Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2165847428', 'doi': 'https://doi.org/10.1186/1471-2105-14-s5-s18', 'title': 'Optimal assembly for high throughput shotgun sequencing', 'display_name': 'Optimal assembly for high throughput shotgun sequencing', 'publication_year': 2013, 'publication_date': '2013-04-01', 'ids': {'openalex': 'https://openalex.org/W2165847428', 'doi': 'https://doi.org/10.1186/1471-2105-14-s5-s18', 'mag': '2165847428', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/23902516', 'pmcid': 'https://www.ncbi.nlm.nih.gov/pmc/articles/3706340'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1186/1471-2105-14-s5-s18', 'pdf_url': 'https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S5-S18', 'source': {'id': 'https://openalex.org/S19032547', 'display_name': 'BMC Bioinformatics', 'issn_l': '1471-2105', 'issn': ['1471-2105'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320256', 'host_organization_name': 'BioMed Central', 'host_organization_lineage': ['https://openalex.org/P4310319965', 'https://openalex.org/P4310320256'], 'host_organization_lineage_names': ['Springer Nature', 'BioMed Central'], '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', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'gold', 'oa_url': 'https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S5-S18', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5060812074', 'display_name': 'Guy Bresler', 'orcid': 'https://orcid.org/0000-0003-1303-582X'}, 'institutions': [{'id': 'https://openalex.org/I95457486', 'display_name': 'University of California, Berkeley', 'ror': 'https://ror.org/01an7q238', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I95457486']}], 'countries': ['US'], 'is_corresponding': True, 'raw_author_name': 'Guy Bresler', 'raw_affiliation_strings': ['Department of EECS, UC Berkeley, California, USA'], 'affiliations': [{'raw_affiliation_string': 'Department of EECS, UC Berkeley, California, USA', 'institution_ids': ['https://openalex.org/I95457486']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5017469189', 'display_name': 'Ma’ayan Bresler', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I95457486', 'display_name': 'University of California, Berkeley', 'ror': 'https://ror.org/01an7q238', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I95457486']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': "Ma'ayan Bresler", 'raw_affiliation_strings': ['Department of EECS, UC Berkeley, California, USA'], 'affiliations': [{'raw_affiliation_string': 'Department of EECS, UC Berkeley, California, USA', 'institution_ids': ['https://openalex.org/I95457486']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5024072566', 'display_name': 'David Tse', 'orcid': 'https://orcid.org/0000-0003-1460-5900'}, 'institutions': [{'id': 'https://openalex.org/I95457486', 'display_name': 'University of California, Berkeley', 'ror': 'https://ror.org/01an7q238', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I95457486']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'David Tse', 'raw_affiliation_strings': ['Department of EECS, UC Berkeley, California, USA'], 'affiliations': [{'raw_affiliation_string': 'Department of EECS, UC Berkeley, California, USA', 'institution_ids': ['https://openalex.org/I95457486']}]}], 'countries_distinct_count': 1, 'institutions_distinct_count': 1, 'corresponding_author_ids': ['https://openalex.org/A5060812074'], 'corresponding_institution_ids': ['https://openalex.org/I95457486'], 'apc_list': {'value': 1690, 'currency': 'GBP', 'value_usd': 2072, 'provenance': 'doaj'}, 'apc_paid': {'value': 1690, 'currency': 'GBP', 'value_usd': 2072, 'provenance': 'doaj'}, 'fwci': 5.266, 'has_fulltext': True, 'fulltext_origin': 'pdf', 'cited_by_count': 97, 'citation_normalized_percentile': {'value': 