-
1
-
-
79956001876
-
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
-
Sorber, K., Dimon, M. T. & DeRisi, J. L. RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. Nucleic Acids Res. 39, 3820-3835 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 3820-3835
-
-
Sorber, K.1
Dimon, M.T.2
Derisi, J.L.3
-
2
-
-
84863229522
-
Targeted disruption of Toxoplasma gondii serine protease inhibitor 1 increases bradyzoite cyst formation in vitro and parasite tissue burden in mice
-
Pszenny, V. et al. Targeted disruption of Toxoplasma gondii serine protease inhibitor 1 increases bradyzoite cyst formation in vitro and parasite tissue burden in mice. Infect. Immun. 80, 1156-1165 (2012).
-
(2012)
Infect. Immun
, vol.80
, pp. 1156-1165
-
-
Pszenny, V.1
-
3
-
-
79953085633
-
Characterization of intronic structures and alternative splicing in Phytophthora sojae by comparative analysis of expressed sequence tags and genomic sequences
-
Shen, D., Ye, W., Dong, S., Wang, Y. & Dou, D. Characterization of intronic structures and alternative splicing in Phytophthora sojae by comparative analysis of expressed sequence tags and genomic sequences. Can. J. Microbiol. 57, 84-90 (2011).
-
(2011)
Can. J. Microbiol
, vol.57
, pp. 84-90
-
-
Shen, D.1
Ye, W.2
Dong, S.3
Wang, Y.4
Dou, D.5
-
4
-
-
77649098171
-
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii
-
Labadorf, A. et al. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics 11, 114 (2010).
-
(2010)
BMC Genomics
, vol.11
, pp. 114
-
-
Labadorf, A.1
-
5
-
-
84861890038
-
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
-
Marquez, Y., Brown, J. W. S., Simpson, C., Barta, A. & Kalyna, M. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22, 1184-1195 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 1184-1195
-
-
Marquez, Y.1
Brown, J.W.S.2
Simpson, C.3
Barta, A.4
Kalyna, M.5
-
6
-
-
84870564943
-
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
-
Curtis, B. A. et al. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492, 59-65 (2012).
-
(2012)
Nature
, vol.492
, pp. 59-65
-
-
Curtis, B.A.1
-
7
-
-
77956107299
-
Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
-
Wang, B. et al. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 38, 5075-5087 (2010).
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 5075-5087
-
-
Wang, B.1
-
8
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
DOI 10.1038/nature07509, PII NATURE07509
-
Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008). (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
-
9
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing
-
Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nat. Genet. 40, 1413-1415 (2008).
-
(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
-
10
-
-
79953043801
-
The developmental transcriptome of Drosophila melanogaster
-
Graveley, B. R. et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473-479 (2011).
-
(2011)
Nature
, vol.471
, pp. 473-479
-
-
Graveley, B.R.1
-
11
-
-
26244435561
-
Mutually exclusive splicing of the insect Dscam Pre-mRNA directed by competing intronic RNA secondary structures
-
DOI 10.1016/j.cell.2005.07.028, PII S0092867405007592
-
Graveley, B. R. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell 123, 65-73 (2005). (Pubitemid 41414529)
-
(2005)
Cell
, vol.123
, Issue.1
, pp. 65-73
-
-
Graveley, B.R.1
-
12
-
-
75849145292
-
Expansion of the eukaryotic proteome by alternative splicing
-
Nilsen, T. W. & Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457-463 (2010).
-
(2010)
Nature
, vol.463
, pp. 457-463
-
-
Nilsen, T.W.1
Graveley, B.R.2
-
13
-
-
5344223383
-
V1.2 calcium channel dysfunction causes a multisystem disorder including arrhythmia and autism
-
DOI 10.1016/j.cell.2004.09.011, PII S0092867404008426
-
Splawski, I. et al. Ca(V)1.2 calcium channel dysfunction causes a multisystem disorder including arrhythmia and autism. Cell 119, 19-31 (2004). (Pubitemid 39349317)
-
(2004)
Cell
, vol.119
, Issue.1
, pp. 19-31
-
-
Splawski, I.1
Timothy, K.W.2
Sharpe, L.M.3
Decher, N.4
Kumar, P.5
Bloise, R.6
Napolitano, C.7
Schwartz, P.J.8
Joseph, R.M.9
Condouris, K.10
Tager-Flusberg, H.11
Priori, S.G.12
Sanguinetti, M.C.13
Keating, M.T.14
-
14
-
-
82455162377
-
Deficiency of the mitochondrial phosphate carrier presenting as myopathy and cardiomyopathy in a family with three affected children
-
Mayr, J. A. et al. Deficiency of the mitochondrial phosphate carrier presenting as myopathy and cardiomyopathy in a family with three affected children. Neuromusc. Disord. 21, 803-808 (2011).
