-
1
-
-
84976498063
-
A survey of the sorghum transcriptome using single-molecule long reads
-
Abdel-Ghany SE, Hamilton M, Jacobi JL, Ngam P, Devitt N, Schilkey F, Ben-Hur A, Reddy AS. 2016. A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun 7: 11706.
-
(2016)
Nat Commun
, vol.7
, pp. 11706
-
-
Abdel-Ghany, S.E.1
Hamilton, M.2
Jacobi, J.L.3
Ngam, P.4
Devitt, N.5
Schilkey, F.6
Ben-Hur, A.7
Reddy, A.S.8
-
2
-
-
84954402887
-
Characterization of glucose-related metabolic pathways in differentiated rat oligodendrocyte lineage cells
-
Amaral AI, Hadera MG, Tavares JM, Kotter MRN, Sonnewald U. 2016. Characterization of glucose-related metabolic pathways in differentiated rat oligodendrocyte lineage cells. Glia 64: 21-34.
-
(2016)
Glia
, vol.64
, pp. 21-34
-
-
Amaral, A.I.1
Hadera, M.G.2
Tavares, J.M.3
Mrn, K.4
Sonnewald, U.5
-
3
-
-
84867121279
-
LSC improving PacBio long read accuracy by short read alignment
-
Au KF, Underwood JG, Lee L, Wong WH. 2012. LSC improving PacBio long read accuracy by short read alignment. PLoS One 7: 1-8.
-
(2012)
PLoS One
, vol.7
, pp. 1-8
-
-
Au, K.F.1
Underwood, J.G.2
Lee, L.3
Wong, W.H.4
-
4
-
-
84890286068
-
Characterization of the human ESC transcriptome by hybrid sequencing
-
Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG, et al. 2013. Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci 110: E4821-E4830.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. E4821-E4830
-
-
Au, K.F.1
Sebastiano, V.2
Afshar, P.T.3
Durruthy, J.D.4
Lee, L.5
Williams, B.A.6
Van Bakel, H.7
Schadt, E.E.8
Reijo-Pera, R.A.9
Underwood, J.G.10
-
5
-
-
0013394889
-
Mechanisms of alternative pre-messenger RNA splicing
-
Black DL. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72: 291-336.
-
(2003)
Annu Rev Biochem
, vol.72
, pp. 291-336
-
-
Black, D.L.1
-
6
-
-
0035478854
-
Random forests
-
Breiman L. 2001. Random forests. Mach Learn 45: 5-32.
-
(2001)
Mach Learn
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
7
-
-
0003802343
-
-
Wadsworth & Brooks/Cole Advanced Books & Software, Monterey, CA.
-
Breiman L, Friedman JH, Olshen RA, Stone CJ. 1984. Classification and regression trees. Wadsworth & Brooks/Cole Advanced Books & Software, Monterey, CA.
-
(1984)
Classification and Regression Trees
-
-
Breiman, L.1
Friedman, J.H.2
Olshen, R.A.3
Stone, C.J.4
-
8
-
-
0347363610
-
Membrane properties of rat embryonic multipotent neural stem cells
-
Cai J, Cheng A, Luo Y, Lu C, Mattson MP, Rao MS, Furukawa K. 2004. Membrane properties of rat embryonic multipotent neural stem cells. J Neurochem 88: 212-226.
-
(2004)
J Neurochem
, vol.88
, pp. 212-226
-
-
Cai, J.1
Cheng, A.2
Luo, Y.3
Lu, C.4
Mattson, M.P.5
Rao, M.S.6
Furukawa, K.7
-
9
-
-
84864518203
-
Pacific Biosciences sequencing technology for genotyping and variation discovery in human data
-
CarneiroMO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA. 2012. Pacific Biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics 13: 375.
-
(2012)
BMC Genomics
, vol.13
, pp. 375
-
-
Carneiro, M.O.1
Russ, C.2
Ross, M.G.3
Gabriel, S.B.4
Nusbaum, C.5
DePristo, M.A.6
-
10
-
-
84976579385
-
CDNA library enrichment of full length transcripts for SMRT long read sequencing
-
Cartolano M, Huettel B, Hartwig B, Reinhardt R, Schneeberger K. 2016. cDNA library enrichment of full length transcripts for SMRT long read sequencing. PLoS One 11: e0157779.
