Computational methods for transcriptome annotation and quantification using RNA-seq

High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational chal...

Celý popis

Uloženo v:

Podrobná bibliografie
Vydáno v:	Nature methods Ročník 8; číslo 6; s. 469 - 477
Hlavní autoři:	Garber, Manuel, Grabherr, Manfred G, Guttman, Mitchell, Trapnell, Cole
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	New York Nature Publishing Group US 01.06.2011 Nature Publishing Group
Témata:	631/114/2184 631/1647/514/1949 631/208/212/2019 Animals Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Cellular biology Computational Biology - methods DNA sequencing Gene Expression Profiling - statistics & numerical data Genomics Genomics - statistics & numerical data High-Throughput Nucleotide Sequencing - statistics & numerical data Humans Life Sciences Nucleotide sequencing Physiological aspects Proteomics review-article Ribonucleic acid RNA Sequence Alignment - statistics & numerical data Sequence Analysis, RNA - statistics & numerical data United States
ISSN:	1548-7091, 1548-7105, 1548-7105
On-line přístup:	Získat plný text
Tagy:	Přidat tag Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!

Abstract	High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications.
AbstractList	High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications. High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications. [PUBLICATION ABSTRACT] High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications.High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications.
Audience	Academic
Author	Garber, Manuel Guttman, Mitchell Grabherr, Manfred G Trapnell, Cole
Author_xml	– sequence: 1 givenname: Manuel surname: Garber fullname: Garber, Manuel email: mgarber@broadinstitute.org organization: Broad Institute of Massachusetts Institute of Technology and Harvard – sequence: 2 givenname: Manfred G surname: Grabherr fullname: Grabherr, Manfred G organization: Broad Institute of Massachusetts Institute of Technology and Harvard – sequence: 3 givenname: Mitchell surname: Guttman fullname: Guttman, Mitchell organization: Broad Institute of Massachusetts Institute of Technology and Harvard, Department of Biology, Massachusetts Institute of Technology – sequence: 4 givenname: Cole surname: Trapnell fullname: Trapnell, Cole organization: Broad Institute of Massachusetts Institute of Technology and Harvard, Department of Stem Cell and Regenerative Biology, Harvard University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/21623353$$D View this record in MEDLINE/PubMed
BookMark	eNqF0luL1DAUB_AgK-5FX_wAUtwHYaVj7j19HAZ1hUXBy3PIJOmYpU1mkvbBb29qdxCXAelDQ_idf9qcc4nOQgwOoZcErwhm8C4Mbvy5IpKwJ-iCCA51Q7A4O65xS87RZc73GDPGqXiGzimRlDHBLtC3TRz206hHH4Puqzkp2lx1MVVj0iGb5PdjHFylQ4gLK0tbHSYdRt95s2xN2Ydd9fXzus7u8Bw97XSf3YuH9xX68eH9981tfffl46fN-q42gvCxltK6BqQBY2TbWMtbwyjlnSTGMk2csUZuAQhsccsJEAdGcuC8aQDAUMuu0Jsld5_iYXJ5VIPPxvW9Di5OWbWYc6C4of-VIFuOy0fM8vUjeR-nVK5mRtBiEIIUdL2gne6d8qGL5a7MHKnWVABngrRQ1OqEKo91gzelhZ0v-_8UvHo4e9oOzqp98oNOv9SxWwXgBZgUc06uU8YvPSnJvlcEq3kg1J-BUPNAlJKbRyXH1JP47YJzQWHn0t-fP6F_A4XZw_c
CitedBy_id	crossref_primary_10_3390_ijms242216450 crossref_primary_10_1093_jxb_eru322 crossref_primary_10_1186_s13068_023_02313_3 crossref_primary_10_1261_rna_059360_116 crossref_primary_10_1093_bib_bbaa045 crossref_primary_10_1111_jfd_13329 crossref_primary_10_1371_journal_pcbi_1013133 crossref_primary_10_1016_j_cpb_2019_02_002 crossref_primary_10_1016_j_actatropica_2015_11_009 crossref_primary_10_3389_fmicb_2016_00408 crossref_primary_10_1371_journal_pone_0145532 crossref_primary_10_3390_f8110420 crossref_primary_10_3389_fpls_2016_01883 crossref_primary_10_1111_imm_12841 crossref_primary_10_4137_EBO_S23873 crossref_primary_10_1186_s13059_016_0881_8 crossref_primary_10_1371_journal_pone_0075323 crossref_primary_10_1007_s10142_020_00732_1 crossref_primary_10_1016_j_gene_2020_144480 crossref_primary_10_1016_j_heares_2012_01_002 crossref_primary_10_1186_1752_0509_7_S2_S10 crossref_primary_10_1016_j_ab_2011_08_013 crossref_primary_10_1016_j_jaci_2019_07_049 crossref_primary_10_1186_s12859_022_05065_3 crossref_primary_10_1016_j_neucom_2014_04_064 crossref_primary_10_1186_1471_2164_13_S8_S11 crossref_primary_10_1007_s11103_012_9992_0 crossref_primary_10_1093_nar_gku1357 crossref_primary_10_1186_1756_0500_6_503 crossref_primary_10_1007_s11295_015_0928_0 crossref_primary_10_1016_j_cell_2015_10_039 crossref_primary_10_1038_s41467_023_41412_5 crossref_primary_10_1101_gr_207902_116 crossref_primary_10_1016_j_aquaculture_2025_742601 crossref_primary_10_3389_fcimb_2019_00017 crossref_primary_10_1158_0008_5472_CAN_12_1054 crossref_primary_10_3389_fpls_2017_01182 crossref_primary_10_1371_journal_pone_0129154 crossref_primary_10_1093_nar_gks804 crossref_primary_10_1134_S199075081601008X crossref_primary_10_1016_j_molcel_2012_07_030 crossref_primary_10_1109_TCBB_2015_2418753 crossref_primary_10_2217_fvl_12_112 crossref_primary_10_3390_life12122027 crossref_primary_10_1007_s00262_012_1354_x crossref_primary_10_1111_odi_14237 crossref_primary_10_1371_journal_pone_0167417 crossref_primary_10_1016_j_cbd_2023_101087 crossref_primary_10_3390_genes12020301 crossref_primary_10_3390_life11080803 crossref_primary_10_1007_s10126_016_9689_5 crossref_primary_10_1371_journal_pone_0066521 crossref_primary_10_1109_TCBB_2015_2392077 crossref_primary_10_1016_j_aquaculture_2024_741362 crossref_primary_10_1097_MOH_0000000000000134 crossref_primary_10_1186_1471_2164_13_193 crossref_primary_10_1186_s12859_017_1831_5 crossref_primary_10_3389_fcell_2020_593007 crossref_primary_10_1016_j_bbrc_2015_05_085 crossref_primary_10_1186_s12864_019_5430_x crossref_primary_10_1038_ng_3840 crossref_primary_10_3390_agriculture14040615 crossref_primary_10_1186_s12859_015_0557_5 crossref_primary_10_1371_journal_pone_0175391 crossref_primary_10_1007_s12374_015_0113_x crossref_primary_10_1093_bib_bbae532 crossref_primary_10_1016_j_anireprosci_2021_106784 crossref_primary_10_1136_gutjnl_2011_301935 crossref_primary_10_3389_fmicb_2025_1520459 crossref_primary_10_3389_fpls_2022_1038109 crossref_primary_10_1016_j_semcancer_2020_09_007 crossref_primary_10_1093_nar_gkaa638 crossref_primary_10_1002_bies_201300100 crossref_primary_10_1007_s00343_020_0176_5 crossref_primary_10_1007_s40484_017_0109_2 crossref_primary_10_3390_ani11041042 crossref_primary_10_1016_j_ijrobp_2016_03_001 crossref_primary_10_1186_s12864_016_3130_3 crossref_primary_10_1038_mi_2013_90 crossref_primary_10_1186_s40246_017_0101_y crossref_primary_10_1016_j_cj_2021_12_008 crossref_primary_10_1016_j_cbd_2021_100883 crossref_primary_10_1017_S1479262116000162 crossref_primary_10_1016_j_preteyeres_2016_06_001 crossref_primary_10_1016_j_envres_2023_115999 crossref_primary_10_1038_srep09453 crossref_primary_10_1128_JVI_00118_15 crossref_primary_10_1261_rna_037473_112 crossref_primary_10_1038_nbt_2671 crossref_primary_10_1371_journal_pone_0078644 crossref_primary_10_3390_ijms21010167 crossref_primary_10_1016_j_biotechadv_2012_12_004 crossref_primary_10_1371_journal_pone_0025279 crossref_primary_10_1016_j_ygeno_2013_10_003 crossref_primary_10_1186_1756_0500_6_559 crossref_primary_10_1038_ncomms7404 crossref_primary_10_1016_j_gene_2018_10_036 crossref_primary_10_1111_plb_12624 crossref_primary_10_1093_nar_gkt1338 crossref_primary_10_1007_s00343_018_7090_0 crossref_primary_10_1016_j_canlet_2012_11_010 crossref_primary_10_1038_s41556_021_00795_7 crossref_primary_10_1371_journal_pone_0188067 crossref_primary_10_1007_s40484_016_0060_7 crossref_primary_10_1186_s12864_016_2564_y crossref_primary_10_1038_s41598_020_64972_8 crossref_primary_10_1186_1756_0500_5_506 crossref_primary_10_3390_genes7030010 crossref_primary_10_1093_molbev_msac096 crossref_primary_10_1016_j_fsi_2020_01_051 crossref_primary_10_1038_s41593_020_0685_8 crossref_primary_10_1038_s41375_025_02562_1 crossref_primary_10_1007_s11427_011_4255_x crossref_primary_10_1016_j_rvsc_2021_01_007 crossref_primary_10_1111_j_1749_6632_2012_06755_x crossref_primary_10_1016_j_livsci_2014_04_028 crossref_primary_10_1002_1878_0261_12528 crossref_primary_10_1038_srep18019 crossref_primary_10_1016_j_aquaculture_2019_734328 crossref_primary_10_1186_s12864_023_09837_w crossref_primary_10_1038_nrg3802 crossref_primary_10_1007_s11105_023_01404_7 crossref_primary_10_1093_pcp_pcv190 crossref_primary_10_1007_s00438_016_1246_4 crossref_primary_10_1093_pcp_pcv071 crossref_primary_10_1093_pcp_pcv074 crossref_primary_10_1038_mi_2015_98 crossref_primary_10_1371_journal_ppat_1006033 crossref_primary_10_3389_fpls_2022_1035266 crossref_primary_10_1111_gbb_12007 crossref_primary_10_1016_j_jaci_2018_03_017 crossref_primary_10_1111_gtc_13119 crossref_primary_10_1371_journal_pone_0143525 crossref_primary_10_1371_journal_pone_0190152 crossref_primary_10_7554_eLife_05996 crossref_primary_10_1534_g3_118_201008 crossref_primary_10_1371_journal_pone_0085284 crossref_primary_10_1371_journal_pcbi_1005851 crossref_primary_10_1182_blood_2014_04_512756 crossref_primary_10_3389_fpls_2016_01784 crossref_primary_10_1016_j_ygeno_2012_07_014 crossref_primary_10_1155_2015_916352 crossref_primary_10_2108_zs220047 crossref_primary_10_1186_s12864_024_10814_0 crossref_primary_10_3389_fgene_2022_884106 crossref_primary_10_1016_j_phymed_2025_156814 crossref_primary_10_2174_1574893614666190410155603 crossref_primary_10_1093_bib_bbab460 crossref_primary_10_1002_wrna_1274 crossref_primary_10_1186_s12864_022_09074_7 crossref_primary_10_3389_fgene_2018_00636 crossref_primary_10_3390_ani12162010 crossref_primary_10_1038_s41598_017_17337_7 crossref_primary_10_3389_fpls_2016_00443 crossref_primary_10_3390_s21041333 crossref_primary_10_1039_D0FO00809E crossref_primary_10_1371_journal_pone_0134837 crossref_primary_10_1038_srep00264 crossref_primary_10_1109_TCBB_2023_3307419 crossref_primary_10_1038_s41598_023_35205_5 crossref_primary_10_1111_jog_14257 crossref_primary_10_1371_journal_pgen_1003997 crossref_primary_10_1007_s00122_019_03419_9 crossref_primary_10_1186_s12870_022_03821_4 crossref_primary_10_1007_s00018_014_1637_9 crossref_primary_10_1371_journal_pone_0070835 crossref_primary_10_1038_s41598_018_21190_7 crossref_primary_10_1038_sdata_2015_51 crossref_primary_10_1007_s11033_019_04879_4 crossref_primary_10_1371_journal_pone_0091418 crossref_primary_10_3390_agronomy12092114 crossref_primary_10_1007_s40484_013_0006_2 crossref_primary_10_1080_17550874_2012_745909 crossref_primary_10_1007_s10681_023_03168_3 crossref_primary_10_1016_j_cbd_2019_03_009 crossref_primary_10_1016_j_plgene_2018_07_002 crossref_primary_10_1016_j_ygeno_2020_11_034 crossref_primary_10_1093_bioinformatics_btx104 crossref_primary_10_1186_s13059_014_0572_2 