-
1
-
-
79959875909
-
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
-
Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Sánchez Alvarado A, Kempa S, Dieterich C, Rajewsky N, Chen W, Alvarado AS. 2011. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Research 21: 1193-1200. doi: 10.1101/gr.113779.110
-
(2011)
Genome Research
, vol.21
, pp. 1193-1200
-
-
Adamidi, C.1
Wang, Y.2
Gruen, D.3
Mastrobuoni, G.4
You, X.5
Tolle, D.6
Dodt, M.7
Mackowiak, S.D.8
Gogol-Doering, A.9
Oenal, P.10
Rybak, A.11
Ross, E.12
Sánchez Alvarado, A.13
Kempa, S.14
Dieterich, C.15
Rajewsky, N.16
Chen, W.17
Alvarado, A.S.18
-
2
-
-
84952684108
-
The ancestral gene repertoire of animal stem cells
-
Alié A, Hayashi T, Sugimura I, Manuel M, Sugano W, Mano A, Satoh N, Agata K, Funayama N. 2015. The ancestral gene repertoire of animal stem cells. PNAS 112: E7093-E7100. doi: 10.1073/pnas.1514789112
-
(2015)
PNAS
, vol.112
, pp. E7093-E7100
-
-
Alié, A.1
Hayashi, T.2
Sugimura, I.3
Manuel, M.4
Sugano, W.5
Mano, A.6
Satoh, N.7
Agata, K.8
Funayama, N.9
-
3
-
-
84928987900
-
HTSeq-a Python framework to work with high-throughput sequencing data
-
Anders S, Pyl PT, Huber W. 2015. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166-169. doi: 10.1093/bioinformatics/btu638
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
4
-
-
0001121524
-
Quantitative analysis of cell types during growth, degrowth and regeneration in the planarians Dugesia mediterranea and Dugesia tigrina
-
Baguñá J, Romero R. 1981. Quantitative analysis of cell types during growth, degrowth and regeneration in the planarians Dugesia mediterranea and Dugesia tigrina. Hydrobiologia 84: 181-194. doi: 10.1007/978-94-009-8668-8_25
-
(1981)
Hydrobiologia
, vol.84
, pp. 181-194
-
-
Baguñá, J.1
Romero, R.2
-
5
-
-
78650774202
-
A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology
-
Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, Evans D, Jowett J, Hall A, Lemay V, Lam S, Aboobaker AA. 2010. A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PLoS One 5: e15617. doi: 10.1371/journal.pone.0015617
-
(2010)
PLoS One
, vol.5
-
-
Blythe, M.J.1
Kao, D.2
Malla, S.3
Rowsell, J.4
Wilson, R.5
Evans, D.6
Jowett, J.7
Hall, A.8
Lemay, V.9
Lam, S.10
Aboobaker, A.A.11
-
6
-
-
84920460444
-
Detained introns are a novel, widespread class of post-transcriptionally spliced introns
-
Boutz PL, Bhutkar A, Sharp PA. 2015. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes & Development 29: 63-80. doi: 10.1101/gad.247361.114
-
(2015)
Genes & Development
, vol.29
, pp. 63-80
-
-
Boutz, P.L.1
Bhutkar, A.2
Sharp, P.A.3
-
7
-
-
84919923534
-
Widespread intron retention in mammals functionally tunes transcriptomes
-
Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ. 2014. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Research 24: 1774-1786. doi: 10.1101/gr.177790.114
-
(2014)
Genome Research
, vol.24
, pp. 1774-1786
-
-
Braunschweig, U.1
Barbosa-Morais, N.L.2
Pan, Q.3
Nachman, E.N.4
Alipanahi, B.5
Gonatopoulos-Pournatzis, T.6
Frey, B.7
Irimia, M.8
Blencowe, B.J.9
-
8
-
-
79551584794
-
Conservation of an RNA regulatory map between Drosophila and mammals
-
Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. 2011. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research 21: 193-202. doi: 10.1101/gr. 108662.110
-
(2011)
Genome Research
, vol.21
, pp. 193-202
-
-
Brooks, A.N.1
Yang, L.2
Duff, M.O.3
Hansen, K.D.4
Park, J.W.5
Dudoit, S.6
Brenner, S.E.7
Graveley, B.R.8
-
9
-
-
84862992463
-
Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks
-
Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM. 2012. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Molecular Cell 46: 871-883. doi: 10.1016/j.molcel.2012.05.039
