{"id":"https://openalex.org/W1494067444","doi":"https://doi.org/10.1093/bib/bbp052","title":"Editorial","display_name":"Editorial","publication_year":2009,"publication_date":"2009-11-01","ids":{"openalex":"https://openalex.org/W1494067444","doi":"https://doi.org/10.1093/bib/bbp052","mag":"1494067444","pmid":"https://pubmed.ncbi.nlm.nih.gov/19933207"},"language":"nl","primary_location":{"id":"doi:10.1093/bib/bbp052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp052","pdf_url":"https://academic.oup.com/bib/article-pdf/10/6/593/723465/bbp052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"editorial","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/10/6/593/723465/bbp052.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076940698","display_name":"Jo Dicks","orcid":"https://orcid.org/0000-0003-1300-5233"},"institutions":[{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"J. Dicks","raw_affiliation_strings":["John Innes Centre, Norwich, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"John Innes Centre, Norwich, UK","institution_ids":["https://openalex.org/I100288624"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5076940698"],"corresponding_institution_ids":["https://openalex.org/I100288624"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":"6","first_page":"593","last_page":"594"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3973289728164673}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3973289728164673}],"mesh":[{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D030821","descriptor_name":"Plants, Genetically Modified","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030821","descriptor_name":"Plants, Genetically Modified","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030821","descriptor_name":"Plants, Genetically Modified","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbp052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp052","pdf_url":"https://academic.oup.com/bib/article-pdf/10/6/593/723465/bbp052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19933207","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19933207","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":"Briefings in bioinformatics","raw_type":"Editorial"}],"best_oa_location":{"id":"doi:10.1093/bib/bbp052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp052","pdf_url":"https://academic.oup.com/bib/article-pdf/10/6/593/723465/bbp052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1494067444.pdf","grobid_xml":"https://content.openalex.org/works/W1494067444.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"A":[0],"few":[1],"years":[2,421],"ago,":[3],"when":[4,38],"asked":[5],"what":[6,125],"I":[7,15,96,155],"worked":[8],"on":[9,327,332,427,482,602,620,665,814,838,1017],"by":[10,533,695,868],"new":[11,457,570,618,720,931,1070,1158,1185,1220,1232],"acquaintances":[12],"at":[13,20,35,44,57],"conferences,":[14],"occasionally":[16],"found":[17],"myself":[18],"looked":[19],"rather":[21,704],"quizzically":[22],"upon":[23,685],"answering":[24],"\u2018Plant":[25],"Bioinformatics\u2019.":[26],"True,":[27],"there":[28],"were":[29,40],"yet":[30],"no":[31,210,219],"plant":[32,53,107,140,207,275,286,293,312,461,470,491,525,667,689,750,795,815,897,1001,1045,1172,1207],"genome":[33,1014,1208],"sequences,":[34],"a":[36,79,285,354,379,490,594,636,693,753,907,1077,1094,1263],"time":[37],"conferences":[39],"buzzing":[41],"with":[42,119,148,378,463,581,849,1082,1175,1203,1218],"excitement":[43],"newly":[45],"sequenced":[46],"mammals":[47],"or":[48],"microbes.":[49],"And":[50],"also":[51,165,233,1149],"true,":[52],"research":[54,208,384,608,643,837,898,1198,1246],"did":[55],"not":[56,318,888,1049