-
1
-
-
84883743509
-
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.
-
Yan L, Yang M, Guo H, Yang L, Wu J, Li RR, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Qiao J, Tang F. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013;20:1131-9.
-
(2013)
Nat Struct Mol Biol.
, vol.20
, pp. 1131-1139
-
-
Yan, L.1
Yang, M.2
Guo, H.3
Yang, L.4
Wu, J.5
Li, R.R.6
Liu, P.7
Lian, Y.8
Zheng, X.9
Yan, J.10
Huang, J.11
Li, M.12
Wu, X.13
Wen, L.14
Lao, K.15
Qiao, J.16
Tang, F.17
-
2
-
-
84900322651
-
Detecting and characterizing circular RNAs
-
Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nature Biotechnology. 2014;32:453-61.
-
(2014)
Nature Biotechnology.
, vol.32
, pp. 453-461
-
-
Jeck, W.R.1
Sharpless, N.E.2
-
3
-
-
84884687363
-
Cell-type specific features of circular RNA expression
-
Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9:e1003777.
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003777
-
-
Salzman, J.1
Chen, R.E.2
Olsen, M.N.3
Wang, P.L.4
Brown, P.O.5
-
4
-
-
33646852092
-
Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing
-
Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res. 2006;34:e63.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. e63
-
-
Suzuki, H.1
Zuo, Y.2
Wang, J.3
Zhang, M.Q.4
Malhotra, A.5
Mayeda, A.6
-
5
-
-
84863045982
-
Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types
-
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One. 2012;7:e30733.
-
(2012)
PLoS One.
, vol.7
, pp. e30733
-
-
Salzman, J.1
Gawad, C.2
Wang, P.L.3
Lacayo, N.4
Brown, P.O.5
-
6
-
-
84884566546
-
Circular intronic long noncoding RNAs.
-
Zhang Y, Zhang X, Chen T, Xiang J, Yin Q-F, Xing Y, Zhu S, Yang L, Chen L-L. Circular intronic long noncoding RNAs. Mol Cell. 2013;51:792-806.
-
(2013)
Mol Cell.
, vol.51
, pp. 792-806
-
-
Zhang, Y.1
Zhang, X.2
Chen, T.3
Xiang, J.4
Yin, Q-F.5
Xing, Y.6
Zhu, S.7
Yang, L.8
Chen, L-L.9
-
7
-
-
84924274183
-
Exon-intron circular RNAs regulate transcription in the nucleus.
-
Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, Zhu P, Chang Z, Wu Q, Zhao Y, Jia Y, Xu P. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015;22:256-64.
-
(2015)
Nat Struct Mol Biol.
, vol.22
, pp. 256-264
-
-
Li, Z.1
Huang, C.2
Bao, C.3
Chen, L.4
Lin, M.5
Wang, X.6
Zhong, G.7
Yu, B.8
Hu, W.9
Dai, L.10
Zhu, P.11
Chang, Z.12
Wu, Q.13
Zhao, Y.14
Jia, Y.15
Xu, P.16
-
8
-
-
84875372911
-
Natural RNA circles function as efficient microRNA sponges.
-
Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495:384-8.
-
(2013)
Nature
, vol.495
, pp. 384-388
-
-
Hansen, T.B.1
Jensen, T.I.2
Clausen, B.H.3
Bramsen, J.B.4
Finsen, B.5
Damgaard, C.K.6
Kjems, J.7
-
9
-
-
84875369248
-
Circular RNAs are a large class of animal RNAs with regulatory potency.
-
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, Noble F, Rajewsky N, le Noble F, Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333-8.
-
(2013)
Nature.
, vol.495
, pp. 333-338
-
-
Memczak, S.1
Jens, M.2
Elefsinioti, A.3
Torti, F.4
Krueger, J.5
Rybak, A.6
Maier, L.7
Mackowiak, S.D.8
Gregersen, L.H.9
Munschauer, M.10
Loewer, A.11
Ziebold, U.12
Landthaler, M.13
Kocks, C.14
Noble, F.15
Rajewsky, N.16
le Noble, F.17
Rajewsky, N.18
-
10
-
-
84911476411
-
circRNA biogenesis competes with pre-mRNA splicing.
-
Ashwal-Fluss R, Meyer M, Pamudurti NRR, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S. circRNA biogenesis competes with pre-mRNA splicing. Mol Cell. 2014;56:55-66.
-
(2014)
Mol Cell.
