{"id":"https://openalex.org/W2149293348","doi":"https://doi.org/10.1142/9789812776136_0051","title":"TRANSCRIPT NORMALIZATION AND SEGMENTATION OF TILING ARRAY DATA","display_name":"TRANSCRIPT NORMALIZATION AND SEGMENTATION OF TILING ARRAY DATA","publication_year":2007,"publication_date":"2007-12-01","ids":{"openalex":"https://openalex.org/W2149293348","doi":"https://doi.org/10.1142/9789812776136_0051","mag":"2149293348","pmid":"https://pubmed.ncbi.nlm.nih.gov/18229713"},"language":"en","primary_location":{"id":"doi:10.1142/9789812776136_0051","doi":"https://doi.org/10.1142/9789812776136_0051","is_oa":false,"landing_page_url":"https://doi.org/10.1142/9789812776136_0051","pdf_url":null,"source":{"id":"https://openalex.org/S7407088813","display_name":"Pacific Symposium on Biocomputing (PSB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2008","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","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/A5031822697","display_name":"Georg Zeller","orcid":"https://orcid.org/0000-0003-1429-7485","observed_orcids":["https://orcid.org/0000-0003-1429-7485"]},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]},{"id":"https://openalex.org/I4210147862","display_name":"Friedrich Miescher Laboratory","ror":"https://ror.org/04vh1tq58","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210147862"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"GEORG ZELLER","raw_affiliation_strings":["Friedrich Miescher Laboratory of the Max Planck Society & Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35 & 39, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Friedrich Miescher Laboratory of the Max Planck Society & Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35 & 39, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I149899117","https://openalex.org/I4210112458","https://openalex.org/I4210147862"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053747370","display_name":"Stefan R. Henz","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"STEFAN R. HENZ","raw_affiliation_strings":["Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210112458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091044256","display_name":"Sascha Laubinger","orcid":"https://orcid.org/0000-0002-6682-0728","observed_orcids":["https://orcid.org/0000-0002-6682-0728"]},"institutions":[{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"SASCHA LAUBINGER","raw_affiliation_strings":["Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210112458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003440649","display_name":"Detlef Weigel","orcid":"https://orcid.org/0000-0002-2114-7963","observed_orcids":["https://orcid.org/0000-0002-2114-7963"]},"institutions":[{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"DETLEF WEIGEL","raw_affiliation_strings":["Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Developmental Biology, Dept. for Molecular Biology, Spemannstr. 35, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210112458"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035416263","display_name":"Gunnar R\u00e4tsch","orcid":"https://orcid.org/0000-0001-5486-8532","observed_orcids":["https://orcid.org/0000-0001-5486-8532"]},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210147862","display_name":"Friedrich Miescher Laboratory","ror":"https://ror.org/04vh1tq58","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210147862"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"GUNNAR R\u00c4TSCH","raw_affiliation_strings":["Friedrich Miescher Laboratory of the Max Planck Society, Spemannstr. 39, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Friedrich Miescher Laboratory of the Max Planck Society, Spemannstr. 39, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I149899117","https://openalex.org/I4210147862"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":7.9149,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.9752809,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"527","last_page":"538"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8403000235557556,"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/T10885","display_name":"Gene expression and cancer classification","score":0.8403000235557556,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.09549999982118607,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0364999994635582,"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/tiling-arrays","display_name":"tiling arrays","score":0.7879999876022339},{"id":"https://openalex.org/keywords/oligonucleotide-probes","display_name":"oligonucleotide probes","score":0.8870000243186951},{"id":"https://openalex.org/keywords/hybridization-intensity","display_name":"hybridization intensity","score":0.8190000057220459},{"id":"https://openalex.org/keywords/transcript-mapping","display_name":"transcript