-
1
-
-
84879987789
-
Linc RNAs: Genomics, evolution, and mechanisms
-
23827673
-
Ulitsky I, Bartel DP (2013) linc RNAs: genomics, evolution, and mechanisms. Cell 154: 26-46. doi: 10.1016/j.cell.2013.06.020 PMID: 23827673
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
2
-
-
84875590101
-
Long noncoding RNAs: Past, present, and future
-
23463798
-
Kung JT, Colognori D, Lee JT (2013) Long noncoding RNAs: past, present, and future. Genetics 193: 651-669. doi: 10.1534/genetics.112.146704 PMID: 23463798
-
(2013)
Genetics
, vol.193
, pp. 651-669
-
-
Kung, J.T.1
Colognori, D.2
Lee, J.T.3
-
3
-
-
18344364099
-
Understanding alternative splicing: Towards a cellular code
-
15956978
-
Matlin AJ, Clark F, Smith CW (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6: 386-398. PMID: 15956978
-
(2005)
Nat Rev Mol Cell Biol
, vol.6
, pp. 386-398
-
-
Matlin, A.J.1
Clark, F.2
Smith, C.W.3
-
4
-
-
80052447253
-
Ending the message: Poly(A) signals then and now
-
21896654
-
Proudfoot NJ (2011) Ending the message: poly(A) signals then and now. Genes Dev 25: 1770-1782. doi: 10.1101/gad.17268411 PMID: 21896654
-
(2011)
Genes Dev
, vol.25
, pp. 1770-1782
-
-
Proudfoot, N.J.1
-
5
-
-
80052979140
-
Mechanisms and consequences of alternative polyadenylation
-
21925375
-
Di Giammartino DC, Nishida K, Manley JL (2011) Mechanisms and consequences of alternative polyadenylation. Mol Cell 43: 853-866. doi: 10.1016/j.molcel.2011.08.017 PMID: 21925375
-
(2011)
Mol Cell
, vol.43
, pp. 853-866
-
-
Di Giammartino, D.C.1
Nishida, K.2
Manley, J.L.3
-
6
-
-
30044445670
-
Tandem chimerism as a means to increase protein complexity in the human genome
-
16344564
-
Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, et al. (2006) Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res 16: 37-44. PMID: 16344564
-
(2006)
Genome Res
, vol.16
, pp. 37-44
-
-
Parra, G.1
Reymond, A.2
Dabbouseh, N.3
Dermitzakis, E.T.4
Castelo, R.5
-
7
-
-
30044431810
-
Transcription-mediated gene fusion in the human genome
-
16344562
-
Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, et al. (2006) Transcription-mediated gene fusion in the human genome. Genome Res 16: 30-36. PMID: 16344562
-
(2006)
Genome Res
, vol.16
, pp. 30-36
-
-
Akiva, P.1
Toporik, A.2
Edelheit, S.3
Peretz, Y.4
Diber, A.5
-
8
-
-
45549105119
-
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes
-
18315870
-
Munk C, Beck T, Zielonka J, Hotz-Wagenblatt A, Chareza S, et al. (2008) Functions, structure, and read-through alternative splicing of feline APOBEC3 genes. Genome Biol 9: R48. doi: 10.1186/gb- 2008-9-3-r48 PMID: 18315870
-
(2008)
Genome Biol
, vol.9
, pp. R48
-
-
Munk, C.1
Beck, T.2
Zielonka, J.3
Hotz-Wagenblatt, A.4
Chareza, S.5
-
9
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
18451266
-
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. doi: 10.1126/science.1158441 PMID: 18451266
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
-
10
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
18516045
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. doi: 10.1038/nmeth.1226 PMID: 18516045
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
11
-
-
80052960863
-
Next-generation transcriptome assembly
-
21897427
-
Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682. doi: 10.1038/nrg3068 PMID: 21897427
-
(2011)
Nat Rev Genet
, vol.12
, pp. 671-682
-
-
Martin, J.A.1
Wang, Z.2
-
12
-
-
84897528076
-
Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing
-
24639501
-
Treutlein B, Gokce O, Quake SR, Sudhof TC (2014) Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proc Natl Acad Sci U S A 111: E1291-1299. doi: 10.1073/pnas.1403244111 PMID: 24639501
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. E1291-1299
-
-
Treutlein, B.1
Gokce, O.2