-
(2016)
PLoS One
, vol.11
, pp. e0157779
-
-
Cartolano, M.1
Huettel, B.2
Hartwig, B.3
Reinhardt, R.4
Schneeberger, K.5
-
11
-
-
84925286546
-
Alternative splicing in cancer: Implications for biology and therapy
-
Chen J, Weiss WA. 2014. Alternative splicing in cancer: implications for biology and therapy. Oncogene 34: 1-14.
-
(2014)
Oncogene
, vol.34
, pp. 1-14
-
-
Chen, J.1
Weiss, W.A.2
-
12
-
-
85021209015
-
Metabolic switching and cell fate decisions: Implications for pluripotency, reprogramming and development
-
Cliff TS, Dalton S. 2017. Metabolic switching and cell fate decisions: implications for pluripotency, reprogramming and development. Curr Opin Genet Dev 46: 44-49.
-
(2017)
Curr Opin Genet Dev
, vol.46
, pp. 44-49
-
-
Cliff, T.S.1
Dalton, S.2
-
13
-
-
33746683274
-
Reverse transcriptase template switching and false alternative transcripts
-
Cocquet J, Chong A, Zhang G, Veitia RA. 2006. Reverse transcriptase template switching and false alternative transcripts. Genomics 88: 127-131.
-
(2006)
Genomics
, vol.88
, pp. 127-131
-
-
Cocquet, J.1
Chong, A.2
Zhang, G.3
Veitia, R.A.4
-
14
-
-
24644503098
-
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
-
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
-
(2005)
Bioinformatics
, vol.21
, pp. 3674-3676
-
-
Conesa, A.1
Götz, S.2
García-Gómez, J.M.3
Terol, J.4
Talón, M.5
Robles, M.6
-
15
-
-
34249753618
-
Support-vector networks
-
Cortes C, VapnikV. 1995. Support-vector networks.MachLearn 20:273-297.
-
(1995)
MachLearn
, vol.20
, pp. 273-297
-
-
Cortes, C.1
Vapnik, V.2
-
16
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig R, Beavis RC. 2004. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20: 1466-1467.
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
17
-
-
84994589431
-
Human proteome project mass spectrometry data interpretation guidelines 2.1
-
Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, et al. 2016. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. J Proteome Res 15: 3961-3970.
-
(2016)
J Proteome Res
, vol.15
, pp. 3961-3970
-
-
Deutsch, E.W.1
Overall, C.M.2
Van Eyk, J.E.3
Baker, M.S.4
Paik, Y.K.5
Weintraub, S.T.6
Lane, L.7
Martens, L.8
Vandenbrouck, Y.9
Kusebauch, U.10
-
18
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15-21.
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
19
-
-
0033545946
-
Missense and silent τ genemutations cause frontotemporal dementiawithparkinsonism-chromosome17type, byaffectingmultiple alternative RNA splicing regulatory elements
-
D'Souza I, Poorkaj P, Hong M, Nochlin D, LeeVM, Bird TD, SchellenbergGD. 1999. Missense and silent τ genemutations cause frontotemporal dementiawithparkinsonism-chromosome17type, byaffectingmultiple alternative RNA splicing regulatory elements. Proc Natl Acad Sci 96: 5598-5603.
-
(1999)
Proc Natl Acad Sci
, vol.96
, pp. 5598-5603
-
-
D'Souza, I.1
Poorkaj, P.2
Hong, M.3
Nochlin, D.4
Lee, V.M.5
Bird, T.D.6
Schellenberg, G.D.7
-
20
-
-
84859254586
-
The human pancreatic islet transcriptome: Expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines
-
Eizirik DL, Sammeth M, Bouckenooghe T, Bottu G, Sisino G, Igoillo-Esteve M, Ortis F, Santin I, Colli ML, Barthson J, et al. 2012. The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines. PLoS Genet 8: e1002552.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002552
-
-
Eizirik, D.L.1
Sammeth, M.2
Bouckenooghe, T.3
Bottu, G.4
Sisino, G.5
Igoillo-Esteve, M.6
Ortis, F.7
Santin, I.8
Colli, M.L.9
Barthson, J.10
-
21
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng JK, McCormack AL, Yates JR. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5: 976-989.
