-
1
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
DOI 10.1038/nature07509, PII NATURE07509
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476. (Pubitemid 352759009)
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
2
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
DOI 10.1038/nmeth.1226, PII NMETH.1226
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
-
(2008)
Nature Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
3
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
-
(2008)
Nat Genet
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
4
-
-
15544379277
-
Are splicing mutations the most frequent cause of hereditary disease?
-
DOI 10.1016/j.febslet.2005.02.047
-
Lopez-Bigas N, Audit B, Ouzounis C, Parra G, Guigo R (2005) Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett 579: 1900-1903. (Pubitemid 40404028)
-
(2005)
FEBS Letters
, vol.579
, Issue.9
, pp. 1900-1903
-
-
Lopez-Bigas, N.1
Audit, B.2
Ouzounis, C.3
Parra, G.4
Guigo, R.5
-
5
-
-
37349089805
-
Insights into the connection between cancer and alternative splicing
-
DOI 10.1016/j.tig.2007.10.001, PII S0168952507003459
-
Kim E, Goren A, Ast G (2008) Insights into the connection between cancer and alternative splicing. Trends Genet 24: 7-10. (Pubitemid 350298628)
-
(2008)
Trends in Genetics
, vol.24
, Issue.1
, pp. 7-10
-
-
Kim, E.1
Goren, A.2
Ast, G.3
-
6
-
-
78650961149
-
Epigenetics in alternative pre-mRNA splicing
-
Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T (2011) Epigenetics in alternative pre-mRNA splicing. Cell 144: 16-26.
-
(2011)
Cell
, vol.144
, pp. 16-26
-
-
Luco, R.F.1
Allo, M.2
Schor, I.E.3
Kornblihtt, A.R.4
Misteli, T.5
-
7
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr MG, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8: 469-477.
-
(2011)
Nat Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
8
-
-
78649714014
-
Analysis and design of RNA sequencing experiments for identifying isoform regulation
-
Katz Y, Wang ET, Airoldi EM, Burge CB (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1015.
-
(2010)
Nat Methods
, vol.7
, pp. 1009-1015
-
-
Katz, Y.1
Wang, E.T.2
Airoldi, E.M.3
Burge, C.B.4
-
9
-
-
80053435328
-
FDM: A graphbased statistical method to detect differential transcription using RNA-seq data
-
Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, et al. (2011) FDM: a graphbased statistical method to detect differential transcription using RNA-seq data. Bioinformatics 27: 2633-2640.
-
(2011)
Bioinformatics
, vol.27
, pp. 2633-2640
-
-
Singh, D.1
Orellana, C.F.2
Hu, Y.3
Jones, C.D.4
Liu, Y.5
-
10
-
-
84865527768
-
Detecting differential usage of exons from RNA-seq data
-
Anders S, Reyes A, Huber W (2012) Detecting differential usage of exons from RNA-seq data. Genome Res 22: 2008-2017.
-
(2012)
Genome Res
, vol.22
, pp. 2008-2017
-
-
Anders, S.1
Reyes, A.2
Huber, W.3
-
11
-
-
84860385776
-
MATS: A Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data
-
Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, et al. (2012) MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 40: e61.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Shen, S.1
Park, J.W.2
Huang, J.3
Dittmar, K.A.4
Lu, Z.X.5
-
12
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
-
13
-
-
84877043834
-
A Hierarchical Bayesian Model for Estimating and Inferring Differential Isoform Expression for Multi-Sample RNA-Seq Data
-
Vardhanabhuti S, Li M, Li H (2013) A Hierarchical Bayesian Model for Estimating and Inferring Differential Isoform Expression for Multi-Sample RNA-Seq Data. Stat Biosci 5: 119-137.
-
(2013)
Stat Biosci
, vol.5
, pp. 119-137
-
-
Vardhanabhuti, S.1
Li, M.2
Li, H.3
-
14
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7: 562-578.
-
(2012)
Nat Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
-
15
-
-
84863992953
-
Identifying differentially expressed transcripts from RNA-seq data with biological variation
-
Glaus P, Honkela A, Rattray M (2012) Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics 28: 1721-1728.