crossref_primary_10_1186_1471_2105_14_370 crossref_primary_10_3389_fpls_2021_723636 crossref_primary_10_1016_j_ajpath_2015_10_023 crossref_primary_10_1007_s44169_024_00072_2 crossref_primary_10_1016_j_ymeth_2015_04_018 crossref_primary_10_3389_fgene_2019_00317 crossref_primary_10_1016_j_psj_2023_103355 crossref_primary_10_1016_j_cbpc_2021_109185 crossref_primary_10_1038_srep13443 crossref_primary_10_1038_nprot_2015_037 crossref_primary_10_1371_journal_pone_0077492 crossref_primary_10_1038_srep42460 crossref_primary_10_1042_EBC20180003 crossref_primary_10_1371_journal_pone_0141220 crossref_primary_10_3389_fmicb_2022_888984 crossref_primary_10_3389_fnins_2021_591122 crossref_primary_10_1186_1471_2105_15_167 crossref_primary_10_1186_1471_2105_13_331 crossref_primary_10_1105_tpc_113_117523 crossref_primary_10_1016_j_fsi_2017_01_025 crossref_primary_10_1371_journal_pone_0040092 crossref_primary_10_1016_j_jhazmat_2021_125928 crossref_primary_10_1186_s12864_024_11118_z crossref_primary_10_1128_msystems_01128_22 crossref_primary_10_1016_j_gpb_2012_09_003 crossref_primary_10_1016_j_scienta_2015_04_008 crossref_primary_10_3390_ijms21051720 crossref_primary_10_1038_nrg3433 crossref_primary_10_3390_genes15010052 crossref_primary_10_1111_jne_70072 crossref_primary_10_3389_fmars_2023_1096407 crossref_primary_10_3390_ijms26062634 crossref_primary_10_13005_bbra_2895 crossref_primary_10_1038_bjc_2017_304 crossref_primary_10_1007_s00425_014_2059_5 crossref_primary_10_1371_journal_pone_0079523 crossref_primary_10_3389_fmicb_2016_00041 crossref_primary_10_1186_s13068_023_02305_3 crossref_primary_10_1038_srep01689 crossref_primary_10_1016_j_actatropica_2017_05_009 crossref_primary_10_1155_2013_481545 crossref_primary_10_1371_journal_pone_0151118 crossref_primary_10_1016_j_gene_2012_11_057 crossref_primary_10_1101_gr_139881_112 crossref_primary_10_3389_fpls_2018_01545 crossref_primary_10_1038_nmeth_3313 crossref_primary_10_1186_s13007_016_0128_4 crossref_primary_10_3389_fgene_2020_00474 crossref_primary_10_1016_j_canlet_2023_216165 crossref_primary_10_1038_nmeth_3317 crossref_primary_10_3389_fgene_2018_00313 crossref_primary_10_3389_fvets_2017_00194 crossref_primary_10_3389_fmicb_2020_00460 crossref_primary_10_1007_s11427_015_0349_4 crossref_primary_10_1186_s12864_017_4054_2 crossref_primary_10_3389_fgene_2016_00011 crossref_primary_10_1165_rcmb_2012_0532OC crossref_primary_10_1161_CIRCRESAHA_111_249433 crossref_primary_10_1186_1471_2164_15_964 crossref_primary_10_32604_phyton_2022_019630 crossref_primary_10_1186_s12864_015_2356_9 crossref_primary_10_1093_bib_bby014 crossref_primary_10_3389_fmicb_2022_993237 crossref_primary_10_4137_GRSB_S13612 crossref_primary_10_1002_mgg3_23 crossref_primary_10_1101_gr_214288_116 crossref_primary_10_1534_g3_112_005298 crossref_primary_10_3390_toxins13070452 crossref_primary_10_7554_eLife_03700 crossref_primary_10_1371_journal_pone_0069401 crossref_primary_10_1007_s00343_017_5305_4 crossref_primary_10_1186_s12870_020_02679_8 crossref_primary_10_1371_journal_pone_0046415 crossref_primary_10_3390_toxins10070292 crossref_primary_10_1002_2211_5463_12724 crossref_primary_10_1146_annurev_genom_090314_045935 crossref_primary_10_3389_fgene_2015_00174 crossref_primary_10_1186_1471_2164_15_854 crossref_primary_10_1007_s00425_013_1850_z crossref_primary_10_3389_fpls_2023_1213642 crossref_primary_10_1371_journal_pone_0091466 crossref_primary_10_1080_16546628_2017_1379861 crossref_primary_10_1049_iet_syb_2012_0060 crossref_primary_10_3390_fishes8030121 crossref_primary_10_1186_s13059_021_02568_9 crossref_primary_10_1016_j_jbi_2016_03_010 crossref_primary_10_1186_1471_2164_15_S5_S7 crossref_primary_10_1016_j_meegid_2021_105015 crossref_primary_10_3389_fmicb_2014_00134 crossref_primary_10_1186_s12864_019_5503_x crossref_primary_10_1186_1471_2164_15_703 crossref_primary_10_1186_s12864_015_1767_y crossref_primary_10_1038_nrg_2016_10 crossref_primary_10_1093_nar_gkx1059 crossref_primary_10_1261_rna_033233_112 crossref_primary_10_1016_j_cardfail_2015_02_005 crossref_primary_10_1111_1462_2920_14029 crossref_primary_10_1016_j_aqrep_2020_100582 crossref_primary_10_1016_j_aquaculture_2024_741041 crossref_primary_10_1016_j_gene_2017_05_058 crossref_primary_10_1182_blood_2014_01_548305 crossref_primary_10_1371_journal_pone_0079448 crossref_primary_10_1016_j_ibmb_2016_02_006 crossref_primary_10_1186_gb4152 crossref_primary_10_1177_2515841419835460 crossref_primary_10_1038_s41597_024_03837_5 crossref_primary_10_1186_s12885_016_2597_2 crossref_primary_10_3390_plants14010120 crossref_primary_10_1016_j_aaf_2023_12_003 crossref_primary_10_1371_journal_pone_0194487 crossref_primary_10_1186_1471_2164_16_S4_S2 crossref_primary_10_1038_s41467_024_48117_3 crossref_primary_10_3390_ijms251810091 crossref_primary_10_1186_s13071_020_04294_w crossref_primary_10_1007_s12374_020_09227_9 crossref_primary_10_1371_journal_pone_0057563 crossref_primary_10_7554_eLife_44360 crossref_primary_10_1186_s12864_025_11212_w crossref_primary_10_1007_s10142_018_0647_3 crossref_primary_10_1016_j_jia_2022_10_010 crossref_primary_10_3389_fphar_2024_1494131 crossref_primary_10_1261_rna_074922_120 crossref_primary_10_1016_j_jaci_2018_10_070 crossref_primary_10_1016_j_jclepro_2024_141653 crossref_primary_10_1038_s41598_020_76881_x crossref_primary_10_3389_fmicb_2017_01830 crossref_primary_10_1146_annurev_biochem_051410_092902 crossref_primary_10_1007_s40495_017_0084_3 crossref_primary_10_1016_j_pneurobio_2012_09_006 crossref_primary_10_1186_s12864_015_1788_6 crossref_primary_10_1016_j_aqrep_2023_101610 crossref_primary_10_1186_s12983_020_0350_9 crossref_primary_10_1186_s12864_017_4324_z crossref_primary_10_1186_s12870_015_0599_x crossref_primary_10_1016_j_pmpp_2016_03_008 crossref_primary_10_3389_fgene_2015_00361 crossref_primary_10_4049_jimmunol_1601299 crossref_primary_10_1093_nar_gkr1249 crossref_primary_10_1186_s40246_016_0084_0 crossref_primary_10_1093_bib_bbv061 crossref_primary_10_1371_journal_pone_0184581 crossref_primary_10_3390_genes10110865 crossref_primary_10_1007_s11427_013_4485_1 crossref_primary_10_1016_j_jaci_2020_06_012 crossref_primary_10_1016_j_ygeno_2016_03_005 crossref_primary_10_3390_ijms161126030 crossref_primary_10_1038_nrg3174 crossref_primary_10_1371_journal_pone_0068233 crossref_primary_10_1016_j_jmoldx_2024_06_010 crossref_primary_10_1093_nar_gku577 crossref_primary_10_1186_1471_2164_14_695 crossref_primary_10_1002_advs_202408054 crossref_primary_10_1016_j_jocs_2022_101572 crossref_primary_10_1038_srep38254 crossref_primary_10_1186_1471_2164_14_578 crossref_primary_10_1186_s13059_015_0777_z crossref_primary_10_1371_journal_pone_0077094 crossref_primary_10_1513_AnnalsATS_201810_716WS crossref_primary_10_26508_lsa_201800156 crossref_primary_10_1038_s41467_021_27021_0 crossref_primary_10_3389_fgene_2018_00297 crossref_primary_10_1155_2018_5804376 crossref_primary_10_1186_s12870_024_05422_9 crossref_primary_10_1186_s13059_018_1571_5 crossref_primary_10_3390_ani11030834 crossref_primary_10_1002_wrna_1865 crossref_primary_10_1002_wrna_1503 crossref_primary_10_1016_j_biopha_2023_115332 crossref_primary_10_3389_fimmu_2018_01403 crossref_primary_10_1007_s00125_012_2797_5 crossref_primary_10_1007_s10126_024_10384_y crossref_primary_10_3389_fmicb_2021_605095 crossref_primary_10_1371_journal_pntd_0010204 crossref_primary_10_1002_cam4_3772 crossref_primary_10_1007_s40484_018_0139_4 crossref_primary_10_1038_nbt_1915 crossref_primary_10_1038_s41396_021_01121_7 crossref_primary_10_3390_genes3030344 crossref_primary_10_3389_fmicb_2021_778190 crossref_primary_10_1007_s00441_014_1885_x crossref_primary_10_1038_s41540_021_00175_9 crossref_primary_10_1007_s13258_016_0391_9 crossref_primary_10_1007_s00438_016_1231_y crossref_primary_10_1371_journal_pone_0119701 crossref_primary_10_3389_fmicb_2018_01235 crossref_primary_10_1038_s41467_021_21894_x crossref_primary_10_1089_cmb_2021_0476 crossref_primary_10_1093_pcp_pcs179 crossref_primary_10_1038_s41598_022_09874_7 crossref_primary_10_1080_10495398_2022_2042306 crossref_primary_10_1002_ddr_21215 crossref_primary_10_1038_s41438_020_0297_1 crossref_primary_10_1186_s12864_021_07450_3 crossref_primary_10_1016_j_bmcl_2020_127102 crossref_primary_10_1016_j_mrfmmm_2015_01_008 crossref_primary_10_1242_bio_028498 crossref_primary_10_4137_BBI_S30884 crossref_primary_10_1109_JPROC_2015_2494198 crossref_primary_10_1038_s41598_020_79086_4 crossref_primary_10_3390_ani14223228 crossref_primary_10_7554_eLife_08384 crossref_primary_10_1080_00288330_2023_2230914 crossref_primary_10_1186_s12870_018_1371_9 crossref_primary_10_1007_s10681_017_1891_7 crossref_primary_10_1186_s12859_019_2786_5 crossref_primary_10_1016_j_molcel_2016_11_029 crossref_primary_10_1016_j_ymben_2016_08_004 crossref_primary_10_1016_j_margen_2015_02_004 crossref_primary_10_1186_s12864_018_5082_2 crossref_primary_10_1007_s12561_012_9068_3 crossref_primary_10_1093_pcp_pcr153 crossref_primary_10_1016_j_ijfoodmicro_2017_07_001 crossref_primary_10_1186_s12859_019_2697_5 crossref_primary_10_1371_journal_pone_0133068 crossref_primary_10_1111_1755_0998_12110 crossref_primary_10_1177_1176935119835522 crossref_primary_10_1186_1471_2105_14_320 crossref_primary_10_1186_1471_2164_14_892 crossref_primary_10_1186_s12864_016_3103_6 crossref_primary_10_3389_fped_2023_1133134 crossref_primary_10_1371_journal_pone_0171451 crossref_primary_10_1093_molbev_msw139 crossref_primary_10_3390_ani15091220 crossref_primary_10_1371_journal_pone_0128951 crossref_primary_10_3390_genes2040689 crossref_primary_10_1186_s13071_018_2983_5 crossref_primary_10_1093_bib_bbt086 crossref_primary_10_1111_age_12332 crossref_primary_10_1371_journal_pone_0071564 crossref_primary_10_3390_pr6010005 crossref_primary_10_1111_ppl_13591 crossref_primary_10_1186_1471_2164_15_324 crossref_primary_10_1016_j_gene_2013_09_014 crossref_primary_10_1371_journal_pone_0058363 crossref_primary_10_1016_j_copbio_2012_09_004 crossref_primary_10_1177_1094342016653243 crossref_primary_10_4137_BBI_S29334 crossref_primary_10_1186_1471_2105_15_135 crossref_primary_10_1186_s12864_019_5830_y crossref_primary_10_3390_genes13061032 crossref_primary_10_1186_2045_3701_2_26 crossref_primary_10_3390_genes13040595 crossref_primary_10_1534_g3_117_040683 crossref_primary_10_1093_nar_gkv227 crossref_primary_10_3390_children8121082 crossref_primary_10_1002_jez_b_22595 crossref_primary_10_3390_ani13010166 crossref_primary_10_1186_1471_2105_15_S9_S3 crossref_primary_10_1186_s12864_015_1308_8 crossref_primary_10_3389_fpls_2025_1544247 crossref_primary_10_1101_gr_133744_111 crossref_primary_10_1093_nar_gks196 crossref_primary_10_1093_nar_gku495 crossref_primary_10_1101_gad_17446611 crossref_primary_10_1007_s43032_020_00259_7 