mapping","score":0.8220000267028809},{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.8059999942779541}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7003781199455261},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6169552206993103},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.4946152865886688},{"id":"https://openalex.org/C119401833","wikidata":"https://www.wikidata.org/wiki/Q7802158","display_name":"Tiling array","level":5,"score":0.468217134475708},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46766912937164307},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35218507051467896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15412327647209167},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13045862317085266},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.0997612476348877},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06259387731552124},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015335","descriptor_name":"Molecular Probes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D046228","descriptor_name":"Microarray Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1142/9789812776136_0051","doi":"https://doi.org/10.1142/9789812776136_0051","is_oa":false,"landing_page_url":"https://doi.org/10.1142/9789812776136_0051","pdf_url":null,"source":{"id":"https://openalex.org/S7407088813","display_name":"Pacific Symposium on Biocomputing (PSB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2008","raw_type":"proceedings-article"},{"id":"pmid:18229713","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18229713","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":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.84.5842","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.84.5842","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://psb.stanford.edu/psb-online/proceedings/psb08/zeller.pdf","raw_type":"text"},{"id":"pmh:oai:edoc.mpg.de:402914","doi":null,"is_oa":false,"landing_page_url":"http://edoc.mpg.de/402914","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:edoc.mpg.de:412731","doi":null,"is_oa":false,"landing_page_url":"http://edoc.mpg.de/412731","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Pacific Symposium on Biocomputing, v.13, 527-538 (2008)","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1494075612","https://openalex.org/W1547068196","https://openalex.org/W1978677326","https://openalex.org/W2009570821","https://openalex.org/W2047028564","https://openalex.org/W2066358615","https://openalex.org/W2077735595","https://openalex.org/W2105644991","https://openalex.org/W2106554405","https://openalex.org/W2111765516","https://openalex.org/W2112276896","https://openalex.org/W2116027790","https://openalex.org/W2120865735","https://openalex.org/W2122150418","https://openalex.org/W2134597218","https://openalex.org/W2139686264","https://openalex.org/W2140022443","https://openalex.org/W2147065940","https://openalex.org/W2151949149","https://openalex.org/W2154462399","https://openalex.org/W3119651796"],"related_works":["https://openalex.org/W7140263048","https://openalex.org/W2122150418","https://openalex.org/W2140022443","https://openalex.org/W7100404470","https://openalex.org/W2114955151","https://openalex.org/W2140347980","https://openalex.org/W7096376687","https://openalex.org/W2442149594","https://openalex.org/W7096623652","https://openalex.org/W2040659174"],"abstract_inverted_index":{"For":[0],"the":[1,28,43,51,101],"analysis":[2],"of":[3,30,105],"transcriptional":[4],"tiling":[5,60,98,128],"arrays":[6,99],"we":[7,19,62],"have":[8],"developed":[9],"two":[10],"methods":[11],"based":[12],"on":[13,34,111,126],"state-of-the-art":[14],"machine":[15],"learning":[16],"algorithms.":[17],"First,":[18],"present":[20],"a":[21,86],"novel":[22],"transcript":[23,89,107],"normalization":[24,56],"technique":[25,57],"to":[26,41,50,58,65,100],"alleviate":[27],"effect":[29],"oligonucleotide":[31],"probe":[32],"sequences":[33],"hybridization":[35],"intensity.":[36],"It":[37,91],"is":[38,85,124],"specifically":[39],"designed":[40],"decrease":[42],"variability":[44],"observed":[45],"for":[46,88,96],"individual":[47],"probes":[48],"complementary":[49],"same":[52],"transcript.":[53],"Applying":[54],"this":[55],"Arabidopsis":[59],"arrays,":[61],"are":[63],"able":[64],"reduce":[66],"sequence":[67],"biases":[68],"and":[69,79],"also":[70],"significantly":[71],"improve":[72],"separation":[73],"in":[74],"signal":[75],"intensity":[76],"between":[77],"exonic":[78],"intronic/intergenic":[80],"probes.":[81],"Our":[82],"second":[83],"contribution":[84],"method":[87,117],"mapping.":[90],"extends":[92],"an":[93],"algorithm":[94],"proposed":[95],"yeast":[97],"more":[102],"challenging":[103],"task":[104],"spliced":[106],"identification.":[108],"When":[109],"evaluated":[110],"raw":[112],"versus":[113],"normalized":[114],"intensities":[115],"our":[116],"achieves":[118],"highest":[119],"prediction":[120],"accuracy":[121],"when":[122],"segmentation":[123],"performed":[125],"transcript-normalized":[127],"array":[129],"data.":[130]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-11-03T10:50:19.383937","created_date":"2016-06-24T00:00:00"}