTOLOGY | COMMUNITIES | NESTEDNESS | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Humans | RNA, Ribosomal, 16S - analysis | Geographic Mapping | Plants - microbiology | Gene Dosage | Archaea - isolation & purification | Biodiversity | Bacteria - genetics | Bacteria - isolation & purification | Ecology - methods | Animals | Microbiota - genetics | RNA, Ribosomal, 16S - genetics | Archaea - genetics | Earth, Planet | Environmental aspects | Observations | Microbial colonies | Biological diversity | International marketing | Nucleotide sequencing | Ribosomal RNA | Catalogs | Analysis | DNA sequencing | Microbiological research | Distribution | Genetic aspects | Research | Identification and classification | Analytical methods | Nucleotide sequence | Microbiology | Taxonomy | rRNA | Ecology | Genomes | Ribonucleic acid--RNA | Gene sequencing | Meta-analysis | Earth | Studies | Microorganisms | Phylogenetics | Bacteria | Deoxyribonucleic acid--DNA | Index Medicus | ENVIRONMENTAL SCIENCES | global | BASIC BIOLOGICAL SCIENCES | microbiome | Geosciences, Multidisciplinary | Climate Research | Klimatforskning | Oceanografi, hydrologi, vattenresurser | Oceanography, Hydrology, Water Resources | Annan geovetenskap och miljövetenskap | Multidisciplinär geovetenskap | Ekologi | Other Earth and Related Environmental Sciences | CVI Infection Biology | CVI Infectiebiologie | Food Quality and Design | VLAG | Infectiebiologie | Infection Biology
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4. Full Text Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
by Asnicar, Francesco and Thomas, Andrew Maltez and Beghini, Francesco and Mengoni, Claudia and Manara, Serena and Manghi, Paolo and Zhu, Qiyun and Bolzan, Mattia and Cumbo, Fabio and May, Uyen and Sanders, Jon G and Zolfo, Moreno and Kopylova, Evguenia and Pasolli, Edoardo and Knight, Rob and Mirarab, Siavash and Huttenhower, Curtis and Segata, Nicola
Nature communications, ISSN 2041-1723, 05/2020, Volume 11, Issue 1, pp. 2500 - 2500
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Microorganisms | Level (quantity) | Divergence | Cultivation | Phylogenetics | Genomes | Phylogeny | Species | Gene sequencing | Index Medicus
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5. Full Text Microbiome analyses of blood and tissues suggest cancer diagnostic approach
by Poore, Gregory D and Kopylova, Evguenia and Zhu, Qiyun and Carpenter, Carolina and Fraraccio, Serena and Wandro, Stephen and Kosciolek, Tomasz and Janssen, Stefan and Metcalf, Jessica and Song, Se Jin and Kanbar, Jad and Miller-Montgomery, Sandrine and Heaton, Robert and Mckay, Rana and Patel, Sandip Pravin and Swafford, Austin D and Knight, Rob
Nature (London), ISSN 0028-0836, 03/2020, Volume 579, Issue 7800, pp. 567 - 574
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Melanoma - blood | Liquid Biopsy | Melanoma - diagnosis | Reproducibility of Results | Datasets as Topic | Humans | Neoplasms - microbiology | Lung Neoplasms - microbiology | Male | Neoplasms - diagnosis | Prostatic Neoplasms - diagnosis | Case-Control Studies | DNA, Viral - blood | Neoplasms - blood | Microbiota - genetics | Plasma - microbiology | DNA, Bacterial - blood | Prostatic Neoplasms - microbiology | Prostatic Neoplasms - blood | Female | Melanoma - microbiology | Lung Neoplasms - blood | Lung Neoplasms - diagnosis | Cohort Studies | Microbiota (Symbiotic organisms) | Physiological aspects | Diagnosis | Tissues | Methods | Blood | Cancer | Care and treatment | Genomics | Machine learning | Genetic aspects | Genomes | Nucleic acids | Biotechnology industry | Adenocarcinoma | Squamous cell carcinoma | Microbiology | Pipelines | Pollution control | Microbial contamination | Melanoma | Microbiomes | Cervix | Gene expression | Contamination | Microorganisms | Diagnostic systems | Prostate | Bayesian analysis | Deoxyribonucleic acid--DNA | Tumors | Index Medicus
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6. Full Text Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