-
(2012)
Molecular Cell
, vol.46
, pp. 871-883
-
-
Buljan, M.1
Chalancon, G.2
Eustermann, S.3
Wagner, G.P.4
Fuxreiter, M.5
Bateman, A.6
Babu, M.M.7
-
10
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421. doi: 10.1186/1471-2105-10-421
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
11
-
-
0023277545
-
Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction
-
Chomczynski P, Sacchi N. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical Biochemistry 162: 156-159. doi: 10.1016/0003-2697(87)90021-2
-
(1987)
Analytical Biochemistry
, vol.162
, pp. 156-159
-
-
Chomczynski, P.1
Sacchi, N.2
-
12
-
-
49749110720
-
Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus
-
D’Aniello S, Irimia M, Maeso I, Pascual-Anaya J, Jiménez-Delgado S, Bertrand S, Garcia-Fernández J. 2008. Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus. Molecular Biology and Evolution 25: 1841-1854. doi: 10.1093/molbev/msn132
-
(2008)
Molecular Biology and Evolution
, vol.25
, pp. 1841-1854
-
-
D’Aniello, S.1
Irimia, M.2
Maeso, I.3
Pascual-Anaya, J.4
Jiménez-Delgado, S.5
Bertrand, S.6
Garcia-Fernández, J.7
-
13
-
-
84858440814
-
The importance of CELF control: Molecular and biological roles of the CUG-BP, Elav-like family of RNA-binding proteins
-
Dasgupta T, Ladd AN. 2012. The importance of CELF control: molecular and biological roles of the CUG-BP, Elav-like family of RNA-binding proteins. Wiley Interdisciplinary Reviews: RNA 3: 104-121. doi: 10.1002/wrna. 107
-
(2012)
Wiley Interdisciplinary Reviews: RNA
, vol.3
, pp. 104-121
-
-
Dasgupta, T.1
Ladd, A.N.2
-
14
-
-
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. doi: 10.1093/bioinformatics/bts635
-
(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
-
15
-
-
84887224285
-
FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms
-
Dodt M, Roehr JT, Ahmed R, Dieterich C. 2012. FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms. Biology 1: 895-905. doi: 10.3390/biology1030895
-
(2012)
Biology
, vol.1
, pp. 895-905
-
-
Dodt, M.1
Roehr, J.T.2
Ahmed, R.3
Dieterich, C.4
-
16
-
-
51049089115
-
Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea
-
Eisenhoffer GT, Kang H, Sánchez Alvarado A, Alvarado AS. 2008. Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell 3: 327-339. doi: 10.1016/j.stem.2008.07.002
-
(2008)
Cell Stem Cell
, vol.3
, pp. 327-339
-
-
Eisenhoffer, G.T.1
Kang, H.2
Sánchez Alvarado, A.3
Alvarado, A.S.4
-
17
-
-
84863003268
-
Tissue-specific alternative splicing remodels protein-protein interaction networks
-
Ellis JD, Barrios-Rodiles M, Colak R, Irimia M, Kim T, Calarco JA, Wang X, Pan Q, O’Hanlon D, Kim PM, Wrana JL, Blencowe BJ. 2012. Tissue-specific alternative splicing remodels protein-protein interaction networks. Molecular Cell 46: 884-892. doi: 10.1016/j.molcel.2012.05.037
-
(2012)
Molecular Cell
, vol.46
, pp. 884-892
-
-
Ellis, J.D.1
Barrios-Rodiles, M.2
Colak, R.3
Irimia, M.4
Kim, T.5
Calarco, J.A.6
Wang, X.7
Pan, Q.8
O’Hanlon, D.9
Kim, P.M.10
Wrana, J.L.11
Blencowe, B.J.12
-
18
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
Falcon S, Gentleman R. 2007. Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258. doi: 10.1093/bioinformatics/btl567
-
(2007)
Bioinformatics
, vol.23
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
-
19
-
-
78650583114
-
Evolution of the mammalian embryonic pluripotency gene regulatory network
-
Fernandez-Tresguerres B, Cañon S, Rayon T, Pernaute B, Crespo M, Torroja C, Manzanares M. 2010. Evolution of the mammalian embryonic pluripotency gene regulatory network. PNAS 107: 19955-19960. doi: 10.1073/pnas.1010708107
