Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2144480915', 'doi': 'https://doi.org/10.1371/journal.pone.0099414', 'title': 'Analysis of Run-to-Run Variation of Bar-Coded Pyrosequencing for Evaluating Bacterial Community Shifts and Individual Taxa Dynamics', 'display_name': 'Analysis of Run-to-Run Variation of Bar-Coded Pyrosequencing for Evaluating Bacterial Community Shifts and Individual Taxa Dynamics', 'publication_year': 2014, 'publication_date': '2014-06-09', 'ids': {'openalex': 'https://openalex.org/W2144480915', 'doi': 'https://doi.org/10.1371/journal.pone.0099414', 'mag': '2144480915', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/24911191', 'pmcid': 'https://www.ncbi.nlm.nih.gov/pmc/articles/4049813'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1371/journal.pone.0099414', 'pdf_url': 'https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0099414&type=printable', 'source': {'id': 'https://openalex.org/S202381698', 'display_name': 'PLoS ONE', 'issn_l': '1932-6203', 'issn': ['1932-6203'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310315706', 'host_organization_name': 'Public Library of Science', 'host_organization_lineage': ['https://openalex.org/P4310315706'], 'host_organization_lineage_names': ['Public Library of Science'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'doaj', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'gold', 'oa_url': 'https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0099414&type=printable', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5066493950', 'display_name': 'Yuan Ge', 'orcid': 'https://orcid.org/0000-0003-0234-5638'}, 'institutions': [{'id': 'https://openalex.org/I154570441', 'display_name': 'University of California, Santa Barbara', 'ror': 'https://ror.org/02t274463', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I154570441']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Yuan Ge', 'raw_affiliation_strings': ['Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America', 'Earth Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America', 'University of California Center for Environmental Implications of Nanotechnology, University of California Santa Barbara, Santa Barbara, California, United States of America'], 'affiliations': [{'raw_affiliation_string': 'University of California Center for Environmental Implications of Nanotechnology, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}, {'raw_affiliation_string': 'Earth Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}, {'raw_affiliation_string': 'Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5020677883', 'display_name': 'Joshua P. Schimel', 'orcid': 'https://orcid.org/0000-0002-1022-6623'}, 'institutions': [{'id': 'https://openalex.org/I154570441', 'display_name': 'University of California, Santa Barbara', 'ror': 'https://ror.org/02t274463', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I154570441']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Joshua P. Schimel', 'raw_affiliation_strings': ['Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, United States of America', 'University of California Center for Environmental Implications of Nanotechnology, University of California Santa Barbara, Santa Barbara, California, United States of America'], 'affiliations': [{'raw_affiliation_string': 'University of California Center for Environmental Implications of Nanotechnology, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}, {'raw_affiliation_string': 'Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5004697086', 'display_name': 'Patricia A. Holden', 'orcid': 'https://orcid.org/0000-0002-6777-5359'}, 'institutions': [{'id': 'https://openalex.org/I154570441', 'display_name': 'University of California, Santa Barbara', 'ror': 'https://ror.org/02t274463', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I154570441']}], 'countries': ['US'], 'is_corresponding': True, 'raw_author_name': 'Patricia A. Holden', 'raw_affiliation_strings': ['Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America', 'Earth Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America', 'University of California Center for