-
(1994)
J Am Soc Mass Spectrom
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates, J.R.3
-
22
-
-
84926443748
-
Most highly expressed protein-coding genes have a single dominant isoform
-
Ezkurdia I, Rodriguez JM, Carrillo-De Santa Pau E, Vázquez J, Valencia A, Tress ML. 2015. Most highly expressed protein-coding genes have a single dominant isoform. J Proteome Res 14: 1880-1887.
-
(2015)
J Proteome Res
, vol.14
, pp. 1880-1887
-
-
Ezkurdia, I.1
Rodriguez, J.M.2
Carrillo-De Santa Pau, E.3
Vázquez, J.4
Valencia, A.5
Tress, M.L.6
-
23
-
-
84862260563
-
The importance of identifying alternative splicing in vertebrate genome annotation
-
Frankish A, Mudge JM, Thomas M, Harrow J. 2012. The importance of identifying alternative splicing in vertebrate genome annotation. Database 2012: bas014.
-
(2012)
Database
, vol.2012
, pp. BAS014
-
-
Frankish, A.1
Mudge, J.M.2
Thomas, M.3
Harrow, J.4
-
24
-
-
84941333926
-
Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing
-
Gordon SP, Tseng E, Salamov A, Zhang J, Meng X, Zhao Z, Kang D, Underwood J, Grigoriev IV, Figueroa M, et al. 2015. Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing. PLoS One 10: e0132628.
-
(2015)
PLoS One
, vol.10
, pp. e0132628
-
-
Gordon, S.P.1
Tseng, E.2
Salamov, A.3
Zhang, J.4
Meng, X.5
Zhao, Z.6
Kang, D.7
Underwood, J.8
Grigoriev, I.V.9
Figueroa, M.10
-
25
-
-
45549089420
-
High-throughput functional annotation and data mining with the Blast2GO suite
-
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A. 2008. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3420-3435
-
-
Götz, S.1
García-Gómez, J.M.2
Terol, J.3
Williams, T.D.4
Nagaraj, S.H.5
Nueda, M.J.6
Robles, M.7
Talón, M.8
Dopazo, J.9
Conesa, A.10
-
26
-
-
84911372793
-
Proovread: Large-scale high-accuracy PacBio correction through iterative short read consensus
-
Hackl T, Hedrich R, Schultz J, Förster F. 2014. proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics 30: 1-8.
-
(2014)
Bioinformatics
, vol.30
, pp. 1-8
-
-
Hackl, T.1
Hedrich, R.2
Schultz, J.3
Förster, F.4
-
27
-
-
84903995739
-
Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation
-
Han D, Jin J, Woo J, Min H, Kim Y. 2014. Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation. Proteomics 14: 1604-1609.
-
(2014)
Proteomics
, vol.14
, pp. 1604-1609
-
-
Han, D.1
Jin, J.2
Woo, J.3
Min, H.4
Kim, Y.5
-
28
-
-
77957893329
-
Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro
-
Houseley J, Tollervey D. 2010. Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS One 5: e12271.
-
(2010)
PLoS One
, vol.5
, pp. e12271
-
-
Houseley, J.1
Tollervey, D.2
-
29
-
-
84919928214
-
A highly conserved program of neuronal microexons is misregulated in autistic brains
-
Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, et al. 2014. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159: 1511-1523.
-
(2014)
Cell
, vol.159
, pp. 1511-1523
-
-
Irimia, M.1
Weatheritt, R.J.2
Ellis, J.D.3
Parikshak, N.N.4
Gonatopoulos-Pournatzis, T.5
Babor, M.6
Quesnel-Vallières, M.7
Tapial, J.8
Raj, B.9
O'Hanlon, D.10
-
30
-
-
0346243804
-
A muscleblind knockout model for myotonic dystrophy
-
Kanadia RN, Johnstone KA, Mankodi A, Lungu C, Thornton CA, Esson D, Timmers AM, Hauswirth WW, Swanson MS. 2003. A muscleblind knockout model for myotonic dystrophy. Science 302: 1978-1980.