-
(2012)
Bioinformatics
, vol.28
, pp. 1721-1728
-
-
Glaus, P.1
Honkela, A.2
Rattray, M.3
-
16
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
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.
-
(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
-
17
-
-
64549119707
-
Statistical inferences for isoform expression in RNASeq
-
Jiang H, Wong WH (2009) Statistical inferences for isoform expression in RNASeq. Bioinformatics 25: 1026-1032.
-
(2009)
Bioinformatics
, vol.25
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.H.2
-
19
-
-
79959262465
-
Transcriptomic analysis of autistic brain reveals convergent molecular pathology
-
Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, et al. (2011) Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474: 380-384.
-
(2011)
Nature
, vol.474
, pp. 380-384
-
-
Voineagu, I.1
Wang, X.2
Johnston, P.3
Lowe, J.K.4
Tian, Y.5
-
20
-
-
84869423417
-
Statistical properties of an early stopping rule for resampling-based multiple testing
-
Jiang H, Salzman J (2012) Statistical properties of an early stopping rule for resampling-based multiple testing. Biometrika 99: 973-980.
-
(2012)
Biometrika
, vol.99
, pp. 973-980
-
-
Jiang, H.1
Salzman, J.2
-
21
-
-
84861302942
-
Genome-wide determination of a broad ESRP-regulated posttranscriptional network by highthroughput sequencing
-
Dittmar KA, Jiang P, Park JW, Amirikian K, Wan J, et al. (2012) Genome-wide determination of a broad ESRP-regulated posttranscriptional network by highthroughput sequencing. Mol Cell Biol 32: 1468-1482.
-
(2012)
Mol Cell Biol
, vol.32
, pp. 1468-1482
-
-
Dittmar, K.A.1
Jiang, P.2
Park, J.W.3
Amirikian, K.4
Wan, J.5
-
23
-
-
35548940665
-
Neuronal regulation of alternative pre-mRNA splicing
-
DOI 10.1038/nrn2237, PII NRN2237
-
Li Q, Lee JA, Black DL (2007) Neuronal regulation of alternative pre-mRNA splicing. Nat Rev Neurosci 8: 819-831. (Pubitemid 350006218)
-
(2007)
Nature Reviews Neuroscience
, vol.8
, Issue.11
, pp. 819-831
-
-
Li, Q.1
Lee, J.-A.2
Black, D.L.3
-
24
-
-
84866428088
-
Emerging Roles of Alternative Pre-mRNA Splicing Regulation in Neuronal Development and Function
-
Norris AD, Calarco JA (2012) Emerging Roles of Alternative Pre-mRNA Splicing Regulation in Neuronal Development and Function. Front Neurosci 6: 122.
-
(2012)
Front Neurosci
, vol.6
, pp. 122
-
-
Norris, A.D.1
Calarco, J.A.2
-
25
-
-
33749054403
-
Splicing Regulation in Neurologic Disease
-
DOI 10.1016/j.neuron.2006.09.017, PII S0896627306007240
-
Licatalosi DD, Darnell RB (2006) Splicing regulation in neurologic disease. Neuron 52: 93-101. (Pubitemid 44466357)
-
(2006)
Neuron
, vol.52
, Issue.1
, pp. 93-101
-
-
Licatalosi, D.D.1
Darnell, R.B.2
-
26
-
-
77952581425
-
Aberrant RNA processing events in neurological disorders
-
Anthony K, Gallo JM (2010) Aberrant RNA processing events in neurological disorders. Brain Res 1338: 67-77.
-
(2010)
Brain Res
, vol.1338
, pp. 67-77
-
-
Anthony, K.1
Gallo, J.M.2
-
27
-
-
84894111292
-
-
Available: Accessed 2013 October 1
-
NIH Genetic Association Database. Available: http://geneticassociationdb. nih.gov/. Accessed 2013 October 1.
-
NIH Genetic Association Database
-
-
-
30
-
-
84856854101
-
The role of NrCAM in neural development and disorders-beyond a simple glue in the brain
-
Sakurai T (2012) The role of NrCAM in neural development and disorders-beyond a simple glue in the brain. Mol Cell Neurosci 49: 351-363.