Environmental Implications of Nanotechnology, University of California Santa Barbara, Santa Barbara, California, United States of America'], 'affiliations': [{'raw_affiliation_string': 'University of California Center for Environmental Implications of Nanotechnology, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}, {'raw_affiliation_string': 'Earth Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}, {'raw_affiliation_string': 'Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America', 'institution_ids': ['https://openalex.org/I154570441']}]}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 1, 'corresponding_author_ids': ['https://openalex.org/A5004697086'], 'corresponding_institution_ids': ['https://openalex.org/I154570441'], 'apc_list': {'value': 1805, 'currency': 'USD', 'value_usd': 1805, 'provenance': 'doaj'}, 'apc_paid': {'value': 1805, 'currency': 'USD', 'value_usd': 1805, 'provenance': 'doaj'}, 'fwci': 2.056, 'has_fulltext': True, 'fulltext_origin': 'pdf', 'cited_by_count': 13, 'citation_normalized_percentile': {'value': 0.712812, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 87, 'max': 88}, 'biblio': {'volume': '9', 'issue': '6', 'first_page': 'e99414', 'last_page': 'e99414'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T11791', 'display_name': 'Microbial Community Ecology and Physiology', 'score': 0.9964, 'subfield': {'id': 'https://openalex.org/subfields/2303', 'display_name': 'Ecology'}, 'field': {'id': 'https://openalex.org/fields/23', 'display_name': 'Environmental Science'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, 'topics': [{'id': 'https://openalex.org/T11791', 'display_name': 'Microbial Community Ecology and Physiology', 'score': 0.9964, 'subfield': {'id': 'https://openalex.org/subfields/2303', 'display_name': 'Ecology'}, 'field': {'id': 'https://openalex.org/fields/23', 'display_name': 'Environmental Science'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, {'id': 'https://openalex.org/T12561', 'display_name': 'bioluminescence and chemiluminescence research', 'score': 0.9786, 'subfield': {'id': 'https://openalex.org/subfields/1312', 'display_name': 'Molecular Biology'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, {'id': 'https://openalex.org/T12640', 'display_name': 'Environmental DNA in Biodiversity Studies', 'score': 0.9731, 'subfield': {'id': 'https://openalex.org/subfields/2303', 'display_name': 'Ecology'}, 'field': {'id': 'https://openalex.org/fields/23', 'display_name': 'Environmental Science'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}], 'keywords': [{'id': 'https://openalex.org/keywords/pyrosequencing', 'display_name': 'Pyrosequencing', 'score': 0.99446464}], 'concepts': [{'id': 'https://openalex.org/C125009961', 'wikidata': 'https://www.wikidata.org/wiki/Q2342248', 'display_name': 'Pyrosequencing', 'level': 3, 'score': 0.99446464}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.70643514}, {'id': 'https://openalex.org/C71640776', 'wikidata': 'https://www.wikidata.org/wiki/Q16521', 'display_name': 'Taxon', 'level': 2, 'score': 0.6639179}, {'id': 'https://openalex.org/C78458016', 'wikidata': 'https://www.wikidata.org/wiki/Q840400', 'display_name': 'Evolutionary biology', 'level': 1, 'score': 0.47670028}, {'id': 'https://openalex.org/C2908647359', 'wikidata': 'https://www.wikidata.org/wiki/Q2625603', 'display_name': 'Population', 'level': 2, 'score': 0.46199086}, {'id': 'https://openalex.org/C54355233', 'wikidata': 'https://www.wikidata.org/wiki/Q7162', 'display_name': 'Genetics', 'level': 1, 'score': 0.286757}, {'id': 'https://openalex.org/C18903297', 'wikidata': 'https://www.wikidata.org/wiki/Q7150', 'display_name': 'Ecology', 'level': 1, 'score': 0.25232992}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.1330896}, {'id': 'https://openalex.org/C149923435', 'wikidata': 'https://www.wikidata.org/wiki/Q37732', 'display_name': 'Demography', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C144024400', 'wikidata': 'https://www.wikidata.org/wiki/Q21201', 'display_name': 'Sociology', 'level': 0, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D001419', 'descriptor_name': 'Bacteria', 