-
(2010)
PNAS
, vol.107
, pp. 19955-19960
-
-
Fernandez-Tresguerres, B.1
Cañon, S.2
Rayon, T.3
Pernaute, B.4
Crespo, M.5
Torroja, C.6
Manzanares, M.7
-
20
-
-
84891782659
-
Pfam: The protein families database
-
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. 2014. Pfam: the protein families database. Nucleic Acids Research 42: D222-D230. doi: 10.1093/nar/gkt1223
-
(2014)
Nucleic Acids Research
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
Heger, A.7
Hetherington, K.8
Holm, L.9
Mistry, J.10
Sonnhammer, E.L.11
Tate, J.12
Punta, M.13
-
21
-
-
80052223272
-
An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming
-
Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O’Hanlon D, Sung HK, Alvarez M, Talukder S, Pan Q, Mazzoni EO, Nedelec S, Wichterle H, Woltjen K, Hughes TR, Zandstra PW, Nagy A, Wrana JL, Blencowe BJ. 2011. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell 147: 132-146. doi: 10.1016/j.cell.2011.08.023
-
(2011)
Cell
, vol.147
, pp. 132-146
-
-
Gabut, M.1
Samavarchi-Tehrani, P.2
Wang, X.3
Slobodeniuc, V.4
O’Hanlon, D.5
Sung, H.K.6
Alvarez, M.7
Talukder, S.8
Pan, Q.9
Mazzoni, E.O.10
Nedelec, S.11
Wichterle, H.12
Woltjen, K.13
Hughes, T.R.14
Zandstra, P.W.15
Nagy, A.16
Wrana, J.L.17
Blencowe, B.J.18
-
22
-
-
84924955867
-
The early expansion and evolutionary dynamics of POU class genes
-
Gold DA, Gates RD, Jacobs DK. 2014. The early expansion and evolutionary dynamics of POU class genes. Molecular Biology and Evolution 31: 3136-3147. doi: 10.1093/molbev/msu243
-
(2014)
Molecular Biology and Evolution
, vol.31
, pp. 3136-3147
-
-
Gold, D.A.1
Gates, R.D.2
Jacobs, D.K.3
-
23
-
-
79953043801
-
The developmental transcriptome of Drosophila melanogaster
-
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, et al. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471: 473-479. doi: 10.1038/nature09715
-
(2011)
Nature
, vol.471
, pp. 473-479
-
-
Graveley, B.R.1
Brooks, A.N.2
Carlson, J.W.3
Duff, M.O.4
Landolin, J.M.5
Yang, L.6
Artieri, C.G.7
van Baren, M.J.8
Boley, N.9
Booth, B.W.10
Brown, J.B.11
Cherbas, L.12
Davis, C.A.13
Dobin, A.14
Li, R.15
Lin, W.16
Malone, J.H.17
Mattiuzzo, N.R.18
Miller, D.19
Sturgill, D.20
more..
-
24
-
-
84939856392
-
An alternative splicing event amplifies evolutionary differences between vertebrates
-
Gueroussov S, Gonatopoulos-Pournatzis T, Irimia M, Raj B, Lin ZY, Gingras AC, Blencowe BJ. 2015. An alternative splicing event amplifies evolutionary differences between vertebrates. Science 349: 868-873. doi: 10. 1126/science.aaa8381
-
(2015)
Science
, vol.349
, pp. 868-873
-
-
Gueroussov, S.1
Gonatopoulos-Pournatzis, T.2
Irimia, M.3
Raj, B.4
Lin, Z.Y.5
Gingras, A.C.6
Blencowe, B.J.7
-
25
-
-
33746518104
-
A Bruno-like gene is required for stem cell maintenance in planarians
-
Guo T, Peters AH, Newmark PA. 2006. A Bruno-like gene is required for stem cell maintenance in planarians. Developmental Cell 11: 159-169. doi: 10.1016/j.devcel.2006.06.004
-
(2006)
Developmental Cell
, vol.11
, pp. 159-169
-
-
Guo, T.1
Peters, A.H.2
Newmark, P.A.3
-
26
-
-
84880266648
-
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
-
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, et al. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols 8: 1494-1512. doi: 10.1038/nprot.2013.084
-
(2013)
Nature Protocols
, vol.8
, pp. 1494-1512
-
-
Haas, B.J.1
Papanicolaou, A.2
Yassour, M.3
Grabherr, M.4
Blood, P.D.5
Bowden, J.6
Couger, M.B.7
Eccles, D.8
Li, B.9
Lieber, M.10
Macmanes, M.D.11
Ott, M.12
Orvis, J.13
Pochet, N.14
Strozzi, F.15
Weeks, N.16
Westerman, R.17
William, T.18
Dewey, C.N.19
Henschel, R.20
more..