crossref_primary_10_1093_bib_bbv007 crossref_primary_10_1016_j_gene_2019_05_021 crossref_primary_10_1007_s00299_012_1295_z crossref_primary_10_1016_j_gene_2016_01_047 crossref_primary_10_1016_j_ijbiomac_2018_01_029 crossref_primary_10_3390_genes8100289 crossref_primary_10_1186_s12859_024_05663_3 crossref_primary_10_3390_ani10020344 crossref_primary_10_1038_nrg3117 crossref_primary_10_1007_s11105_019_01137_6 crossref_primary_10_1186_s12864_016_2646_x crossref_primary_10_3390_cimb46100645 crossref_primary_10_1513_AnnalsATS_201302_035AW crossref_primary_10_1007_s10142_015_0447_y crossref_primary_10_1186_1471_2164_14_866 crossref_primary_10_1186_s12859_017_1992_2 crossref_primary_10_1371_journal_pone_0101374 crossref_primary_10_1007_s00418_020_01936_z crossref_primary_10_1007_s11227_025_07563_6 crossref_primary_10_1186_s12920_024_01842_6 crossref_primary_10_1016_j_ymben_2019_05_007 crossref_primary_10_1111_1755_0998_12465 crossref_primary_10_1016_j_coph_2019_04_012 crossref_primary_10_1093_nar_gkt145 crossref_primary_10_1371_journal_pone_0141910 crossref_primary_10_3389_fmicb_2015_00896 crossref_primary_10_1016_j_aquaculture_2020_736255 crossref_primary_10_1007_s11738_017_2569_4 crossref_primary_10_1371_journal_pone_0127755 crossref_primary_10_1111_1755_0998_12109 crossref_primary_10_1016_j_aquaculture_2016_08_003 crossref_primary_10_1016_j_aquaculture_2020_735733 crossref_primary_10_3390_genes11080935 crossref_primary_10_1242_dev_111617 crossref_primary_10_1016_j_gene_2020_145061 crossref_primary_10_1016_j_ygeno_2016_01_002 crossref_primary_10_3390_jpm13081242 crossref_primary_10_1016_j_gene_2016_06_003 crossref_primary_10_1093_nar_gku166 crossref_primary_10_1111_mec_16286 crossref_primary_10_1371_journal_pone_0124432 crossref_primary_10_1155_2014_450621 crossref_primary_10_1038_gene_2014_27 crossref_primary_10_1111_jpi_12095 crossref_primary_10_1016_j_foodchem_2020_128410 crossref_primary_10_1016_j_drudis_2013_06_003 crossref_primary_10_1371_journal_pone_0115964 crossref_primary_10_1049_nbt2_12115 crossref_primary_10_12688_f1000research_18276_1 crossref_primary_10_31083_j_fbl2811283 crossref_primary_10_1007_s00344_024_11238_6 crossref_primary_10_1038_jid_2014_28 crossref_primary_10_3390_horticulturae7120522 crossref_primary_10_3389_fped_2021_751204 crossref_primary_10_1172_JCI65171 crossref_primary_10_2478_bile_2022_0009 crossref_primary_10_3389_fpls_2021_764978 crossref_primary_10_1371_journal_pone_0104709 crossref_primary_10_1371_journal_pone_0123691 crossref_primary_10_1016_j_fsi_2017_09_054 crossref_primary_10_1186_s12864_016_2745_8 crossref_primary_10_1016_j_ympev_2024_108138 crossref_primary_10_3389_fmars_2021_754588 crossref_primary_10_1002_jor_23661 crossref_primary_10_1186_1752_0509_7_S5_S7 crossref_primary_10_1016_j_jbc_2025_108496 crossref_primary_10_1101_gr_162537_113 crossref_primary_10_1038_srep15184 crossref_primary_10_1016_j_fsi_2019_02_030 crossref_primary_10_1016_j_bbadis_2014_03_011 crossref_primary_10_1186_1471_2164_14_394 crossref_primary_10_7717_peerj_13670 crossref_primary_10_1111_trf_16418 crossref_primary_10_1186_s12864_016_3161_9 crossref_primary_10_7717_peerj_11135 crossref_primary_10_1073_pnas_1216108110 crossref_primary_10_1093_nar_gkv594 crossref_primary_10_1186_1471_2164_15_1008 crossref_primary_10_1016_j_ympev_2020_106878 crossref_primary_10_3389_fmicb_2021_630013 crossref_primary_10_1095_biolreprod_112_099127 crossref_primary_10_1038_nprot_2012_086 crossref_primary_10_1002_biot_201500107 crossref_primary_10_1007_s00705_021_05313_6 crossref_primary_10_1007_s10695_019_00693_8 crossref_primary_10_1289_EHP13217 crossref_primary_10_3389_fmicb_2023_1238855 crossref_primary_10_1093_jisesa_iex002 crossref_primary_10_1371_journal_pone_0228623 crossref_primary_10_1002_bies_201900187 crossref_primary_10_1038_nrmicro2852 crossref_primary_10_1161_CIRCULATIONAHA_120_046789 crossref_primary_10_1182_blood_2014_06_582700 crossref_primary_10_1186_1471_2164_13_116 crossref_primary_10_1007_s00439_013_1300_9 crossref_primary_10_1089_cmb_2017_0244 crossref_primary_10_1002_mbo3_120 crossref_primary_10_1371_journal_pone_0134246 crossref_primary_10_7717_peerj_13669 crossref_primary_10_1038_onc_2013_424 crossref_primary_10_1038_s41467_023_36383_6 crossref_primary_10_3390_genes10040280 crossref_primary_10_1016_j_ymeth_2014_06_008 crossref_primary_10_1002_ece3_8866 crossref_primary_10_1038_srep20758 crossref_primary_10_1371_journal_pcbi_1004393 crossref_primary_10_1186_s12859_015_0492_5 crossref_primary_10_1002_pro_4979 crossref_primary_10_1371_journal_pcbi_1006453 crossref_primary_10_1371_journal_pone_0066902 crossref_primary_10_7717_peerj_3797 crossref_primary_10_1186_1471_2164_13_361 crossref_primary_10_1038_s41576_021_00326_y crossref_primary_10_1093_hr_uhad214 crossref_primary_10_1016_j_phymed_2024_155509 crossref_primary_10_1038_nbt_3122 crossref_primary_10_3390_ani12091061 crossref_primary_10_1186_s12859_016_1457_z crossref_primary_10_1007_s00344_023_11064_2 crossref_primary_10_1016_j_funbio_2016_02_003 crossref_primary_10_1016_j_aquaculture_2021_737710 crossref_primary_10_1038_nprot_2012_016 crossref_primary_10_1016_j_gene_2013_02_023 crossref_primary_10_1038_onc_2015_269 crossref_primary_10_1111_j_1365_2796_2011_02508_x crossref_primary_10_1109_TCBB_2015_2403355 crossref_primary_10_1016_j_margen_2018_08_007 crossref_primary_10_1097_COH_0b013e32834dde1c crossref_primary_10_1186_gb_2013_14_12_r134 crossref_primary_10_1186_s12864_015_1553_x crossref_primary_10_3390_plants12061378 crossref_primary_10_1016_j_cell_2011_11_058 crossref_primary_10_1038_s41598_019_51041_y crossref_primary_10_1002_2211_5463_12033 crossref_primary_10_1111_gcbb_13040 crossref_primary_10_1186_1471_2164_13_696 crossref_primary_10_1016_j_aaf_2020_06_013 crossref_primary_10_1109_TCBB_2016_2591533 crossref_primary_10_1007_s11427_013_4442_z crossref_primary_10_1007_s00343_021_0364_y crossref_primary_10_1534_g3_114_012526 crossref_primary_10_1038_srep16597 crossref_primary_10_1093_gigascience_giy093 crossref_primary_10_1371_journal_pcbi_1003000 crossref_primary_10_3389_fpls_2023_1213086 crossref_primary_10_1038_s41598_017_09334_7 crossref_primary_10_3390_ijms241713198 crossref_primary_10_1089_omi_2013_0110 crossref_primary_10_1186_1471_2164_15_154 crossref_primary_10_1371_journal_pone_0094270 crossref_primary_10_1371_journal_pone_0030646 crossref_primary_10_1016_j_fsi_2015_03_032 crossref_primary_10_1038_s41438_021_00520_3 crossref_primary_10_1111_acel_14151 crossref_primary_10_3389_fphys_2019_00125 crossref_primary_10_1186_1471_2164_13_547 crossref_primary_10_1371_journal_pone_0087613 crossref_primary_10_1016_j_jep_2020_113551 crossref_primary_10_1186_1471_2164_14_230 crossref_primary_10_3390_ijms232113351 crossref_primary_10_1177_0300985817709887 crossref_primary_10_1080_01621459_2017_1423074 crossref_primary_10_1016_j_gene_2014_05_059 crossref_primary_10_3390_ijms232314984 crossref_primary_10_1186_s12864_016_3402_y crossref_primary_10_1038_s41598_020_74567_y crossref_primary_10_7717_peerj_10074 crossref_primary_10_1186_s12864_016_3118_z crossref_primary_10_1038_s41467_018_06063_x crossref_primary_10_1016_j_compbiomed_2021_104646 crossref_primary_10_1371_journal_pone_0101418 crossref_primary_10_1016_j_ejphar_2019_172789 crossref_primary_10_1371_journal_pgen_1006482 crossref_primary_10_1371_journal_pone_0124638 crossref_primary_10_1038_nrg3198 crossref_primary_10_1104_pp_112_201962 crossref_primary_10_1186_s12915_023_01617_y crossref_primary_10_1186_s13068_018_1164_2 crossref_primary_10_1186_1471_2164_14_31 crossref_primary_10_1186_1471_2164_15_279 crossref_primary_10_1515_biol_2022_0613
Cites_doi	10.1126/science.1191244 10.1093/bioinformatics/btm453 10.1093/bioinformatics/btq485 10.1093/bioinformatics/btp459 10.1101/gr.079558.108 10.1093/bioinformatics/btq057 10.1186/gb-2010-11-10-r106 10.1038/nature07509 10.1101/gr.078212.108 10.1038/nmeth.1517 10.1101/gr.074492.107 10.1038/nature05805 10.1142/S0219720010005178 10.1186/gb-2009-10-3-r25 10.1038/nmeth.1223 10.1093/bioinformatics/btp113 10.1186/gb-2010-11-8-r83 10.1186/gb-2010-11-3-r25 10.1093/bioinformatics/btp120 10.1093/bioinformatics/btp692 10.1186/gb-2008-9-12-r175 10.1038/nmeth.1503 10.1093/nar/gkq1015 10.1126/science.286.5439.531 10.1093/bioinformatics/btp367 10.1182/blood-2010-07-293332 10.1186/1745-6150-4-14 10.1093/bioinformatics/btn025 10.1093/bioinformatics/btp336 10.1093/bioinformatics/btp324 10.1093/bioinformatics/btn300 10.1101/gr.103846.109 10.1038/ng.264 10.1101/gad.1788009 10.1038/5976 10.1038/nmeth.1491 10.1093/bioinformatics/bti310 10.1126/science.270.5235.467 10.1093/nar/gkg770 10.1101/gr.229202 10.1101/gr.103697.109 10.1093/bioinformatics/bti407 10.1038/nature07638 10.1101/gr.111120.110 10.1038/nbt.1621 10.1093/nar/gkq211 10.1038/nmeth.1371 10.1038/nmeth.1470 10.1016/j.cell.2008.03.029 10.1093/bioinformatics/btn429 10.1371/journal.pone.0007767 10.1038/nrg2484 10.1016/j.molcel.2004.12.004 10.1038/nmeth.1528 10.1093/bioinformatics/btp579 10.1038/nature09616 10.1126/science.2047873 10.1101/gr.099226.109 10.1101/gr.1119703 10.1073/pnas.97.23.12690 10.1186/1471-2105-11-94 10.1038/nmeth.1226 10.1016/j.pbi.2008.11.004 10.1126/science.1068597 10.1371/journal.pcbi.1000386 10.1101/gr.111021.110 10.1038/nature07672 10.1093/nar/gkq622 10.1126/science.1160342 10.1038/nbt.1633 10.1093/bioinformatics/btp612 10.1126/science.1158441 10.1016/S0020-0255(01)00098-6 10.1080/07391102.1989.10507752 10.1073/pnas.091062498 10.1093/bioinformatics/btp616 10.1073/pnas.0812841106 10.1186/1471-2105-9-128 10.1002/0471250953.bi1105s31
ContentType	Journal Article
Copyright	Springer Nature America, Inc. 2011 COPYRIGHT 2011 Nature Publishing Group Copyright Nature Publishing Group Jun 2011
Copyright_xml	– notice: Springer Nature America, Inc. 2011 – notice: COPYRIGHT 2011 Nature Publishing Group – notice: Copyright Nature Publishing Group Jun 2011
DBID	AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7QL 7QO 7SS 7TK 7U9 7X2 7X7 7XB 88E 88I 8AO 8FD 8FE 8FG 8FH 8FI 8FJ 8FK ABJCF ABUWG AEUYN AFKRA ARAPS ATCPS AZQEC BBNVY BENPR BGLVJ BHPHI BKSAR C1K CCPQU D1I DWQXO FR3 FYUFA GHDGH GNUQQ H94 HCIFZ K9. KB. L6V LK8 M0K M0S M1P M2P M7N M7P M7S P5Z P62 P64 PATMY PCBAR PDBOC PHGZM PHGZT PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS PTHSS PYCSY Q9U RC3 7X8 7TM
DOI	10.1038/nmeth.1613