'qualifier_ui': 'Q000235', 'qualifier_name': 'genetics', 'is_major_topic': True}, {'descriptor_ui': 'D001419', 'descriptor_name': 'Bacteria', 'qualifier_ui': 'Q000145', 'qualifier_name': 'classification', 'is_major_topic': True}, {'descriptor_ui': 'D058893', 'descriptor_name': 'DNA Barcoding, Taxonomic', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D059014', 'descriptor_name': 'High-Throughput Nucleotide Sequencing', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D054892', 'descriptor_name': 'Metagenome', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D000704', 'descriptor_name': 'Analysis of Variance', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D001419', 'descriptor_name': 'Bacteria', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D044822', 'descriptor_name': 'Biodiversity', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D059014', 'descriptor_name': 'High-Throughput Nucleotide Sequencing', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': False}, {'descriptor_ui': 'D059014', 'descriptor_name': 'High-Throughput Nucleotide Sequencing', 'qualifier_ui': 'Q000592', 'qualifier_name': 'standards', 'is_major_topic': False}, {'descriptor_ui': 'D015203', 'descriptor_name': 'Reproducibility of Results', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D012988', 'descriptor_name': 'Soil Microbiology', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 6, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1371/journal.pone.0099414', 'pdf_url': 'https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0099414&type=printable', 'source': {'id': 'https://openalex.org/S202381698', 'display_name': 'PLoS ONE', 'issn_l': '1932-6203', 'issn': ['1932-6203'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310315706', 'host_organization_name': 'Public Library of Science', 'host_organization_lineage': ['https://openalex.org/P4310315706'], 'host_organization_lineage_names': ['Public Library of Science'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://doaj.org/article/cc45b04436494f588325e2c374e1afa7', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306401280', 'display_name': 'DOAJ (DOAJ: Directory of Open Access Journals)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': None, 'host_organization_name': None, 'host_organization_lineage': [], 'host_organization_lineage_names': [], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}, {'is_oa': True, 'landing_page_url': 'https://europepmc.org/articles/pmc4049813', 'pdf_url': 'https://europepmc.org/articles/pmc4049813?pdf=render', 'source': {'id': 'https://openalex.org/S4306400806', 'display_name': 'Europe PMC (PubMed Central)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1303153112', 'host_organization_name': 'European Bioinformatics Institute', 'host_organization_lineage': ['https://openalex.org/I1303153112'], 'host_organization_lineage_names': ['European Bioinformatics Institute'], 'type': 'repository'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://www.escholarship.org/uc/item/14j9z823', 'pdf_url': 'https://escholarship.org/content/qt14j9z823/qt14j9z823.pdf?t=nuqlc5', 'source': {'id': 'https://openalex.org/S4306400115', 'display_name': 'eScholarship (California Digital Library)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I2801248553', 'host_organization_name': 'California Digital Library', 'host_organization_lineage': ['https://openalex.org/I2801248553'], 'host_organization_lineage_names': ['California Digital Library'], 'type': 'repository'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049813', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S2764455111', 'display_name': 'PubMed Central', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/24911191', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306525036', 'display_name': 'PubMed', 'issn_l': None, 'issn': None, 'is_oa': False, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}], 'best_oa_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1371/journal.pone.0099414', 'pdf_url': 'https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0099414&type=printable', 'source': {'id': 'https://openalex.org/S202381698', 