{"id":"https://openalex.org/W2102937449","doi":"https://doi.org/10.1093/bioinformatics/btt428","title":"ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq","display_name":"ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq","publication_year":2013,"publication_date":"2013-08-08","ids":{"openalex":"https://openalex.org/W2102937449","doi":"https://doi.org/10.1093/bioinformatics/btt428","mag":"2102937449","pmid":"https://pubmed.ncbi.nlm.nih.gov/23929032"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt428","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt428","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033094491","display_name":"Alper K\u00fc\u00e7\u00fckural","orcid":"https://orcid.org/0000-0001-9983-394X"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]},{"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/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alper Kucukural","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I166722992","https://openalex.org/I97018004","https://openalex.org/I1344073410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028208583","display_name":"Hakan \u00d6zadam","orcid":"https://orcid.org/0000-0001-6571-1661"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]},{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hakan \u00d6zadam","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I166722992","https://openalex.org/I97018004","https://openalex.org/I1344073410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050267692","display_name":"Guramrit Singh","orcid":"https://orcid.org/0000-0002-5283-9540"},"institutions":[{"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/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guramrit Singh","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I166722992","https://openalex.org/I97018004","https://openalex.org/I1344073410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040309185","display_name":"Melissa J. Moore","orcid":"https://orcid.org/0000-0002-4905-8727"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"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/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa J. Moore","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I166722992","https://openalex.org/I97018004","https://openalex.org/I1344073410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047557155","display_name":"Can Cenik","orcid":"https://orcid.org/0000-0001-6370-0889"},"institutions":[{"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/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Can Cenik","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605 and 2Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I166722992","https://openalex.org/I97018004","https://openalex.org/I1344073410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5033094491"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I166722992","https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9433,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.861164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"19","first_page":"2485","last_page":"2486"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"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/T11482","display_name":"RNA modifications and cancer","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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7299019694328308},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6898490190505981},{"id":"https://openalex.org/keywords/parallelizable-manifold","display_name":"Parallelizable manifold","score":0.5473832488059998},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5277279615402222},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5124083161354065},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5104831457138062},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4576590955257416},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4317765235900879},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.4190126061439514},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40966564416885376},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20869800448417664},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.18324095010757446},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13228768110275269}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7299019694328308},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6898490190505981},{"id":"https://openalex.org/C148047603","wikidata":"https://www.wikidata.org/wiki/Q1014612","display_name":"Parallelizable manifold","level":2,"score":0.5473832488059998},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5277279615402222},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5124083161354065},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5104831457138062},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4576590955257416},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4317765235900879},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.4190126061439514},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40966564416885376},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20869800448417664},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.18324095010757446},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13228768110275269},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"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":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt428","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt428","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:23929032","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23929032","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:escholarship.umassmed.edu:faculty_pubs-1513","is_oa":false,"landing_page_url":"https://escholarship.umassmed.edu/faculty_pubs/514","pdf_url":null,"source":{"id":"https://openalex.org/S4306400883","display_name":"The Journal of the American Medical Association (JAMA) Network (American Medical Association)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173654999","host_organization_name":"American Medical Association","host_organization_lineage":["https://openalex.org/I173654999"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"University of Massachusetts Medical School Faculty Publications","raw_type":"text"},{"id":"pmh:oai:europepmc.org:3147569","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3777114","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1544691147","https://openalex.org/W1967656072","https://openalex.org/W1996212302","https://openalex.org/W2009935171","https://openalex.org/W2012827801","https://openalex.org/W2024694407","https://openalex.org/W2041341260","https://openalex.org/W2042936984","https://openalex.org/W2082102894","https://openalex.org/W2095855903","https://openalex.org/W2097220641","https://openalex.org/W2098832713","https://openalex.org/W2127982146","https://openalex.org/W2128016314","https://openalex.org/W2131226388","https://openalex.org/W2167866392","https://openalex.org/W2171808845"],"related_works":["https://openalex.org/W4285069850","https://openalex.org/W2891970004","https://openalex.org/W1996916724","https://openalex.org/W4240963716","https://openalex.org/W1974634278","https://openalex.org/W1596637634","https://openalex.org/W2321918740","https://openalex.org/W2058965144","https://openalex.org/W2046419983","https://openalex.org/W2604408404"],"abstract_inverted_index":{"ASPeak":[0,15,28,43],"is":[1,17,37],"implemented":[2],"in":[3],"Perl":[4],"as":[5,13],"a":[6,33],"complete":[7],"pipeline":[8],"that":[9],"takes":[10],"bedGraph":[11],"files":[12],"input.":[14],"implementation":[16],"freely":[18],"available":[19],"at":[20],"https://sourceforge.net/projects/as-peak":[21],"under":[22],"the":[23],"GNU":[24],"General":[25],"Public":[26],"License.":[27],"can":[29,44,60],"be":[30,40,61],"run":[31,46],"on":[32,47],"personal":[34],"computer,":[35],"yet":[36],"designed":[38],"to":[39],"easily":[41],"parallelizable.":[42],"also":[45],"high":[48],"performance":[49],"computing":[50],"clusters":[51],"providing":[52],"efficient":[53],"speedup.":[54],"The":[55],"documentation":[56],"and":[57],"user":[58],"manual":[59],"obtained":[62],"from":[63],"http://master.dl.sourceforge.net/project/as-peak/manual.pdf.":[64]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
