Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2150856587', 'doi': 'https://doi.org/10.1093/bioinformatics/bth057', 'title': 'Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites', 'display_name': 'Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites', 'publication_year': 2004, 'publication_date': '2004-02-05', 'ids': {'openalex': 'https://openalex.org/W2150856587', 'doi': 'https://doi.org/10.1093/bioinformatics/bth057', 'mag': '2150856587', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/14764556'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/bth057', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/20/7/1198/48905397/bioinformatics_20_7_1198.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, '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': 'bronze', 'oa_url': 'https://academic.oup.com/bioinformatics/article-pdf/20/7/1198/48905397/bioinformatics_20_7_1198.pdf', 'any_repository_has_fulltext': False}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5109277906', 'display_name': 'Han Yu', 'orcid': None}, 'institutions': [], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Han Yu', 'raw_affiliation_strings': ['Wave Systems Corp., 19925 Stevens Creek Blvd, Cupertino, CA 95014, USA.'], 'affiliations': [{'raw_affiliation_string': 'Wave Systems Corp., 19925 Stevens Creek Blvd, Cupertino, CA 95014, USA.', 'institution_ids': []}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5091747215', 'display_name': 'Andrew S. Yoo', 'orcid': 'https://orcid.org/0000-0002-0304-3247'}, 'institutions': [], 'countries': [], 'is_corresponding': False, 'raw_author_name': 'Andrew S Yoo', 'raw_affiliation_strings': [], 'affiliations': []}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5069328543', 'display_name': 'Iva Greenwald', 'orcid': 'https://orcid.org/0000-0001-7180-3706'}, 'institutions': [], 'countries': [], 'is_corresponding': False, 'raw_author_name': 'Iva Greenwald', 'raw_affiliation_strings': [], 'affiliations': []}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 0, 'corresponding_author_ids': [], 'corresponding_institution_ids': [], 'apc_list': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'apc_paid': None, 'fwci': 0.713, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 9, 'citation_normalized_percentile': {'value': 0.512086, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 80, 'max': 81}, 'biblio': {'volume': '20', 'issue': '7', 'first_page': '1198', 'last_page': '1200'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10222', 'display_name': 'Genomics and Chromatin Dynamics', 'score': 0.9998, '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/T10222', 'display_name': 'Genomics and Chromatin Dynamics', 'score': 0.9998, '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/T10521', 'display_name': 'RNA and protein synthesis mechanisms', 'score': 0.9996, '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/T10604', 'display_name': 'RNA Research and Splicing', 'score': 0.9991, '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/dna-binding-site', 'display_name': 'DNA binding site', 'score': 0.6828656}, {'id': 'https://openalex.org/keywords/transcription', 'display_name': 'Transcription', 'score': 0.5060715}], 'concepts': [{'id': 'https://openalex.org/C86339819', 'wikidata': 'https://www.wikidata.org/wiki/Q407384', 'display_name': 'Transcription factor', 'level': 3, 'score': 0.6840334}, {'id': 'https://openalex.org/C3662595', 'wikidata': 'https://www.wikidata.org/wiki/Q5205743', 'display_name': 'DNA binding site', 'level': 5, 'score': 0.6828656}, {'id': 'https://openalex.org/C54985914', 'wikidata': 'https://www.wikidata.org/wiki/Q1295754', 'display_name': 'Consensus sequence', 'level': 4, 'score': 0.6542314}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.6174741}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.5551465}, {'id': 'https://openalex.org/C179926584', 'wikidata': 'https://www.wikidata.org/wiki/Q207714', 'display_name': 'Transcription (linguistics)', 'level': 2, 'score': 0.5060715}, {'id': 'https://openalex.org/C141231307', 'wikidata': 'https://www.wikidata.org/wiki/Q7020', 'display_name': 'Genome', 'level': 3, 'score': 0.45714903}, {'id': 'https://openalex.org/C107824862', 'wikidata': 'https://www.wikidata.org/wiki/Q616005', 'display_name': 'Binding site', 'level': 2, 'score': 0.44935912}, {'id': 'https://openalex.org/C2779904517', 'wikidata': 'https://www.wikidata.org/wiki/Q5008900', 'display_name': 'CATS', 'level': 2, 'score': 0.4270749}, {'id': 'https://openalex.org/C552990157', 'wikidata': 'https://www.wikidata.org/wiki/Q7430', 'display_name': 'DNA', 'level': 2, 'score': 0.4268859}, {'id': 'https://openalex.org/C54355233', 'wikidata': 'https://www.wikidata.org/wiki/Q7162', 'display_name': 'Genetics', 'level': 1, 'score': 0.42287445}, {'id': 'https://openalex.org/C51679486', 'wikidata': 'https://www.wikidata.org/wiki/Q380546', 'display_name': 'DNA sequencing', 'level': 3, 'score': 0.4148111}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.3652891}, {'id': 'https://openalex.org/C101762097', 'wikidata': 'https://www.wikidata.org/wiki/Q224093', 'display_name': 'Promoter', 'level': 4, 'score': 0.27889696}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.27078515}, {'id': 'https://openalex.org/C3017666073', 'wikidata': 'https://www.wikidata.org/wiki/Q1764062', 'display_name': 'Base sequence', 'level': 3, 