'display_name': 'PLoS ONE', 'issn_l': '1932-6203', 'issn': ['1932-6203'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310315706', 'host_organization_name': 'Public Library of Science', 'host_organization_lineage': ['https://openalex.org/P4310315706'], 'host_organization_lineage_names': ['Public Library of Science'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 25, 'referenced_works': ['https://openalex.org/W1922909364', 'https://openalex.org/W1969435169', 'https://openalex.org/W1982599457', 'https://openalex.org/W1991829808', 'https://openalex.org/W1995393174', 'https://openalex.org/W2062866524', 'https://openalex.org/W2067537975', 'https://openalex.org/W2072970694', 'https://openalex.org/W2102718644', 'https://openalex.org/W2103412200', 'https://openalex.org/W2106308757', 'https://openalex.org/W2108718991', 'https://openalex.org/W2114859967', 'https://openalex.org/W2116781551', 'https://openalex.org/W2119441056', 'https://openalex.org/W2124625449', 'https://openalex.org/W2125400741', 'https://openalex.org/W2127602818', 'https://openalex.org/W2128114769', 'https://openalex.org/W2131927212', 'https://openalex.org/W2132543522', 'https://openalex.org/W2140106443', 'https://openalex.org/W2155688991', 'https://openalex.org/W2168442789', 'https://openalex.org/W2317346336'], 'related_works': ['https://openalex.org/W2359295417', 'https://openalex.org/W2161558410', 'https://openalex.org/W2156417649', 'https://openalex.org/W2144480915', 'https://openalex.org/W2130076355', 'https://openalex.org/W2119695867', 'https://openalex.org/W2082860237', 'https://openalex.org/W2061542922', 'https://openalex.org/W2005015095', 'https://openalex.org/W2001808934'], 'abstract_inverted_index': {'Bar-coded': [0], 'pyrosequencing': [1, 31, 44, 62, 92, 101, 126], 'has': [2], 'been': [3], 'increasingly': [4], 'used': [5, 128], 'due': [6], 'to': [7, 105, 116, 121, 151], 'its': [8], 'fine': [9], 'taxonomic': [10], 'resolution': [11], 'and': [12, 37], 'high': [13], 'throughput.': [14], 'Yet,': [15], 'concerns': [16], 'arise': [17], 'regarding': [18], 'the': [19, 26, 59, 107, 135, 145], 'reproducibility': [20, 60], 'of': [21, 29, 61, 71, 156], 'bar-coded': [22, 30], 'pyrosequencing.': [23], 'We': [24], 'evaluated': [25], 'run-to-run': [27], 'variation': [28, 158], 'in': [32, 47, 63], 'detecting': [33, 64], 'bacterial': [34, 131], 'community': [35, 49], 'shifts': [36, 50], 'taxa': [38, 66, 72, 137], 'dynamics.': [39], 'Our': [40], 'results': [41], 'demonstrate': [42], 'that': [43, 88], 'is': [45, 86, 127], 'reproducible': [46], 'evaluating': [48], 'within': [51], 'a': [52, 69], 'run,': [53], 'but': [54], 'not': [55], 'between': [56], 'runs.': [57], 'Also,': [58], 'individual': [65], 'increased': [67, 150], 'as': [68], 'function': [70], 'abundance.': [73], 'Based': [74], 'on': [75], 'our': [76], 'findings:': [77], '(1)': [78], 'for': [79, 129, 142], 'studies': [80], 'with': [81], 'modest': [82], 'sequencing': [83, 108, 111, 146], 'depth,': [84, 109], 'it': [85], 'doubtful': [87], 'data': [89], 'from': [90], 'different': [91], 'runs': [93, 102], 'can': [94], 'be': [95, 114, 139, 149], 'considered': [96], 'comparable;': [97], '(2)': [98], 'if': [99, 125], 'multiple': [100], 'are': [103], 'needed': [104], 'increase': [106], 'additional': [110], 'efforts': [112], 'should': [113, 138, 148], 'applied': [115], 'all': [117], 'samples,': [118], 'rather': [119], 'than': [120], 'selected': [122], 'samples;': [123], '(3)': [124], 'estimating': [130], 'population': [132], 'dynamics,': [133], 'only': [134], 'abundant': [136], 'considered;': [140], '(4)': [141], 'less-abundant': [143], 'taxa,': [144], 'depth': [147], 'ensure': [152], 'an': [153], 'accurate': [154], 'evaluation': [155], 'taxon': [157], 'trends': [159], 'across': [160], 'samples.': [161]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2144480915', 'counts_by_year': [{'year': 2023, 'cited_by_count': 1}, {'year': 2020, 'cited_by_count': 1}, {'year': 2018, 'cited_by_count': 2}, {'year': 2017, 'cited_by_count': 3}, {'year': 2016, 'cited_by_count': 1}, {'year': 2015, 'cited_by_count': 5}], 'updated_date': '2024-12-08T23:25:34.407258', 'created_date': '2016-06-24'}