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For: Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. ACTA ACUST UNITED AC 2012;29:15-21. [PMID: 23104886 DOI: 10.1093/bioinformatics/bts635] [Citation(s) in RCA: 32199] [Impact Index Per Article: 2476.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
32001
Combs PA, Eisen MB. Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols. PeerJ 2015;3:e869. [PMID: 25834775 PMCID: PMC4380159 DOI: 10.7717/peerj.869] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/11/2015] [Indexed: 01/23/2023]  Open
32002
Therapy-induced tumour secretomes promote resistance and tumour progression. Nature 2015;520:368-72. [PMID: 25807485 PMCID: PMC4507807 DOI: 10.1038/nature14336] [Citation(s) in RCA: 381] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/12/2015] [Indexed: 12/11/2022]
32003
Farlow JL, Lin H, Sauerbeck L, Lai D, Koller DL, Pugh E, Hetrick K, Ling H, Kleinloog R, van der Vlies P, Deelen P, Swertz MA, Verweij BH, Regli L, Rinkel GJE, Ruigrok YM, Doheny K, Liu Y, Broderick J, Foroud T, FIA Study Investigators. Lessons learned from whole exome sequencing in multiplex families affected by a complex genetic disorder, intracranial aneurysm. PLoS One 2015;10:e0121104. [PMID: 25803036 PMCID: PMC4372548 DOI: 10.1371/journal.pone.0121104] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/10/2015] [Indexed: 12/30/2022]  Open
32004
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 2015;112:4322-7. [PMID: 25787252 DOI: 10.1073/pnas.1503587112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
32005
Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV. Natural variation of gene models in Drosophila melanogaster. BMC Genomics 2015;16:198. [PMID: 25888292 PMCID: PMC4373058 DOI: 10.1186/s12864-015-1415-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/28/2015] [Indexed: 01/10/2025]  Open
32006
HEB associates with PRC2 and SMAD2/3 to regulate developmental fates. Nat Commun 2015;6:6546. [PMID: 25775035 DOI: 10.1038/ncomms7546] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/05/2015] [Indexed: 11/09/2022]  Open
32007
Jalali S, Kapoor S, Sivadas A, Bhartiya D, Scaria V. Computational approaches towards understanding human long non-coding RNA biology. Bioinformatics 2015;31:2241-51. [DOI: 10.1093/bioinformatics/btv148] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 03/10/2015] [Indexed: 12/18/2022]  Open
32008
DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, Jamieson CHM, Carson D, Kipps TJ, Frazer KA. Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PLoS Comput Biol 2015;11:e1004105. [PMID: 25768983 PMCID: PMC4358997 DOI: 10.1371/journal.pcbi.1004105] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/29/2014] [Indexed: 01/12/2023]  Open
32009
Gabel HW, Kinde B, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH, Greenberg ME. Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature 2015;522:89-93. [PMID: 25762136 PMCID: PMC4480648 DOI: 10.1038/nature14319] [Citation(s) in RCA: 440] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 02/12/2015] [Indexed: 12/29/2022]
32010
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 2015;12:357-60. [PMID: 25751142 DOI: 10.1038/nmeth.3317] [Citation(s) in RCA: 14630] [Impact Index Per Article: 1463.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/16/2015] [Indexed: 02/06/2023]
32011
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nat Methods 2015;12:339-42. [PMID: 25751143 DOI: 10.1038/nmeth.3321] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/01/2015] [Indexed: 12/20/2022]
32012
Arboleda VA, Lee H, Dorrani N, Zadeh N, Willis M, Macmurdo CF, Manning MA, Kwan A, Hudgins L, Barthelemy F, Miceli MC, Quintero-Rivera F, Kantarci S, Strom SP, Deignan JL, Grody WW, Vilain E, Nelson SF. De novo nonsense mutations in KAT6A, a lysine acetyl-transferase gene, cause a syndrome including microcephaly and global developmental delay. Am J Hum Genet 2015;96:498-506. [PMID: 25728775 DOI: 10.1016/j.ajhg.2015.01.017] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/20/2015] [Indexed: 12/19/2022]  Open
32013
