{"id":"https://openalex.org/W7117619268","doi":"https://doi.org/10.1016/j.compbiolchem.2025.108874","title":"Improved somatic mutation profiling in small-cell lung cancer using RNA-sequencing and the T2T-CHM13 genome reference","display_name":"Improved somatic mutation profiling in small-cell lung cancer using RNA-sequencing and the T2T-CHM13 genome reference","publication_year":2025,"publication_date":"2025-12-30","ids":{"openalex":"https://openalex.org/W7117619268","doi":"https://doi.org/10.1016/j.compbiolchem.2025.108874","pmid":"https://pubmed.ncbi.nlm.nih.gov/41485300"},"language":"en","primary_location":{"id":"doi:10.1016/j.compbiolchem.2025.108874","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.compbiolchem.2025.108874","pdf_url":null,"source":{"id":"https://openalex.org/S104924063","display_name":"Computational Biology and Chemistry","issn_l":"1476-9271","issn":["1476-9271","1476-928X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Biology and Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113968016","display_name":"Pragya Kashyap","orcid":null},"institutions":[{"id":"https://openalex.org/I154549908","display_name":"Indian Institute of Technology Jodhpur","ror":"https://ror.org/03yacj906","country_code":"IN","type":"education","lineage":["https://openalex.org/I154549908"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Pragya Kashyap","raw_affiliation_strings":["Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India","institution_ids":["https://openalex.org/I154549908"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Dinesh Kumar Ahirwar","orcid":"https://orcid.org/0000-0002-0518-7156"},"institutions":[{"id":"https://openalex.org/I154549908","display_name":"Indian Institute of Technology Jodhpur","ror":"https://ror.org/03yacj906","country_code":"IN","type":"education","lineage":["https://openalex.org/I154549908"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Dinesh Kumar Ahirwar","raw_affiliation_strings":["Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India; Interdisciplinary Research Platform-Smart Healthcare, Indian Institute of Technology, Jodhpur, Rajasthan, India. Electronic address: dineshahirwar@iitj.ac.in"],"raw_orcid":"https://orcid.org/0000-0002-0518-7156","affiliations":[{"raw_affiliation_string":"Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India; Interdisciplinary Research Platform-Smart Healthcare, Indian Institute of Technology, Jodhpur, Rajasthan, India. Electronic address: dineshahirwar@iitj.ac.in","institution_ids":["https://openalex.org/I154549908"]}]},{"author_position":"last","author":{"id":null,"display_name":"Pankaj Yadav","orcid":"https://orcid.org/0000-0001-7160-9209"},"institutions":[{"id":"https://openalex.org/I154549908","display_name":"Indian Institute of Technology Jodhpur","ror":"https://ror.org/03yacj906","country_code":"IN","type":"education","lineage":["https://openalex.org/I154549908"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Pankaj Yadav","raw_affiliation_strings":["Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India; School of Artificial Intelligence and Data Science, Indian Institute of Technology, Jodhpur, Rajasthan, India. Electronic address: pyadav@iitj.ac.in"],"raw_orcid":"https://orcid.org/0000-0001-7160-9209","affiliations":[{"raw_affiliation_string":"Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India; School of Artificial Intelligence and Data Science, Indian Institute of Technology, Jodhpur, Rajasthan, India. Electronic address: pyadav@iitj.ac.in","institution_ids":["https://openalex.org/I154549908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I154549908"],"apc_list":{"value":2960,"currency":"USD","value_usd":2960},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.68147654,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"121","issue":null,"first_page":"108874","last_page":"108874"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12334","display_name":"Lung Cancer Research Studies","score":0.9753999710083008,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T12334","display_name":"Lung Cancer Research Studies","score":0.9753999710083008,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10417","display_name":"Lung Cancer Treatments and Mutations","score":0.014100000262260437,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.00139999995008111,"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/somatic-cell","display_name":"Somatic cell","score":0.7010999917984009},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.6661999821662903},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6025000214576721},{"id":"https://openalex.org/keywords/lung-cancer","display_name":"Lung cancer","score":0.4350999891757965},{"id":"https://openalex.org/keywords/dbsnp","display_name":"dbSNP","score":0.40130001306533813},{"id":"https://openalex.org/keywords/germline-mutation","display_name":"Germline mutation","score":0.3984000086784363},{"id":"https://openalex.org/keywords/cosmic-cancer-database","display_name":"COSMIC cancer database","score":0.3984000086784363}],"concepts":[{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.7010999917984009},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.6661999821662903},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6367999911308289},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6025000214576721},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.565500020980835},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5390999913215637},{"id":"https://openalex.org/C2776256026","wikidata":"https://www.wikidata.org/wiki/Q47912","display_name":"Lung