-
27
-
-
84878995293
-
MBNL proteins repress ES-cell-specific alternative splicing and reprogramming
-
Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O’Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, et al. 2013. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature 498: 241-245. doi: 10.1038/nature12270
-
(2013)
Nature
, vol.498
, pp. 241-245
-
-
Han, H.1
Irimia, M.2
Ross, P.J.3
Sung, H.K.4
Alipanahi, B.5
David, L.6
Golipour, A.7
Gabut, M.8
Michael, I.P.9
Nachman, E.N.10
Wang, E.11
Trcka, D.12
Thompson, T.13
O’Hanlon, D.14
Slobodeniuc, V.15
Barbosa-Morais, N.L.16
Burge, C.B.17
Moffat, J.18
Frey, B.J.19
Nagy, A.20
more..
-
28
-
-
33745816717
-
Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting
-
Hayashi T, Asami M, Higuchi S, Shibata N, Agata K. 2006. Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting. Development, Growth and Differentiation 48: 371-380. doi: 10.1111/j.1440-169X.2006.00876.x
-
(2006)
Development, Growth and Differentiation
, vol.48
, pp. 371-380
-
-
Hayashi, T.1
Asami, M.2
Higuchi, S.3
Shibata, N.4
Agata, K.5
-
29
-
-
79955121833
-
Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain
-
Irimia M, Denuc A, Burguera D, Somorjai I, Martiín-Durán JM, Genikhovich G, Jimenez-Delgado S, Technau U, Roy SW, Marfany G, Garcia-Fernández J. 2011. Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain. PNAS 108: 5319-5324. doi: 10.1073/pnas.1012333108
-
(2011)
PNAS
, vol.108
, pp. 5319-5324
-
-
Irimia, M.1
Denuc, A.2
Burguera, D.3
Somorjai, I.4
Martiín-Durán, J.M.5
Genikhovich, G.6
Jimenez-Delgado, S.7
Technau, U.8
Roy, S.W.9
Marfany, G.10
Garcia-Fernández, J.11
-
30
-
-
59849108350
-
Quantitative regulation of alternative splicing in evolution and development
-
Irimia M, Rukov JL, Roy SW, Vinther J, Garcia-Fernandez J. 2009. Quantitative regulation of alternative splicing in evolution and development. BioEssays 31: 40-50. doi: 10.1002/bies.080092
-
(2009)
BioEssays
, vol.31
, pp. 40-50
-
-
Irimia, M.1
Rukov, J.L.2
Roy, S.W.3
Vinther, J.4
Garcia-Fernandez, J.5
-
31
-
-
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-Valliéres M, Tapial J, Raj B, O’Hanlon D, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ. 2014. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159: 1511-1523. doi: 10.1016/j.cell.2014.11.035
-
(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-Valliéres, M.7
Tapial, J.8
Raj, B.9
O’Hanlon, D.10
Barrios-Rodiles, M.11
Sternberg, M.J.12
Cordes, S.P.13
Roth, F.P.14
Wrana, J.L.15
Geschwind, D.H.16
Blencowe, B.J.17
-
32
-
-
58149492467
-
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart
-
Kalsotra A, Xiao X, Ward AJ, Castle JC, Johnson JM, Burge CB, Cooper TA. 2008. A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. PNAS 105: 20333-20338. doi: 10. 1073/pnas.0809045105
-
(2008)
PNAS
, vol.105
, pp. 20333-20338
-
-
Kalsotra, A.1
Xiao, X.2
Ward, A.J.3
Castle, J.C.4
Johnson, J.M.5
Burge, C.B.6
Cooper, T.A.7
-
33
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Article published online before March 2002
-
Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Research 12: 656-664. Article published online before March 2002. doi: 10.1101/gr.229202.