-
(2003)
Science
, vol.302
, pp. 1978-1980
-
-
Kanadia, R.N.1
Johnstone, K.A.2
Mankodi, A.3
Lungu, C.4
Thornton, C.A.5
Esson, D.6
Timmers, A.M.7
Hauswirth, W.W.8
Swanson, M.S.9
-
31
-
-
50149117169
-
Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases
-
Kim S, Gupta N, Pevzner PA. 2008. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res 7: 3354-3363.
-
(2008)
J Proteome Res
, vol.7
, pp. 3354-3363
-
-
Kim, S.1
Gupta, N.2
Pevzner, P.A.3
-
32
-
-
84922332663
-
Increasing the coding potential of genomes through alternative splicing: The case of PARK2 gene
-
La Cognata V, Iemmolo R, D'Agata V, Scuderi S, Drago F, Zappia M, Cavallaro S. 2014. Increasing the coding potential of genomes through alternative splicing: the case of PARK2 gene. Curr Genomics 15: 203-216.
-
(2014)
Curr Genomics
, vol.15
, pp. 203-216
-
-
La Cognata, V.1
Iemmolo, R.2
D'Agata, V.3
Scuderi, S.4
Drago, F.5
Zappia, M.6
Cavallaro, S.7
-
33
-
-
84884814617
-
CUG-BP, Elav-like family (CELF)-mediated alternative splicing regulation in the brain during health and disease
-
Ladd AN. 2013. CUG-BP, Elav-like family (CELF)-mediated alternative splicing regulation in the brain during health and disease. Mol Cell Neurosci 56: 456-464.
-
(2013)
Mol Cell Neurosci
, vol.56
, pp. 456-464
-
-
Ladd, A.N.1
-
34
-
-
84885354288
-
Aberrant alternative splicing is another hallmark of cancer
-
Ladomery M. 2013. Aberrant alternative splicing is another hallmark of cancer. Int J Cell Biol 2013: 463786.
-
(2013)
Int J Cell Biol
, vol.2013
, pp. 463786
-
-
Ladomery, M.1
-
35
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
36
-
-
84953835989
-
Cytoplasmic Rbfox1 regulates the expression of synaptic and autism-related genes
-
Lee JA, Damianov A, Lin CH, Fontes M, Parikshak NN, Anderson ES, Geschwind DH, Black DL, Martin KC. 2016. Cytoplasmic Rbfox1 regulates the expression of synaptic and autism-related genes. Neuron 89: 113-128.
-
(2016)
Neuron
, vol.89
, pp. 113-128
-
-
Lee, J.A.1
Damianov, A.2
Lin, C.H.3
Fontes, M.4
Parikshak, N.N.5
Anderson, E.S.6
Geschwind, D.H.7
Black, D.L.8
Martin, K.C.9
-
37
-
-
79961123152
-
RSEM: Accurate transcript quantification from RNASeq data with or without a reference genome
-
Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNASeq data with or without a reference genome. BMC Bioinformatics 12: 323.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
38
-
-
84997207303
-
High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation
-
Li S, Yamada M, Han X, Ohler U, Benfey PN. 2016. High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation. Dev Cell 39: 508-522.
-
(2016)
Dev Cell
, vol.39
, pp. 508-522
-
-
Li, S.1
Yamada, M.2
Han, X.3
Ohler, U.4
Benfey, P.N.5
-
39
-
-
84882268443
-
Alternative RNA splicing and cancer
-
Liu S, Cheng C. 2013. Alternative RNA splicing and cancer. Wiley Interdiscip Rev RNA 4: 547-566.
-
(2013)
Wiley Interdiscip Rev RNA
, vol.4
, pp. 547-566
-
-
Liu, S.1
Cheng, C.2
-
40
-
-
0031312210
-
Split selection methods for classification trees
-
Loh W-Y, Shih Y-S. 1997. Split selection methods for classification trees. Stat Sin 7: 815-840.