Quake, S.R.3
Sudhof, T.C.4
-
13
-
-
19444377759
-
Transcriptional interference-A crash course
-
15922833
-
Shearwin KE, Callen BP, Egan JB (2005) Transcriptional interference-a crash course. Trends Genet 21: 339-345. PMID: 15922833
-
(2005)
Trends Genet
, vol.21
, pp. 339-345
-
-
Shearwin, K.E.1
Callen, B.P.2
Egan, J.B.3
-
14
-
-
84899669874
-
Long-read sequencing of chicken transcripts and identification of new transcript isoforms
-
24736250
-
Thomas S, Underwood JG, Tseng E, Holloway AK (2014) Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLOS ONE 9: e94650. doi: 10.1371/journal.pone. 0094650 PMID: 24736250
-
(2014)
PLOS ONE
, vol.9
, pp. e94650
-
-
Thomas, S.1
Underwood, J.G.2
Tseng, E.3
Holloway, A.K.4
-
15
-
-
84887412533
-
A single-molecule long-read survey of the human transcriptome
-
24108091
-
Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 31: 1009-1014. doi: 10.1038/nbt.2705 PMID: 24108091
-
(2013)
Nat Biotechnol
, vol.31
, pp. 1009-1014
-
-
Sharon, D.1
Tilgner, H.2
Grubert, F.3
Snyder, M.4
-
16
-
-
84890286068
-
Characterization of the human ESC transcriptome by hybrid sequencing
-
24282307
-
Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, et al. (2013) Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A 110: E4821-4830. doi: 10.1073/pnas. 1320101110 PMID: 24282307
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. E4821-4830
-
-
Au, K.F.1
Sebastiano, V.2
Afshar, P.T.3
Durruthy, J.D.4
Lee, L.5
-
17
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
22750884
-
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, et al. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30: 693-700. doi: 10.1038/nbt. 2280 PMID: 22750884
-
(2012)
Nat Biotechnol
, vol.30
, pp. 693-700
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
-
18
-
-
84862977387
-
The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes
-
22745431
-
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, et al. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719. doi: 10.1126/science.1221748 PMID: 22745431
-
(2012)
Science
, vol.336
, pp. 1715-1719
-
-
Floudas, D.1
Binder, M.2
Riley, R.3
Barry, K.4
Blanchette, R.A.5
-
19
-
-
84894576802
-
Fungal alternative splicing is associated with multicellular complexity and virulence: A genome-wide multi-species study
-
24122896
-
Grutzmann K, Szafranski K, Pohl M, Voigt K, Petzold A, et al. (2014) Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study. DNA Res 21: 27-39. doi: 10.1093/dnares/dst038 PMID: 24122896
-
(2014)
DNA Res
, vol.21
, pp. 27-39
-
-
Grutzmann, K.1
Szafranski, K.2
Pohl, M.3
Voigt, K.4
Petzold, A.5
-
20
-
-
84891752209
-
Myco cosm portal: Gearing up for 1000 fungal genomes
-
24297253
-
Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, et al. (2014) Myco Cosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42: D699-704. doi: 10.1093/nar/gkt1183 PMID: 24297253
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D699-704
-
-
Grigoriev, I.V.1
Nikitin, R.2
Haridas, S.3
Kuo, A.4
Ohm, R.5
-
21
-
-
18744383071
-
GMAP: A genomic mapping and alignment program form RNA and EST sequences
-
15728110
-
Wu TD, Watanabe CK (2005) GMAP: a genomic mapping and alignment program form RNA and EST sequences. Bioinformatics 21: 1859-1875. PMID: 15728110
-
(2005)
Bioinformatics
, vol.21
, pp. 1859-1875
-
-
Wu, T.D.1
Watanabe, C.K.2
-
22
-
-
74949084336
-
Genome-wide mapping of alternative splicing in Arabidopsis thaliana
-
19858364
-
Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, et al. (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20: 45-58. doi: 10.1101/gr.093302.109 PMID: 19858364
-
(2010)
Genome Res
, vol.20
, pp. 45-58
-
-
Filichkin, S.A.1
Priest, H.D.2
Givan, S.A.3
Shen, R.4
Bryant, D.W.5
-
23
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
