{"id":"https://openalex.org/W2914184348","doi":"https://doi.org/10.1093/bioinformatics/btz080","title":"ChimeraUGEM: unsupervised gene expression modeling in any given organism","display_name":"ChimeraUGEM: unsupervised gene expression modeling in any given organism","publication_year":2019,"publication_date":"2019-01-30","ids":{"openalex":"https://openalex.org/W2914184348","doi":"https://doi.org/10.1093/bioinformatics/btz080","mag":"2914184348","pmid":"https://pubmed.ncbi.nlm.nih.gov/30715207"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz080","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz080","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091136913","display_name":"Alon Diament","orcid":"https://orcid.org/0000-0002-3939-5703"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alon Diament","raw_affiliation_strings":["Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065324696","display_name":"Iddo Weiner","orcid":"https://orcid.org/0000-0001-9554-346X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Iddo Weiner","raw_affiliation_strings":["Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","institution_ids":[]},{"raw_affiliation_string":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057713570","display_name":"Noam Shahar","orcid":"https://orcid.org/0000-0001-9929-7622"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Noam Shahar","raw_affiliation_strings":["School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089001632","display_name":"Shira Landman","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shira Landman","raw_affiliation_strings":["School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071850715","display_name":"Yael Feldman","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yael Feldman","raw_affiliation_strings":["School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052792602","display_name":"Shimshi Atar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shimshi Atar","raw_affiliation_strings":["Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015796551","display_name":"Meital Avitan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Meital Avitan","raw_affiliation_strings":["Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","institution_ids":[]},{"raw_affiliation_string":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049207723","display_name":"Shira Schweitzer","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shira Schweitzer","raw_affiliation_strings":["School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018652889","display_name":"Iftach Yacoby","orcid":"https://orcid.org/0000-0003-0177-0624"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Iftach Yacoby","raw_affiliation_strings":["School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021278923","display_name":"Tamir Tuller","orcid":"https://orcid.org/0000-0003-4194-7068"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Tamir Tuller","raw_affiliation_strings":["Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","The Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel","institution_ids":[]},{"raw_affiliation_string":"The Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5018652889","https://openalex.org/A5021278923"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6819,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.67870668,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"18","first_page":"3365","last_page":"3371"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"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/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/organism","display_name":"Organism","score":0.7192422747612},{"id":"https://openalex.org/keywords/chlamydomonas-reinhardtii","display_name":"Chlamydomonas reinhardtii","score":0.6852988600730896},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.6413061022758484},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6332255601882935},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6254928112030029},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6037867069244385},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5493268370628357},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4982430934906006},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4552539587020874},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4516351819038391},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4425901472568512},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.4125097990036011},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23246410489082336},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20465809106826782}],"concepts":[{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.7192422747612},{"id":"https://openalex.org/C2777727519","wikidata":"https://www.wikidata.org/wiki/Q291827","display_name":"Chlamydomonas reinhardtii","level":4,"score":0.6852988600730896},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.6413061022758484},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6332255601882935},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6254928112030029},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6037867069244385},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5493268370628357},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4982430934906006},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4552539587020874},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4516351819038391},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4425901472568512},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.4125097990036011},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23246410489082336},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20465809106826782},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz080","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz080","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30715207","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30715207","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5600000023841858,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320948","display_name":"Ministry of Science, Technology and Space","ror":"https://ror.org/02heb2n75"},{"id":"https://openalex.org/F4320322596","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49"},{"id":"https://openalex.org/F4320323139","display_name":"Azrieli Foundation","ror":"https://ror.org/009svts64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1820328344","https://openalex.org/W1841471854","https://openalex.org/W1879501137","https://openalex.org/W1939771252","https://openalex.org/W1966618675","https://openalex.org/W1968569455","https://openalex.org/W1990228304","https://openalex.org/W1995352318","https://openalex.org/W1999143685","https://openalex.org/W2016214324","https://openalex.org/W2018330825","https://openalex.org/W2018590530","https://openalex.org/W2025569664","https://openalex.org/W2025836692","https://openalex.org/W2035475950","https://openalex.org/W2046872786","https://openalex.org/W2049322319","https://openalex.org/W2051242197","https://openalex.org/W2058426472","https://openalex.org/W2058864686","https://openalex.org/W2063779182","https://openalex.org/W2064295826","https://openalex.org/W2065248572","https://openalex.org/W2078624174","https://openalex.org/W2078755055","https://openalex.org/W2085522899","https://openalex.org/W2086471971","https://openalex.org/W2092035637","https://openalex.org/W2093676487","https://openalex.org/W2105100203","https://openalex.org/W2107804881","https://openalex.org/W2109036608","https://openalex.org/W2118540273","https://openalex.org/W2120368500","https://openalex.org/W2122438081","https://openalex.org/W2123035829","https://openalex.org/W2129217817","https://openalex.org/W2141643127","https://openalex.org/W2143078019","https://openalex.org/W2145147173","https://openalex.org/W2147837708","https://openalex.org/W2157815481","https://openalex.org/W2161616648","https://openalex.org/W2512653639","https://openalex.org/W2534106100","https://openalex.org/W2583341722","https://openalex.org/W2603991019","https://openalex.org/W2739217157","https://openalex.org/W2769217290","https://openalex.org/W2782537090","https://openalex.org/W2787023214","https://openalex.org/W2794154969","https://openalex.org/W4250359879"],"related_works":["https://openalex.org/W4223896405","https://openalex.org/W2059629050","https://openalex.org/W2074740504","https://openalex.org/W3013644380","https://openalex.org/W1996935079","https://openalex.org/W2205963160","https://openalex.org/W3210243923","https://openalex.org/W2145833061","https://openalex.org/W2258998699","https://openalex.org/W1998405066"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