cancer","level":2,"score":0.4350999891757965},{"id":"https://openalex.org/C35794970","wikidata":"https://www.wikidata.org/wiki/Q5243761","display_name":"dbSNP","level":5,"score":0.40130001306533813},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.3984000086784363},{"id":"https://openalex.org/C59375849","wikidata":"https://www.wikidata.org/wiki/Q5013513","display_name":"COSMIC cancer database","level":2,"score":0.3984000086784363},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.36730000376701355},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3447999954223633},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.31529998779296875},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3095000088214874},{"id":"https://openalex.org/C181561989","wikidata":"https://www.wikidata.org/wiki/Q2581905","display_name":"Heteroplasmy","level":4,"score":0.2865000069141388},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2782999873161316},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.2721000015735626},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26249998807907104},{"id":"https://openalex.org/C205270622","wikidata":"https://www.wikidata.org/wiki/Q17082639","display_name":"Cancer genome sequencing","level":5,"score":0.2517000138759613},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.25130000710487366}],"mesh":[{"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":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055752","descriptor_name":"Small Cell Lung Carcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D055752","descriptor_name":"Small Cell Lung Carcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1016/j.compbiolchem.2025.108874","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.compbiolchem.2025.108874","pdf_url":null,"source":{"id":"https://openalex.org/S104924063","display_name":"Computational Biology and Chemistry","issn_l":"1476-9271","issn":["1476-9271","1476-928X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Biology and Chemistry","raw_type":"journal-article"},{"id":"pmid:41485300","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41485300","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":"Computational biology and chemistry","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8474935293197632,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G3471621552","display_name":null,"funder_award_id":"I/SEED/DKA/20230044","funder_id":"https://openalex.org/F4320319038","funder_display_name":"Indian Institute of Technology Jodhpur"},{"id":"https://openalex.org/G4402659260","display_name":null,"funder_award_id":"I/SEED/PY/20200037","funder_id":"https://openalex.org/F4320319038","funder_display_name":"Indian Institute of Technology Jodhpur"},{"id":"https://openalex.org/G6247938119","display_name":null,"funder_award_id":"SRG/2023/002556","funder_id":"https://openalex.org/F4320320719","funder_display_name":"Department of Science and Technology, Ministry of Science and Technology, India"}],"funders":[{"id":"https://openalex.org/F4320319038","display_name":"Indian Institute of Technology Jodhpur","ror":null},{"id":"https://openalex.org/F4320320719","display_name":"Department of Science and Technology, Ministry of Science and Technology, India","ror":"https://ror.org/0101xrq71"},{"id":"https://openalex.org/F4320334771","display_name":"Science and Engineering Research Board","ror":"https://ror.org/03ffdsr55"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1903523058","https://openalex.org/W1984068087","https://openalex.org/W2022714591","https://openalex.org/W2056631765","https://openalex.org/W2072684537","https://openalex.org/W2073576377","https://openalex.org/W2104549677","https://openalex.org/W2116041602","https://openalex.org/W2131271579","https://openalex.org/W2143238378","https://openalex.org/W2169105660","https://openalex.org/W2342358015","https://openalex.org/W2614443510","https://openalex.org/W2751686252","https://openalex.org/W2770026599","https://openalex.org/W2888569999","https://openalex.org/W2890862599","https://openalex.org/W2898789672","https://openalex.org/W2901888495","https://openalex.org/W2942610007","https://openalex.org/W3121328438","https://openalex.org/W3124749091","https://openalex.org/W3139667391","https://openalex.org/W3152632772","https://openalex.org/W3155102387","https://openalex.org/W3169081530","https://openalex.org/W3170143789","https://openalex.org/W3188286147","https://openalex.org/W3197579678","https://openalex.org/W4210594651","https://openalex.org/W4210647614","https://openalex.org/W4224262913","https://openalex.org/W4224437644","https://openalex.org/W4229072282","https://openalex.org/W4281250846","https://openalex.org/W4281741884","https://openalex.org/W4288736489","https://openalex.org/W4289704912","https://openalex.org/W4294216483","https://openalex.org/W4298089008","https://openalex.org/W4376131110","https://openalex.org/W4392739921","https://openalex.org/W4395006784","https://openalex.org/W4396865652","https://openalex.org/W4398252689","https://openalex.org/W4401544998","https://openalex.org/W4401868660","https://openalex.org/W4406363150","https://openalex.org/W4408510039"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-01-19T04:01:09.351973","created_date":"2025-12-30T00:00:00"}