, vol.56
, pp. 55-66
-
-
Ashwal-Fluss, R.1
Meyer, M.2
Pamudurti, N.R.R.3
Ivanov, A.4
Bartok, O.5
Hanan, M.6
Evantal, N.7
Memczak, S.8
Rajewsky, N.9
Kadener, S.10
-
11
-
-
0029585914
-
Inverted repeats are necessary for circularization of the mouse testis Sry transcript
-
Dubin RA, Kazmi MA, Ostrer H. Inverted repeats are necessary for circularization of the mouse testis Sry transcript. Gene. 1995;167:245-8.
-
(1995)
Gene.
, vol.167
, pp. 245-248
-
-
Dubin, R.A.1
Kazmi, M.A.2
Ostrer, H.3
-
12
-
-
84907509527
-
Complementary sequence-mediated exon circularization
-
Zhang X, Wang H-B, Zhang Y, Lu X, Chen L-L, Yang L. Complementary sequence-mediated exon circularization. Cell. 2014;159:1-14.
-
(2014)
Cell.
, vol.159
, pp. 1-14
-
-
Zhang, X.1
Wang, H.-B.2
Zhang, Y.3
Lu, X.4
Chen, L.-L.5
Yang, L.6
-
13
-
-
84939419124
-
Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed.
-
Rybak-Wolf A, Stottmeister C, Glažar P, Jens M, Pino N, Giusti S, Hanan M, Behm M, Bartok O, Ashwal-Fluss R, Herzog M, Schreyer L, Papavasileiou P, Ivanov A, Öhman M, Refojo D, Kadener S, Rajewsky N. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58:870-85.
-
(2015)
Mol Cell.
, vol.58
, pp. 870-885
-
-
Rybak-Wolf, A.1
Stottmeister, C.2
Glažar, P.3
Jens, M.4
Pino, N.5
Giusti, S.6
Hanan, M.7
Behm, M.8
Bartok, O.9
Ashwal-Fluss, R.10
Herzog, M.11
Schreyer, L.12
Papavasileiou, P.13
Ivanov, A.14
Öhman, M.15
Refojo, D.16
Kadener, S.17
Rajewsky, N.18
-
14
-
-
84946544407
-
Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development.
-
Venø MT, Hansen TB, Venø ST, Clausen BH, Grebing M, Finsen B, Holm IE, Kjems J. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. Genome Biol. 2015;16:245.
-
(2015)
Genome Biol.
, vol.16
, pp. 245
-
-
Venø, M.T.1
Hansen, T.B.2
Venø, S.T.3
Clausen, B.H.4
Grebing, M.5
Finsen, B.6
Holm, I.E.7
Kjems, J.8
-
15
-
-
79953288433
-
Development and applications of single-cell transcriptome analysis.
-
Tang F, Lao K, Surani MA. Development and applications of single-cell transcriptome analysis. Nat Methods. 2011;8:S6-11.
-
(2011)
Nat Methods.
, vol.8
, pp. S6-S11
-
-
Tang, F.1
Lao, K.2
Surani, M.A.3
-
16
-
-
84887101406
-
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
-
Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods. 2013;10:1096-8.
-
(2013)
Nat Methods.
, vol.10
, pp. 1096-1098
-
-
Picelli, S.1
Björklund, K.2
Faridani, O.R.3
Sagasser, S.4
Winberg, G.5
Sandberg, R.6
-
17
-
-
84866953427
-
CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification
-
Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012;2:666-73.
-
(2012)
Cell Rep.
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
Yanai, I.4
-
18
-
-
84937703271
-
Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.
-
Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F, Huang Y. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 2015;16:148.
-
(2015)
Genome Biol.
, vol.16
, pp. 148
-
-
Fan, X.1
Zhang, X.2
Wu, X.3
Guo, H.4
Hu, Y.5
Tang, F.6
Huang, Y.7
-
19
-
-
84923647450
-
Computational and analytical challenges in single-cell transcriptomics
-
Stegle O, Teichmann S, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet. 2015;16(3):133-45.
-
(2015)
Nat Rev Genet
, vol.16
, Issue.3
, pp. 133-145
-
-
Stegle, O.1
Teichmann, S.2
Marioni, J.C.3
-
20
-
-
84920550975
-
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
-
Su Z, Łabaj PP, Li S, Thierry-Mieg J, Thierry-Mieg D, Shi W, Wang C, Schroth GP, Setterquist R a, Thompson JF, Jones WD, Xiao W, Xu W, Jensen R V, Kelly R, Xu J, Conesa A, Furlanello C, Gao H, Hong H, Jafari N, Letovsky S, Liao Y, Lu F, Oakeley EJ, Peng Z, Praul C a, Santoyo-Lopez J, Scherer A, Shi T, et al. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014;32:903-14.