DatabaseName	CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Bacteriology Abstracts (Microbiology B) Biotechnology Research Abstracts Entomology Abstracts (Full archive) Neurosciences Abstracts Virology and AIDS Abstracts Agricultural Science Collection Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) Science Database (Alumni Edition) ProQuest Pharma Collection Technology Research Database ProQuest SciTech Collection ProQuest Technology Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) Materials Science & Engineering Collection ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland Advanced Technologies & Computer Science Collection Agricultural & Environmental Science Collection ProQuest Central Essentials Biological Science Collection ProQuest Central Technology Collection Natural Science Collection ProQuest Earth, Atmospheric & Aquatic Science Collection Environmental Sciences and Pollution Management ProQuest One Community College ProQuest Materials Science Collection ProQuest Central Engineering Research Database Proquest Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student AIDS and Cancer Research Abstracts SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) Materials Science Database ProQuest Engineering Collection Biological Sciences Agricultural Science Database ProQuest Health & Medical Collection Medical Database Science Database Algology Mycology and Protozoology Abstracts (Microbiology C) Biological Science Database Engineering Database Advanced Technologies & Aerospace Database ProQuest Advanced Technologies & Aerospace Collection Biotechnology and BioEngineering Abstracts Environmental Science Database Earth, Atmospheric & Aquatic Science Database Materials Science Collection Proquest Central Premium ProQuest One Academic ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China Engineering collection Environmental Science Collection ProQuest Central Basic Genetics Abstracts MEDLINE - Academic Nucleic Acids Abstracts
DatabaseTitle	CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Agricultural Science Database ProQuest Central Student ProQuest Advanced Technologies & Aerospace Collection ProQuest Central Essentials SciTech Premium Collection ProQuest Central China Environmental Sciences and Pollution Management ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) Engineering Collection Advanced Technologies & Aerospace Collection Engineering Database Virology and AIDS Abstracts ProQuest Science Journals (Alumni Edition) ProQuest Biological Science Collection ProQuest One Academic Eastern Edition Earth, Atmospheric & Aquatic Science Database Agricultural Science Collection ProQuest Hospital Collection ProQuest Technology Collection Health Research Premium Collection (Alumni) Biological Science Database Neurosciences Abstracts ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts Environmental Science Collection Entomology Abstracts ProQuest Health & Medical Complete ProQuest One Academic UKI Edition Environmental Science Database Engineering Research Database ProQuest One Academic ProQuest One Academic (New) Technology Collection Technology Research Database ProQuest One Academic Middle East (New) Materials Science Collection ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Pharma Collection ProQuest Central Earth, Atmospheric & Aquatic Science Collection ProQuest Health & Medical Research Collection Genetics Abstracts ProQuest Engineering Collection Biotechnology Research Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Bacteriology Abstracts (Microbiology B) Algology Mycology and Protozoology Abstracts (Microbiology C) Agricultural & Environmental Science Collection AIDS and Cancer Research Abstracts Materials Science Database ProQuest Materials Science Collection ProQuest Central Basic ProQuest Science Journals ProQuest SciTech Collection Advanced Technologies & Aerospace Database ProQuest Medical Library Materials Science & Engineering Collection ProQuest Central (Alumni) MEDLINE - Academic Nucleic Acids Abstracts
DatabaseTitleList	Nucleic Acids Abstracts Agricultural Science Database MEDLINE - Academic MEDLINE
Database_xml	– sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: BENPR name: ProQuest Central url: https://www.proquest.com/central sourceTypes: Aggregation Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Biology
EISSN	1548-7105
EndPage	477
ExternalDocumentID	2360085891 A258435198 21623353 10_1038_nmeth_1613
Genre	Journal Article Review
GeographicLocations	United States
GeographicLocations_xml	– name: United States
GroupedDBID	--- -~X 0R~ 123 29M 39C 3V. 4.4 53G 5BI 7X2 7X7 7XC 88E 88I 8AO 8CJ 8FE 8FG 8FH 8FI 8FJ 8R4 8R5 AAEEF AAHBH AARCD AAYZH AAZLF ABAWZ ABDBF ABJCF ABJNI ABLJU ABUWG ACBWK ACGFS ACGOD ACIWK ACPRK ACUHS ADBBV AENEX AEUYN AFANA AFBBN AFKRA AFRAH AFSHS AGAYW AHBCP AHMBA AHSBF AIBTJ ALFFA ALIPV ALMA_UNASSIGNED_HOLDINGS ARAPS ARMCB ASPBG ATCPS AVWKF AXYYD AZFZN AZQEC BBNVY BENPR BGLVJ BHPHI BKKNO BKSAR BPHCQ BVXVI CCPQU CS3 D1I D1J D1K DB5 DU5 DWQXO EBS EE. EJD EMOBN ESX F5P FEDTE FSGXE FYUFA FZEXT GNUQQ HCIFZ HMCUK HVGLF HZ~ IAO IHR INH INR ITC K6- KB. L6V LK5 LK8 M0K M1P M2P M7P M7R M7S NNMJJ O9- ODYON P2P P62 PATMY PCBAR PDBOC PQQKQ PROAC PSQYO PTHSS PYCSY Q2X RNS RNT RNTTT SHXYY SIXXV SJN SNYQT SOJ SV3 TAOOD TBHMF TDRGL TSG TUS UKHRP ~8M AAYXX AFFHD ATHPR CITATION PHGZM PHGZT PJZUB PPXIY PQGLB CGR CUY CVF ECM EIF NFIDA NPM 7QL 7QO 7SS 7TK 7U9 7XB 8FD 8FK C1K FR3 H94 K9. M7N P64 PKEHL PQEST PQUKI PRINS Q9U RC3 7X8 PUEGO 7TM
ID	FETCH-LOGICAL-c514t-66de786c8cc697dd49c3224f61cd3a1ecdc6b8818b094181e8c6484477888c2d3
IEDL.DBID	M7S
ISICitedReferencesCount	745
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000291031800015&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	1548-7091 1548-7105
IngestDate	Thu Oct 02 06:48:45 EDT 2025 Thu Oct 02 14:30:11 EDT 2025 Mon Oct 06 16:59:46 EDT 2025 Tue Nov 11 11:03:43 EST 2025 Tue Nov 04 18:16:35 EST 2025 Mon Jul 21 05:49:12 EDT 2025 Sat Nov 29 02:49:25 EST 2025 Tue Nov 18 22:19:38 EST 2025 Fri Feb 21 02:37:43 EST 2025
IsPeerReviewed	true
IsScholarly	true
Issue	6
Language	English
License	http://www.springer.com/tdm
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c514t-66de786c8cc697dd49c3224f61cd3a1ecdc6b8818b094181e8c6484477888c2d3
Notes	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 ObjectType-Review-3 content type line 23
PMID	21623353
PQID	868908551
PQPubID	28015
PageCount	9
ParticipantIDs	proquest_miscellaneous_904482072 proquest_miscellaneous_869406972 proquest_journals_868908551 gale_infotracmisc_A258435198 gale_infotracacademiconefile_A258435198 pubmed_primary_21623353 crossref_citationtrail_10_1038_nmeth_1613 crossref_primary_10_1038_nmeth_1613 springer_journals_10_1038_nmeth_1613
PublicationCentury	2000
PublicationDate	2011-06-01
PublicationDateYYYYMMDD	2011-06-01
PublicationDate_xml	– month: 06 year: 2011 text: 2011-06-01 day: 01
PublicationDecade	2010
PublicationPlace	New York
PublicationPlace_xml	– name: New York – name: United States
PublicationSubtitle	Techniques for life scientists and chemists
PublicationTitle	Nature methods
PublicationTitleAbbrev	Nat Methods
PublicationTitleAlternate	Nat Methods
PublicationYear	2011
Publisher	Nature Publishing Group US Nature Publishing Group
Publisher_xml	– name: Nature Publishing Group US – name: Nature Publishing Group
References	Jiang, Wong (CR66) 2009; 25 Yassour (CR23) 2009; 106 Grant, Manduchi, Stoeckert (CR71) 2007; 19 Berger (CR26) 2010; 20 de Souza (CR3) 2000; 97 Nagalakshmi (CR21) 2008; 320 Mortazavi (CR27) 2010; 20 Li, Li, Kristiansen, Wang (CR34) 2008; 24 Kent (CR8) 2002; 12 Li (CR41) 2009; 25 Plessy (CR81) 2010; 7 Robertson (CR53) 2010; 7 Robinson, McCarthy, Smyth (CR75) 2010; 26 Golub (CR14) 1999; 286 Rumble (CR37) 2009; 5 Oshlack, Wakefield (CR64) 2009; 4 Denoeud (CR16) 2008; 9 Blencowe, Ahmad, Lee (CR60) 2009; 23 Pepke, Wold, Mortazavi (CR62) 2009; 6 Jiang, Wong (CR32) 2008; 24 Katz, Wang, Airoldi, Burge (CR30) 2010; 7 Trapnell, Pachter, Salzberg (CR48) 2009; 25 Ferragina, Manzini (CR43) 2001; 135 Trapnell (CR29) 2010; 28 Langmead, Trapnell, Pop, Salzberg (CR39) 2009; 10 Carninci (CR2) 2003; 13 Wang, Wu, Zhang (CR69) 2010; 8 Wang (CR5) 2008; 456 Zerbino, Birney (CR58) 2008; 18 De Bona, Ossowski, Schneeberger, Ratsch (CR51) 2008; 24 Au, Jiang, Lin, Xing, Wong (CR47) 2010; 38 Li, Ruotti, Stewart, Thomson, Dewey (CR67) 2010; 26 Robinson, Smyth (CR74) 2007; 23 Smith, Xuan, Zhang (CR38) 2008; 9 CR42 Wang, Feng, Wang, Zhang (CR77) 2010; 26 Guttman (CR4) 2009; 458 Lee (CR82) 2010; 39 Haas (CR7) 2003; 31 Schena, Shalon, Davis, Brown (CR13) 1995; 270 Wu, Nacu (CR50) 2010; 26 Kapranov (CR10) 2002; 296 Pan (CR11) 2004; 16 Wang, Gerstein, Snyder (CR63) 2009; 10 De Bruijn (CR56) 1946; 46 Wilhelm (CR25) 2010; 117 Cloonan (CR45) 2009; 25 Li, Durbin (CR40) 2009; 25 Wang (CR49) 2010; 38 Degner (CR46) 2009; 25 Zerbino (CR59) 2010; 31 Jan, Friedman, Ruby, Bartel (CR79) 2011; 469 Tusher, Tibshirani, Chu (CR70) 2001; 98 Wu, Watanabe (CR9) 2005; 21 Cloonan (CR15) 2008; 5 Mangone (CR80) 2010; 329 Surget-Groba, Montoya-Burgos (CR55) 2010; 20 Homer, Merriman, Nelson (CR31) 2009; 4 Maher (CR18) 2009; 458 Li, Ruan, Durbin (CR33) 2008; 18 Adams (CR6) 1991; 252 Grant, Liu, Stoeckert (CR72) 2005; 21 Lister (CR17) 2008; 133 Sultan (CR22) 2008; 321 Guttman (CR28) 2010; 28 Langmead, Hansen, Leek (CR73) 2010; 11 Bullard, Purdom, Hansen, Dudoit (CR68) 2010; 11 Pevzner (CR57) 1989; 7 Lister, Gregory, Ecker (CR61) 2009; 12 Marra (CR1) 1999; 21 Marioni, Mason, Mane, Stephens, Gilad (CR19) 2008; 18 Lunter, Goodson (CR35) 2010; 21 Griffith (CR44) 2010; 7 Anders, Huber (CR76) 2010; 11 Rizk, Lavenier (CR36) 2010; 26 Mortazavi, Williams, McCue, Schaeffer, Wold (CR20) 2008; 5 Blekhman, Marioni, Zumbo, Stephens, Gilad (CR24) 2010; 20 Mikkelsen (CR52) 2007; 447 Birol (CR54) 2009; 25 Robinson, Oshlack (CR65) 2010; 11 Castle (CR12) 2008; 40 Levin (CR78) 2010; 7 BJ Haas (BFnmeth1613_CR7) 2003; 31 A Oshlack (BFnmeth1613_CR64) 2009; 4 TD Wu (BFnmeth1613_CR9) 2005; 21 A Mortazavi (BFnmeth1613_CR27) 2010; 20 M Mangone (BFnmeth1613_CR80) 2010; 329 N Cloonan (BFnmeth1613_CR15) 2008; 5 B Langmead (BFnmeth1613_CR39) 2009; 10 BT Wilhelm (BFnmeth1613_CR25) 2010; 117 TS Mikkelsen (BFnmeth1613_CR52) 2007; 447 TD Wu (BFnmeth1613_CR50) 2010; 26 MD Robinson (BFnmeth1613_CR74) 2007; 23 MD Adams (BFnmeth1613_CR6) 1991; 252 JC Marioni (BFnmeth1613_CR19) 2008; 18 Y Surget-Groba (BFnmeth1613_CR55) 2010; 20 JH Bullard (BFnmeth1613_CR68) 2010; 11 X Wang (BFnmeth1613_CR69) 2010; 8 M Griffith (BFnmeth1613_CR44) 2010; 7 NG De Bruijn (BFnmeth1613_CR56) 1946; 46 H Jiang (BFnmeth1613_CR66) 2009; 25 WJ Kent (BFnmeth1613_CR8) 2002; 12 R Blekhman (BFnmeth1613_CR24) 2010; 20 H Li (BFnmeth1613_CR40) 2009; 25 F Denoeud (BFnmeth1613_CR16) 2008; 9 Z Wang (BFnmeth1613_CR63) 2009; 10 BFnmeth1613_CR42 K Wang (BFnmeth1613_CR49) 2010; 38 H Li (BFnmeth1613_CR33) 2008; 18 JC Castle (BFnmeth1613_CR12) 2008; 40 JZ Levin (BFnmeth1613_CR78) 2010; 7 R Li (BFnmeth1613_CR34) 2008; 24 B Langmead (BFnmeth1613_CR73) 2010; 11 S Lee (BFnmeth1613_CR82) 2010; 39 M Sultan (BFnmeth1613_CR22) 2008; 321 S Pepke (BFnmeth1613_CR62) 2009; 6 R Lister (BFnmeth1613_CR61) 2009; 12 L Wang (BFnmeth1613_CR77) 2010; 26 JF Degner (BFnmeth1613_CR46) 2009; 25 B Li (BFnmeth1613_CR67) 2010; 26 S Anders (BFnmeth1613_CR76) 2010; 11 U Nagalakshmi (BFnmeth1613_CR21) 2008; 320 CH Jan (BFnmeth1613_CR79) 2011; 469 MD Robinson (BFnmeth1613_CR65) 2010; 11 N Homer (BFnmeth1613_CR31) 2009; 4 F De Bona (BFnmeth1613_CR51) 2008; 24 VG Tusher (BFnmeth1613_CR70) 2001; 98 P Carninci (BFnmeth1613_CR2) 2003; 13 BJ Blencowe (BFnmeth1613_CR60) 2009; 23 CA Maher (BFnmeth1613_CR18) 2009; 458 M Yassour (BFnmeth1613_CR23) 2009; 106 C Trapnell (BFnmeth1613_CR48) 2009; 25 DR Zerbino (BFnmeth1613_CR59) 2010; 31 R Li (BFnmeth1613_CR41) 2009; 25 M Guttman (BFnmeth1613_CR4) 2009; 458 G Robertson (BFnmeth1613_CR53) 2010; 7 Y Katz (BFnmeth1613_CR30) 2010; 7 SM Rumble (BFnmeth1613_CR37) 2009; 5 PA Pevzner (BFnmeth1613_CR57) 1989; 7 A Mortazavi (BFnmeth1613_CR20) 2008; 5 N Cloonan (BFnmeth1613_CR45) 2009; 25 TR Golub (BFnmeth1613_CR14) 1999; 286 G. Lunter (BFnmeth1613_CR35) 2010; 21 M Guttman (BFnmeth1613_CR28) 2010; 28 C Trapnell (BFnmeth1613_CR29) 2010; 28 I Birol (BFnmeth1613_CR54) 2009; 25 P Ferragina (BFnmeth1613_CR43) 2001; 135 GR Grant (BFnmeth1613_CR72) 2005; 21 R Lister (BFnmeth1613_CR17) 2008; 133 AD Smith (BFnmeth1613_CR38) 2008; 9 MF Berger (BFnmeth1613_CR26) 2010; 20 GR Grant (BFnmeth1613_CR71) 2007; 19 M Schena (BFnmeth1613_CR13) 1995; 270 MD Robinson (BFnmeth1613_CR75) 2010; 26 DR Zerbino (BFnmeth1613_CR58) 2008; 18 C Plessy (BFnmeth1613_CR81) 2010; 7 ET Wang (BFnmeth1613_CR5) 2008; 456 SJ de Souza (BFnmeth1613_CR3) 2000; 97 H Jiang (BFnmeth1613_CR32) 2008; 24 P Kapranov (BFnmeth1613_CR10) 2002; 296 Q Pan (BFnmeth1613_CR11) 2004; 16 G Rizk (BFnmeth1613_CR36) 2010; 26 M Marra (BFnmeth1613_CR1) 1999; 21 KF Au (BFnmeth1613_CR47) 2010; 38 19844228 - Nat Methods. 2009 Nov;6(11 Suppl):S22-32 17881408 - Bioinformatics. 2007 Nov 1;23(21):2881-7 20979621 - Genome Biol. 2010;11(10):R106 20802226 - Nucleic Acids Res. 2010 Oct;38(18):e178 19528315 - Genes Dev. 2009 Jun 15;23(12):1379-86 11988577 - Science. 2002 May 3;296(5569):916-9 19015660 - Nat Rev Genet. 2009 Jan;10(1):57-63 17495919 - Nature. 2007 May 10;447(7141):167-77 20980554 - Genome Res. 2010 Dec;20(12):1740-7 19182780 - Nature. 2009 Mar 12;458(7235):223-7 20147302 - Bioinformatics. 2010 Apr 1;26(7):873-81 18423832 - Cell. 2008 May 2;133(3):523-36 20701754 - Genome Biol. 2010;11(8):R83 21059678 - Nucleic Acids Res. 2011 Jan;39(2):e9 19808877 - Bioinformatics. 2009 Dec 15;25(24):3207-12 7569999 - Science. 1995 Oct 20;270(5235):467-70 20739310 - Bioinformatics. 2010 Oct 15;26(20):2534-40 14500829 - Nucleic Acids Res. 2003 Oct 1;31(19):5654-66 20935650 - Nat Methods. 2010 Nov;7(11):909-12 18599741 - Science. 2008 Aug 15;321(5891):956-60 20371516 - Nucleic Acids Res. 2010 Aug;38(14):4570-8 20693479 - Genome Res. 2010 Oct;20(10):1432-40 19497933 - Bioinformatics. 2009 Aug 1;25(15):1966-7 18516045 - Nat Methods. 2008 Jul;5(7):621-8 2047873 - Science. 1991 Jun 21;252(5013):1651-6 20436464 - Nat Biotechnol. 2010 May;28(5):511-5 18265395 - Curr Protoc Mol Biol. 2007 Jan;Chapter 19:Unit 19.6 20196867 - Genome Biol. 2010;11(3):R25 19648138 - Bioinformatics. 2009 Oct 1;25(19):2615-6 11309499 - Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 Nat Methods. 2011 Jun;8(6):following 477 19136943 - Nature. 2009 Mar 5;458(7234):97-101 19855105 - Bioinformatics. 2010 Jan 1;26(1):136-8 20980556 - Genome Res. 2011 Jun;21(6):936-9 11932250 - Genome Res. 2002 Apr;12(4):656-64 19208812 - Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9 21155027 - J Bioinform Comput Biol. 2010 Dec;8 Suppl 1:177-92 20522740 - Science. 2010 Jul 23;329(5990):432-5 19087247 - Genome Biol. 2008;9(12):R175 20179022 - Genome Res. 2010 Apr;20(4):413-27 19461883 - PLoS Comput Biol. 2009 May;5(5):e1000386 19451168 - Bioinformatics. 2009 Jul 15;25(14):1754-60 20711195 - Nat Methods. 2010 Sep;7(9):709-15 21085120 - Nature. 2011 Jan 6;469(7328):97-101 19907642 - PLoS One. 2009 Nov 11;4(11):e7767 9988271 - Nat Genet. 1999 Feb;21(2):191-4 20836074 - Curr Protoc Bioinformatics. 2010 Sep;Chapter 11:Unit 11.5 18978772 - Nature. 2008 Nov 27;456(7221):470-6 12819125 - Genome Res. 2003 Jun;13(6B):1273-89 19289445 - Bioinformatics. 2009 May 1;25(9):1105-11 18697769 - Bioinformatics. 2008 Oct 15;24(20):2395-6 15610736 - Mol Cell. 2004 Dec 22;16(6):929-41 18689821 - Bioinformatics. 2008 Aug 15;24(16):i174-80 20022975 - Bioinformatics. 2010 Feb 15;26(4):493-500 20980679 - Blood. 2011 Jan 13;117(2):e27-38 2684223 - J Biomol Struct Dyn. 1989 Aug;7(1):63-73 15797908 - Bioinformatics. 2005 Jun 1;21(11):2684-90 18451266 - Science. 2008 Jun 6;320(5881):1344-9 18227114 - Bioinformatics. 2008 Mar 1;24(5):713-4 19910308 - Bioinformatics. 2010 Jan 1;26(1):139-40 11070084 - Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12690-3 20167110 - BMC Bioinformatics. 2010 Feb 18;11:94 20835245 - Nat Methods. 2010 Oct;7(10):843-7 19261174 - Genome Biol. 2009;10(3):R25 18714091 - Genome Res. 2008 Nov;18(11):1851-8 19371405 - Biol Direct. 2009 Apr 16;4:14 19244387 - Bioinformatics. 2009 Apr 15;25(8):1026-32 18516046 - Nat Methods. 2008 Jul;5(7):613-9 19528083 - Bioinformatics. 2009 Nov 1;25(21):2872-7 19157957 - Curr Opin Plant Biol. 2009 Apr;12(2):107-18 18349386 - Genome Res. 2008 May;18(5):821-9 15728110 - Bioinformatics. 2005 May 1;21(9):1859-75 18978788 - Nat Genet. 2008 Dec;40(12):1416-25 18550803 - Genome Res. 2008 Sep;18(9):1509-17 20436462 - Nat Biotechnol. 2010 May;28(5):503-10 20009012 - Genome Res. 2010 Feb;20(2):180-9 18307793 - BMC Bioinformatics. 2008 Feb 28;9:128 20543846 - Nat Methods. 2010 Jul;7(7):528-34 10521349 - Science. 1999 Oct 15;286(5439):531-7
References_xml	– volume: 329 start-page: 432 year: 2010 end-page: 435 ident: CR80 article-title: The landscape of 3′UTRs publication-title: Science doi: 10.1126/science.1191244 – volume: 23 start-page: 2881 year: 2007 end-page: 2887 ident: CR74 article-title: Moderated statistical tests for assessing differences in tag abundance publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm453 – volume: 26 start-page: 2534 year: 2010 end-page: 2540 ident: CR36 article-title: GASSST: global alignment short sequence search tool publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq485 – volume: 25 start-page: 2615 year: 2009 end-page: 2616 ident: CR45 article-title: RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp459 – volume: 18 start-page: 1509 year: 2008 end-page: 1517 ident: CR19 article-title: RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays publication-title: Genome Res. doi: 10.1101/gr.079558.108 – volume: 26 start-page: 873 year: 2010 end-page: 881 ident: CR50 article-title: Fast and SNP-tolerant detection of complex variants and splicing in short reads publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq057 – volume: 11 start-page: R106 year: 2010 ident: CR76 article-title: Differential expression analysis for sequence count data publication-title: Genome Biol. doi: 10.1186/gb-2010-11-10-r106 – volume: 456 start-page: 470 year: 2008 end-page: 476 ident: CR5 article-title: Alternative isoform regulation in human tissue transcriptomes publication-title: Nature doi: 10.1038/nature07509 – volume: 18 start-page: 1851 year: 2008 end-page: 1858 ident: CR33 article-title: Mapping short DNA sequencing reads and calling variants using mapping quality scores publication-title: Genome Res. doi: 10.1101/gr.078212.108 – volume: 7 start-page: 909 year: 2010 end-page: 912 ident: CR53 article-title: De novo assembly and analysis of RNA-seq data publication-title: Nat. Methods doi: 10.1038/nmeth.1517 – volume: 18 start-page: 821 year: 2008 end-page: 829 ident: CR58 article-title: Velvet: algorithms for de novo short read assembly using de Bruijn graphs publication-title: Genome Res. doi: 10.1101/gr.074492.107 – volume: 447 start-page: 167 year: 2007 end-page: 177 ident: CR52 article-title: Genome of the marsupial reveals innovation in non-coding sequences publication-title: Nature doi: 10.1038/nature05805 – volume: 8 start-page: 177 issue: Suppl. 1 year: 2010 end-page: 192 ident: CR69 article-title: Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq publication-title: J. Bioinform. Comput. Biol. doi: 10.1142/S0219720010005178 – volume: 10 start-page: R25 year: 2009 ident: CR39 article-title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome publication-title: Genome Biol. doi: 10.1186/gb-2009-10-3-r25 – volume: 5 start-page: 613 year: 2008 end-page: 619 ident: CR15 article-title: Stem cell transcriptome profiling via massive-scale mRNA sequencing publication-title: Nat. Methods doi: 10.1038/nmeth.1223 – ident: CR42 – volume: 25 start-page: 1026 year: 2009 end-page: 1032 ident: CR66 article-title: Statistical inferences for isoform expression in RNA-Seq publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp113 – volume: 11 start-page: R83 year: 2010 ident: CR73 article-title: Cloud-scale RNA-sequencing differential expression analysis with Myrna publication-title: Genome Biol. doi: 10.1186/gb-2010-11-8-r83 – volume: 11 start-page: R25 year: 2010 ident: CR65 article-title: A scaling normalization method for differential expression analysis of RNA-seq data publication-title: Genome Biol. doi: 10.1186/gb-2010-11-3-r25 – volume: 25 start-page: 1105 year: 2009 end-page: 1111 ident: CR48 article-title: TopHat: discovering splice junctions with RNA-Seq publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp120 – volume: 26 start-page: 493 year: 2010 end-page: 500 ident: CR67 article-title: RNA-Seq gene expression estimation with read mapping uncertainty publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp692 – volume: 9 start-page: R175 year: 2008 ident: CR16 article-title: Annotating genomes with massive-scale RNA sequencing publication-title: Genome Biol. doi: 10.1186/gb-2008-9-12-r175 – volume: 7 start-page: 843 year: 2010 end-page: 847 ident: CR44 article-title: Alternative expression analysis by RNA sequencing publication-title: Nat. Methods doi: 10.1038/nmeth.1503 – volume: 39 start-page: e9 year: 2010 ident: CR82 article-title: Accurate quantification of transcriptome from RNA-Seq data by effective length normalization publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq1015 – volume: 286 start-page: 531 year: 1999 end-page: 537 ident: CR14 article-title: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring publication-title: Science doi: 10.1126/science.286.5439.531 – volume: 25 start-page: 2872 year: 2009 end-page: 2877 ident: CR54 article-title: De novo transcriptome assembly with ABySS publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp367 – volume: 19 start-page: 6 year: 2007 ident: CR71 article-title: Jr. Analysis and management of microarray gene expression data publication-title: Curr. Protoc. Mol. Biol. – volume: 117 start-page: e27 year: 2010 end-page: e38 ident: CR25 article-title: RNA-seq analysis of two closely related leukemia clones that differ in their self-renewal capacity publication-title: Blood doi: 10.1182/blood-2010-07-293332 – volume: 4 start-page: 14 year: 2009 ident: CR64 article-title: Transcript length bias in RNA-seq data confounds systems biology publication-title: Biol. Direct doi: 10.1186/1745-6150-4-14 – volume: 24 start-page: 713 year: 2008 end-page: 714 ident: CR34 article-title: SOAP: short oligonucleotide alignment program publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn025 – volume: 25 start-page: 1966 year: 2009 end-page: 1967 ident: CR41 article-title: SOAP2: an improved ultrafast tool for short read alignment publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp336 – volume: 25 start-page: 1754 year: 2009 end-page: 1760 ident: CR40 article-title: Fast and accurate short read alignment with Burrows-Wheeler transform publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 24 start-page: i174 year: 2008 end-page: i180 ident: CR51 article-title: Optimal spliced alignments of short sequence reads publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn300 – volume: 20 start-page: 1432 year: 2010 end-page: 1440 ident: CR55 article-title: Optimization of de novo transcriptome assembly from next-generation sequencing data publication-title: Genome Res. doi: 10.1101/gr.103846.109 – volume: 40 start-page: 1416 year: 2008 end-page: 1425 ident: CR12 article-title: Expression of 24,426 human alternative splicing events and predicted regulation in 48 tissues and cell lines publication-title: Nat. Genet. doi: 10.1038/ng.264 – volume: 23 start-page: 1379 year: 2009 end-page: 1386 ident: CR60 article-title: Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes publication-title: Genes Dev. doi: 10.1101/gad.1788009 – volume: 21 start-page: 191 year: 1999 end-page: 194 ident: CR1 article-title: An encyclopedia of mouse genes publication-title: Nat. Genet. doi: 10.1038/5976 – volume: 7 start-page: 709 year: 2010 end-page: 715 ident: CR78 article-title: Comprehensive comparative analysis of strand-specific RNA sequencing methods publication-title: Nat. Methods doi: 10.1038/nmeth.1491 – volume: 21 start-page: 1859 year: 2005 end-page: 1875 ident: CR9 article-title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti310 – volume: 270 start-page: 467 year: 1995 end-page: 470 ident: CR13 article-title: Quantitative monitoring of gene expression patterns with a complementary DNA microarray publication-title: Science doi: 10.1126/science.270.5235.467 – volume: 31 start-page: 5654 year: 2003 end-page: 5666 ident: CR7 article-title: Improving the genome annotation using maximal transcript alignment assemblies publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkg770 – volume: 12 start-page: 656 year: 2002 end-page: 664 ident: CR8 article-title: BLAT—the BLAST-like alignment tool publication-title: Genome Res. doi: 10.1101/gr.229202 – volume: 20 start-page: 413 year: 2010 end-page: 427 ident: CR26 article-title: Integrative analysis of the melanoma transcriptome publication-title: Genome Res. doi: 10.1101/gr.103697.109 – volume: 21 start-page: 2684 year: 2005 end-page: 2690 ident: CR72 article-title: Jr. A practical false discovery rate approach to identifying patterns of differential expression in microarray data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti407 – volume: 458 start-page: 97 year: 2009 end-page: 101 ident: CR18 article-title: Transcriptome sequencing to detect gene fusions in cancer publication-title: Nature doi: 10.1038/nature07638 – volume: 21 start-page: 936 issue: 6 year: 2010 end-page: 939 ident: CR35 article-title: Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads publication-title: Genome Research doi: 10.1101/gr.111120.110 – volume: 28 start-page: 511 year: 2010 end-page: 515 ident: CR29 article-title: Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1621 – volume: 38 start-page: 4570 year: 2010 end-page: 4578 ident: CR47 article-title: Detection of splice junctions from paired-end RNA-seq data by SpliceMap publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq211 – volume: 6 start-page: S22 year: 2009 end-page: S32 ident: CR62 article-title: Computation for ChIP-seq and RNA-seq studies publication-title: Nat. Methods doi: 10.1038/nmeth.1371 – volume: 7 start-page: 528 year: 2010 end-page: 534 ident: CR81 article-title: Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan publication-title: Nat. Methods doi: 10.1038/nmeth.1470 – volume: 133 start-page: 523 year: 2008 end-page: 536 ident: CR17 article-title: Highly integrated single-base resolution maps of the epigenome in publication-title: Cell doi: 10.1016/j.cell.2008.03.029 – volume: 24 start-page: 2395 year: 2008 end-page: 2396 ident: CR32 article-title: SeqMap: mapping massive amount of oligonucleotides to the genome publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn429 – volume: 4 start-page: e7767 year: 2009 ident: CR31 article-title: BFAST: an alignment tool for large scale genome resequencing publication-title: PLoS ONE doi: 10.1371/journal.pone.0007767 – volume: 10 start-page: 57 year: 2009 end-page: 63 ident: CR63 article-title: RNA-Seq: a revolutionary tool for transcriptomics publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2484 – volume: 16 start-page: 929 year: 2004 end-page: 941 ident: CR11 article-title: Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform publication-title: Mol. Cell doi: 10.1016/j.molcel.2004.12.004 – volume: 7 start-page: 1009 year: 2010 end-page: 1015 ident: CR30 article-title: Analysis and design of RNA sequencing experiments for identifying isoform regulation publication-title: Nat. Methods doi: 10.1038/nmeth.1528 – volume: 25 start-page: 3207 year: 2009 end-page: 3212 ident: CR46 article-title: Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp579 – volume: 469 start-page: 97 year: 2011 end-page: 101 ident: CR79 article-title: Formation, regulation and evolution of 3′UTRs publication-title: Nature doi: 10.1038/nature09616 – volume: 252 start-page: 1651 year: 1991 end-page: 1656 ident: CR6 article-title: Complementary DNA sequencing: expressed sequence tags and human genome project publication-title: Science doi: 10.1126/science.2047873 – volume: 20 start-page: 180 year: 2010 end-page: 189 ident: CR24 article-title: Sex-specific and lineage-specific alternative splicing in primates publication-title: Genome Res. doi: 10.1101/gr.099226.109 – volume: 13 start-page: 1273 year: 2003 end-page: 1289 ident: CR2 article-title: Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia publication-title: Genome Res. doi: 10.1101/gr.1119703 – volume: 97 start-page: 12690 year: 2000 end-page: 12693 ident: CR3 article-title: Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.97.23.12690 – volume: 11 start-page: 94 year: 2010 ident: CR68 article-title: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-94 – volume: 5 start-page: 621 year: 2008 end-page: 628 ident: CR20 article-title: Mapping and quantifying mammalian transcriptomes by RNA-seq publication-title: Nat. Methods doi: 10.1038/nmeth.1226 – volume: 12 start-page: 107 year: 2009 end-page: 118 ident: CR61 article-title: Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond publication-title: Curr. Opin. Plant Biol. doi: 10.1016/j.pbi.2008.11.004 – volume: 296 start-page: 916 year: 2002 end-page: 919 ident: CR10 article-title: Large-scale transcriptional activity in chromosomes 21 and 22 publication-title: Science doi: 10.1126/science.1068597 – volume: 5 start-page: e1000386 year: 2009 ident: CR37 article-title: SHRiMP: accurate mapping of short color-space reads publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1000386 – volume: 46 start-page: 6 year: 1946 ident: CR56 article-title: A combinatorial problem. publication-title: Wetenschappen – volume: 20 start-page: 1740 year: 2010 end-page: 1747 ident: CR27 article-title: Scaffolding a Caenorhabditis nematode genome with RNA-seq publication-title: Genome Res. doi: 10.1101/gr.111021.110 – volume: 31 start-page: 11.5.1 year: 2010 end-page: 11.5.12 ident: CR59 article-title: Using the Velvet assembler for short-read sequencing technologies publication-title: Curr. Protoc. Bioinformatics – volume: 458 start-page: 223 year: 2009 end-page: 227 ident: CR4 article-title: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals publication-title: Nature doi: 10.1038/nature07672 – volume: 38 start-page: e178 year: 2010 ident: CR49 article-title: MapSplice: accurate mapping of RNA-seq reads for splice junction discovery publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq622 – volume: 321 start-page: 956 year: 2008 end-page: 960 ident: CR22 article-title: A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome publication-title: Science doi: 10.1126/science.1160342 – volume: 28 start-page: 503 year: 2010 end-page: 510 ident: CR28 article-title: Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1633 – volume: 26 start-page: 136 year: 2010 end-page: 138 ident: CR77 article-title: DEGseq: an R package for identifying differentially expressed genes from RNA-seq data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp612 – volume: 320 start-page: 1344 year: 2008 end-page: 1349 ident: CR21 article-title: The transcriptional landscape of the yeast genome defined by RNA sequencing publication-title: Science doi: 10.1126/science.1158441 – volume: 135 start-page: 13 year: 2001 end-page: 28 ident: CR43 article-title: An experimental study of a compressed index publication-title: Inf. Sci. doi: 10.1016/S0020-0255(01)00098-6 – volume: 7 start-page: 63 year: 1989 end-page: 73 ident: CR57 article-title: 1-Tuple DNA sequencing: computer analysis publication-title: J. Biomol. Struct. Dyn. doi: 10.1080/07391102.1989.10507752 – volume: 98 start-page: 5116 year: 2001 end-page: 5121 ident: CR70 article-title: Significance analysis of microarrays applied to the ionizing radiation response publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.091062498 – volume: 26 start-page: 139 year: 2010 end-page: 140 ident: CR75 article-title: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp616 – volume: 106 start-page: 3264 year: 2009 end-page: 3269 ident: CR23 article-title: Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.0812841106 – volume: 9 start-page: 128 year: 2008 ident: CR38 article-title: Using quality scores and