{"id":"https://openalex.org/W2963538344","doi":"https://doi.org/10.17615/yazw-zn17","title":"Computational Methods for Inferring Transcriptome Dynamics","display_name":"Computational Methods for Inferring Transcriptome Dynamics","publication_year":2019,"publication_date":"2019-08-08","ids":{"openalex":"https://openalex.org/W2963538344","doi":"https://doi.org/10.17615/yazw-zn17","mag":"2963538344"},"language":"en","primary_location":{"id":"pmh:oai:cdr.lib.unc.edu:uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","doi":null,"is_oa":true,"landing_page_url":"https://cdr.lib.unc.edu/record/uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","pdf_url":"https://cdr.lib.unc.edu/record/uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"volume":null,"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://cdr.lib.unc.edu/record/uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032755605","display_name":"Joshua D. Welch","orcid":"https://orcid.org/0000-0002-5869-2391","observed_orcids":["https://orcid.org/0000-0002-5869-2391"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Welch, Joshua","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5032755605"],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06515711,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9839000105857849,"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":0.9839000105857849,"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":0.009800000116229057,"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/T10885","display_name":"Gene expression and cancer classification","score":0.002400000113993883,"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/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.8299999833106995},{"id":"https://openalex.org/keywords/transcriptome-dynamics","display_name":"transcriptome dynamics","score":0.8450000286102295},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"alternative splicing","score":0.9129999876022339},{"id":"https://openalex.org/keywords/single-cell-heterogeneity","display_name":"single-cell heterogeneity","score":0.7459999918937683},{"id":"https://openalex.org/keywords/slicer","display_name":"Slicer","score":0.9570000171661377},{"id":"https://openalex.org/keywords/manifold-alignment","display_name":"manifold alignment","score":0.5350000262260437},{"id":"https://openalex.org/keywords/pseudogene-expression","display_name":"pseudogene expression","score":0.765999972820282},{"id":"https://openalex.org/keywords/competing-endogenous-rna","display_name":"competing endogenous RNA","score":0.7670000195503235},{"id":"https://openalex.org/keywords/rna-degradation","display_name":"RNA degradation","score":0.9290000200271606},{"id":"https://openalex.org/keywords/embryonic-stem-cells","display_name":"embryonic stem cells","score":0.8500000238418579},{"id":"https://openalex.org/keywords/gene-expression-trajectories","display_name":"gene expression trajectories","score":0.42899999022483826}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5502578616142273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5464353561401367},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.48578837513923645},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41723811626434326},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3113379180431366},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14966094493865967},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.10423684120178223},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09664535522460938},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:cdr.lib.unc.edu:uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","doi":null,"is_oa":true,"landing_page_url":"https://cdr.lib.unc.edu/record/uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","pdf_url":"https://cdr.lib.unc.edu/record/uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:cdr.lib.unc.edu:v118rd67s","doi":null,"is_oa":true,"landing_page_url":"https://doi.org/10.17615/yazw-zn17","pdf_url":"https://doi.org/10.17615/yazw-zn17","source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"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":"Dissertation"},{"id":"mag:2963538344","doi":null,"is_oa":false,"landing_page_url":"https://cdr.lib.unc.edu/concern/dissertations/v118rd67s","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"doi:10.17615/yazw-zn17","doi":"https://doi.org/10.17615/yazw-zn17","is_oa":true,"landing_page_url":"https://doi.org/10.17615/yazw-zn17","pdf_url":null,"source":{"id":"https://openalex.org/S7407051488","display_name":"UNC