],"first":[58],"glance":[59],"have":[60,113,145,166,926],"the":[61,71,75,136,151,175,181,194,204,227,292,348,360,363,387,392,408,424,428,434,439,484,504,530,546,553,561,610,621,630,634,649,666,686,700,703,725,741,745,793,818,828,877,893,914,920,971,975,982,992,997,1018,1031,1062,1105,1130,1151,1170,1188,1204,1235,1249],"relevance":[62,205,340],"to":[63,92,98,144,193,279,311,324,341,460,466,469,473,483,518,545,590,651,670,732,767,836,875,1044,1052,1058,1084,1100,1103,1120,1133,1145,1177,1184,1229,1258],"human":[64],"medical":[65],"advancement":[66],"that":[67,81,123,135,154,236,274,306,744,802,858,925,942,1026,1096,1115],"motivates":[68],"many":[69,146,189,396,556,1028,1085],"in":[70,89,117,150,159,188,212,225,263,291,346,358,414,438,476,540,552,567,593,641,659,832,929,981,1036,1067,1156,1169,1187,1234],"bioinformatics":[72,108,276,308,631,668,800,816,921,948],"field.":[73],"Indeed,":[74],"former":[76],"fact":[77],"was":[78],"frustration":[80],"has":[82,616,1097],"only":[83],"been":[84,157,927],"remedied":[85],"relatively":[86],"recently.":[87],"However,":[88,314],"my":[90,93,132,160,382],"responses":[91],"new-found":[94],"friends,":[95],"tried":[97],"get":[99],"across":[100,1122],"just":[101],"how":[102,605,645,762,1227],"fascinating,":[103],"relevant":[104,323],"and":[105,171,180,259,281,283,351,356,370,400,405,455,468,488,494,508,512,515,522,559,572,580,588,633,644,648,672,677,709,774,782,798,824,870,886,923,950,964,967,1039,1050,1075,1136,1138,1182,1195,1210,1223,1251],"rewarding":[106],"can":[109,218,277,296,656,764,841],"be.":[110],"Plant":[111,1197,1245],"genomes":[112,369,554,577,615],"an":[114,785,810],"awful":[115],"lot":[116],"common":[118,234,711,737],"other":[120,333,678],"genomes.":[121,526],"Indeed":[122],"is":[124,209,232,418,451,692,899,1199,1247],"brought":[126],"me":[127],"into":[128],"this":[129,375,453,477,564,1113],"field":[130,454],"after":[131],"PhD,":[133],"discovering":[134],"evolutionary":[137,661,786],"processes":[138],"underlying":[139],"genomic":[141,397,796],"evolution":[142],"appeared":[143],"similarities":[147],"those":[149,799,839,865,940,951,1110],"mammalian":[152],"species":[153],"had":[156],"analysing":[158],"previous":[161],"studies.":[162,682],"But":[163],"plants":[164],"their":[167,255,261,342,366,513,606,625,642,719,1178],"own":[168,343,367,383,1179],"special":[169,301,376],"characteristics":[170],"idiosyncrasies,":[172],"such":[173,265,739,776,863,969,1108,1154],"as":[174,257,266,284,321,740,777,864,970,1109],"ubiquitous":[176],"nature":[177],"of":[178,184,206,216,229,247,339,353,365,371,395,410,430,436,443,486,524,537,549,555,563,569,596,613,624,688,707,736,755,771,779,879,892,896,909,916,977,995,1000,1020,1030,1061,1069,1079,1116,1129,1153,1190,1206,1253],"polyploidy":[179],"extraordinary":[182],"expansion":[183],"repeat":[185],"sequences":[186,1209],"seen":[187,320],"crops,":[190,558,881],"which":[191,652,724,833,953,1141],"add":[192],"analytical":[195,403,1032,1221],"challenge":[196],"but":[197,423],"always":[198],"keep":[199],"you":[200],"interested.":[201],"Perhaps":[202],"today":[203],"longer":[211,220],"doubt.":[213],"An":[214],"abundance":[215],"food":[217,237],"be":[221,240,297,319,657,730,765,842,889,944,1053],"taken":[222],"for":[223,254,260,407,542,675,680,817,845,913,952,1008],"granted":[224],"even":[226],"wealthiest":[228],"nations.":[230],"It":[231],"knowledge":[235,932,983],"production":[238],"must":[239],"further":[241],"stepped":[242],"up":[243],"while":[244,1040,1148],"improving":[245],"methods":[246,632,1140],"sustainable":[248],"agriculture.":[249],"Plants":[250],"are":[251,270,654,956,1034,1142],"being":[252,1143],"scrutinized":[253],"potential":[256],"biofuels":[258],"role