-
(2012)
Mol Cell Neurosci
, vol.49
, pp. 351-363
-
-
Sakurai, T.1
-
31
-
-
33751027533
-
Association analysis of the NrCAM gene in autism and in subsets of families with severe obsessive-compulsive or self-stimulatory behaviors
-
DOI 10.1097/01.ypg.0000242196.81891.c9, PII 0004144420061200000011
-
Sakurai T, Ramoz N, Reichert JG, Corwin TE, Kryzak L, et al. (2006) Association analysis of the NrCAM gene in autism and in subsets of families with severe obsessive-compulsive or self-stimulatory behaviors. Psychiatr Genet 16: 251-257. (Pubitemid 44760305)
-
(2006)
Psychiatric Genetics
, vol.16
, Issue.6
, pp. 251-257
-
-
Sakurai, T.1
Ramoz, N.2
Reichert, J.G.3
Corwin, T.E.4
Kryzak, L.5
Smith, C.J.6
Silverman, J.M.7
Hollander, E.8
Buxbaum, J.D.9
-
32
-
-
61949123986
-
Association of the neuronal cell adhesion molecule (NRCAM) gene variants with autism
-
Marui T, Funatogawa I, Koishi S, Yamamoto K, Matsumoto H, et al. (2009) Association of the neuronal cell adhesion molecule (NRCAM) gene variants with autism. Int J Neuropsychopharmacol 12: 1-10.
-
(2009)
Int J Neuropsychopharmacol
, vol.12
, pp. 1-10
-
-
Marui, T.1
Funatogawa, I.2
Koishi, S.3
Yamamoto, K.4
Matsumoto, H.5
-
33
-
-
38349107593
-
The Alzheimer's disease beta-secretase enzyme, BACE1
-
Cole SL, Vassar R (2007) The Alzheimer's disease beta-secretase enzyme, BACE1. Mol Neurodegener 2: 22.
-
(2007)
Mol Neurodegener
, vol.2
, pp. 22
-
-
Cole, S.L.1
Vassar, R.2
-
34
-
-
49649103244
-
Promotion of BACE1 mRNA alternative splicing reduces amyloid beta-peptide production
-
Mowrer KR, Wolfe MS (2008) Promotion of BACE1 mRNA alternative splicing reduces amyloid beta-peptide production. J Biol Chem 283: 18694-18701.
-
(2008)
J Biol Chem
, vol.283
, pp. 18694-18701
-
-
Mowrer, K.R.1
Wolfe, M.S.2
-
35
-
-
0035816492
-
Three novel alternatively spliced isoforms of the human beta-site amyloid precursor protein cleaving enzyme (BACE) and their effect on amyloid beta-peptide production
-
DOI 10.1016/S0304-3940(01)01912-7, PII S0304394001019127
-
Tanahashi H, Tabira T (2001) Three novel alternatively spliced isoforms of the human beta-site amyloid precursor protein cleaving enzyme (BACE) and their effect on amyloid beta-peptide production. Neurosci Lett 307: 9-12. (Pubitemid 32539296)
-
(2001)
Neuroscience Letters
, vol.307
, Issue.1
, pp. 9-12
-
-
Tanahashi, H.1
Tabira, T.2
-
36
-
-
0038411339
-
Quantification and distribution of beta-secretase alternative splice variants in the rat and human brain
-
DOI 10.1016/S0169-328X(03)00182-7
-
Zohar O, Cavallaro S, D'Agata V, Alkon DL (2003) Quantification and distribution of beta-secretase alternative splice variants in the rat and human brain. Brain Res Mol Brain Res 115: 63-68. (Pubitemid 36725036)
-
(2003)
Molecular Brain Research
, vol.115
, Issue.1
, pp. 63-68
-
-
Zohar, O.1
Cavallaro, S.2
D'Agata, V.3
Alkon, D.L.4
-
37
-
-
79959407483
-
Increased secreted amyloid precursor protein-alpha (sAPPalpha) in severe autism: Proposal of a specific, anabolic pathway and putative biomarker
-
Ray B, Long JM, Sokol DK, Lahiri DK (2011) Increased secreted amyloid precursor protein-alpha (sAPPalpha) in severe autism: proposal of a specific, anabolic pathway and putative biomarker. PLoS One 6: e20405.