Libraries","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":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"thesis"}],"best_oa_location":{"id":"pmh:oai:cdr.lib.unc.edu:uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","doi":null,"is_oa":true,"landing_page_url":"https://cdr.lib.unc.edu/record/uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","pdf_url":"https://cdr.lib.unc.edu/record/uuid:0ffc9c2d-6027-40a5-b9bb-8f04c81058f4","source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2963538344.pdf","grobid_xml":"https://content.openalex.org/works/W2963538344.grobid-xml"},"referenced_works_count":154,"referenced_works":["https://openalex.org/W66306528","https://openalex.org/W147750835","https://openalex.org/W194200989","https://openalex.org/W1504052604","https://openalex.org/W1512834934","https://openalex.org/W1542927170","https://openalex.org/W1552434751","https://openalex.org/W1565088669","https://openalex.org/W1574083126","https://openalex.org/W1602702667","https://openalex.org/W1666901150","https://openalex.org/W1746819321","https://openalex.org/W1792532087","https://openalex.org/W1965659632","https://openalex.org/W1965863160","https://openalex.org/W1967064280","https://openalex.org/W1967220865","https://openalex.org/W1967327758","https://openalex.org/W1968931043","https://openalex.org/W1969865366","https://openalex.org/W1971623350","https://openalex.org/W1972989638","https://openalex.org/W1974352732","https://openalex.org/W1975437957","https://openalex.org/W1978893674","https://openalex.org/W1981509058","https://openalex.org/W1982349215","https://openalex.org/W1984883254","https://openalex.org/W1986365556","https://openalex.org/W1986944049","https://openalex.org/W1988391018","https://openalex.org/W1988925753","https://openalex.org/W1991230146","https://openalex.org/W1993287310","https://openalex.org/W1997379339","https://openalex.org/W2001141328","https://openalex.org/W2006594553","https://openalex.org/W2009458183","https://openalex.org/W2010653277","https://openalex.org/W2011637823","https://openalex.org/W2012254260","https://openalex.org/W2013785611","https://openalex.org/W2014077036","https://openalex.org/W2024626836","https://openalex.org/W2030328593","https://openalex.org/W2039995567","https://openalex.org/W2040914426","https://openalex.org/W2041677964","https://openalex.org/W2045565555","https://openalex.org/W2046387002","https://openalex.org/W2046965780","https://openalex.org/W2047395651","https://openalex.org/W2053186076","https://openalex.org/W2059073003","https://openalex.org/W2059794606","https://openalex.org/W2060608189","https://openalex.org/W2060613703","https://openalex.org/W2061261750","https://openalex.org/W2063530272","https://openalex.org/W2065340354","https://openalex.org/W2065530211","https://openalex.org/W2067360285","https://openalex.org/W2068751516","https://openalex.org/W2068881679","https://openalex.org/W2069295116","https://openalex.org/W2070178871","https://openalex.org/W2070339716","https://openalex.org/W2072770570","https://openalex.org/W2074114726","https://openalex.org/W2074231493","https://openalex.org/W2076687510","https://openalex.org/W2078531707","https://openalex.org/W2081267527","https://openalex.org/W2081516821","https://openalex.org/W2082714048","https://openalex.org/W2084942072","https://openalex.org/W2087616533","https://openalex.org/W2090461073","https://openalex.org/W2097065948","https://openalex.org/W2097255042","https://openalex.org/W2097308346","https://openalex.org/W2098454110","https://openalex.org/W2102212449","https://openalex.org/W2104005232","https://openalex.org/W2104563967","https://openalex.org/W2106292881","https://openalex.org/W2107680358","https://openalex.org/W2110768394","https://openalex.org/W2111882541","https://openalex.org/W2112888168","https://openalex.org/W2115918762","https://openalex.org/W2116196682","https://openalex.org/W2116804945","https://openalex.org/W2117688129","https://openalex.org/W2118020210","https://openalex.org/W2118031210","https://openalex.org/W2121040919","https://openalex.org/W2122795897","https://openalex.org/W2126302009","https://openalex.org/W2126419817","https://openalex.org/W2127905518","https://openalex.org/W2128034264","https://openalex.org/W2129108350","https://openalex.org/W2129524208","https://openalex.org/W2132619562","https://openalex.org/W2135398049","https://openalex.org/W2135937351","https://openalex.org/W2136453810","https://openalex.org/W2137564327","https://openalex.org/W2138773756","https://openalex.org/W2140258573","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2144135883","https://openalex.org/W2144571044","https://openalex.org/W2145808141","https://openalex.org/W2145931730","https://openalex.org/W2151631165","https://openalex.org/W2152239989","https://openalex.org/W2152352881","https://openalex.org/W2153004457","https://openalex.org/W2156838815","https://openalex.org/W2157795344","https://openalex.org/W2158162711","https://openalex.org/W2161076846","https://openalex.org/W2162521231","https://openalex.org/W2165782989","https://openalex.org/W2169456326","https://openalex.org/W2169528473","https://openalex.org/W2170551349","https://openalex.org/W2174049393","https://openalex.org/W2187089797","https://openalex.org/W2195967731","https://openalex.org/W2198371822","https://openalex.org/W2211104821","https://openalex.org/W2222000795","https://openalex.org/W2269309710","https://openalex.org/W2286667211","https://openalex.org/W2287379375","https://openalex.org/W2397338926","https://openalex.org/W2407916594","https://openalex.org/W2422879816","https://openalex.org/W2463727689","https://openalex.org/W2471959288","https://openalex.org/W2517636946","https://openalex.org/W2518030906","https://openalex.org/W2522699003","https://openalex.org/W2525507785","https://openalex.org/W2555892463","https://openalex.org/W2572662684","https://openalex.org/W2591733518","https://openalex.org/W2612519453","https://openalex.org/W2951268343","https://openalex.org/W4298284232"],"related_works":["https://openalex.org/W2911108160","https://openalex.org/W4410590734","https://openalex.org/W4401331071","https://openalex.org/W4390707040","https://openalex.org/W4403387080","https://openalex.org/W431300332","https://openalex.org/W2950030509","https://openalex.org/W7055598029","https://openalex.org/W4414623050","https://openalex.org/W3005435954"],"abstract_inverted_index":{"The":[0,52],"sequencing":[1,120,257],"of":[2,13,21,46,55,60,87,101,111,123,137,155,190,232,251,270],"the":[3,7,22,88,124,169,208,233,249,268],"human":[4],"genome":[5],"paved":[6],"way":[8],"for":[9,34,242,263],"a":[10,17,44,109,134,141,153,163,172,239],"new":[11],"type":[12],"medicine,":[14],"in":[15,91,149,176,248],"which":[16],"molecular-level,":[18],"cell-by-cell":[19],"understanding":[20,37],"genomic":[23],"control":[24],"system":[25],"informs":[26],"diagnosis":[27],"and":[28,49,64,114,224],"treatment.":[29],"A":[30],"key":[31],"experimental":[32,75],"approach":[33],"achieving":[35],"such":[36,74],"is":[38],"measuring":[39],"gene":[40,178],"expression":[41,179,246],"dynamics":[42],"across":[43],"range":[45],"cell":[47,192],"types":[48,100,189],"biological":[50,106,147,165,218],"conditions.":[51],"raw":[53],"outputs":[54],"these":[56],"experiments":[57],"are":[58,67,126],"millions":[59],"short":[61],"DNA":[62],"sequences,":[63],"computational":[65,82,240],"methods":[66,83,125,212],"required":[68],"to":[69,84,128,144,185],"draw":[70],"scientific":[71],"conclusions":[72],"from":[73,119,195],"data.":[76],"In":[77],"this":[78],"dissertation,":[79],"I":[80,237],"present":[81],"address":[85],"some":[86],"challenges":[89],"involved":[90],"inferring":[92],"dynamic":[93],"transcriptome":[94,160],"changes.":[95],"My":[96],"work":[97],"focuses":[98],"two":[99],"challenges:":[102],"(1)":[103],"discovering":[104],"important":[105,217],"variation":[107,148],"within":[108,152],"population":[110,154],"single":[112,156,191],"cells":[113,198,223],"(2)":[115],"robustly":[116,243],"extracting":[117],"information":[118],"reads.":[121],"Three":[122],"designed":[127],"identify":[129],"biologically":[130],"relevant":[131],"differences":[132],"among":[133],"heterogenous":[135],"mixture":[136],"cells.":[138,157],"SingleSplice":[139],"uses":[140,182],"statistical":[142],"model":[143],"detect":[145],"true":[146],"alternative":[150],"splicing":[151],"SLICER":[158],"elucidates":[159],"changes":[161],"during":[162,273],"sequential":[164],"process":[166,170],"by":[167],"positing":[168],"as":[171],"nonlinear":[173],"manifold":[174,183],"embedded":[175],"high-dimensional":[177],"space.":[180],"MATCHER":[181],"alignment":[184],"infer":[186],"what":[187],"multiple":[188],"measurements":[193],"obtained":[194],"different":[196],"individual":[197],"would":[199],"look":[200],"like":[201],"if":[202],"they":[203],"were":[204],"performed":[205],"simultaneously":[206],"on":[207],"same":[209],"cell.":[210],"These":[211],"gave":[213],"insight":[214],"into":[215],"several":[216],"systems,":[219],"including":[220],"embryonic":[221],"stem":[222],"cardiac":[225],"fibroblasts":[226],"undergoing":[227],"reprogramming.":[228],"To":[229],"enable":[230],"study":[231,269],"pseudogene":[234,245],"ceRNA":[235],"effect,":[236],"developed":[238],"method":[241],"computing":[244],"levels":[247],"presence":[250],"high":[252],"sequence":[253],"similarity":[254],"that":[255],"confounds":[256],"read":[258],"alignment.":[259],"AppEnD,":[260],"an":[261],"algorithm":[262],"detecting":[264],"untemplated":[265],"additions,":[266],"allowed":[267],"transcript":[271],"modifications":[272],"RNA":[274],"degradation.":[275]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2019-07-30T00:00:00"}