longer reads improves accuracy of Solexa read mapping publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-9-128 – volume: 21 start-page: 191 year: 1999 ident: BFnmeth1613_CR1 publication-title: Nat. Genet. doi: 10.1038/5976 – volume: 31 start-page: 5654 year: 2003 ident: BFnmeth1613_CR7 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkg770 – volume: 26 start-page: 136 year: 2010 ident: BFnmeth1613_CR77 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp612 – volume: 39 start-page: e9 year: 2010 ident: BFnmeth1613_CR82 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq1015 – volume: 458 start-page: 97 year: 2009 ident: BFnmeth1613_CR18 publication-title: Nature doi: 10.1038/nature07638 – volume: 25 start-page: 3207 year: 2009 ident: BFnmeth1613_CR46 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp579 – volume: 7 start-page: 909 year: 2010 ident: BFnmeth1613_CR53 publication-title: Nat. Methods doi: 10.1038/nmeth.1517 – volume: 117 start-page: e27 year: 2010 ident: BFnmeth1613_CR25 publication-title: Blood doi: 10.1182/blood-2010-07-293332 – volume: 5 start-page: e1000386 year: 2009 ident: BFnmeth1613_CR37 publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1000386 – volume: 38 start-page: e178 year: 2010 ident: BFnmeth1613_CR49 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq622 – volume: 270 start-page: 467 year: 1995 ident: BFnmeth1613_CR13 publication-title: Science doi: 10.1126/science.270.5235.467 – volume: 18 start-page: 1509 year: 2008 ident: BFnmeth1613_CR19 publication-title: Genome Res. doi: 10.1101/gr.079558.108 – volume: 20 start-page: 1432 year: 2010 ident: BFnmeth1613_CR55 publication-title: Genome Res. doi: 10.1101/gr.103846.109 – volume: 18 start-page: 1851 year: 2008 ident: BFnmeth1613_CR33 publication-title: Genome Res. doi: 10.1101/gr.078212.108 – volume: 10 start-page: 57 year: 2009 ident: BFnmeth1613_CR63 publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2484 – volume: 24 start-page: 713 year: 2008 ident: BFnmeth1613_CR34 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn025 – volume: 20 start-page: 413 year: 2010 ident: BFnmeth1613_CR26 publication-title: Genome Res. doi: 10.1101/gr.103697.109 – volume: 19 start-page: 6 year: 2007 ident: BFnmeth1613_CR71 publication-title: Curr. Protoc. Mol. Biol. – volume: 25 start-page: 1966 year: 2009 ident: BFnmeth1613_CR41 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp336 – volume: 40 start-page: 1416 year: 2008 ident: BFnmeth1613_CR12 publication-title: Nat. Genet. doi: 10.1038/ng.264 – volume: 7 start-page: 528 year: 2010 ident: BFnmeth1613_CR81 publication-title: Nat. Methods doi: 10.1038/nmeth.1470 – volume: 133 start-page: 523 year: 2008 ident: BFnmeth1613_CR17 publication-title: Cell doi: 10.1016/j.cell.2008.03.029 – volume: 106 start-page: 3264 year: 2009 ident: BFnmeth1613_CR23 publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.0812841106 – volume: 25 start-page: 2872 year: 2009 ident: BFnmeth1613_CR54 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp367 – volume: 25 start-page: 1026 year: 2009 ident: BFnmeth1613_CR66 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp113 – volume: 97 start-page: 12690 year: 2000 ident: BFnmeth1613_CR3 publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.97.23.12690 – volume: 5 start-page: 621 year: 2008 ident: BFnmeth1613_CR20 publication-title: Nat. Methods doi: 10.1038/nmeth.1226 – volume: 458 start-page: 223 year: 2009 ident: BFnmeth1613_CR4 publication-title: Nature doi: 10.1038/nature07672 – volume: 9 start-page: R175 year: 2008 ident: BFnmeth1613_CR16 publication-title: Genome Biol. doi: 10.1186/gb-2008-9-12-r175 – volume: 24 start-page: 2395 year: 2008 ident: BFnmeth1613_CR32 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn429 – volume: 23 start-page: 1379 year: 2009 ident: BFnmeth1613_CR60 publication-title: Genes Dev. doi: 10.1101/gad.1788009 – volume: 26 start-page: 873 year: 2010 ident: BFnmeth1613_CR50 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq057 – volume: 98 start-page: 5116 year: 2001 ident: BFnmeth1613_CR70 publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.091062498 – volume: 296 start-page: 916 year: 2002 ident: BFnmeth1613_CR10 publication-title: Science doi: 10.1126/science.1068597 – volume: 320 start-page: 1344 year: 2008 ident: BFnmeth1613_CR21 publication-title: Science doi: 10.1126/science.1158441 – volume: 10 start-page: R25 year: 2009 ident: BFnmeth1613_CR39 publication-title: Genome Biol. doi: 10.1186/gb-2009-10-3-r25 – volume: 7 start-page: 709 year: 2010 ident: BFnmeth1613_CR78 publication-title: Nat. Methods doi: 10.1038/nmeth.1491 – volume: 26 start-page: 2534 year: 2010 ident: BFnmeth1613_CR36 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq485 – ident: BFnmeth1613_CR42 – volume: 8 start-page: 177 issue: Suppl. 1 year: 2010 ident: BFnmeth1613_CR69 publication-title: J. Bioinform. Comput. Biol. doi: 10.1142/S0219720010005178 – volume: 24 start-page: i174 year: 2008 ident: BFnmeth1613_CR51 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn300 – volume: 11 start-page: R106 year: 2010 ident: BFnmeth1613_CR76 publication-title: Genome Biol. doi: 10.1186/gb-2010-11-10-r106 – volume: 447 start-page: 167 year: 2007 ident: BFnmeth1613_CR52 publication-title: Nature doi: 10.1038/nature05805 – volume: 4 start-page: e7767 year: 2009 ident: BFnmeth1613_CR31 publication-title: PLoS ONE doi: 10.1371/journal.pone.0007767 – volume: 11 start-page: R83 year: 2010 ident: BFnmeth1613_CR73 publication-title: Genome Biol. doi: 10.1186/gb-2010-11-8-r83 – volume: 26 start-page: 139 year: 2010 ident: BFnmeth1613_CR75 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp616 – volume: 18 start-page: 821 year: 2008 ident: BFnmeth1613_CR58 publication-title: Genome Res. doi: 10.1101/gr.074492.107 – volume: 46 start-page: 6 year: 1946 ident: BFnmeth1613_CR56 publication-title: Wetenschappen – volume: 135 start-page: 13 year: 2001 ident: BFnmeth1613_CR43 publication-title: Inf. Sci. doi: 10.1016/S0020-0255(01)00098-6 – volume: 9 start-page: 128 year: 2008 ident: BFnmeth1613_CR38 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-9-128 – volume: 4 start-page: 14 year: 2009 ident: BFnmeth1613_CR64 publication-title: Biol. Direct doi: 10.1186/1745-6150-4-14 – volume: 12 start-page: 107 year: 2009 ident: BFnmeth1613_CR61 publication-title: Curr. Opin. Plant Biol. doi: 10.1016/j.pbi.2008.11.004 – volume: 469 start-page: 97 year: 2011 ident: BFnmeth1613_CR79 publication-title: Nature doi: 10.1038/nature09616 – volume: 25 start-page: 2615 year: 2009 ident: BFnmeth1613_CR45 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp459 – volume: 11 start-page: R25 year: 2010 ident: BFnmeth1613_CR65 publication-title: Genome Biol. doi: 10.1186/gb-2010-11-3-r25 – volume: 26 start-page: 493 year: 2010 ident: BFnmeth1613_CR67 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp692 – volume: 28 start-page: 503 year: 2010 ident: BFnmeth1613_CR28 publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1633 – volume: 252 start-page: 1651 year: 1991 ident: BFnmeth1613_CR6 publication-title: Science doi: 10.1126/science.2047873 – volume: 31 start-page: 11.5.1 year: 2010 ident: BFnmeth1613_CR59 publication-title: Curr. Protoc. Bioinformatics doi: 10.1002/0471250953.bi1105s31 – volume: 12 start-page: 656 year: 2002 ident: BFnmeth1613_CR8 publication-title: Genome Res. doi: 10.1101/gr.229202 – volume: 7 start-page: 63 year: 1989 ident: BFnmeth1613_CR57 publication-title: J. Biomol. Struct. Dyn. doi: 10.1080/07391102.1989.10507752 – volume: 329 start-page: 432 year: 2010 ident: BFnmeth1613_CR80 publication-title: Science doi: 10.1126/science.1191244 – volume: 7 start-page: 1009 year: 2010 ident: BFnmeth1613_CR30 publication-title: Nat. Methods doi: 10.1038/nmeth.1528 – volume: 6 start-page: S22 year: 2009 ident: BFnmeth1613_CR62 publication-title: Nat. Methods doi: 10.1038/nmeth.1371 – volume: 21 start-page: 1859 year: 2005 ident: BFnmeth1613_CR9 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti310 – volume: 16 start-page: 929 year: 2004 ident: BFnmeth1613_CR11 publication-title: Mol. Cell doi: 10.1016/j.molcel.2004.12.004 – volume: 20 start-page: 180 year: 2010 ident: BFnmeth1613_CR24 publication-title: Genome Res. doi: 10.1101/gr.099226.109 – volume: 11 start-page: 94 year: 2010 ident: BFnmeth1613_CR68 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-94 – volume: 38 start-page: 4570 year: 2010 ident: BFnmeth1613_CR47 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq211 – volume: 25 start-page: 1105 year: 2009 ident: BFnmeth1613_CR48 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp120 – volume: 20 start-page: 1740 year: 2010 ident: BFnmeth1613_CR27 publication-title: Genome Res. doi: 10.1101/gr.111021.110 – volume: 23 start-page: 2881 year: 2007 ident: BFnmeth1613_CR74 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm453 – volume: 7 start-page: 843 year: 2010 ident: BFnmeth1613_CR44 publication-title: Nat. Methods doi: 10.1038/nmeth.1503 – volume: 25 start-page: 1754 year: 2009 ident: BFnmeth1613_CR40 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 456 start-page: 470 year: 2008 ident: BFnmeth1613_CR5 publication-title: Nature doi: 10.1038/nature07509 – volume: 321 start-page: 956 year: 2008 ident: BFnmeth1613_CR22 publication-title: Science doi: 10.1126/science.1160342 – volume: 5 start-page: 613 year: 2008 ident: BFnmeth1613_CR15 publication-title: Nat. Methods doi: 10.1038/nmeth.1223 – volume: 28 start-page: 511 year: 2010 ident: BFnmeth1613_CR29 publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1621 – volume: 21 start-page: 936 issue: 6 year: 2010 ident: BFnmeth1613_CR35 publication-title: Genome Research doi: 10.1101/gr.111120.110 – volume: 13 start-page: 1273 year: 2003 ident: BFnmeth1613_CR2 publication-title: Genome Res. doi: 10.1101/gr.1119703 – volume: 21 start-page: 2684 year: 2005 ident: BFnmeth1613_CR72 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti407 – volume: 286 start-page: 531 year: 1999 ident: BFnmeth1613_CR14 publication-title: Science doi: 10.1126/science.286.5439.531 – reference: 15610736 - Mol Cell. 2004 Dec 22;16(6):929-41 – reference: 19182780 - Nature. 2009 Mar 12;458(7235):223-7 – reference: 2684223 - J Biomol Struct Dyn. 1989 Aug;7(1):63-73 – reference: 18599741 - Science. 2008 Aug 15;321(5891):956-60 – reference: 20167110 - BMC Bioinformatics. 2010 Feb 18;11:94 – reference: 20980679 - Blood. 2011 Jan 13;117(2):e27-38 – reference: 20543846 - Nat Methods. 2010 Jul;7(7):528-34 – reference: 20522740 - Science. 2010 Jul 23;329(5990):432-5 – reference: 19208812 - Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9 – reference: 18307793 - BMC Bioinformatics. 