by Zhu, Qiyun and Mai, Uyen and Pfeiffer, Wayne and Janssen, Stefan and Asnicar, Francesco and Sanders, Jon G and Belda-Ferre, Pedro and Al-Ghalith, Gabriel A and Kopylova, Evguenia and McDonald, Daniel and Kosciolek, Tomasz and Yin, John B and Huang, Shi and Salam, Nimaichand and Jiao, Jian-Yu and Wu, Zijun and Xu, Zhenjiang Z and Cantrell, Kalen and Yang, Yimeng and Sayyari, Erfan and Rabiee, Maryam and Morton, James T and Podell, Sheila and Knights, Dan and Li, Wen-Jun and Huttenhower, Curtis and Segata, Nicola and Smarr, Larry and Mirarab, Siavash and Knight, Rob
Nature communications, ISSN 2041-1723, 12/2019, Volume 10, Issue 1, pp. 5477 - 14
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Genome, Bacterial | Genome, Archaeal | Bacteria - classification | Archaea - genetics | Phylogeny | Archaea - classification | Bacteria - genetics | Evolution, Molecular | Genes | Biological evolution | Archaea | Radiation | Evolutionary genetics | Genomes | Amino acid substitution | Domains | Heterogeneity | Microorganisms | Ribosomal proteins | Bacteria | Index Medicus
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7. Full Text A comparison of index-based lempel-Ziv LZ77 factorization algorithms
by Al-Hafeedh, Anisa and Crochemore, Maxime and Ilie, Lucian and Kopylova, Evguenia and Smyth, W.F and Tischler, German and Yusufu, Munina
ACM computing surveys, ISSN 0360-0300, 11/2012, Volume 45, Issue 1, pp. 1 - 17
suffix array | Lempel-Ziv factorization | periodicity | String | suffix tree | longest common prefix | algorithm | Computer Science, Theory & Methods | Technology | Computer Science | Science & Technology | Signal and communications theory | Speech and sound recognition and synthesis. Linguistics | Telecommunications and information theory | Exact sciences and technology | Applied sciences | Information, signal and communications theory | Cryptography | Artificial intelligence | Computer science; control theory; systems | Data structures | Algorithms | Research | Methods | Text processing | Studies | Mathematics | Efficiency | Data compression | Compressing | Computation | Mathematical analysis | Texts | Computational efficiency | Strings | Factorization | Data Structures and Algorithms
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8. Full Text Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
by He, Yan and Caporaso, J. Gregory and Jiang, Xiao-Tao and Sheng, Hua-Fang and Huse, Susan M and Rideout, Jai Ram and Edgar, Robert C and Kopylova, Evguenia and Walters, William A and Knight, Rob and Zhou, Hong-Wei
Microbiome, ISSN 2049-2618, 05/2015, Volume 3, Issue 1, pp. 20 - 20
Life Sciences & Biomedicine | Microbiology | Science & Technology | RNA | Analysis | Biological diversity
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9. Full Text American Gut: An open platform for citizen science microbiome research
by Vázquez-Baeza, Yoshiki and Vrbanac, Alison and Wischmeyer, Paul and Wolfe, Elaine and Zhu, Qiyun and Knight, Rob and McDonald, Daniel and Hyde, Embriette and Debelius, Justine W and Morton, James T and Gonzalez, Antonio and Ackermann, Gail and Aksenov, Alexander A and Behsaz, Bahar and Brennan, Caitriona and Chen, Yingfeng and Goldasich, Lindsay DeRight and Dorrestein, Pieter C and Dunn, Robert R and Fahimipour, Ashkaan K and Gaffney, James and Gilbert, Jack A and Gogul, Grant and Green, Jessica L and Hugenholtz, Philip and Humphrey, Greg and Huttenhower, Curtis and Jackson, Matthew A and Janssen, Stefan and Jeste, Dilip V and Jiang, Lingjing and Kelley, Scott T and Knights, Dan and Kosciolek, Tomasz and Ladau, Joshua and Leach, Jeff and Marotz, Clarisse and Meleshko, Dmitry and Melnik, Alexey V and Metcalf, Jessica L and Mohimani, Hosein and Montassier, Emmanuel and Navas-Molina, Jose and Nguyen, Tanya T and Peddada, Shyamal and Pevzner, Pavel and Pollard, Katherine S and Rahnavard, Gholamali and Robbins-Pianka, Adam and Sangwan, Naseer and Shorenstein, Joshua and Smarr, Larry and Song, Se Jin and Spector, Timothy and Swafford, Austin D and Thackray, Varykina G and Thompson, Luke R and Tripathi, Anupriya and Amer Gut Consortium and American Gut Consortium and Argonne National Lab. (ANL), Argonne, IL (United States) and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
mSystems, ISSN 2379-5077, 06/2018, Volume 3, Issue 3, p. e00031-18
Citizen science | Microbiome | Life Sciences & Biomedicine | Microbiology | Science & Technology | BASIC BIOLOGICAL SCIENCES | citizen science | microbiome
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