-
(2011)
Neuromusc. Disord
, vol.21
, pp. 803-808
-
-
Mayr, J.A.1
-
15
-
-
23044441734
-
Voltage-gated sodium channel expression and potentiation of human breast cancer metastasis
-
DOI 10.1158/1078-0432.CCR-05-0327
-
Fraser, S. P. et al. Voltage-gated sodium channel expression and potentiation of human breast cancer metastasis. Clin. Cancer Res. 11, 5381-5389 (2005). (Pubitemid 41060811)
-
(2005)
Clinical Cancer Research
, vol.11
, Issue.15
, pp. 5381-5389
-
-
Fraser, S.P.1
Diss, J.K.J.2
Chioni, A.-M.3
Mycielska, M.E.4
Pan, H.5
Yamaci, R.F.6
Pani, F.7
Siwy, Z.8
Krasowska, M.9
Grzywna, Z.10
Brackenbury, W.J.11
Theodorou, D.12
Koyuturk, M.13
Kaya, H.14
Battaloglu, E.15
De Bella, M.T.16
Slade, M.J.17
Tolhurst, R.18
Palmieri, C.19
Jiang, J.20
Latchman, D.S.21
Coombes, R.C.22
Djamgoz, M.B.A.23
more..
-
16
-
-
75149150660
-
HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer
-
David, C. J., Chen, M., Assanah, M., Canoll, P. & Manley, J. L. HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer. Nature 463, 364-368 (2010).
-
(2010)
Nature
, vol.463
, pp. 364-368
-
-
David, C.J.1
Chen, M.2
Assanah, M.3
Canoll, P.4
Manley, J.L.5
-
18
-
-
79551653312
-
RNA secondary structure in mutually exclusive splicing
-
Yang, Y. et al. RNA secondary structure in mutually exclusive splicing. Nat. Struct. Mol. Biol. 18, 159-168 (2011).
-
(2011)
Nat. Struct. Mol. Biol
, vol.18
, pp. 159-168
-
-
Yang, Y.1
-
19
-
-
84865448443
-
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function
-
Ezkurdia, I. et al. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Mol. Biol. Evol. 29, 2265-2283 (2012).
-
(2012)
Mol. Biol. Evol
, vol.29
, pp. 2265-2283
-
-
Ezkurdia, I.1
-
20
-
-
34249717879
-
A high-quality catalog of the Drosophila melanogaster proteome
-
DOI 10.1038/nbt1300, PII NBT1300
-
Brunner, E. et al. A high-quality catalog of the Drosophila melanogaster proteome. Nat. Biotechnol. 25, 576-583 (2007). (Pubitemid 46834841)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.5
, pp. 576-583
-
-
Brunner, E.1
Ahrens, C.H.2
Mohanty, S.3
Baetschmann, H.4
Loevenich, S.5
Potthast, F.6
Deutsch, E.W.7
Panse, C.8
De Lichtenberg, U.9
Rinner, O.10
Lee, H.11
Pedrioli, P.G.A.12
Malmstrom, J.13
Koehler, K.14
Schrimpf, S.15
Krijgsveld, J.16
Kregenow, F.17
Heck, A.J.R.18
Hafen, E.19
Schlapbach, R.20
Aebersold, R.21
more..
-
21
-
-
80155171417
-
A protein complex network of Drosophila melanogaster
-
Guruharsha, K. G. et al. A protein complex network of Drosophila melanogaster. Cell 147, 690-703 (2011).
-
(2011)
Cell
, vol.147
, pp. 690-703
-
-
Guruharsha, K.G.1
-
22
-
-
19044365796
-
The Drosophila gene collection: Identification of putative full-length cDNAs for 70% of D. melanogaster genes
-
DOI 10.1101/gr.269102
-
Stapleton, M. et al. The Drosophila Gene Collection: Identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 12, 1294-1300 (2002). (Pubitemid 41264431)
-
(2002)
Genome Research
, vol.12
, Issue.8
, pp. 1294-1300
-
-
Stapleton, M.1
Liao, G.2
Brokstein, P.3
Hong, L.4
Carninci, P.5
Shiraki, T.6
Hayashizaki, Y.7
Champe, M.8
Pacleb, J.9
Wan, K.10
Yu, C.11
Carlson, J.12
George, R.13
Celniker, S.14
Rubin, G.M.15
-
24
-
-
0037183901
-
Gene expression during the life cycle of Drosophila melanogaster
-
Arbeitman, M. N. et al. Gene expression during the life cycle of Drosophila melanogaster. Science 297, 2270-2275 (2002).