-
(2002)
Genome Research
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
34
-
-
84874805648
-
In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea
-
King RS, Newmark PA. 2013. In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea. BMC Developmental Biology 13: 8. doi: 10.1186/1471-213X-13-8
-
(2013)
BMC Developmental Biology
, vol.13
, pp. 8
-
-
King, R.S.1
Newmark, P.A.2
-
35
-
-
84864376995
-
A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals
-
Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ. 2012. A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells 30: 1734-1745. doi: 10.1002/stem.1144
-
(2012)
Stem Cells
, vol.30
, pp. 1734-1745
-
-
Labbé, R.M.1
Irimia, M.2
Currie, K.W.3
Lin, A.4
Zhu, S.J.5
Brown, D.D.6
Ross, E.J.7
Voisin, V.8
Bader, G.D.9
Blencowe, B.J.10
Pearson, B.J.11
-
36
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357-359. doi: 10.1038/nmeth.1923
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
37
-
-
84988288865
-
Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible
-
Lareau LF, Brenner SE. 2015. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Molecular Biology and Evolution 32: 1072-1079. doi: 10.1093/molbev/msv002
-
(2015)
Molecular Biology and Evolution
, vol.32
, pp. 1072-1079
-
-
Lareau, L.F.1
Brenner, S.E.2
-
38
-
-
70450203364
-
Pathogenic mechanisms of myotonic dystrophy
-
Lee JE, Cooper TA. 2009. Pathogenic mechanisms of myotonic dystrophy. Biochemical Society Transactions 37: 1281-1286. doi: 10.1042/BST0371281
-
(2009)
Biochemical Society Transactions
, vol.37
, pp. 1281-1286
-
-
Lee, J.E.1
Cooper, T.A.2
-
39
-
-
33745248133
-
Failure of MBNL1-dependent post-natal splicing transitions in myotonic dystrophy
-
Lin X, Miller JW, Mankodi A, Kanadia RN, Yuan Y, Moxley RT, Swanson MS, Thornton CA. 2006. Failure of MBNL1-dependent post-natal splicing transitions in myotonic dystrophy. Human Molecular Genetics 15: 2087-2097. doi: 10.1093/hmg/ddl132
-
(2006)
Human Molecular Genetics
, vol.15
, pp. 2087-2097
-
-
Lin, X.1
Miller, J.W.2
Mankodi, A.3
Kanadia, R.N.4
Yuan, Y.5
Moxley, R.T.6
Swanson, M.S.7
Thornton, C.A.8
-
40
-
-
84881481616
-
Reactivating head regrowth in a regeneration-deficient planarian species
-
Liu SY, Selck C, Friedrich B, Lutz R, Vila-Farré M, Dahl A, Brandl H, Lakshmanaperumal N, Henry I, Rink JC. 2013. Reactivating head regrowth in a regeneration-deficient planarian species. Nature 500: 81-84. doi: 10.1038/nature12414
-
(2013)
Nature
, vol.500
, pp. 81-84
-
-
Liu, S.Y.1
Selck, C.2
Friedrich, B.3
Lutz, R.4
Vila-Farré, M.5
Dahl, A.6
Brandl, H.7
Lakshmanaperumal, N.8
Henry, I.9
Rink, J.C.10
-
41
-
-
0042701918
-
Two neuronal, nuclear-localized RNA binding proteins involved in synaptic transmission
-
Loria PM, Duke A, Rand JB, Hobert O. 2003. Two neuronal, nuclear-localized RNA binding proteins involved in synaptic transmission. Current Biology 13: 1317-1323. doi: 10.1016/S0960-9822(03)00532-3
-
(2003)
Current Biology
, vol.13
, pp. 1317-1323
-
-
Loria, P.M.1
Duke, A.2
Rand, J.B.3
Hobert, O.4
-
42
-
-
80053374662
-
Schmidtea mediterranea phylogeography: An old species surviving on a few Mediterranean islands?
