{"id":"https://openalex.org/W4379196640","doi":"https://doi.org/10.1093/bioinformatics/btad362","title":"Optimization-based decoding of Imaging Spatial Transcriptomics data","display_name":"Optimization-based decoding of Imaging Spatial Transcriptomics data","publication_year":2023,"publication_date":"2023-06-01","ids":{"openalex":"https://openalex.org/W4379196640","doi":"https://doi.org/10.1093/bioinformatics/btad362","pmid":"https://pubmed.ncbi.nlm.nih.gov/37267161"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad362","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad362/50513505/btad362.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/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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad362/50513505/btad362.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031693097","display_name":"John Bryan","orcid":"https://orcid.org/0000-0003-1388-7731"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John P Bryan","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, MA 02139, USA","Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St , Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St , Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044900278","display_name":"Lo\u00efc Binan","orcid":"https://orcid.org/0000-0002-3886-5873"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lo\u00efc Binan","raw_affiliation_strings":["Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St , Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St , Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056756087","display_name":"Cai McCann","orcid":"https://orcid.org/0000-0003-2010-9794"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cai McCann","raw_affiliation_strings":["Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St , Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St , Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005913897","display_name":"Yonina C. Eldar","orcid":"https://orcid.org/0000-0003-4358-5304"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]},{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Yonina C Eldar","raw_affiliation_strings":["Department of Computer Science and Applied Mathematics, Weizmann Institute of Science , 218 Ullman, Rehovot 7610001, Israel","Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, MA 02139, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Applied Mathematics, Weizmann Institute of Science , 218 Ullman, Rehovot 7610001, Israel","institution_ids":["https://openalex.org/I53964585"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077897775","display_name":"Samouil L. Farhi","orcid":"https://orcid.org/0000-0003-1359-4568"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samouil L Farhi","raw_affiliation_strings":["Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St, Cambridge, MA 02142, USA"],"affiliations":[{"raw_affiliation_string":"Klarman Cell Observatory, Broad Institute of MIT and Harvard , 415 Main St, Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080433291","display_name":"Brian Cleary","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brian Cleary","raw_affiliation_strings":["Program in Bioinformatics, Departments of Biomedical Engineering and Biology, Faculty of Computing and Data Sciences, Boston University , 665 Commonwealth Ave., Boston, MA 02215, USA"],"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics, Departments of Biomedical Engineering and Biology, Faculty of Computing and Data Sciences, Boston University , 665 Commonwealth Ave., Boston, MA 02215, USA","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5005913897","https://openalex.org/A5077897775","https://openalex.org/A5080433291"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I111088046","https://openalex.org/I53964585","https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1051,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.77616607,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9965000152587891,"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/T11393","display_name":"Biosensors and Analytical Detection","score":0.9894999861717224,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7632273435592651},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.6592455506324768},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5373892188072205},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48455730080604553},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.45139971375465393},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.43380647897720337},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.421907901763916},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4200412333011627},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.40532898902893066},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3504837155342102},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2206343710422516},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09426367282867432}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7632273435592651},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.6592455506324768},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5373892188072205},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48455730080604553},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.45139971375465393},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.43380647897720337},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.421907901763916},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4200412333011627},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.40532898902893066},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3504837155342102},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2206343710422516},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09426367282867432},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017404","descriptor_name":"In Situ Hybridization, Fluorescence","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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad362","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad362/50513505/btad362.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/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:37267161","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37267161","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:10287917","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10287917","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10287917/pdf/btad362.pdf","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad362","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad362/50513505/btad362.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/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":[{"id":"https://openalex.org/G2990047757","display_name":null,"funder_award_id":"RF1MH121289","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4379196640.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W649866511","https://openalex.org/W1987371344","https://openalex.org/W2025818287","https://openalex.org/W2042789810","https://openalex.org/W2123491442","https://openalex.org/W2131681506","https://openalex.org/W2271221198","https://openalex.org/W2520858613","https://openalex.org/W2800392236","https://openalex.org/W2809368942","https://openalex.org/W2810581099","https://openalex.org/W2810682944","https://openalex.org/W2899224111","https://openalex.org/W2969922972","https://openalex.org/W2972445800","https://openalex.org/W3048671742","https://openalex.org/W3099768174","https://openalex.org/W3102464072","https://openalex.org/W3108118546","https://openalex.org/W3133902371","https://openalex.org/W3134482219","https://openalex.org/W3135740182","https://openalex.org/W3163420826","https://openalex.org/W3178113810","https://openalex.org/W3203364159","https://openalex.org/W4205213118","https://openalex.org/W4213416970","https://openalex.org/W4291021133","https://openalex.org/W4300263211","https://openalex.org/W4300862018","https://openalex.org/W4302362633","https://openalex.org/W4311684329","https://openalex.org/W6673959690","https://openalex.org/W6845303433","https://openalex.org/W6931149909"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W188202134","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520"],"abstract_inverted_index":{"Software":[0],"implementation":[1],"of":[2],"JSIT,":[3],"together":[4],"with":[5],"example":[6],"files,":[7],"is":[8],"available":[9],"at":[10],"https://github.com/jpbryan13/JSIT.":[11]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