-
(2002)
Science
, vol.297
, pp. 2270-2275
-
-
Arbeitman, M.N.1
-
25
-
-
7444233156
-
A gene expression map for the euchromatic genome of Drosophila melanogaster
-
DOI 10.1126/science.1101312
-
Stolc, V. et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306, 655-660 (2004). (Pubitemid 39440907)
-
(2004)
Science
, vol.306
, Issue.5696
, pp. 655-660
-
-
Stolc, V.1
Gauhar, Z.2
Mason, C.3
Halasz, G.4
Van Batenburg, M.F.5
Rifkin, S.A.6
Hua, S.7
Herreman, T.8
Tongprasit, W.9
Barbano, P.E.10
Bussemaker, H.J.11
White, K.P.12
-
26
-
-
33749153857
-
Biological function of unannotated transcription during the early development of Drosophila melanogaster
-
DOI 10.1038/ng1875, PII NG1875
-
Manak, J. R. et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat. Genet. 38, 1151-1158 (2006). (Pubitemid 44470360)
-
(2006)
Nature Genetics
, vol.38
, Issue.10
, pp. 1151-1158
-
-
Manak, J.R.1
Dike, S.2
Sementchenko, V.3
Kapranov, P.4
Biemar, F.5
Long, J.6
Cheng, J.7
Bell, I.8
Ghosh, S.9
Piccolboni, A.10
Gingeras, T.R.11
-
27
-
-
19944434180
-
Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
-
Richards, S. et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15, 1-18 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1-18
-
-
Richards, S.1
-
28
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
DOI 10.1038/nature06341, PII NATURE06341
-
Clark, A. G. et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (2007). (Pubitemid 351972300)
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 203-218
-
-
Clark, A.G.1
Eisen, M.B.2
Smith, D.R.3
Bergman, C.M.4
Oliver, B.5
Markow, T.A.6
Kaufman, T.C.7
Kellis, M.8
Gelbart, W.9
Iyer, V.N.10
Pollard, D.A.11
Sackton, T.B.12
Larracuente, A.M.13
Singh, N.D.14
Abad, J.P.15
Abt, D.N.16
Adryan, B.17
Aguade, M.18
Akashi, H.19
Anderson, W.W.20
Aquadro, C.F.21
Ardell, D.H.22
Arguello, R.23
Artieri, C.G.24
Barbash, D.A.25
Barker, D.26
Barsanti, P.27
Batterham, P.28
Batzoglou, S.29
Begun, D.30
Bhutkar, A.31
Blanco, E.32
Bosak, S.A.33
Bradley, R.K.34
Brand, A.D.35
Brent, M.R.36
Brooks, A.N.37
Brown, R.H.38
Butlin, R.K.39
Caggese, C.40
Calvi, B.R.41
Bernardo De Carvalho, A.42
Caspi, A.43
Castrezana, S.44
Celniker, S.E.45
Chang, J.L.46
Chapple, C.47
Chatterji, S.48
Chinwalla, A.49
Civetta, A.50
Clifton, S.W.51
Comeron, J.M.52
Costello, J.C.53
Coyne, J.A.54
Daub, J.55
David, R.G.56
Delcher, A.L.57
Delehaunty, K.58
Do, C.B.59
Ebling, H.60
Edwards, K.61
Eickbush, T.62
Evans, J.D.63
Filipski, A.64
Findeiss, S.65
Freyhult, E.66
Fulton, L.67
Fulton, R.68
more..
-
29
-
-
84858707057
-
Sex-specific adaptation drives early sex chromosome evolution in Drosophila
-
Zhou, Q. & Bachtrog, D. Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science 337, 341-345 (2012).
-
(2012)
Science
, vol.337
, pp. 341-345
-
-
Zhou, Q.1
Bachtrog, D.2
-
30
-
-
79959670380
-
Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology
-
Pillmann, H., Hatje, K., Odronitz, F., Hammesfahr, B. & Kollmar, M. Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology. BMC Bioinformatics 12, 270 (2011).
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 270
-
-
Pillmann, H.1
Hatje, K.2
Odronitz, F.3
Hammesfahr, B.4
Kollmar, M.5
-
31
-
-
2942527473
-
Gene prediction with a hidden Markov model and a new intron submodel
-
DOI 10.1093/bioinformatics/btg1080
-
Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19(Suppl 2): ii215-ii225 (2003). (Pubitemid 41296659)
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Stanke, M.1
Waack, S.2
-
32
-
-
0347224274
-
Cell-specific alternative splicing increases calcium channel current density in the pain pathway
-
DOI 10.1016/S0896-6273(03)00801-8
-
Bell, T. J., Thaler, C., Castiglioni, A. J., Helton, T. D. & Lipscombe, D. Cellspecific alternative splicing increases calcium channel current density in the pain pathway. Neuron 41, 127-138 (2004). (Pubitemid 38068440)
-
(2004)
Neuron
, vol.41
, Issue.1
, pp. 127-138
-
-
Bell, T.J.1
Thaler, C.2
Castiglioni, A.J.3
Helton, T.D.4
Lipscombe, D.5
-
33
-
-
78751475623
-
Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster
-
May, G. E., Olson, S., McManus, C. J. & Graveley, B. R. Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. RNA. 17, 222-229 (2011).