-
(2011)
PLoS One
, vol.6
-
-
Ray, B.1
Long, J.M.2
Sokol, D.K.3
Lahiri, D.K.4
-
38
-
-
33746049824
-
High levels of Alzheimer beta-amyloid precursor protein (APP) in children with severely autistic behavior and aggression
-
DOI 10.2310/7010.2006.00130
-
Sokol DK, Chen D, Farlow MR, Dunn DW, Maloney B, et al. (2006) High levels of Alzheimer beta-amyloid precursor protein (APP) in children with severely autistic behavior and aggression. J Child Neurol 21: 444-449. (Pubitemid 44069791)
-
(2006)
Journal of Child Neurology
, vol.21
, Issue.6
, pp. 444-449
-
-
Sokol, D.K.1
Chen, D.2
Farlow, M.R.3
Dunn, D.W.4
Maloney, B.5
Zimmer, J.A.6
Lahiri, D.K.7
-
39
-
-
76749111279
-
Peripheral biomarkers in Autism: Secreted amyloid precursor protein-alpha as a probable key player in early diagnosis
-
Bailey AR, Giunta BN, Obregon D, Nikolic WV, Tian J, et al. (2008) Peripheral biomarkers in Autism: secreted amyloid precursor protein-alpha as a probable key player in early diagnosis. Int J Clin Exp Med 1: 338-344.
-
(2008)
Int J Clin Exp Med
, vol.1
, pp. 338-344
-
-
Bailey, A.R.1
Giunta, B.N.2
Obregon, D.3
Nikolic, W.V.4
Tian, J.5
-
40
-
-
79954627454
-
Autism, Alzheimer disease, and fragile X: APP, FMRP, and mGluR5 are molecular links
-
Sokol DK, Maloney B, Long JM, Ray B, Lahiri DK (2011) Autism, Alzheimer disease, and fragile X: APP, FMRP, and mGluR5 are molecular links. Neurology 76: 1344-1352.
-
(2011)
Neurology
, vol.76
, pp. 1344-1352
-
-
Sokol, D.K.1
Maloney, B.2
Long, J.M.3
Ray, B.4
Lahiri, D.K.5
-
41
-
-
0033621875
-
2+-dependent actin filament severing protein that controls cortical actin network dynamics during secretion
-
DOI 10.1023/A:1007503919265
-
Trifaro JM, Rose SD, Marcu MG (2000) Scinderin, a Ca2+-dependent actin filament severing protein that controls cortical actin network dynamics during secretion. Neurochem Res 25: 133-144. (Pubitemid 30074284)
-
(2000)
Neurochemical Research
, vol.25
, Issue.1
, pp. 133-144
-
-
Trifaro, J.-M.1
Rose, S.D.2
Marcu, M.G.3
-
42
-
-
84858041341
-
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
-
McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40: 4288-4297.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 4288-4297
-
-
McCarthy, D.J.1
Chen, Y.2
Smyth, G.K.3
-
43
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
44
-
-
84874912212
-
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
-
Wu H, Wang C, Wu Z (2013) A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics 14: 232-243.
-
(2013)
Biostatistics
, vol.14
, pp. 232-243
-
-
Wu, H.1
Wang, C.2
Wu, Z.3
-
45
-
-
77954473082
-
CisGenome Browser: A flexible tool for genomic data visualization
-
Jiang H, Wang F, Dyer NP, Wong WH (2010) CisGenome Browser: a flexible tool for genomic data visualization. Bioinformatics 26: 1781-1782.
-
(2010)
Bioinformatics
, vol.26
, pp. 1781-1782
-
-
Jiang, H.1
Wang, F.2
Dyer, N.P.3
Wong, W.H.4
|