0.999986, 'is_in_top_1_percent': True, 'is_in_top_10_percent': True}, 'cited_by_percentile_year': {'min': 98, 'max': 99}, 'biblio': {'volume': '14', 'issue': 'S5', 'first_page': None, 'last_page': None}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10015', 'display_name': 'RNA Sequencing Data Analysis', 'score': 0.9995, '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'}}, 'topics': [{'id': 'https://openalex.org/T10015', 'display_name': 'RNA Sequencing Data Analysis', 'score': 0.9995, '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/T10434', 'display_name': 'Genome Evolution and Polyploidy in Plants', 'score': 0.9845, 'subfield': {'id': 'https://openalex.org/subfields/1110', 'display_name': 'Plant Science'}, 'field': {'id': 'https://openalex.org/fields/11', 'display_name': 'Agricultural and Biological Sciences'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, {'id': 'https://openalex.org/T10521', 'display_name': 'Ribosome Structure and Translation Mechanisms', 'score': 0.9577, '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'}}], 'keywords': [{'id': 'https://openalex.org/keywords/k-mer', 'display_name': 'k-mer', 'score': 0.7323893}, {'id': 'https://openalex.org/keywords/sequence-assembly', 'display_name': 'Sequence assembly', 'score': 0.70950055}, {'id': 'https://openalex.org/keywords/hybrid-genome-assembly', 'display_name': 'Hybrid genome assembly', 'score': 0.70832485}, {'id': 'https://openalex.org/keywords/shotgun', 'display_name': 'Shotgun', 'score': 0.6837771}, {'id': 'https://openalex.org/keywords/sequence-alignment', 'display_name': 'sequence alignment', 'score': 0.564948}, {'id': 'https://openalex.org/keywords/metagenomics-assembly', 'display_name': 'metagenomics assembly', 'score': 0.549796}], 'concepts': [{'id': 'https://openalex.org/C101985253', 'wikidata': 'https://www.wikidata.org/wiki/Q1073526', 'display_name': 'Shotgun sequencing', 'level': 4, 'score': 0.9119642}, {'id': 'https://openalex.org/C2279292', 'wikidata': 'https://www.wikidata.org/wiki/Q6322851', 'display_name': 'k-mer', 'level': 4, 'score': 0.7323893}, {'id': 'https://openalex.org/C18949551', 'wikidata': 'https://www.wikidata.org/wiki/Q740578', 'display_name': 'Sequence assembly', 'level': 5, 'score': 0.70950055}, {'id': 'https://openalex.org/C113425843', 'wikidata': 'https://www.wikidata.org/wiki/Q5953213', 'display_name': 'Hybrid genome assembly', 'level': 5, 'score': 0.70832485}, {'id': 'https://openalex.org/C2781434637', 'wikidata': 'https://www.wikidata.org/wiki/Q486396', 'display_name': 'Shotgun', 'level': 3, 'score': 0.6837771}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.53220624}, {'id': 'https://openalex.org/C141231307', 'wikidata': 'https://www.wikidata.org/wiki/Q7020', 'display_name': 'Genome', 'level': 3, 'score': 0.5022516}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.48237196}, {'id': 'https://openalex.org/C51679486', 'wikidata': 'https://www.wikidata.org/wiki/Q380546', 'display_name': 'DNA sequencing', 'level': 3, 'score': 0.48206788}, {'id': 'https://openalex.org/C177264268', 'wikidata': 'https://www.wikidata.org/wiki/Q1514741', 'display_name': 'Set (abstract data type)', 'level': 2, 'score': 0.43819606}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.3567865}, {'id': 'https://openalex.org/C11413529', 'wikidata': 'https://www.wikidata.org/wiki/Q8366', 'display_name': 'Algorithm', 'level': 1, 'score': 0.34889752}, {'id': 'https://openalex.org/C54355233', 'wikidata': 'https://www.wikidata.org/wiki/Q7162', 'display_name': 'Genetics', 'level': 1, 'score': 0.23411804}, {'id': 'https://openalex.org/C552990157', 'wikidata': 'https://www.wikidata.org/wiki/Q7430', 'display_name': 'DNA', 'level': 2, 'score': 0.16462448}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.12481031}, {'id': 