-
(2014)
Nat Biotechnol.
, vol.32
, pp. 903-914
-
-
Su, Z.1
Łabaj, P.P.2
Li, S.3
Thierry-Mieg, J.4
Thierry-Mieg, D.5
Shi, W.6
Wang, C.7
Schroth, G.P.8
Setterquist, R.A.9
Thompson, J.F.10
Jones, W.D.11
Xiao, W.12
Xu, W.13
Jensen, R.V.14
Kelly, R.15
Xu, J.16
Conesa, A.17
Furlanello, C.18
Gao, H.19
Hong, H.20
Jafari, N.21
Letovsky, S.22
Liao, Y.23
Lu, F.24
Oakeley, E.J.25
Peng, Z.26
Praul, C.A.27
Santoyo-Lopez, J.28
Scherer, A.29
Shi, T.30
more..
-
21
-
-
84861960860
-
Digital PCR, hits its stride
-
Baker M. Digital PCR, hits its stride. Nat Methods. 2012;9:541-4.
-
(2012)
Nat Methods.
, vol.9
, pp. 541-544
-
-
Baker, M.1
-
22
-
-
84855982119
-
Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification.
-
Pinheiro LB, Coleman VA, Hindson CM, Herrmann J, Hindson BJ, Bhat S, Emslie KR. Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal Chem. 2012;84:1003-11.
-
(2012)
Anal Chem.
, vol.84
, pp. 1003-1011
-
-
Pinheiro, L.B.1
Coleman, V.A.2
Hindson, C.M.3
Herrmann, J.4
Hindson, B.J.5
Bhat, S.6
Emslie, K.R.7
-
23
-
-
84919471287
-
Transcriptome-wide variability in single embryonic development cells
-
Piras V, Tomita M, Selvarajoo K. Transcriptome-wide variability in single embryonic development cells. Sci Rep. 2014;4:7137.
-
(2014)
Sci Rep.
, vol.4
, pp. 7137
-
-
Piras, V.1
Tomita, M.2
Selvarajoo, K.3
-
24
-
-
80051493701
-
Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development.
-
Vassena R, Boué S, González-Roca E, Aran B, Auer H, Veiga A, Izpisua Belmonte JC. Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development. Development. 2011;138:3699-709.
-
(2011)
Development.
, vol.138
, pp. 3699-3709
-
-
Vassena, R.1
Boué, S.2
González-Roca, E.3
Aran, B.4
Auer, H.5
Veiga, A.6
Izpisua Belmonte, J.C.7
-
25
-
-
84856750425
-
Human pre-implantation embryo development
-
Niakan KK, Han J, Pedersen R, Simon C, Pera RR. Human pre-implantation embryo development. Development. 2012;139:829-41.
-
(2012)
Development.
, vol.139
, pp. 829-841
-
-
Niakan, K.K.1
Han, J.2
Pedersen, R.3
Simon, C.4
Pera, R.R.5
-
26
-
-
3543056889
-
The unique transcriptome through day 3 of human preimplantation development.
-
Dobson AT, Raja R, Abeyta MJ, Taylor T, Shen S, Haqq C, Reijo Pera RA. The unique transcriptome through day 3 of human preimplantation development. Hum Mol Genet. 2004;13:1461-70.
-
(2004)
Hum Mol Genet.
, vol.13
, pp. 1461-1470
-
-
Dobson, A.T.1
Raja, R.2
Abeyta, M.J.3
Taylor, T.4
Shen, S.5
Haqq, C.6
Reijo Pera, R.A.7
-
27
-
-
84933041690
-
Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development.
-
Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J. Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biol. 2015;16:126.
-
(2015)
Genome Biol.
, vol.16
, pp. 126
-
-
Szabo, L.1
Morey, R.2
Palpant, N.J.3
Wang, P.L.4
Afari, N.5
Jiang, C.6
Parast, M.M.7
Murry, C.E.8
Laurent, L.C.9
Salzman, J.10
-
28
-
-
84911491114
-
Circular RNAs: diversity of form and function
-
Lasda E, Parker R. Circular RNAs: diversity of form and function. RNA. 2014;20:1829-42.
-
(2014)
RNA.
, vol.20
, pp. 1829-1842
-
-
Lasda, E.1
Parker, R.2
-
29
-
-
84941067776
-
RNA circularization strategies in vivo and in vitro
-
Petkovic S, Muller S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res. 2015;43:2454-65.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 2454-2465
-
-
Petkovic, S.1
Muller, S.2
-
30
-
-
84915820022
-
Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation.