'score': 0.1395658}, {'id': 'https://openalex.org/C150194340', 'wikidata': 'https://www.wikidata.org/wiki/Q26972', 'display_name': 'Gene expression', 'level': 3, 'score': 0.13750711}, {'id': 'https://openalex.org/C41895202', 'wikidata': 'https://www.wikidata.org/wiki/Q8162', 'display_name': 'Linguistics', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C138885662', 'wikidata': 'https://www.wikidata.org/wiki/Q5891', 'display_name': 'Philosophy', 'level': 0, 'score': 0.0}, {'id': 'https://openalex.org/C149635348', 'wikidata': 'https://www.wikidata.org/wiki/Q193040', 'display_name': 'Embedded system', 'level': 1, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D020869', 'descriptor_name': 'Gene Expression Profiling', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D016415', 'descriptor_name': 'Sequence Alignment', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D017421', 'descriptor_name': 'Sequence Analysis', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D012984', 'descriptor_name': 'Software', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D014157', 'descriptor_name': 'Transcription Factors', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': True}, {'descriptor_ui': 'D014584', 'descriptor_name': 'User-Computer Interface', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D001665', 'descriptor_name': 'Binding Sites', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016000', 'descriptor_name': 'Cluster Analysis', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D020869', 'descriptor_name': 'Gene Expression Profiling', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D011381', 'descriptor_name': 'Programming Languages', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D011485', 'descriptor_name': 'Protein Binding', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016415', 'descriptor_name': 'Sequence Alignment', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D017421', 'descriptor_name': 'Sequence Analysis', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D014157', 'descriptor_name': 'Transcription Factors', 'qualifier_ui': 'Q000235', 'qualifier_name': 'genetics', 'is_major_topic': False}, {'descriptor_ui': 'D014157', 'descriptor_name': 'Transcription Factors', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 2, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/bth057', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/20/7/1198/48905397/bioinformatics_20_7_1198.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, '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/14764556', '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/10.1093/bioinformatics/bth057', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/20/7/1198/48905397/bioinformatics_20_7_1198.pdf', 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 7, 'referenced_works': ['https://openalex.org/W1597226907', 'https://openalex.org/W1987179641', 'https://openalex.org/W2034719432', 'https://openalex.org/W2112221859', 'https://openalex.org/W2117549173', 'https://openalex.org/W2136726922', 'https://openalex.org/W2165228646'], 'related_works': ['https://openalex.org/W2412031876', 'https://openalex.org/W2236968607', 'https://openalex.org/W2165899269', 'https://openalex.org/W2153561273', 'https://openalex.org/W2152664145', 'https://openalex.org/W2146393977', 'https://openalex.org/W2079197459', 'https://openalex.org/W2058896391', 'https://openalex.org/W2036927633', 'https://openalex.org/W1485150548'], 'abstract_inverted_index': {'Abstract': [0], 'Summary:': [1], 'We': [2], 'have': [3, 75], 'developed': [4], 'a': [5, 38, 55, 110], 'program,': [6], 'Cluster': [7], 'Analyzer': [8], 'for': [9, 28, 34, 65, 71, 92], 'Transcription': [10], 'Sites': [11], '(CATS),': [12], 'which': [13, 72], 'identifies': [14], 'clusters': [15, 29, 93], 'of': [16, 30, 41, 51, 90, 94, 104], 'transcription': [17, 69, 96], 'factor': [18, 97], 'binding': [19, 36, 98], 'sites': [20, 99], 'in': [21, 109], 'any': [22, 127], 'genome': [23], 'sequence.': [24], 'The': [25, 43, 88], 'program': [26], 'searches': [27], 'the': [31, 47, 102], 'consensus': [32, 52, 73], 'sequence': [33], 'DNA': [35], 'within': [37, 54], 'window': [39, 44], '(length': [40], 'DNA).': [42], 'size': [45, 49], 'and': [46, 81, 122], 'cluster': [48], '(number': [50], 'sequences': [53, 74], 'given': [56], 'window)': [57], 'can': [58, 62], 'be': [59, 63], 'varied.': [60], 'CATS': [61, 91, 117], 'used': [64], 'single': [66], 'or': [67, 84, 113], 'multiple': [68], 'factors': [70], 'been': [76], 'deduced': [77], 'based': [78], 'on': [79, 124], 'biochemical': [80], 'mutational': [82], 'analysis,': [83], 'by': [85], 'comparative': [86], 'genomics.': [87], 'use': [89, 123], 'different': [95], 'may': [100], 'facilitate': [101], 'identification': [103], 'genes': [105], 'that': [106], 'are': [107], 'co-regulated': [108], 'cell': [111], 'type-specific': [112], 'developmental': [114], 'stage-specific': [115], 'manner.': [116], 'is': [118], 'simple': [119], 'to': [120], 'install': [121], 'computers': [125], 'running': [126], 'Windows': [128], 'NT-platforms.': [129], 'Availability:': [130], 'http://www.healthsciences.columbia.edu/dept/greenwaldlab/links.html': [131]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2150856587', 'counts_by_year': [{'year': 2018, 'cited_by_count': 1}], 'updated_date': '2024-12-10T05:43:11.293316', 'created_date': '2016-06-24'}