Gibb EA, Warren RL, Wilson GW, Brown SD, Robertson GA, Morin GB, Holt RA. Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. Genome Med 2015;7:22. [PMID: 25821520 PMCID: PMC4375928 DOI: 10.1186/s13073-015-0142-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/12/2015] [Indexed: 11/15/2022]  Open
32014
Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, Buettner F, Macaulay IC, Jawaid W, Diamanti E, Nishikawa SI, Piterman N, Kouskoff V, Theis FJ, Fisher J, Göttgens B. Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol 2015;33:269-276. [PMID: 25664528 PMCID: PMC4374163 DOI: 10.1038/nbt.3154] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 01/16/2015] [Indexed: 11/16/2022]
32015
Lai KP, Li JW, Wang SY, Chiu JMY, Tse A, Lau K, Lok S, Au DWT, Tse WKF, Wong CKC, Chan TF, Kong RYC, Wu RSS. Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes. BMC Genomics 2015;16:135. [PMID: 25765076 PMCID: PMC4352242 DOI: 10.1186/s12864-015-1325-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 02/06/2015] [Indexed: 11/12/2022]  Open
32016
Farkas MH, Au ED, Sousa ME, Pierce EA. RNA-Seq: Improving Our Understanding of Retinal Biology and Disease. Cold Spring Harb Perspect Med 2015;5:a017152. [PMID: 25722474 PMCID: PMC4561396 DOI: 10.1101/cshperspect.a017152] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
32017
mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer. PLoS One 2015;10:e0117818. [PMID: 25710561 PMCID: PMC4339844 DOI: 10.1371/journal.pone.0117818] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/30/2014] [Indexed: 12/30/2022]  Open
32018
Olarerin-George AO, Hogenesch JB. Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive. Nucleic Acids Res 2015;43:2535-42. [PMID: 25712092 PMCID: PMC4357728 DOI: 10.1093/nar/gkv136] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
32019
Lin IH, Chen DT, Chang YF, Lee YL, Su CH, Cheng C, Tsai YC, Ng SC, Chen HT, Lee MC, Chen HW, Suen SH, Chen YC, Liu TT, Chang CH, Hsu MT. Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes. PLoS One 2015;10:e0118453. [PMID: 25706888 PMCID: PMC4338251 DOI: 10.1371/journal.pone.0118453] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/20/2015] [Indexed: 01/18/2023]  Open
32020
Wei YN, Hu HY, Xie GC, Fu N, Ning ZB, Zeng R, Khaitovich P. Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. Genome Biol 2015;16:41. [PMID: 25853883 PMCID: PMC4375924 DOI: 10.1186/s13059-015-0608-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 02/09/2015] [Indexed: 12/21/2022]  Open
32021
Zhao S, Zhang B. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC Genomics 2015;16:97. [PMID: 25765860 PMCID: PMC4339237 DOI: 10.1186/s12864-015-1308-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/30/2015] [Indexed: 01/09/2023]  Open
32022
Neeland MR, Elhay MJ, Powell DR, Rossello FJ, Meeusen ENT, de Veer MJ. Transcriptional profile in afferent lymph cells following vaccination with liposomes incorporating CpG. Immunology 2015;144:518-529. [PMID: 25308816 DOI: 10.1111/imm.12401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/14/2014] [Accepted: 10/02/2014] [Indexed: 12/17/2022]  Open
32023
Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JAD, Hoffmann A. A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide. Mol Syst Biol 2015;11:783. [PMID: 25680807 PMCID: PMC4358656 DOI: 10.15252/msb.20145554] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
32024
Lim J, Ha M, Chang H, Kwon SC, Simanshu DK, Patel DJ, Kim VN. Uridylation by TUT4 and TUT7 marks mRNA for degradation. Cell 2015;159:1365-76. [PMID: 25480299 DOI: 10.1016/j.cell.2014.10.055] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/24/2014] [Accepted: 10/20/2014] [Indexed: 02/05/2023]
32025
Park SM, Gönen M, Vu L, Minuesa G, Tivnan P, Barlowe TS, Taggart J, Lu Y, Deering RP, Hacohen N, Figueroa ME, Paietta E, Fernandez HF, Tallman MS, Melnick A, Levine R, Leslie C, Lengner CJ, Kharas MG. Musashi2 sustains the mixed-lineage leukemia-driven stem cell regulatory program. J Clin Invest 2015;125:1286-98. [PMID: 25664853 DOI: 10.1172/jci78440] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/05/2015] [Indexed: 01/15/2023]  Open
32026
Discovery of CTCF-sensitive Cis-spliced fusion RNAs between adjacent genes in human prostate cells. PLoS Genet 2015;11:e1005001. [PMID: 25658338 PMCID: PMC4450057 DOI: 10.1371/journal.pgen.1005001] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/13/2015] [Indexed: 11/19/2022]  Open