-
Westholm JO, Miura P, Graveley BR, Lai EC, Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep. 2014;9:1966-80.
-
(2014)
Cell Rep.
, vol.9
, pp. 1966-1980
-
-
Westholm, J.O.1
Miura, P.2
Graveley, B.R.3
Lai, E.C.4
Westholm, J.O.5
Miura, P.6
Olson, S.7
Shenker, S.8
Joseph, B.9
Sanfilippo, P.10
-
31
-
-
84929322923
-
Regulation of circRNA biogenesis
-
Chen L-L, Yang L. Regulation of circRNA biogenesis. RNA Biol. 2015;12:381-8.
-
(2015)
RNA Biol.
, vol.12
, pp. 381-388
-
-
Chen, L.-L.1
Yang, L.2
-
32
-
-
13444267841
-
NONCODE: An integrated knowledge database of non-coding RNAs.
-
Liu C, Bai B, Skogerbø G, Cai L, Deng W, Zhang Y, Bu D, Zhao Y, Chen R. NONCODE: An integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 2005;33:D112-5.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. D112-D115
-
-
Liu, C.1
Bai, B.2
Skogerbø, G.3
Cai, L.4
Deng, W.5
Zhang, Y.6
Bu, D.7
Zhao, Y.8
Chen, R.9
-
33
-
-
84878282421
-
Resource epigenomic analysis of multilineage differentiation of human embryonic stem cells.
-
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, et al. Resource epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013;153:1134-48.
-
(2013)
Cell.
, vol.153
, pp. 1134-1148
-
-
Xie, W.1
Schultz, M.D.2
Lister, R.3
Hou, Z.4
Rajagopal, N.5
Ray, P.6
Whitaker, J.W.7
Tian, S.8
Hawkins, R.D.9
Leung, D.10
Yang, H.11
Wang, T.12
Lee, A.Y.13
Swanson, S.A.14
Zhang, J.15
Zhu, Y.16
Kim, A.17
Nery, J.R.18
Urich, M.A.19
Kuan, S.20
Yen, C.21
Klugman, S.22
Yu, P.23
Suknuntha, K.24
Propson, N.E.25
Chen, H.26
Edsall, L.E.27
Wagner, U.28
Li, Y.29
Ye, Z.30
more..
-
34
-
-
66349086264
-
Identifying novel constrained elements by exploiting biased substitution patterns
-
Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics. 2009;25:54-62.
-
(2009)
Bioinformatics.
, vol.25
, pp. 54-62
-
-
Garber, M.1
Guttman, M.2
Clamp, M.3
Zody, M.C.4
Friedman, N.5
Xie, X.6
-
35
-
-
34547582418
-
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
-
Kong L, Zhang Y, Ye Z, Liu X, Zhao S, Wei L. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35:345-9.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 345-349
-
-
Kong, L.1
Zhang, Y.2
Ye, Z.3
Liu, X.4
Zhao, S.5
Wei, L.6
-
36
-
-
84905030212
-
The DNA methylation landscape of human early embryos.
-
Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y, Yan J, Ren X, Lin S, Li J, Jin X, Shi X, Liu P, Wang X, Wang W, Wei Y, Li X, Guo F, Wu X, Fan X, Yong J, Wen L, Xie SX, Tang F, Qiao J. The DNA methylation landscape of human early embryos. Nature. 2014;511:606-10.
-
(2014)
Nature.
, vol.511
, pp. 606-610
-
-
Guo, H.1
Zhu, P.2
Yan, L.3
Li, R.4
Hu, B.5
Lian, Y.6
Yan, J.7
Ren, X.8
Lin, S.9
Li, J.10
Jin, X.11
Shi, X.12
Liu, P.13
Wang, X.14
Wang, W.15
Wei, Y.16
Li, X.17
Guo, F.18
Wu, X.19
Fan, X.20
Yong, J.21
Wen, L.22
Xie, S.X.23
Tang, F.24
Qiao, J.25
more..
-
37
-
-
84928987900
-
HTSeq--a Python framework to work with high-throughput sequencing data
-
Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166-9.
-
(2015)
Bioinformatics.
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
39
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
-
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 2014;15:550.
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
40
-
-
3142665525
-
GOstat: Find statistically overrepresented Gene Ontologies with a group of genes
-
Beißbarth T, Speed TP. GOstat: Find statistically overrepresented Gene Ontologies with a group of genes. Bioinformatics. 2004;20:1464-5.
-
(2004)
Bioinformatics.
, vol.20
, pp. 1464-1465
-
-
Beißbarth, T.1
Speed, T.P.2
|