'https://openalex.org/C150194340', 'wikidata': 'https://www.wikidata.org/wiki/Q26972', 'display_name': 'Gene expression', 'level': 3, 'score': 0.0}, {'id': 'https://openalex.org/C162317418', 'wikidata': 'https://www.wikidata.org/wiki/Q252857', 'display_name': 'Transcriptome', 'level': 4, 'score': 0.0}, {'id': 'https://openalex.org/C199360897', 'wikidata': 'https://www.wikidata.org/wiki/Q9143', 'display_name': 'Programming language', 'level': 1, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D000465', 'descriptor_name': 'Algorithms', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D059014', 'descriptor_name': 'High-Throughput Nucleotide Sequencing', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D017422', 'descriptor_name': 'Sequence Analysis, DNA', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D020451', 'descriptor_name': 'Contig Mapping', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D059014', 'descriptor_name': 'High-Throughput Nucleotide Sequencing', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D006801', 'descriptor_name': 'Humans', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D017422', 'descriptor_name': 'Sequence Analysis, DNA', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 7, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1186/1471-2105-14-s5-s18', 'pdf_url': 'https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S5-S18', 'source': {'id': 'https://openalex.org/S19032547', 'display_name': 'BMC Bioinformatics', 'issn_l': '1471-2105', 'issn': ['1471-2105'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320256', 'host_organization_name': 'BioMed Central', 'host_organization_lineage': ['https://openalex.org/P4310319965', 'https://openalex.org/P4310320256'], 'host_organization_lineage_names': ['Springer Nature', 'BioMed Central'], 'type': 'journal'}, '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://europepmc.org/articles/pmc3706340', 'pdf_url': 'https://europepmc.org/articles/pmc3706340?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://escholarship.org/uc/item/5981t594', 'pdf_url': 'https://escholarship.org/content/qt5981t594/qt5981t594.pdf?t=mpo6yc', '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/PMC3706340', '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': True, 'landing_page_url': 'https://arxiv.org/abs/1301.0068', 'pdf_url': 'https://arxiv.org/pdf/1301.0068', 'source': {'id': 'https://openalex.org/S4306400194', 'display_name': 'arXiv (Cornell University)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I205783295', 'host_organization_name': 'Cornell University', 'host_organization_lineage': ['https://openalex.org/I205783295'], 'host_organization_lineage_names': ['Cornell University'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': 'submittedVersion', 'is_accepted': False, 'is_published': False}, {'is_oa': True, 'landing_page_url': None, 'pdf_url': 'https://arxiv.org/pdf/1301.0068.pdf', 'source': {'id': 'https://openalex.org/S4306400194', 'display_name': 'arXiv (Cornell University)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I205783295', 'host_organization_name': 'Cornell University', 'host_organization_lineage': ['https://openalex.org/I205783295'], 'host_organization_lineage_names': ['Cornell University'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': 'submittedVersion', 'is_accepted': False, 'is_published': False}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/23902516', '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/10.1186/1471-2105-14-s5-s18', 'pdf_url': 'https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S5-S18', 'source': {'id': 'https://openalex.org/S19032547', 'display_name': 'BMC Bioinformatics', 'issn_l': '1471-2105', 'issn': ['1471-2105'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320256', 