-
(1997)
Stat Sin
, vol.7
, pp. 815-840
-
-
Loh, W.-Y.1
Shih, Y.-S.2
-
41
-
-
84871392152
-
Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene
-
Loomis EW, Eid JS, Peluso P, Yin J, Hickey L, Rank D, McCalmon S, Hagerman RJ, Tassone F, Hagerman PJ. 2013. Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res 23: 121-128.
-
(2013)
Genome Res
, vol.23
, pp. 121-128
-
-
Loomis, E.W.1
Eid, J.S.2
Peluso, P.3
Yin, J.4
Hickey, L.5
Rank, D.6
McCalmon, S.7
Hagerman, R.J.8
Tassone, F.9
Hagerman, P.J.10
-
42
-
-
77956277181
-
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
-
Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W, et al. 2010. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res 20: 1238-1249.
-
(2010)
Genome Res
, vol.20
, pp. 1238-1249
-
-
Lu, T.1
Lu, G.2
Fan, D.3
Zhu, C.4
Li, W.5
Zhao, Q.6
Feng, Q.7
Zhao, Y.8
Guo, Y.9
Li, W.10
-
43
-
-
23944526367
-
PRIDE: The proteomics identifications database
-
Martens L, Hermjakob H, Jones P, Adamsk M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R. 2005. PRIDE: the proteomics identifications database. Proteomics 5: 3537-3545.
-
(2005)
Proteomics
, vol.5
, pp. 3537-3545
-
-
Martens, L.1
Hermjakob, H.2
Jones, P.3
Adamsk, M.4
Taylor, C.5
States, D.6
Gevaert, K.7
Vandekerckhove, J.8
Apweiler, R.9
-
44
-
-
84875798204
-
Control of alternative splicing in immune responses: Many regulators, many predictions, much still to learn
-
Martinez NM, Lynch KW. 2013. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol Rev 253: 216-236.
-
(2013)
Immunol Rev
, vol.253
, pp. 216-236
-
-
Martinez, N.M.1
Lynch, K.W.2
-
46
-
-
84874597027
-
IReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data
-
Mezlini AM, Smith EJM, Fiume M, Buske O, Savich GL, Shah S, Aparicio S, Chiang DY, Goldenberg A, Brudno M. 2013. IReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res 23: 519-529.
-
(2013)
Genome Res
, vol.23
, pp. 519-529
-
-
Mezlini, A.M.1
Ejm, S.2
Fiume, M.3
Buske, O.4
Savich, G.L.5
Shah, S.6
Aparicio, S.7
Chiang, D.Y.8
Goldenberg, A.9
Brudno, M.10
-
47
-
-
80053204000
-
The origins, evolution, and functional potential of alternative splicing in vertebrates
-
Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J. 2011. The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol 28: 2949-2959.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2949-2959
-
-
Mudge, J.M.1
Frankish, A.2
Fernandez-Banet, J.3
Alioto, T.4
Derrien, T.5
Howald, C.6
Reymond, A.7
Guigó, R.8
Hubbard, T.9
Harrow, J.10
-
48
-
-
0037197827
-
Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
-
Nam DK, Lee S, Zhou G, Cao X, Wang C, Clark T, Chen J, Rowley JD, Wang SM. 2002. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci 99: 6152-6156.
-
(2002)
Proc Natl Acad Sci
, vol.99
, pp. 6152-6156
-
-
Nam, D.K.1
Lee, S.2
Zhou, G.3
Cao, X.4
Wang, C.5
Clark, T.6
Chen, J.7
Rowley, J.D.8
Wang, S.M.9
-
49
-
-
84983605356
-
Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
-
Oikonomopoulos S, Wang YC, Djambazian H, Badescu D, Ragoussis J. 2016. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 6: 31602.
-
(2016)
Sci Rep
, vol.6
, pp. 31602
-
-
Oikonomopoulos, S.1
Wang, Y.C.2
Djambazian, H.3
Badescu, D.4
Ragoussis, J.5
-
50
-
-
84921334197
-
A comprehensive survey of non-canonical splice sites in the human transcriptome
-
Parada GE, Munita R, Cerda CA, Gysling K. 2014. A comprehensive survey of non-canonical splice sites in the human transcriptome. Nucleic Acids Res 42: 10564-10578.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 10564-10578
-
-
Parada, G.E.1
Munita, R.2
Cerda, C.A.3
Gysling, K.4
-
51
-
-
84964927929
-
-
R Core Team., R Foundation for Statistical Computing, Vienna, Austria.