2008 Feb 28;9:128 – reference: 18714091 - Genome Res. 2008 Nov;18(11):1851-8 – reference: 20371516 - Nucleic Acids Res. 2010 Aug;38(14):4570-8 – reference: 20836074 - Curr Protoc Bioinformatics. 2010 Sep;Chapter 11:Unit 11.5 – reference: 18978772 - Nature. 2008 Nov 27;456(7221):470-6 – reference: 18516045 - Nat Methods. 2008 Jul;5(7):621-8 – reference: 11309499 - Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 – reference: 19648138 - Bioinformatics. 2009 Oct 1;25(19):2615-6 – reference: 19497933 - Bioinformatics. 2009 Aug 1;25(15):1966-7 – reference: 19910308 - Bioinformatics. 2010 Jan 1;26(1):139-40 – reference: 11932250 - Genome Res. 2002 Apr;12(4):656-64 – reference: 19157957 - Curr Opin Plant Biol. 2009 Apr;12(2):107-18 – reference: 20835245 - Nat Methods. 2010 Oct;7(10):843-7 – reference: 15797908 - Bioinformatics. 2005 Jun 1;21(11):2684-90 – reference: 20022975 - Bioinformatics. 2010 Feb 15;26(4):493-500 – reference: 19136943 - Nature. 2009 Mar 5;458(7234):97-101 – reference: 20980556 - Genome Res. 2011 Jun;21(6):936-9 – reference: 20979621 - Genome Biol. 2010;11(10):R106 – reference: 19015660 - Nat Rev Genet. 2009 Jan;10(1):57-63 – reference: 18451266 - Science. 2008 Jun 6;320(5881):1344-9 – reference: 11070084 - Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12690-3 – reference: 15728110 - Bioinformatics. 2005 May 1;21(9):1859-75 – reference: 21085120 - Nature. 2011 Jan 6;469(7328):97-101 – reference: 20179022 - Genome Res. 2010 Apr;20(4):413-27 – reference: 18265395 - Curr Protoc Mol Biol. 2007 Jan;Chapter 19:Unit 19.6 – reference: 19528315 - Genes Dev. 2009 Jun 15;23(12):1379-86 – reference: 19261174 - Genome Biol. 2009;10(3):R25 – reference: 7569999 - Science. 1995 Oct 20;270(5235):467-70 – reference: 11988577 - Science. 2002 May 3;296(5569):916-9 – reference: 20196867 - Genome Biol. 2010;11(3):R25 – reference: 20436462 - Nat Biotechnol. 2010 May;28(5):503-10 – reference: - Nat Methods. 2011 Jun;8(6):following 477 – reference: 21155027 - J Bioinform Comput Biol. 2010 Dec;8 Suppl 1:177-92 – reference: 19844228 - Nat Methods. 2009 Nov;6(11 Suppl):S22-32 – reference: 2047873 - Science. 1991 Jun 21;252(5013):1651-6 – reference: 20739310 - Bioinformatics. 2010 Oct 15;26(20):2534-40 – reference: 19087247 - Genome Biol. 2008;9(12):R175 – reference: 19808877 - Bioinformatics. 2009 Dec 15;25(24):3207-12 – reference: 19907642 - PLoS One. 2009 Nov 11;4(11):e7767 – reference: 19244387 - Bioinformatics. 2009 Apr 15;25(8):1026-32 – reference: 19461883 - PLoS Comput Biol. 2009 May;5(5):e1000386 – reference: 18349386 - Genome Res. 2008 May;18(5):821-9 – reference: 20701754 - Genome Biol. 2010;11(8):R83 – reference: 20147302 - Bioinformatics. 2010 Apr 1;26(7):873-81 – reference: 20711195 - Nat Methods. 2010 Sep;7(9):709-15 – reference: 20693479 - Genome Res. 2010 Oct;20(10):1432-40 – reference: 18227114 - Bioinformatics. 2008 Mar 1;24(5):713-4 – reference: 17495919 - Nature. 2007 May 10;447(7141):167-77 – reference: 18423832 - Cell. 2008 May 2;133(3):523-36 – reference: 12819125 - Genome Res. 2003 Jun;13(6B):1273-89 – reference: 19855105 - Bioinformatics. 2010 Jan 1;26(1):136-8 – reference: 20009012 - Genome Res. 2010 Feb;20(2):180-9 – reference: 17881408 - Bioinformatics. 2007 Nov 1;23(21):2881-7 – reference: 19371405 - Biol Direct. 2009 Apr 16;4:14 – reference: 18550803 - Genome Res. 2008 Sep;18(9):1509-17 – reference: 18689821 - Bioinformatics. 2008 Aug 15;24(16):i174-80 – reference: 20436464 - Nat Biotechnol. 2010 May;28(5):511-5 – reference: 19289445 - Bioinformatics. 2009 May 1;25(9):1105-11 – reference: 10521349 - Science. 1999 Oct 15;286(5439):531-7 – reference: 19528083 - Bioinformatics. 2009 Nov 1;25(21):2872-7 – reference: 18978788 - Nat Genet. 2008 Dec;40(12):1416-25 – reference: 20935650 - Nat Methods. 2010 Nov;7(11):909-12 – reference: 18516046 - Nat Methods. 2008 Jul;5(7):613-9 – reference: 14500829 - Nucleic Acids Res. 2003 Oct 1;31(19):5654-66 – reference: 20802226 - Nucleic Acids Res. 2010 Oct;38(18):e178 – reference: 19451168 - Bioinformatics. 2009 Jul 15;25(14):1754-60 – reference: 9988271 - Nat Genet. 1999 Feb;21(2):191-4 – reference: 20980554 - Genome Res. 2010 Dec;20(12):1740-7 – reference: 21059678 - Nucleic Acids Res. 2011 Jan;39(2):e9 – reference: 18697769 - Bioinformatics. 2008 Oct 15;24(20):2395-6
SSID	ssj0033425
Score	2.5787978
SecondaryResourceType	review_article
Snippet	High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all...
SourceID	proquest gale pubmed crossref springer
SourceType	Aggregation Database Index Database Enrichment Source Publisher
StartPage	469
SubjectTerms	631/114/2184 631/1647/514/1949 631/208/212/2019 Animals Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Cellular biology Computational Biology - methods DNA sequencing Gene Expression Profiling - statistics & numerical data Genomics Genomics - statistics & numerical data High-Throughput Nucleotide Sequencing - statistics & numerical data Humans Life Sciences Nucleotide sequencing Physiological aspects Proteomics review-article Ribonucleic acid RNA Sequence Alignment - statistics & numerical data Sequence Analysis, RNA - statistics & numerical data
Title	Computational methods for transcriptome annotation and quantification using RNA-seq
URI	https://link.springer.com/article/10.1038/nmeth.1613 https://www.ncbi.nlm.nih.gov/pubmed/21623353 https://www.proquest.com/docview/868908551 https://www.proquest.com/docview/869406972 https://www.proquest.com/docview/904482072
Volume	8
WOSCitedRecordID	wos000291031800015&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
journalDatabaseRights	– providerCode: PRVPQU databaseName: Advanced Technologies & Aerospace Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: P5Z dateStart: 20041001 isFulltext: true titleUrlDefault: https://search.proquest.com/hightechjournals providerName: ProQuest – providerCode: PRVPQU databaseName: Agricultural Science Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: M0K dateStart: 20041001 isFulltext: true titleUrlDefault: https://search.proquest.com/agriculturejournals providerName: ProQuest – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: M7P dateStart: 20041001 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Earth, Atmospheric & Aquatic Science Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: PCBAR dateStart: 20041001 isFulltext: true titleUrlDefault: https://search.proquest.com/eaasdb providerName: ProQuest – providerCode: PRVPQU databaseName: Engineering Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: M7S dateStart: 20041001 isFulltext: true titleUrlDefault: http://search.proquest.com providerName: ProQuest – providerCode: PRVPQU databaseName: Environmental Science Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: PATMY dateStart: 20041001 isFulltext: true titleUrlDefault: http://search.proquest.com/environmentalscience providerName: ProQuest – providerCode: PRVPQU databaseName: Materials Science Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: KB. dateStart: 20041001 isFulltext: true titleUrlDefault: http://search.proquest.com/materialsscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: BENPR dateStart: 20041001 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Health & Medical Collection customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: 7X7 dateStart: 20041001 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: Science Database customDbUrl: eissn: 1548-7105 dateEnd: 20171231 omitProxy: false ssIdentifier: ssj0033425 issn: 1548-7091 databaseCode: M2P dateStart: 20041001 isFulltext: true titleUrlDefault: https://search.proquest.com/sciencejournals providerName: ProQuest
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1La9wwEBZN0kIufTfdJg2GBkoPTmxL1uNUNiGhELos2RaWXow90oZCa2fj3UL_fWcke_No0ksvg2yPbckjzYyk8XyM7TlIOagqjW2Zy1hInsWVSXIsGcGdmCW6LD3YhBqN9HRqxl1sTtuFVfY60Stq2wCtkR9oqQ3FVKUfL-YxgUbR5mqHoLHGNihJQuYj9ya9IuZceMxVcspjhXaxz07K9UFN-Mz7qUc1uGaPbmvla2bp1j6pNz8nT_6z4k_Z487vjIahozxjD1z9nD0KSJS_X7BJQHfoVgajgCvdRujRRguyZl63ND9dVNZ1E9iwaKP5sgzRRuEURdGfR2ejYdy6-Uv29eT4y9GnuMNbiAHdpkUspXVKS9AA0ihrhQEc7mImU7C8TB1YkJVGC1_hnBA9A6dBCi2Eomk0ZJa_Yut1U7vXLLIzZROL3gFOqEQlS5NUZgYVKtMcOGRywD70X72ALhk5YWL8KPymONeFl1BBEhqwdyvei5CC406u9yS8gsYlPgnK7vcCrA9luCqGGbpahEaoB2znBieOJ7hxebuXY9GN57ZYCXHAotVVupFC1GrXLInF0F_EKrufxSQ4Gc4SYtkK_WrVoCxFP5Tn2Iy9vqNdvf3v1r75ZyW32WZY-qbFoh22vrhcurfsIfxafG8vd9mamipP9S7bODwejc_w6PRwH-nn5JRoNiaqAp0gHeff_gBAoSPF
linkProvider	ProQuest
linkToHtml	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9QwEB6VAoIL78fSApEoQhxCk9jrxwGhFVC1alkhKNLeQjL2IiTIdptdUH8U_5GZOAltedx64BYlk4eTL_PN2GN_ABseU4G6TGNXDFUslcji0iZD2rJSeDlNTFE0YhN6PDaTiX27Aj-6uTBcVtn5xMZRuxlyH_mmUcZyTVX64mAes2gUD652ChoBFbv-6DtlbPXznVf0eR9n2dbr_ZfbcSsqECPFBotYKee1UWgQldXOSYuEaTlVKTpRpB4dqtIQjZWU-BD9eYNKGik154qYOUHXPQfnyY1rriDTkz6_E0I2Gq-cBMSaeLhbDVWYzYr1oJ-ljYrCMf47zQLHaPDUuGxDd1tX_7MXdQ2utHF1NAo_wnVY8dUNuBiUNo9uwvugXtH2fEZBN7uOKGKPFszWje-cffVRUVWzYEabLpovi1BNFXbxLIFP0bvxKK79_BZ8OJMW3YbValb5uxC5qXaJo-iHEkZZqsImpZ1iSWQxRIGZGsDT7ivn2C62zpofX_Jm0F-YvEFEzogYwKPe9iAsMfJHqycMlpz9Dl0Ji3b6BD0Pr-CVjzIKJVlt0Qxg_YQl-Qs8cXitw03e-qs670EzgKg_yidyCV7lZ0s2sTxLWmd_N7EJJftZwiZ3Ao77BmUpxdliSM3Y6ID96-6_t_bePx_yIVza3n-zl-_tjHfX4HLo5ueOsXVYXRwu_X24gN8Wn-vDB80PGsHHswb6T9CKd5Q
linkToPdf	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9NAEB6V8hAX3o_QApYoQhxMbO96vXtAKKJEVEVRxEOqejH27BohgdPUCag_jX_HjNcObXnceuBm2RPbE3-eb2Y9ux_AlsNYYFbGoS1SFUolkrA0UUpbRgonq0gXRSs2kU0mem_PTNfgRz8Xhtsq-5jYBmo7Qx4jH2qlDfdUxcOq64qYbo9fHMxDFpDiD629moZHyK47-k7VW_N8Z5se9eMkGb96__J12AkMhEh5wiJUyrpMK9SIymTWSoOEb1mpGK0oYocWVamJ0koqgogKnUYltZQZ142YWEHnPQfnM3KM675put-TgBCy1XvlgiDMiJP7lVGFHtasDf0sbhUVjnHhaUY4RomnvtG21De--h__adfgSpdvByP_glyHNVffgItegfPoJrzzqhbdiGjg9bSbgDL5YMEs3sbU2VcXFHU982a0aYP5svBdVn4Xzx74FLydjMLGzW_BhzPx6Das17Pa3YXAVpmNLGVFVEjKUhUmKk2FJZFIigITNYCn_RPPsVuEnbVAvuRtM4DQeYuOnNExgEcr2wO_9MgfrZ4wcHKOR3QmLLppFXQ_vLJXPkooxWQVRj2AzROWFEfwxOGNHkN5F8eafAWgAQSro_xDbs2r3WzJJoZnT2fJ301MJCVlmmxyx2N65VASU_4tUnJjqwf5r6v_7u29f97kQ7hE-M7f7Ex2N-CyH_3n8bJNWF8cLt19uIDfFp-bwwftuxrAx7PG-U8Br4CH
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Computational+methods+for+transcriptome+annotation+and+quantification+using+RNA-seq&rft.jtitle=Nature+methods&rft.au=Garber%2C+Manuel&rft.au=Grabherr%2C+Manfred+G&rft.au=Guttman%2C+Mitchell&rft.au=Trapnell%2C+Cole&rft.date=2011-06-01&rft.issn=1548-7091&rft.volume=8&rft.issue=6&rft.spage=469&rft.epage=477&rft_id=info:doi/10.1038%2Fnmeth.1613&rft.externalDBID=NO_FULL_TEXT
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1548-7091&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1548-7091&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1548-7091&client=summon