-
(2011)
RNA
, vol.17
, pp. 222-229
-
-
May, G.E.1
Olson, S.2
McManus, C.J.3
Graveley, B.R.4
-
34
-
-
45549107329
-
Use and misuse of the gene ontology annotations
-
DOI 10.1038/nrg2363, PII NRG2363
-
Rhee, S. Y., Wood, V., Dolinski, K. & Draghici, S. Use and misuse of the gene ontology annotations. Nat. Rev. Genet. 9, 509-515 (2008). (Pubitemid 351861540)
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.7
, pp. 509-515
-
-
Yon Rhee, S.1
Wood, V.2
Dolinski, K.3
Draghici, S.4
-
35
-
-
1642385302
-
Evolutionary convergence of alternative splicing in ion channels
-
DOI 10.1016/j.tig.2004.02.001, PII S016895250400037X
-
Copley, R. R. Evolutionary convergence of alternative splicing in ion channels. Trends Genet. 20, 171-176 (2004). (Pubitemid 38369186)
-
(2004)
Trends in Genetics
, vol.20
, Issue.4
, pp. 171-176
-
-
Copley, R.R.1
-
36
-
-
20444368053
-
Neuronal proteins custom designed by alternative splicing
-
DOI 10.1016/j.conb.2005.04.002, PII S0959438805000656
-
Lipscombe, D. Neuronal proteins custom designed by alternative splicing. Curr. Opin. Neurobiol. 15, 358-363 (2005). (Pubitemid 40806449)
-
(2005)
Current Opinion in Neurobiology
, vol.15
, Issue.3 SPEC. ISS.
, pp. 358-363
-
-
Lipscombe, D.1
-
37
-
-
39849089591
-
Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene
-
Odronitz, F. & Kollmar, M. Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene. BMC Mol. Biol. 9, 21 (2008).
-
(2008)
BMC Mol. Biol
, vol.9
, pp. 21
-
-
Odronitz, F.1
Kollmar, M.2
-
38
-
-
84871436996
-
Evolutionary dynamics of gene and isoform regulation in mammalian tissues
-
Merkin, J., Russell, C., Chen, P. & Burge, C. B. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338, 1593-1599 (2012).
-
(2012)
Science
, vol.338
, pp. 1593-1599
-
-
Merkin, J.1
Russell, C.2
Chen, P.3
Burge, C.B.4
-
39
-
-
84871410405
-
The evolutionary landscape of alternative splicing in vertebrate species
-
Barbosa-Morais, N. L. et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 338, 1587-1593 (2012).
-
(2012)
Science
, vol.338
, pp. 1587-1593
-
-
Barbosa-Morais, N.L.1
-
40
-
-
58149199579
-
FlyBase: Enhancing Drosophila Gene Ontology annotations
-
Tweedie, S. et al. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 37, D555-D559 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Tweedie, S.1
-
41
-
-
84861207340
-
WormBase 2012: More genomes, more data, new website
-
Yook, K. et al. WormBase 2012: more genomes, more data, new website. Nucleic Acids Res. 40, D735-D741 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Yook, K.1
-
42
-
-
84862234802
-
The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools
-
Lamesch, P. et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40, D1202-D1210 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Lamesch, P.1
-
43
-
-
46649114758
-
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
-
Keller, O., Odronitz, F., Stanke, M., Kollmar, M. & Waack, S. Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinformatics 9, 278 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 278
-
-
Keller, O.1
Odronitz, F.2
Stanke, M.3
Kollmar, M.4
Waack, S.5
-
44
-
-
39549090389
-
SeqAn An efficient, generic C+ + library for sequence analysis
-
Döring, A., Weese, D., Rausch, T. & Reinert, K. SeqAn An efficient, generic C+ + library for sequence analysis. BMC Bioinformatics 9, 11 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 11
-
-
Döring, A.1
Weese, D.2
Rausch, T.3
Reinert, K.4
-
45
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
46
-
-
82055164092
-
ViennaRNA package 2.0
-
Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. Biol. 6, 26 (2011).
-
(2011)
Algorithms Mol. Biol
, vol.6
, pp. 26
-
-
Lorenz, R.1
-
47
-
-
58349111875
-
AmiGO: Online access to ontology and annotation data
-
Carbon, S. et al. AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288-289 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 288-289
-
-
Carbon, S.1
|