-
R Core Team. 2016. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.Rproject.org/.
-
(2016)
R: A Language and Environment for Statistical Computing
-
-
-
52
-
-
84937405196
-
Alternative splicing in the mammalian nervous system: Recent insights into mechanisms and functional roles
-
Raj B, Blencowe BJ. 2015. Alternative splicing in the mammalian nervous system: recent insights into mechanisms and functional roles. Neuron 87: 14-27.
-
(2015)
Neuron
, vol.87
, pp. 14-27
-
-
Raj, B.1
Blencowe, B.J.2
-
53
-
-
84876513019
-
APPRIS: Annotation of principal and alternative splice isoforms
-
Database issue
-
Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML. 2013. APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res 41(Database issue): D110-D117.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D110-D117
-
-
Rodriguez, J.M.1
Maietta, P.2
Ezkurdia, I.3
Pietrelli, A.4
Wesselink, J.J.5
Lopez, G.6
Valencia, A.7
Tress, M.L.8
-
54
-
-
84863419877
-
SpliceGrapher: Detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data
-
Rogers MF, Thomas J, Reddy AS, Ben-Hur A. 2012. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol 13: R4.
-
(2012)
Genome Biol
, vol.13
, pp. R4
-
-
Rogers, M.F.1
Thomas, J.2
Reddy, A.S.3
Ben-Hur, A.4
-
55
-
-
84913539196
-
LoRDEC: Accurate and efficient long read error correction
-
Salmela L, Rivals E. 2014. LoRDEC: accurate and efficient long read error correction. Bioinformatics 30: 3506-3514.
-
(2014)
Bioinformatics
, vol.30
, pp. 3506-3514
-
-
Salmela, L.1
Rivals, E.2
-
56
-
-
0034243471
-
Boosting neural networks
-
Schwenk H, Bengio Y. 2000. Boosting neural networks. Neural Comput 12: 1869-1887.
-
(2000)
Neural Comput
, vol.12
, pp. 1869-1887
-
-
Schwenk, H.1
Bengio, Y.2
-
57
-
-
84949104386
-
Cell type-and brain region-resolved mouse brain proteome
-
Sharma K, Schmitt S, Bergner CG, Tyanova S, Kannaiyan N, Manrique-Hoyos N, Kongi K, Cantuti L, Hanisch UK, Philips MA, et al. 2015. Cell type-and brain region-resolved mouse brain proteome. Nat Neurosci 18: 1819-1831.
-
(2015)
Nat Neurosci
, vol.18
, pp. 1819-1831
-
-
Sharma, K.1
Schmitt, S.2
Bergner, C.G.3
Tyanova, S.4
Kannaiyan, N.5
Manrique-Hoyos, N.6
Kongi, K.7
Cantuti, L.8
Hanisch, U.K.9
Philips, M.A.10
-
58
-
-
84887412533
-
A single-molecule longread survey of the human transcriptome
-
Sharon D, Tilgner H, Grubert F, Snyder M. 2013. A single-molecule longread survey of the human transcriptome. Nat Biotechnol 31: 1009-1014.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 1009-1014
-
-
Sharon, D.1
Tilgner, H.2
Grubert, F.3
Snyder, M.4
-
59
-
-
85021206966
-
Glial and neuronal protein tyrosine phosphatase α (PTPα) regulate oligodendrocyte differentiation and myelination
-
Shih Y, Ly PTT, Wang J, Pallen CJ. 2017. Glial and neuronal protein tyrosine phosphatase α (PTPα) regulate oligodendrocyte differentiation and myelination. J Mol Neurosci 62: 329-343.
-
(2017)
J Mol Neurosci
, vol.62
, pp. 329-343
-
-
Shih, Y.1
Ptt, L.2
Wang, J.3
Pallen, C.J.4
-
60
-
-
84956574798
-
Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
-
Soneson C, Matthes KL, Nowicka M, LawCW, Robinson MD. 2016. Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage. Genome Biol 17: 12.