32027
Molineaux AC, Maier JA, Schecker T, Sears KE. Exogenous retinoic acid induces digit reduction in opossums (Monodelphis domestica) by disrupting cell death and proliferation, and apical ectodermal ridge and zone of polarizing activity function. ACTA ACUST UNITED AC 2015;103:225-34. [PMID: 25656823 DOI: 10.1002/bdra.23347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/25/2014] [Accepted: 12/04/2014] [Indexed: 01/25/2023]
32028
Genetic inactivation of TRAF3 in canine and human B-cell lymphoma. Blood 2015;125:999-1005. [DOI: 10.1182/blood-2014-10-602714] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
32029
Zheng CL, Wilmot B, Walter NA, Oberbeck D, Kawane S, Searles RP, McWeeney SK, Hitzemann R. Splicing landscape of the eight collaborative cross founder strains. BMC Genomics 2015;16:52. [PMID: 25652416 PMCID: PMC4320832 DOI: 10.1186/s12864-015-1267-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/22/2015] [Indexed: 12/20/2022]  Open
32030
Casey ME, Meade KG, Nalpas NC, Taraktsoglou M, Browne JA, Killick KE, Park SDE, Gormley E, Hokamp K, Magee DA, MacHugh DE. Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq. Front Immunol 2015;6:23. [PMID: 25699042 PMCID: PMC4316787 DOI: 10.3389/fimmu.2015.00023] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/10/2015] [Indexed: 12/28/2022]  Open
32031
Ramaswamy K, Spitzer B, Kentsis A. Therapeutic Re-Activation of Protein Phosphatase 2A in Acute Myeloid Leukemia. Front Oncol 2015;5:16. [PMID: 25699237 PMCID: PMC4313608 DOI: 10.3389/fonc.2015.00016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 01/13/2015] [Indexed: 11/13/2022]  Open
32032
Legeai F, Derrien T. Identification of long non-coding RNAs in insects genomes. CURRENT OPINION IN INSECT SCIENCE 2015;7:37-44. [PMID: 32846672 DOI: 10.1016/j.cois.2015.01.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 06/11/2023]
32033
Hoff KJ, Stanke M. Current methods for automated annotation of protein-coding genes. CURRENT OPINION IN INSECT SCIENCE 2015;7:8-14. [PMID: 32846689 DOI: 10.1016/j.cois.2015.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/08/2014] [Accepted: 02/18/2015] [Indexed: 06/11/2023]
32034
Fang S, Suh JM, Reilly SM, Yu E, Osborn O, Lackey D, Yoshihara E, Perino A, Jacinto S, Lukasheva Y, Atkins AR, Khvat A, Schnabl B, Yu RT, Brenner DA, Coulter S, Liddle C, Schoonjans K, Olefsky JM, Saltiel AR, Downes M, Evans RM. Intestinal FXR agonism promotes adipose tissue browning and reduces obesity and insulin resistance. Nat Med 2015;21:159-65. [PMID: 25559344 PMCID: PMC4320010 DOI: 10.1038/nm.3760] [Citation(s) in RCA: 579] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/21/2014] [Indexed: 12/14/2022]
32035
Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI. Omics Pipe: a community-based framework for reproducible multi-omics data analysis. ACTA ACUST UNITED AC 2015;31:1724-8. [PMID: 25637560 DOI: 10.1093/bioinformatics/btv061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/25/2015] [Indexed: 01/08/2023]
32036
Ranzani V, Rossetti G, Panzeri I, Arrigoni A, Bonnal RJ, Curti S, Gruarin P, Provasi E, Sugliano E, Marconi M, De Francesco R, Geginat J, Bodega B, Abrignani S, Pagani M. The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. Nat Immunol 2015;16:318-325. [PMID: 25621826 PMCID: PMC4333215 DOI: 10.1038/ni.3093] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 12/18/2014] [Indexed: 12/14/2022]
32037
Nowak MD, Russo G, Schlapbach R, Huu CN, Lenhard M, Conti E. The draft genome of Primula veris yields insights into the molecular basis of heterostyly. Genome Biol 2015;16:12. [PMID: 25651398 PMCID: PMC4305239 DOI: 10.1186/s13059-014-0567-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 12/11/2014] [Indexed: 12/04/2022]  Open
32038
Structural insights into mis-regulation of protein kinase A in human tumors. Proc Natl Acad Sci U S A 2015;112:1374-9. [PMID: 25605907 DOI: 10.1073/pnas.1424206112] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
32039
Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun 2015;6:5903. [PMID: 25582907 PMCID: PMC4308717 DOI: 10.1038/ncomms6903] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 12/13/2022]  Open