'host_organization_name': 'BioMed Central', 'host_organization_lineage': ['https://openalex.org/P4310319965', 'https://openalex.org/P4310320256'], 'host_organization_lineage_names': ['Springer Nature', 'BioMed Central'], 'type': 'journal'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [{'id': 'https://metadata.un.org/sdg/11', 'display_name': 'Sustainable cities and communities', 'score': 0.58}], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 25, 'referenced_works': ['https://openalex.org/W1579791898', 'https://openalex.org/W1598134722', 'https://openalex.org/W1850079471', 'https://openalex.org/W1966711026', 'https://openalex.org/W1966822396', 'https://openalex.org/W1970939265', 'https://openalex.org/W1984236772', 'https://openalex.org/W2021134019', 'https://openalex.org/W2022910024', 'https://openalex.org/W2022986961', 'https://openalex.org/W2035596374', 'https://openalex.org/W2036145579', 'https://openalex.org/W2041391522', 'https://openalex.org/W2043481183', 'https://openalex.org/W2078331392', 'https://openalex.org/W2121911035', 'https://openalex.org/W2127768708', 'https://openalex.org/W2135361281', 'https://openalex.org/W2136651963', 'https://openalex.org/W2156104322', 'https://openalex.org/W2157888653', 'https://openalex.org/W2159497035', 'https://openalex.org/W2160969485', 'https://openalex.org/W2166265186', 'https://openalex.org/W2171475724'], 'related_works': ['https://openalex.org/W4256345205', 'https://openalex.org/W2417514914', 'https://openalex.org/W2213265806', 'https://openalex.org/W2166654698', 'https://openalex.org/W2165847428', 'https://openalex.org/W2132414125', 'https://openalex.org/W2047803783', 'https://openalex.org/W2047656369', 'https://openalex.org/W2010454899', 'https://openalex.org/W2008090296'], 'abstract_inverted_index': {'We': [0, 20], 'present': [1], 'a': [2, 22, 51, 71, 86], 'framework': [3], 'for': [4, 11, 34, 67, 100, 118], 'the': [5, 15, 26, 30, 39, 43, 64, 78, 94, 98, 108], 'design': [6, 50], 'of': [7, 17, 38, 42, 70, 74, 88, 112], 'optimal': [8], 'assembly': [9, 56], 'algorithms': [10], 'shotgun': [12, 109], 'sequencing': [13, 110], 'under': [14], 'criterion': [16], 'complete': [18], 'reconstruction.': [19, 101], 'derive': [21], 'lower': [23, 65], 'bound': [24, 66], 'on': [25, 46, 85, 93], 'read': [27], 'length': [28], 'and': [29, 90, 97, 115], 'coverage': [31], 'depth': [32], 'required': [33], 'reconstruction': [35], 'in': [36], 'terms': [37], 'repeat': [40, 68], 'statistics': [41, 69], 'genome.': [44], 'Building': [45], 'earlier': [47], 'works,': [48], 'we': [49], 'de': [52], 'Brujin': [53], 'graph': [54], 'based': [55, 84], 'algorithm': [57], 'which': [58], 'can': [59, 104], 'achieve': [60], 'very': [61], 'close': [62], 'to': [63], 'wide': [72], 'range': [73], 'sequenced': [75], 'genomes,': [76], 'including': [77], 'GAGE': [79], 'datasets.': [80], 'The': [81, 102], 'results': [82], 'are': [83], 'set': [87], 'necessary': [89, 114], 'sufficient': [91, 116], 'conditions': [92, 103, 117], 'DNA': [95], 'sequence': [96], 'reads': [99], 'be': [105], 'viewed': [106], 'as': [107], 'analogue': [111], "Ukkonen-Pevzner's": [113], 'Sequencing': [119], 'by': [120], 'Hybridization.': [121]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2165847428', 'counts_by_year': [{'year': 2024, 'cited_by_count': 3}, {'year': 2023, 'cited_by_count': 9}, {'year': 2022, 'cited_by_count': 6}, {'year': 2021, 'cited_by_count': 9}, {'year': 2020, 'cited_by_count': 8}, {'year': 2019, 'cited_by_count': 6}, {'year': 2018, 'cited_by_count': 6}, {'year': 2017, 'cited_by_count': 7}, {'year': 2016, 'cited_by_count': 19}, {'year': 2015, 'cited_by_count': 11}, {'year': 2014, 'cited_by_count': 7}, {'year': 2013, 'cited_by_count': 5}], 'updated_date': '2024-09-13T11:21:47.611966', 'created_date': '2016-06-24'}