-
(2016)
Genome Biol
, vol.17
, pp. 12
-
-
Soneson, C.1
Matthes, K.L.2
Nowicka, M.3
Law, C.W.4
Robinson, M.D.5
-
61
-
-
84890494960
-
3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts
-
Spies N, Burge CB, Bartel DP. 2013. 3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res 23: 2078-2090.
-
(2013)
Genome Res
, vol.23
, pp. 2078-2090
-
-
Spies, N.1
Burge, C.B.2
Bartel, D.P.3
-
62
-
-
84888871954
-
Assessment of transcript reconstruction methods for RNA-seq
-
Steijger T, Abril JF, Engström PG, Kokocinski F, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P, et al. 2013. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10: 1177-1184.
-
(2013)
Nat Methods
, vol.10
, pp. 1177-1184
-
-
Steijger, T.1
Abril, J.F.2
Engström, P.G.3
Kokocinski, F.4
Akerman, M.5
Alioto, T.6
Ambrosini, G.7
Antonarakis, S.E.8
Behr, J.9
Bertone, P.10
-
63
-
-
84885038939
-
Frac-seq reveals isoform-specific recruitment to polyribosomes
-
Sterne-Weiler T, Martinez-Nunez RT, Howard JM, Cvitovik I, Katzman S, Tariq MA, Pourmand N, Sanford JR. 2013. Frac-seq reveals isoform-specific recruitment to polyribosomes. Genome Res 23: 1615-1623.
-
(2013)
Genome Res
, vol.23
, pp. 1615-1623
-
-
Sterne-Weiler, T.1
Martinez-Nunez, R.T.2
Howard, J.M.3
Cvitovik, I.4
Katzman, S.5
Tariq, M.A.6
Pourmand, N.7
Sanford, J.R.8
-
64
-
-
33847401893
-
MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
-
Tabb DL, Fernando CG, Chambers MC. 2007. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res 6: 654-661.
-
(2007)
J Proteome Res
, vol.6
, pp. 654-661
-
-
Tabb, D.L.1
Fernando, C.G.2
Chambers, M.C.3
-
65
-
-
85046105874
-
Identification of protein coding regions in RNA transcripts
-
Tang S, Lomsadze A, Borodovsky M. 2015. Identification of protein coding regions in RNA transcripts. Nucleic Acids Res 248: 1-18.
-
(2015)
Nucleic Acids Res
, vol.248
, pp. 1-18
-
-
Tang, S.1
Lomsadze, A.2
Borodovsky, M.3
-
66
-
-
84969752477
-
The role of telomeres and telomerase reverse transcriptase isoforms in pluripotency induction and maintenance
-
Teichroeb JH, Kim J, Betts DH. 2016. The role of telomeres and telomerase reverse transcriptase isoforms in pluripotency induction and maintenance. RNA Biol 13: 707-719.
-
(2016)
RNA Biol
, vol.13
, pp. 707-719
-
-
Teichroeb, J.H.1
Kim, J.2
Betts, D.H.3
-
67
-
-
84883216800
-
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing
-
Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M. 2013. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda) 3: 387-397.
-
(2013)
G3 (Bethesda)
, vol.3
, pp. 387-397
-
-
Tilgner, H.1
Raha, D.2
Habegger, L.3
Mohiuddin, M.4
Gerstein, M.5
Snyder, M.6
-
68
-
-
85046090275
-
Defining a personal, allele-specific, and single-molecule long-read transcriptome
-
Tilgner H, Grubert F, Sharon D, Snyder MP. 2014. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci 1640: 10-12.