18978772
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476. doi: 10.1038/nature07509 PMID: 18978772
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
-
24
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
23222703
-
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31: 46-53. doi: 10.1038/nbt.2450 PMID: 23222703
-
(2013)
Nat Biotechnol
, vol.31
, pp. 46-53
-
-
Trapnell, C.1
Hendrickson, D.G.2
Sauvageau, M.3
Goff, L.4
Rinn, J.L.5
-
25
-
-
78549246241
-
Rnnotator: An automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
-
21106091
-
Martin J, Bruno VM, Fang Z, Meng X, Blow M, et al. (2010) Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics 11: 663. doi: 10.1186/1471-2164-11-663 PMID: 21106091
-
(2010)
BMC Genomics
, vol.11
, pp. 663
-
-
Martin, J.1
Bruno, V.M.2
Fang, Z.3
Meng, X.4
Blow, M.5
-
26
-
-
84859768479
-
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
-
22368243
-
Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092. doi: 10.1093/bioinformatics/bts094 PMID: 22368243
-
(2012)
Bioinformatics
, vol.28
, pp. 1086-1092
-
-
Schulz, M.H.1
Zerbino, D.R.2
Vingron, M.3
Birney, E.4
-
27
-
-
66149118241
-
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
-
19372376
-
Calvo SE, Pagliarini DJ, Mootha VK (2009) Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci U S A 106: 7507-7512. doi: 10.1073/pnas.0810916106 PMID: 19372376
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 7507-7512
-
-
Calvo, S.E.1
Pagliarini, D.J.2
Mootha, V.K.3
-
29
-
-
52049086511
-
Unique features of nuclearm RNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii
-
18493049
-
Shen Y, Liu Y, Liu L, Liang C, Li QQ (2008) Unique features of nuclearm RNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics 179: 167-176. doi: 10.1534/genetics. 108.088971 PMID: 18493049
-
(2008)
Genetics
, vol.179
, pp. 167-176
-
-
Shen, Y.1
Liu, Y.2
Liu, L.3
Liang, C.4
Li, Q.Q.5
-
30
-
-
79958855346
-
In silico analysis of 3'-end-processing signals in Aspergillus oryzae using expressed sequence tags and genomic sequencing data
-
21586533
-
Tanaka M, Sakai Y, Yamada O, Shintani T, Gomi K (2011) In silico analysis of 3'-end-processing signals in Aspergillus oryzae using expressed sequence tags and genomic sequencing data. DNA Res 18: 189-200. doi: 10.1093/dnares/dsr011 PMID: 21586533
-
(2011)
DNA Res
, vol.18
, pp. 189-200
-
-
Tanaka, M.1
Sakai, Y.2
Yamada, O.3
Shintani, T.4
Gomi, K.5
-
31
-
-
77950929337
-
Diverse pathways generate micro RNA-like RNAs and Dicer-independent small interfering RNAs in fungi
-
20417140
-
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, et al. (2010) Diverse pathways generate micro RNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38: 803-814. doi: 10.1016/j. molcel.2010.04.005 PMID: 20417140
-
(2010)
Mol Cell
, vol.38
, pp. 803-814
-
-
Lee, H.C.1
Li, L.2
Gu, W.3
Xue, Z.4
Crosthwaite, S.K.5
-
32
-
-
40749094018
-
Cohesin complex promotes transcriptional termination between convergent genes in S
-
18358811
-
Gullerova M, Proudfoot NJ (2008) Cohesin complex promotes transcriptional termination between convergent genes in S. pombe. Cell 132: 983-995. doi: 10.1016/j.cell.2008.02.040 PMID: 18358811
-
(2008)
Pombe. Cell
, vol.132
, pp. 983-995
-
-
Gullerova, M.1
Proudfoot, N.J.2
-
33
-
-
78650873365
-
Intergenic transcription causes repression by directing nucleosome assembly
-
21156811
-
Hainer SJ, Pruneski JA, Mitchell RD, Monteverde RM, Martens JA (2011) Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 25: 29-40. doi: 10.1101/gad. 1975011 PMID: 21156811
-
(2011)
Genes Dev
, vol.25
, pp. 29-40
-
-
Hainer, S.J.1
Pruneski, J.A.2
Mitchell, R.D.3
Monteverde, R.M.4
Martens, J.A.5
-
34
-
-
66449107633
-
Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter
-
19524535
-
Palmer AC, Ahlgren-Berg A, Egan JB, Dodd IB, Shearwin KE (2009) Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter. Mol Cell 34: 545-555. doi: 10.1016/j. molcel.2009.04.018 PMID: 19524535
-
(2009)
Mol Cell
, vol.34
, pp. 545-555
-
-
Palmer, A.C.1
Ahlgren-Berg, A.2
Egan, J.B.3
Dodd, I.B.4
Shearwin, K.E.5
-
35
-
-
84930838411
-
Long-read, whole-genome shotgun sequence data for five model organisms: E
-
25977796
-
Kim K, Peluso P, Baybayan P, Yeadon J, Yu C, et al. (2014) Long-read, whole-genome shotgun sequence data for five model organisms: E. coli, S. cerevisiae, N. crassa, A. thaliana, and D. melanogaster. Scientific Data 1: 140045. doi: 10.1038/sdata.2014.45 PMID: 25977796
-
(2014)
Coli, S. Cerevisiae, N. Crassa, A. Thaliana, and D. Melanogaster. Scientific Data
, vol.1
, pp. 140045
-
-
Kim, K.1
Peluso, P.2
Baybayan, P.3
Yeadon, J.4
Yu, C.5
-
36
-
-
20044380139
-
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
-
15653466
-
Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, et al. (2005) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307: 1321-1324. PMID: 15653466
-
(2005)
Science
, vol.307
, pp. 1321-1324
-
-
Loftus, B.J.1
Fung, E.2
Roncaglia, P.3
Rowley, D.4
Amedeo, P.5
-
37
-
-
84877574893
-
Extensive transcriptional heterogeneity revealed by isoform profiling
-
23615609
-
Pelechano V, Wei W, Steinmetz LM (2013) Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 497: 127-131. doi: 10.1038/nature12121 PMID: 23615609
-
(2013)
Nature
, vol.497
, pp. 127-131
-
-
Pelechano, V.1
Wei, W.2
Steinmetz, L.M.3
-
38
-
-
4143050271
-
RIP: The evolutionary cost of genome defense
-
15313550
-
Galagan JE, Selker EU (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20: 417-423. PMID: 15313550
-
(2004)
Trends Genet
, vol.20
, pp. 417-423
-
-
Galagan, J.E.1
Selker, E.U.2
-
39
-
-
84861188156
-
Patterns of repeat-induced point mutation in transposable elements of basidiomycete fungi
-
22250128
-
Horns F, Petit E, Yockteng R, Hood ME (2012) Patterns of repeat-induced point mutation in transposable elements of basidiomycete fungi. Genome Biol Evol 4: 240-247. doi: 10.1093/gbe/evs005 PMID: 22250128
-
(2012)
Genome Biol Evol
, vol.4
, pp. 240-247
-
-
Horns, F.1
Petit, E.2
Yockteng, R.3
Hood, M.E.4
-
40
-
-
84883353135
-
Anti SMASH 2.0-A versatile platform for genome mining of secondary metabolite producers
-
23737449
-
Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, et al. (2013) anti SMASH 2.0-a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41: W204-212. doi: 10.1093/nar/gkt449 PMID: 23737449
-
(2013)
Nucleic Acids Res
, vol.41
, pp. W204-212
-
-
Blin, K.1
Medema, M.H.2
Kazempour, D.3
Fischbach, M.A.4
Breitling, R.5
-
41
-
-
84879900635
-
Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds
-
23798424
-
McGary KL, Slot JC, Rokas A (2013) Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds. Proc Natl Acad Sci U S A 110: 11481-11486. doi: 10.1073/pnas.1304461110 PMID: 23798424
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 11481-11486
-
-
McGary, K.L.1
Slot, J.C.2
Rokas, A.3
-
42
-
-
26844440157
-
Regulating gene expression through RNA nuclear retention
-
16239143
-
Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, et al. (2005) Regulating gene expression through RNA nuclear retention. Cell 123: 249-263. PMID: 16239143
-
(2005)
Cell
, vol.123
, pp. 249-263
-
-
Prasanth, K.V.1
Prasanth, S.G.2
Xuan, Z.3
Hearn, S.4
Freier, S.M.5
-
43
-
-
84880266648
-
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
-
23845962
-
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8: 1494-1512. doi: 10.1038/nprot.2013.084 PMID: 23845962
-
(2013)
Nat Protoc
, vol.8
, pp. 1494-1512
-
-
Haas, B.J.1
Papanicolaou, A.2
Yassour, M.3
Grabherr, M.4
Blood, P.D.5
|