{"id":"https://openalex.org/W3206418085","doi":"https://doi.org/10.1038/s41589-021-00876-6","title":"Reconstruction of evolving gene variants and fitness from short sequencing reads","display_name":"Reconstruction of evolving gene variants and fitness from short sequencing reads","publication_year":2021,"publication_date":"2021-10-11","ids":{"openalex":"https://openalex.org/W3206418085","doi":"https://doi.org/10.1038/s41589-021-00876-6","mag":"3206418085","pmid":"https://pubmed.ncbi.nlm.nih.gov/34635842","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8551035"},"language":"en","primary_location":{"id":"doi:10.1038/s41589-021-00876-6","doi":"https://doi.org/10.1038/s41589-021-00876-6","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s41589-021-00876-6","pdf_url":null,"source":{"id":"https://openalex.org/S51309854","display_name":"Nature Chemical Biology","issn_l":"1552-4450","issn":["1552-4450","1552-4469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Chemical Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8551035","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041272819","display_name":"Max W. Shen","orcid":"https://orcid.org/0000-0002-4226-1861","observed_orcids":["https://orcid.org/0000-0002-4226-1861"]},"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/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Max W. Shen","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA","Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA","Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037445024","display_name":"Kevin Tianmeng Zhao","orcid":"https://orcid.org/0000-0003-3440-2094","observed_orcids":["https://orcid.org/0000-0003-3440-2094"]},"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/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin T. Zhao","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA","Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA","Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0003-3440-2094","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065535610","display_name":"David R. Liu","orcid":"https://orcid.org/0000-0002-9943-7557","observed_orcids":["https://orcid.org/0000-0002-9943-7557","https://orcid.org/0000-0003-0346-5033","https://orcid.org/0000-0002-6078-6506"]},"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/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David R. Liu","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu","Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu","Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA. drliu@fas.harvard.edu","Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0003-0346-5033","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA. drliu@fas.harvard.edu","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065535610"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I1344073410","https://openalex.org/I136199984"],"apc_list":{"value":11390,"currency":"USD","value_usd":11390},"apc_paid":null,"fwci":1.6162,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.83564591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"17","issue":"11","first_page":"1188","last_page":"1198"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.8687000274658203,"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"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.8687000274658203,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.053300000727176666,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.025100000202655792,"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/directed-evolution","display_name":"directed evolution","score":0.7279999852180481},{"id":"https://openalex.org/keywords/fitness-prediction","display_name":"fitness prediction","score":0.6140000224113464},{"id":"https://openalex.org/keywords/short-read-sequencing","display_name":"short-read sequencing","score":0.9210000038146973},{"id":"https://openalex.org/keywords/phage-assisted-continuous-evolution","display_name":"phage-assisted continuous evolution","score":0.9139999747276306},{"id":"https://openalex.org/keywords/adenine-base-editors","display_name":"adenine base editors","score":0.9940000176429749},{"id":"https://openalex.org/keywords/machine-learning","display_name":"machine learning","score":0.4860000014305115}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6045149564743042},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5176161527633667},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5160707831382751},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5019500255584717},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4793744385242462},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3297198414802551}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000243","descriptor_name":"Adenosine Deaminase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1038/s41589-021-00876-6","doi":"https://doi.org/10.1038/s41589-021-00876-6","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s41589-021-00876-6","pdf_url":null,"source":{"id":"https://openalex.org/S51309854","display_name":"Nature Chemical Biology","issn_l":"1552-4450","issn":["1552-4450","1552-4469"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Chemical Biology","raw_type":"journal-article"},{"id":"pmid:34635842","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34635842","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,"listed_in":[],"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":"Nature chemical biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8551035","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8551035","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Nat Chem Biol","raw_type":"Text"},{"id":"pmh:oai:dash.harvard.edu:1/37370767","doi":null,"is_oa":false,"landing_page_url":"https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37370767","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8551035","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8551035","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Nat Chem Biol","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1810876930","display_name":"Graduate Training in Computational and Systems Biology","funder_award_id":"T32GM087237","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2304256781","display_name":null,"funder_award_id":"R01 EB027793","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G4630203202","display_name":null,"funder_award_id":"R35GM118062","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G6316350344","display_name":null,"funder_award_id":"R01 EB031172","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G6955413390","display_name":"Continuous Evolution of Proteins with Novel Therapeutic Potential","funder_award_id":"R01EB031172","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G9000895816","display_name":"ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential","funder_award_id":"R01EB027793","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G9000908732","display_name":"Integrating Chemistry and Evolution to Illuminate Biology and Enable Novel Therapeutics","funder_award_id":"R35GM118062","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000912514","display_name":"Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human Disease","funder_award_id":"RM1HG009490","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W69475100","https://openalex.org/W1635391495","https://openalex.org/W1788245842","https://openalex.org/W1832802542","https://openalex.org/W1954202239","https://openalex.org/W1965175390","https://openalex.org/W1986888627","https://openalex.org/W2003910843","https://openalex.org/W2009427029","https://openalex.org/W2017002214","https://openalex.org/W2034287217","https://openalex.org/W2036815225","https://openalex.org/W2051866702","https://openalex.org/W2064676287","https://openalex.org/W2065266611","https://openalex.org/W2097861808","https://openalex.org/W2105218193","https://openalex.org/W2117737648","https://openalex.org/W2118265845","https://openalex.org/W2127935122","https://openalex.org/W2138270253","https://openalex.org/W2150951085","https://openalex.org/W2151265018","https://openalex.org/W2156454061","https://openalex.org/W2160082846","https://openalex.org/W2160986529","https://openalex.org/W2169436065","https://openalex.org/W2188853907","https://openalex.org/W2212407137","https://openalex.org/W2253465175","https://openalex.org/W2345218814","https://openalex.org/W2583377988","https://openalex.org/W2586921983","https://openalex.org/W2599417231","https://openalex.org/W2766599608","https://openalex.org/W2767044445","https://openalex.org/W2781256610","https://openalex.org/W2792138005","https://openalex.org/W2793309516","https://openalex.org/W2809042973","https://openalex.org/W2902111471","https://openalex.org/W2914453394","https://openalex.org/W2917580301","https://openalex.org/W2918965813","https://openalex.org/W2938803199","https://openalex.org/W2952224179","https://openalex.org/W2952856897","https://openalex.org/W2954007457","https://openalex.org/W2963629338","https://openalex.org/W2970971581","https://openalex.org/W2980789587","https://openalex.org/W2985687430","https://openalex.org/W2987444673","https://openalex.org/W3004632840","https://openalex.org/W3012327875","https://openalex.org/W3087650361"],"related_works":["https://openalex.org/W4412661277","https://openalex.org/W7155626569","https://openalex.org/W7096166233","https://openalex.org/W3206320462","https://openalex.org/W4406942547","https://openalex.org/W4404125138","https://openalex.org/W3096739358","https://openalex.org/W4322720299","https://openalex.org/W4405609184","https://openalex.org/W4405743923"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2021-10-25T00:00:00"}