-
(2014)
Proc Natl Acad Sci
, vol.1640
, pp. 10-12
-
-
Tilgner, H.1
Grubert, F.2
Sharon, D.3
Snyder, M.P.4
-
69
-
-
84929697731
-
Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events
-
Tilgner H, Jahanbani F, Blauwkamp T, Moshrefi A, Jaeger E, Chen F, Harel I, Bustamante CD, Rasmussen M, Snyder MP. 2015. Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events. Nat Biotechnol 33: 736-742.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 736-742
-
-
Tilgner, H.1
Jahanbani, F.2
Blauwkamp, T.3
Moshrefi, A.4
Jaeger, E.5
Chen, F.6
Harel, I.7
Bustamante, C.D.8
Rasmussen, M.9
Snyder, M.P.10
-
70
-
-
85000842751
-
Alternative splicing may not be the key to proteome complexity
-
Tress ML, Abascal F, Valencia A. 2016. Alternative splicing may not be the key to proteome complexity. Trends Biochem Sci 42: 98-110.
-
(2016)
Trends Biochem Sci
, vol.42
, pp. 98-110
-
-
Tress, M.L.1
Abascal, F.2
Valencia, A.3
-
71
-
-
85058198174
-
Full length cDNA sequencing on the PacBio RS
-
Tseng E, Underwood JG. 2013. Full length cDNA sequencing on the PacBio RS. J Biomol Tech 24(Suppl): S45.
-
(2013)
J Biomol Tech
, vol.24
, pp. S45
-
-
Tseng, E.1
Underwood, J.G.2
-
72
-
-
79951750784
-
SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X! Tandem searches
-
Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. 2011. SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X! Tandem searches. Proteomics 11: 996-999.
-
(2011)
Proteomics
, vol.11
, pp. 996-999
-
-
Vaudel, M.1
Barsnes, H.2
Berven, F.S.3
Sickmann, A.4
Martens, L.5
-
73
-
-
84923897273
-
PeptideShaker enables reanalysis of MS-derived proteomics data sets
-
Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H. 2015. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol 33: 22-24.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 22-24
-
-
Vaudel, M.1
Burkhart, J.M.2
Zahedi, R.P.3
Oveland, E.4
Berven, F.S.5
Sickmann, A.6
Martens, L.7
Barsnes, H.8
-
74
-
-
84960379718
-
Pladipus enables universal distributed computing in proteomics bioinformatics
-
Verheggen K, Maddelein D, Hulstaert N, Martens L, Barsnes H, Vaudel M. 2016. Pladipus enables universal distributed computing in proteomics bioinformatics. J Proteome Res 15: 707-712.
-
(2016)
J Proteome Res
, vol.15
, pp. 707-712
-
-
Verheggen, K.1
Maddelein, D.2
Hulstaert, N.3
Martens, L.4
Barsnes, H.5
Vaudel, M.6
-
75
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
76
-
-
84976503037
-
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing
-
Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D. 2016. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun 7: 11708.
-
(2016)
Nat Commun
, vol.7
, pp. 11708
-
-
Wang, B.1
Tseng, E.2
Regulski, M.3
Clark, T.A.4
Hon, T.5
Jiao, Y.6
Lu, Z.7
Olson, A.8
Stein, J.C.9
Ware, D.10
-
78
-
-
18744383071
-
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
-
Wu TD, Watanabe CK. 2005. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859-1875.
-
(2005)
Bioinformatics
, vol.21
, pp. 1859-1875
-
-
Wu, T.D.1
Watanabe, C.K.2
-
79
-
-
13144293035
-
The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia
-
Yang YY, Yin GL, Darnell RB. 1998. The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia. Proc Natl Acad Sci 95: 13254-13259.
-
(1998)
Proc Natl Acad Sci
, vol.95
, pp. 13254-13259
-
-
Yang, Y.Y.1
Yin, G.L.2
Darnell, R.B.3
-
80
-
-
84862245279
-
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
-
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. 2012. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13: 134.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 134
-
-
Ye, J.1
Coulouris, G.2
Zaretskaya, I.3
Cutcutache, I.4
Rozen, S.5
Madden, T.L.6
-
82
-
-
85027186700
-
Evaluation and comparison of computational tools for RNA-seq isoform quantification
-
Zhang C, Zhang B, Lin L-L, Zhao S. 2017. Evaluation and comparison of computational tools for RNA-seq isoform quantification. BMC Genomics 18: 583.
-
(2017)
BMC Genomics
, vol.18
, pp. 583
-
-
Zhang, C.1
Zhang, B.2
Lin, L.-L.3
Zhao, S.4
|