":[262,290,976],"areas":[264],"healthy":[267],"ageing.":[268],"These":[269],"all":[271,1240],"scientific":[272],"challenges":[273,458,531,883,895,1057,1186,1222],"help":[278,874],"advance":[280],"underpin,":[282],"bioinformatician,":[287],"understanding":[288,347,996],"your":[289],"improvement":[294,1237],"process":[295,485,1033],"deeply":[298],"rewarding.":[299],"This":[300,416,1215],"issue":[302,377],"contains":[303],"eight":[304,749],"reviews":[305],"showcase":[307],"themes":[309],"related":[310],"genomics.":[313],"these":[315,676,934,1231],"papers":[316],"should":[317,336,887],"solely":[322],"researchers":[325,330],"working":[326,331],"plants.":[328,372,415],"Rather,":[329],"organism":[334],"groups":[335],"find":[337],"much":[338],"research,":[344],"both":[345,459,566,586],"broad":[349],"mechanisms":[350],"techniques":[352],"theme,":[355],"then":[357],"recognizing":[359],"differences":[361],"between":[362,713,939],"analysis":[364,915],"favourite":[368],"We":[373],"begin":[374],"paper":[380,694],"from":[381,433,448,748,804,902,933],"group,":[385],"because":[386],"area":[388,565],"it":[389,584,1219,1242],"discusses":[390,959],"represents":[391],"starting":[393,432],"point":[394],"analyses.":[398],"Cheema":[399],"Dicks":[401],"review":[402],"approaches":[404,922,1155],"software":[406,1059,1080,1118],"construction":[409],"genetic":[411,998],"linkage":[412],"maps":[413],"problem":[417,706,1095],"almost":[419],"100":[420],"old":[422],"authors":[425,528,628,701,746,829,1024,1126],"focus":[426,601,990],"history":[429],"solutions":[431,955],"proliferation":[435],"computers":[437],"1980s.":[440],"The":[441,527,627,1023,1125],"generation":[442,500,860,1205],"dense":[444],"marker":[445,1072,1212],"data":[446,464,935,1073,1106,1134,1165,1192,1213,1233],"sets":[447,465,1107],"high-throughput":[449,1071,1191,1211],"technologies":[450,571,862],"reinvigorating":[452],"presents":[456],"geneticists":[462],"analyse":[467],"bioinformaticians":[471],"wishing":[472],"make":[474],"advances":[475],"area.":[478],"Next,":[479,986],"we":[480,789,987],"move":[481],"sequencing":[487,501,506,521,861],"assembling":[489],"genome.":[492],"Imelfort":[493,869],"Edwards":[495,871],"cover":[496],"second":[497,859],"(or":[498],"next)":[499],"technologies,":[502],"describing":[503,604,919],"different":[505,705,769],"systems":[507,1119],"assembly":[509,523,536],"algorithms":[510],"available":[511],"current":[514],"future":[516,562,681],"application":[517],"de":[519,534],"novo":[520,535],"discuss":[529,629,702,1056,1076,1137,1161],"presented":[532],"short":[538],"reads":[539],"plants,":[541],"example":[543],"due":[544,1099],"large":[547],"number":[548,878,1078],"intergenic":[550],"repeats":[551],"key":[557,960,1086],"explore":[560],"terms":[568],"algorithms.":[573],"With":[574],"several":[575],"cereal":[576],"now":[578],"sequenced,":[579],"more":[582],"underway,":[583],"becomes":[585],"possible":[587],"desirable":[589],"compare":[591],"them":[592],"variety":[595],"ways.":[597],"Salse":[598],"et":[599,697,759,807,855,1004,1091],"al.":[600,698,760,808,856,1005,1092],"paleogenomics,":[603],"recent":[607],"comparing":[609],"coding":[611],"regions":[612],"grass":[614,823],"given":[617],"insights":[619],"chromosomal":[622],"structure":[623],"ancestor.":[626],"Narcisse-Cereals,":[635],"web-based":[637,979],"tool":[638],"they":[639,653],"developed":[640],"various":[646,1063],"parameters,":[647],"values":[650],"set,":[655],"influential":[658,928],"making":[660],"inferences.":[662],"They":[663,717,1055,1160],"call":[664],"community":[669],"investigate":[671,768],"establish":[673],"standards":[674,1194],"parameters":[679],"Also":[683],"drawing":[684],"theme":[687,994],"comparative