{"id":"https://openalex.org/W3197020116","doi":"https://doi.org/10.1093/bioinformatics/btab653","title":"VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories","display_name":"VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories","publication_year":2021,"publication_date":"2021-09-08","ids":{"openalex":"https://openalex.org/W3197020116","doi":"https://doi.org/10.1093/bioinformatics/btab653","mag":"3197020116","pmid":"https://pubmed.ncbi.nlm.nih.gov/34500455"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab653","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab653","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8723140","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025156938","display_name":"Lyla Atta","orcid":"https://orcid.org/0000-0002-6113-0082"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lyla Atta","raw_affiliation_strings":["Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD 21211, USA","Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA","Medical Scientist Training Program, Johns Hopkins University School of Medicine , Baltimore, MD 21205, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD 21211, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Medical Scientist Training Program, Johns Hopkins University School of Medicine , Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101570227","display_name":"Arpan Sahoo","orcid":"https://orcid.org/0000-0002-6375-3048"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arpan Sahoo","raw_affiliation_strings":["Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA","Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033929431","display_name":"Jean Fan","orcid":"https://orcid.org/0000-0002-0212-5451"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jean Fan","raw_affiliation_strings":["Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD 21211, USA","Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA","Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD 21211, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5033929431"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3014,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.80161004,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"2","first_page":"391","last_page":"396"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9905999898910522,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.9894000291824341,"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/bioconductor","display_name":"Bioconductor","score":0.8527704477310181},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6405367851257324},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5931060314178467},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5922316312789917},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5086973309516907},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.48494890332221985},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47079458832740784},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.46883028745651245},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.43837636709213257},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34527429938316345},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3353330194950104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29424071311950684},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21745970845222473},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21456748247146606},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2086133360862732},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1748816967010498}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8527704477310181},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6405367851257324},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5931060314178467},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5922316312789917},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5086973309516907},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.48494890332221985},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47079458832740784},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.46883028745651245},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.43837636709213257},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34527429938316345},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3353330194950104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29424071311950684},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21745970845222473},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21456748247146606},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2086133360862732},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1748816967010498},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab653","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab653","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:34500455","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34500455","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:8723140","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8723140","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":"pmh:oai:pubmedcentral.nih.gov:8723140","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8723140","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1458437600","display_name":null,"funder_award_id":"2047611","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6576735694","display_name":null,"funder_award_id":"T32-GM136577","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W2006554089","https://openalex.org/W2167482691","https://openalex.org/W2187089797","https://openalex.org/W2273101790","https://openalex.org/W2279350325","https://openalex.org/W2605810679","https://openalex.org/W2766437506","https://openalex.org/W2791058611","https://openalex.org/W2801820889","https://openalex.org/W2813292791","https://openalex.org/W2889326414","https://openalex.org/W2899224111","https://openalex.org/W2900354600","https://openalex.org/W2927507212","https://openalex.org/W2948300330","https://openalex.org/W2952840385","https://openalex.org/W2953405766","https://openalex.org/W2972445800","https://openalex.org/W2982638381","https://openalex.org/W2989747508","https://openalex.org/W3005127469","https://openalex.org/W3021861803","https://openalex.org/W3023126733","https://openalex.org/W3047141442","https://openalex.org/W3087223457"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W4223449272","https://openalex.org/W2978247079","https://openalex.org/W2166887457","https://openalex.org/W2148708580","https://openalex.org/W3037604406","https://openalex.org/W2140163842"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
