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1. Full Text Accurate contact predictions using covariation techniques and machine learning
by Kosciolek, Tomasz and Jones, David T
Proteins, structure, function, and bioinformatics, ISSN 0887-3585, 09/2016, Volume 84, Issue S1, pp. 145 - 151
ab initio prediction | CASP | protein structure prediction | amino acid covariation | residue–residue contact prediction | Residue-residue contact prediction | Protein structure prediction | Amino acid covariation | Amino Acid Sequence | Computational Biology - methods | Bacteria - chemistry | Protein Structure, Secondary | Humans | Models, Molecular | Computational Biology - statistics & numerical data | Models, Statistical | Machine Learning | Protein Folding | Sequence Alignment | Viruses - chemistry | Computer Simulation | Databases, Protein | Protein Interaction Domains and Motifs | Software | Internet | Proteins - chemistry | Neural Networks (Computer) | Index Medicus
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2. Full Text MetaPSICOV: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
by Jones, David T and Singh, Tanya and Kosciolek, Tomasz and Tetchner, Stuart
Bioinformatics, ISSN 1367-4803, 04/2015, Volume 31, Issue 7, pp. 999 - 1006
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 | Sequence Alignment - methods | Sequence Analysis, Protein - methods | Computational Biology - methods | Algorithms | Hydrogen Bonding | Databases, Protein | Humans | Software | Proteins - chemistry | Protein Folding | Index Medicus | Proteins | Alignment | Hydrogen bonds | Evolutionary | Mathematical models | Hydrogen bonding | Three dimensional models | Bioinformatics | Original Papers
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3. Full Text Best practices for analysing microbiomes
by Knight, Rob and Vrbanac, Alison and Taylor, Bryn C and Aksenov, Alexander and Callewaert, Chris and Debelius, Justine and Gonzalez, Antonio and Kosciolek, Tomasz and McCall, Laura-Isobel and McDonald, Daniel and Melnik, Alexey V and Morton, James T and Navas, Jose and Quinn, Robert A and Sanders, Jon G and Swafford, Austin D and Thompson, Luke R and Tripathi, Anupriya and Xu, Zhenjiang Z and Zaneveld, Jesse R and Zhu, Qiyun and Caporaso, J. Gregory and Dorrestein, Pieter C
Nature reviews. Microbiology, ISSN 1740-1526, 07/2018, Volume 16, Issue 7, pp. 410 - 422
Life Sciences & Biomedicine | Microbiology | Science & Technology | Microbial activity | Data analysis | Taxonomy | Microbiomes | Data processing | Gastrointestinal tract | Molecular chains | Gene sequencing | Microorganisms | Reproducibility | Experimental design | Data sets | Technology assessment | Deoxyribonucleic acid--DNA | DNA sequencing | Index Medicus
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4. Full Text Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
by Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian C and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, Titus C and Callahan, Benjamin J and Caraballo-Roíguez, Anés Mauricio and Chase, John and Cope, Emily K and Silva, da, Ricardo and Diener, Christian and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibbons, Sean M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin A and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin D and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan G.I and Lee, Joslynn and Ley, Ruth and Liu, Yong Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie T and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Peo J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and Hooft, van der, Justin J.J and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and Hippel, von, Max and Walters, William and ...
Nature biotechnology, ISSN 1087-0156, 2019, Volume 37, Issue 8, pp. 852 - 857
Bioinformatics | Bioinformatica | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Data Science | Microbiota | Software | Humans | Computational Biology | Databases, Factual | Physiological aspects | Biotechnology | Microbiota (Symbiotic organisms) | Analysis | Computational biology | Microbiomes | Index Medicus
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5. 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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6. Full Text Accurate contact predictions using covariation techniques and machine learning
: CONSIP2 Contact Predictions in CASP11
by Kosciolek, Tomasz and Jones, David T
Proteins, structure, function, and bioinformatics, ISSN 0887-3585, 09/2016, Volume 84, pp. 145 - 151
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7. Full Text Qiita: rapid, web-enabled microbiome meta-analysis
by Gonzalez, Antonio and Navas-Molina, Jose A and Kosciolek, Tomasz and McDonald, Daniel and Vázquez-Baeza, Yoshiki and Ackermann, Gail and DeReus, Jeff and Janssen, Stefan and Swafford, Austin D and Orchanian, Stephanie B and Sanders, Jon G and Shorenstein, Joshua and Holste, Hannes and Petrus, Semar and Robbins-Pianka, Adam and Brislawn, Colin J and Wang, Mingxun and Rideout, Jai Ram and Bolyen, Evan and Dillon, Matthew and Caporaso, J. Gregory and Dorrestein, Pieter C and Knight, Rob and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Nature methods, ISSN 1548-7091, 10/2018, Volume 15, Issue 10, pp. 796 - 798
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Metagenomics | User-Computer Interface | Computational Biology - methods | Microbiota | Humans | Software | Internet | Usage | Public software | Research | Microbiota (Symbiotic organisms) | Analysis | Meta-analysis | Webs | Microbiomes | Index Medicus | microbiome, bioinformatics software, open source software
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8. 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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