32040
Ran L, Sirota I, Cao Z, Murphy D, Chen Y, Shukla S, Xie Y, Kaufmann MC, Gao D, Zhu S, Rossi F, Wongvipat J, Taguchi T, Tap WD, Mellinghoff IK, Besmer P, Antonescu CR, Chen Y, Chi P. Combined inhibition of MAP kinase and KIT signaling synergistically destabilizes ETV1 and suppresses GIST tumor growth. Cancer Discov 2015;5:304-15. [PMID: 25572173 DOI: 10.1158/2159-8290.cd-14-0985] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
32041
Madsen JGS, Schmidt SF, Larsen BD, Loft A, Nielsen R, Mandrup S. iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic Acids Res 2015;43:e40. [PMID: 25564527 PMCID: PMC4381047 DOI: 10.1093/nar/gku1365] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/19/2014] [Indexed: 11/21/2022]  Open
32042
Fernandez-Cuesta L, Sun R, Menon R, George J, Lorenz S, Meza-Zepeda LA, Peifer M, Plenker D, Heuckmann JM, Leenders F, Zander T, Dahmen I, Koker M, Schöttle J, Ullrich RT, Altmüller J, Becker C, Nürnberg P, Seidel H, Böhm D, Göke F, Ansén S, Russell PA, Wright GM, Wainer Z, Solomon B, Petersen I, Clement JH, Sänger J, Brustugun OT, Helland Å, Solberg S, Lund-Iversen M, Buettner R, Wolf J, Brambilla E, Vingron M, Perner S, Haas SA, Thomas RK. Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biol 2015;16:7. [PMID: 25650807 PMCID: PMC4300615 DOI: 10.1186/s13059-014-0558-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 12/03/2014] [Indexed: 02/08/2023]  Open
32043
Bolser DM, Kerhornou A, Walts B, Kersey P. Triticeae resources in Ensembl Plants. PLANT & CELL PHYSIOLOGY 2015;56:e3. [PMID: 25432969 PMCID: PMC4301745 DOI: 10.1093/pcp/pcu183] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/12/2014] [Indexed: 05/21/2023]
32044
Li Q, Zheng Q, Shen W, Cram D, Fowler DB, Wei Y, Zou J. Understanding the biochemical basis of temperature-induced lipid pathway adjustments in plants. THE PLANT CELL 2015;27:86-103. [PMID: 25564555 PMCID: PMC4330585 DOI: 10.1105/tpc.114.134338] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/11/2014] [Accepted: 12/16/2014] [Indexed: 05/20/2023]
32045
López García de Lomana A, Schäuble S, Valenzuela J, Imam S, Carter W, Bilgin DD, Yohn CB, Turkarslan S, Reiss DJ, Orellana MV, Price ND, Baliga NS. Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2015;8:207. [PMID: 26633994 PMCID: PMC4667458 DOI: 10.1186/s13068-015-0391-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/17/2015] [Indexed: 05/08/2023]
32046
Geula S, Moshitch-Moshkovitz S, Dominissini D, Mansour AA, Kol N, Salmon-Divon M, Hershkovitz V, Peer E, Mor N, Manor YS, Ben-Haim MS, Eyal E, Yunger S, Pinto Y, Jaitin DA, Viukov S, Rais Y, Krupalnik V, Chomsky E, Zerbib M, Maza I, Rechavi Y, Massarwa R, Hanna S, Amit I, Levanon EY, Amariglio N, Stern-Ginossar N, Novershtern N, Rechavi G, Hanna JH. Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 2015;347:1002-6. [PMID: 25569111 DOI: 10.1126/science.1261417] [Citation(s) in RCA: 1236] [Impact Index Per Article: 123.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
32047
Kim SY, Park C, Kim HJ, Park J, Hwang J, Kim JI, Choi MG, Kim S, Kim KM, Kang MS. Deregulation of immune response genes in patients with Epstein-Barr virus-associated gastric cancer and outcomes. Gastroenterology 2015;148:137-147.e9. [PMID: 25254613 DOI: 10.1053/j.gastro.2014.09.020] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 09/14/2014] [Accepted: 09/15/2014] [Indexed: 12/13/2022]
32048
Love MI, Anders S, Kim V, Huber W. RNA-Seq workflow: gene-level exploratory analysis and differential expression. F1000Res 2015. [PMID: 26674615 DOI: 10.12688/f1000r.esearch.7035.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]  Open
32049
Li YI, Sanchez-Pulido L, Haerty W, Ponting CP. RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts. Genome Res 2015;25:1-13. [PMID: 25524026 PMCID: PMC4317164 DOI: 10.1101/gr.181990.114] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/27/2014] [Indexed: 11/24/2022]
32050
Koepfli KP, Paten B, O'Brien SJ. The Genome 10K Project: a way forward. Annu Rev Anim Biosci 2015;3:57-111. [PMID: 25689317 PMCID: PMC5837290 DOI: 10.1146/annurev-animal-090414-014900] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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