":[690,847],"genomics":[691,848],"Wilkerson":[696,758],"Here":[699],"identifying":[708],"classifying":[710],"introns":[712],"orthologous":[714],"gene":[715],"sequences.":[716],"introduce":[718],"CIWOG":[721,763],"software,":[722],"within":[723],"user-customizable":[726],"CIDA":[727],"algorithm":[728],"may":[729,943],"used":[731,766,1144],"generate":[733,747],"MySQL":[734],"databases":[735,966],"introns,":[738],"ciwogPlants":[742],"database":[743],"species.":[751],"In":[752],"series":[754],"case":[756,826,1167],"studies,":[757,827,1015,1046],"describe":[761,830,1006,1093,1127],"aspects":[770],"intron":[772,780],"variation":[773],"evolution,":[775],"inference":[778],"gain":[781],"loss":[783],"over":[784],"tree.":[787],"Before":[788],"become":[790],"complacent":[791],"about":[792,1226],"burgeoning":[794],"resources":[797,801,961,980],"derive":[803],"them,":[805,1147],"Armstead":[806,854],"offer":[809],"insightful":[811],"\u2018reality":[812],"check\u2019":[813],"orphan":[819,880],"crops.":[820],"Using":[821],"illustrative":[822],"legume":[825],"ways":[831],"information":[834,1123],"valuable":[835],"crops":[840,901],"leveraged":[843],"through,":[844],"example,":[846],"better":[850],"resourced":[851],"relatives.":[852],"Although":[853],"note":[857],"described":[866,1111],"here":[867],"will":[872,884],"undoubtedly":[873],"reduce":[876],"significant":[882],"remain":[885],"underestimated.":[890],"One":[891],"great":[894],"protecting":[900],"pathogenic":[903],"attack.":[904],"Soderlund":[905,958],"describes":[906],"range":[908],"large-scale":[910],"experimental":[911],"studies":[912,1038,1168],"plant\u2013pathogen":[917],"interactions,":[918],"tools":[924,1081],"gaining":[930],"sets.":[936,1214],"She":[937],"distinguishes":[938],"problems":[941,1131],"solved":[945],"using":[946],"generic":[947],"methodologies":[949,1007,1064],"bespoke":[954],"required.":[957],"including":[962],"fungal":[963],"oomycete":[965],"initiatives":[968],"PAMGO":[972],"ontology,":[973],"emphasizing":[974],"improved":[978],"discovery":[984],"process.":[985,1238],"shift":[988],"our":[989,1101,1259],"towards":[991],"important":[993],"basis":[999],"traits.":[1002],"Zhang":[1003],"inferring":[1009],"genotype\u2013phenotype":[1010],"associations":[1011],"through":[1012],"whole":[1013],"focusing":[1016],"use":[1019],"mixed":[1021],"model.":[1022],"show":[1025],"although":[1027],"parts":[1029],"rooted":[1035],"animal":[1037],"some":[1041,1128,1252],"transfer":[1042],"directly":[1043],"others":[1047],"do":[1048,1261],"need":[1051],"adapted.":[1054],"engineering":[1060],"involved,":[1065],"particularly":[1066],"light":[1068,1265],"sets,":[1074,1193],"regard":[1083],"user":[1087],"requirements.":[1088],"Finally,":[1089],"Lysenko":[1090],"arisen":[1098],"capability":[1102],"develop":[1104],"throughout":[1112],"issue,":[1114],"developing":[1117],"integrate":[1121],"resources.":[1124],"inherent":[1132],"integration":[1135,1166],"contrast":[1139],"solve":[1146],"noting":[1150],"benefits":[1152],"generating":[1157],"knowledge.":[1159],"two":[1162],"distinct,":[1163],"plant-oriented":[1164],"model":[1171],"Arabidopsis":[1173],"thaliana":[1174],"reference":[1176],"Ondex":[1180],"system,":[1181],"look":[1183],"form":[1189],"ontologies.":[1196],"undergoing":[1200],"enormous":[1201],"change":[1202,1216],"brings":[1217,1243],"difficult":[1224],"decisions":[1225],"best":[1228],"exploit":[1230],"crop":[1236],"Above":[1239],"though,":[1241],"excitement.":[1244],"under":[1248],"spotlight":[1250],"us":[1254],"bioinformaticians,":[1255],"perhaps":[1256],"contrary":[1257],"stereotypes,":[1260],"like":[1262],"little":[1264],"sometimes.":[1266]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}
