{"id":"https://openalex.org/W2735632796","doi":"https://doi.org/10.1093/bioinformatics/btx232","title":"HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington\u2019s epigenetic landscape","display_name":"HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington\u2019s epigenetic landscape","publication_year":2017,"publication_date":"2017-04-13","ids":{"openalex":"https://openalex.org/W2735632796","doi":"https://doi.org/10.1093/bioinformatics/btx232","mag":"2735632796","pmid":"https://pubmed.ncbi.nlm.nih.gov/28881967"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx232","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx232","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i102/25156835/btx232.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i102/25156835/btx232.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100609679","display_name":"Jing Guo","orcid":"https://orcid.org/0000-0002-3159-584X"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Jing Guo","raw_affiliation_strings":["Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore","Biomedical Informatics Laboratory, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"Biomedical Informatics Laboratory, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014529529","display_name":"Jie Zheng","orcid":"https://orcid.org/0000-0001-6774-9786"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Jie Zheng","raw_affiliation_strings":["Biomedical Informatics Laboratory, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore","Complexity Institute, Nanyang Technological University, Singapore, Singapore","Genome Institute of Singapore, Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore"],"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Laboratory, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Complexity Institute, Nanyang Technological University, Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Genome Institute of Singapore, Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I66068411"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5014529529"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I172675005","https://openalex.org/I66068411"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6842,"has_fulltext":true,"cited_by_count":43,"citation_normalized_percentile":{"value":0.84276684,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"33","issue":"14","first_page":"i102","last_page":"i109"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9966999888420105,"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/computer-science","display_name":"Computer science","score":0.7068886160850525},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.5102148056030273},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4560002386569977},{"id":"https://openalex.org/keywords/hopfield-network","display_name":"Hopfield network","score":0.42301851511001587},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41319942474365234},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3559056520462036},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32522040605545044},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31365787982940674},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.2648128271102905},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2597808837890625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21121558547019958},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11359050869941711}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7068886160850525},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5102148056030273},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4560002386569977},{"id":"https://openalex.org/C46421273","wikidata":"https://www.wikidata.org/wiki/Q1407668","display_name":"Hopfield network","level":3,"score":0.42301851511001587},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41319942474365234},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3559056520462036},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32522040605545044},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31365787982940674},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2648128271102905},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2597808837890625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21121558547019958},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11359050869941711}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx232","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx232","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i102/25156835/btx232.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28881967","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28881967","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5870541","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870541","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx232","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx232","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i102/25156835/btx232.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1482925484","display_name":null,"funder_award_id":"Tier 1","funder_id":"https://openalex.org/F4320320751","funder_display_name":"Ministry of Education - Singapore"},{"id":"https://openalex.org/G15471654","display_name":null,"funder_award_id":"MOE AcRF Tier 1","funder_id":"https://openalex.org/F4320320751","funder_display_name":"Ministry of Education - Singapore"}],"funders":[{"id":"https://openalex.org/F4320320751","display_name":"Ministry of Education - Singapore","ror":"https://ror.org/01kcva023"},{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2735632796.pdf","grobid_xml":"https://content.openalex.org/works/W2735632796.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W66306528","https://openalex.org/W1984883254","https://openalex.org/W1986944049","https://openalex.org/W1988391018","https://openalex.org/W1993287310","https://openalex.org/W2001246746","https://openalex.org/W2006554089","https://openalex.org/W2007222211","https://openalex.org/W2007439698","https://openalex.org/W2010653277","https://openalex.org/W2023315677","https://openalex.org/W2023887100","https://openalex.org/W2039617089","https://openalex.org/W2054113582","https://openalex.org/W2067413718","https://openalex.org/W2080914918","https://openalex.org/W2087242711","https://openalex.org/W2088861927","https://openalex.org/W2097389802","https://openalex.org/W2112246162","https://openalex.org/W2123649031","https://openalex.org/W2124439606","https://openalex.org/W2124609748","https://openalex.org/W2124972241","https://openalex.org/W2127788692","https://openalex.org/W2128084896","https://openalex.org/W2128120736","https://openalex.org/W2128227827","https://openalex.org/W2142806844","https://openalex.org/W2149573463","https://openalex.org/W2153453980","https://openalex.org/W2163092257","https://openalex.org/W2169187183","https://openalex.org/W2169779569","https://openalex.org/W2177721432","https://openalex.org/W2273101790","https://openalex.org/W2344887288","https://openalex.org/W2395347108","https://openalex.org/W2577025303","https://openalex.org/W2951890476","https://openalex.org/W4232310547","https://openalex.org/W6602631663","https://openalex.org/W6684785420"],"related_works":["https://openalex.org/W4366603091","https://openalex.org/W2485141070","https://openalex.org/W2411374999","https://openalex.org/W2083798468","https://openalex.org/W2117614743","https://openalex.org/W2218979613","https://openalex.org/W4380318195","https://openalex.org/W2008978345","https://openalex.org/W2325094346","https://openalex.org/W3093680309"],"abstract_inverted_index":{"zhengjie@ntu.edu.sg.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6}],"updated_date":"2026-04-19T08:26:33.389920","created_date":"2025-10-10T00:00:00"}
