{"id":"https://openalex.org/W2106626761","doi":"https://doi.org/10.1093/bioinformatics/btt638","title":"Topological augmentation to infer hidden processes in biological systems","display_name":"Topological augmentation to infer hidden processes in biological systems","publication_year":2013,"publication_date":"2013-12-02","ids":{"openalex":"https://openalex.org/W2106626761","doi":"https://doi.org/10.1093/bioinformatics/btt638","mag":"2106626761","pmid":"https://pubmed.ncbi.nlm.nih.gov/24297519"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/2/221/17146193/btt638.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/2/221/17146193/btt638.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018922897","display_name":"Mikael Sunn\u00e5ker","orcid":"https://orcid.org/0009-0003-5881-4998"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Mikael Sunn\u00e5ker","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077497422","display_name":"El\u00edas Zamora-Sillero","orcid":null},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Elias Zamora-Sillero","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069227992","display_name":"Adri\u00e1n L\u00f3pez Garc\u00eda de Lomana","orcid":"https://orcid.org/0000-0002-9748-347X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Adri\u00e1n L\u00f3pez Garc\u00eda de Lomana","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007748962","display_name":"Florian Rudroff","orcid":"https://orcid.org/0000-0002-6680-8200"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Florian Rudroff","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014164691","display_name":"Uwe Sauer","orcid":"https://orcid.org/0000-0002-5923-0770"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Uwe Sauer","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064223365","display_name":"Joerg Stelling","orcid":"https://orcid.org/0000-0002-1145-891X"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Joerg Stelling","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079730045","display_name":"Andreas Wagner","orcid":"https://orcid.org/0000-0003-4299-3840"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Andreas Wagner","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering/Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, 2Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, 3Institute of Evolutionary Biology and Environmental Studies/Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, 4Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and 5The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5018922897"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423","https://openalex.org/I35440088"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8987,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.74662239,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"30","issue":"2","first_page":"221","last_page":"227"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9973999857902527,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9969000220298767,"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":0.6449738144874573},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.6322103142738342},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.5538731813430786},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.48957476019859314},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39326804876327515},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32626432180404663},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.3174703121185303},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.25223761796951294}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6449738144874573},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6322103142738342},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.5538731813430786},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.48957476019859314},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39326804876327515},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32626432180404663},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.3174703121185303},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.25223761796951294},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000008","qualifier_name":"administration & dosage","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000008","qualifier_name":"administration & dosage","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000008","qualifier_name":"administration & dosage","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000008","qualifier_name":"administration & dosage","is_major_topic":false},{"descriptor_ui":"D005973","descriptor_name":"Glutamine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005973","descriptor_name":"Glutamine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005973","descriptor_name":"Glutamine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005973","descriptor_name":"Glutamine","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D026923","descriptor_name":"Amino Acid Transport Systems, Basic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D026923","descriptor_name":"Amino Acid Transport Systems, Basic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D026923","descriptor_name":"Amino Acid Transport Systems, Basic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D026923","descriptor_name":"Amino Acid Transport Systems, Basic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btt638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/2/221/17146193/btt638.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24297519","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24297519","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:www.zora.uzh.ch:88306","is_oa":true,"landing_page_url":null,"pdf_url":"https://www.zora.uzh.ch/id/eprint/88306/1/Bioinformatics-2013-Sunn%C3%A5ker-bioinformatics_btt638.pdf","source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Sunnaker, M; Zamora-Sillero, E; de Lomana, A Lopez Garcia; Rudroff, F; Sauer, U; Stelling, J; Wagner, A  (2014). Topological augmentation to infer hidden processes in biological systems.  Bioinformatics, 30(2):221-227.","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:europepmc.org:2878440","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3892687","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"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":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3892687","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3892687","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/78659","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/78659","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 30 (2)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000078659","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000078659","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5167/uzh-88306","is_oa":true,"landing_page_url":"https://doi.org/10.5167/uzh-88306","pdf_url":null,"source":{"id":"https://openalex.org/S7407051291","display_name":"Universit\u00e4t Z\u00fcrich, ZORA","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/2/221/17146193/btt638.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320327577","display_name":"SystemsX.ch","ror":"https://ror.org/02s09gf16"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106626761.pdf","grobid_xml":"https://content.openalex.org/works/W2106626761.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1964215490","https://openalex.org/W1978641328","https://openalex.org/W2014810706","https://openalex.org/W2026174841","https://openalex.org/W2032616735","https://openalex.org/W2046203659","https://openalex.org/W2051784711","https://openalex.org/W2058815839","https://openalex.org/W2063183241","https://openalex.org/W2070717509","https://openalex.org/W2071413187","https://openalex.org/W2103041540","https://openalex.org/W2103369609","https://openalex.org/W2126351705","https://openalex.org/W2134092975","https://openalex.org/W2149142170","https://openalex.org/W2149695944","https://openalex.org/W2151098983","https://openalex.org/W2153208554","https://openalex.org/W2153568634","https://openalex.org/W2158257740","https://openalex.org/W2161525721","https://openalex.org/W2162317699","https://openalex.org/W2170316986","https://openalex.org/W4211177544","https://openalex.org/W4238187298","https://openalex.org/W4239090616","https://openalex.org/W6641465514","https://openalex.org/W6665272994"],"related_works":["https://openalex.org/W1017828488","https://openalex.org/W2158838630","https://openalex.org/W2373227583","https://openalex.org/W3106514255","https://openalex.org/W560728131","https://openalex.org/W2374267234","https://openalex.org/W118700700","https://openalex.org/W2375988701","https://openalex.org/W2185238563","https://openalex.org/W2002229964"],"abstract_inverted_index":{"Matlab":[0],"code":[1],"and":[2],"examples":[3],"are":[4],"available":[5],"at:":[6],"http://www.csb.ethz.ch/tools/index":[7]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":3}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