-
Lázaro EM, Harrath AH, Stocchino GA, Pala M, Baguñá J, Riutort M. 2011. Schmidtea mediterranea phylogeography: an old species surviving on a few Mediterranean islands? BMC Evolutionary Biology 11: 274. doi: 10.1186/1471-2148-11-274
-
(2011)
BMC Evolutionary Biology
, vol.11
, pp. 274
-
-
Lázaro, E.M.1
Harrath, A.H.2
Stocchino, G.A.3
Pala, M.4
Baguñá, J.5
Riutort, M.6
-
44
-
-
34547588704
-
KAAS: An automatic genome annotation and pathway reconstruction server
-
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research 35: W182-W185. doi: 10.1093/nar/gkm321
-
(2007)
Nucleic Acids Research
, vol.35
, pp. W182-W185
-
-
Moriya, Y.1
Itoh, M.2
Okuda, S.3
Yoshizawa, A.C.4
Kanehisa, M.5
-
45
-
-
84957537166
-
Unusually Large number of mutations in asexually reproducing clonal planarian dugesia japonica
-
Nishimura O, Hosoda K, Kawaguchi E, Yazawa S, Hayashi T, Inoue T, Umesono Y, Agata K. 2015. Unusually Large number of mutations in asexually reproducing clonal planarian dugesia japonica. PLoS one 10: e0143525. doi: 10.1371/journal.pone.0143525
-
(2015)
PLoS one
, vol.10
-
-
Nishimura, O.1
Hosoda, K.2
Kawaguchi, E.3
Yazawa, S.4
Hayashi, T.5
Inoue, T.6
Umesono, Y.7
Agata, K.8
-
46
-
-
84887016186
-
Global splicing pattern reversion during somatic cell reprogramming
-
Ohta S, Nishida E, Yamanaka S, Yamamoto T. 2013. Global splicing pattern reversion during somatic cell reprogramming. Cell Reports 5: 357-366. doi: 10.1016/j.celrep.2013.09.016
-
(2013)
Cell Reports
, vol.5
, pp. 357-366
-
-
Ohta, S.1
Nishida, E.2
Yamanaka, S.3
Yamamoto, T.4
-
47
-
-
84862214826
-
Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells
-
Onal P, Grün D, Adamidi C, Rybak A, Solana J, Mastrobuoni G, Wang Y, Rahn HP, Chen W, Kempa S, Ziebold U, Rajewsky N. 2012. Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells. The EMBO Journal 31: 2755-2769. doi: 10.1038/emboj.2012.110
-
(2012)
The EMBO Journal
, vol.31
, pp. 2755-2769
-
-
Onal, P.1
Grün, D.2
Adamidi, C.3
Rybak, A.4
Solana, J.5
Mastrobuoni, G.6
Wang, Y.7
Rahn, H.P.8
Chen, W.9
Kempa, S.10
Ziebold, U.11
Rajewsky, N.12
-
48
-
-
75549086594
-
InParanoid 7: New algorithms and tools for eukaryotic orthology analysis
-
Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, Frings O, Sonnhammer EL. 2010. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Research 38: D196-D203. doi: 10. 1093/nar/gkp931
-
(2010)
Nucleic Acids Research
, vol.38
, pp. D196-D203
-
-
Ostlund, G.1
Schmitt, T.2
Forslund, K.3
Köstler, T.4
Messina, D.N.5
Roopra, S.6
Frings, O.7
Sonnhammer, E.L.8
-
49
-
-
67650484984
-
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
-
Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR. 2009. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nature Biotechnology 27: 667-670. doi: 10.1038/nbt.1550
-
(2009)
Nature Biotechnology
, vol.27
, pp. 667-670
-
-
Ray, D.1
Kazan, H.2
Chan, E.T.3
Peña Castillo, L.4
Chaudhry, S.5
Talukder, S.6
Blencowe, B.J.7
Morris, Q.8
Hughes, T.R.9
-
50
-
-
84880427394
-
A compendium of RNA-binding motifs for decoding gene regulation
-
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, et al. 2013. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499: 172-177. doi: 10.1038/nature12311
-
(2013)
Nature
, vol.499
, pp. 172-177
-
-
Ray, D.1
Kazan, H.2
Cook, K.B.3
Weirauch, M.T.4
Najafabadi, H.S.5
Li, X.6
Gueroussov, S.7
Albu, M.8
Zheng, H.9
Yang, A.10
Na, H.11
Irimia, M.12
Matzat, L.H.13
Dale, R.K.14
Smith, S.A.15
Yarosh, C.A.16
Kelly, S.M.17
Nabet, B.18
Mecenas, D.19
Li, W.20
more..
-
51
-
-
28144464878
-
SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells
-
Reddien PW, Oviedo NJ, Jennings JR, Jenkin JC, Sánchez Alvarado A. 2005. SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells. Science 310: 1327-1330. doi: 10.1126/science.1116110
-
(2005)
Science
, vol.310
, pp. 1327-1330
-
-
Reddien, P.W.1
Oviedo, N.J.2
Jennings, J.R.3
Jenkin, J.C.4
Sánchez Alvarado, A.5
-
52
-
-
84859355786
-
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea
-
Resch AM, Palakodeti D, Lu YC, Horowitz M, Graveley BR. 2012. Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One 7: e34447. doi: 10.1371/journal.pone. 0034447
-
(2012)
PLoS One
, vol.7
-
-
Resch, A.M.1
Palakodeti, D.2
Lu, Y.C.3
Horowitz, M.4
Graveley, B.R.5
-
53
-
-
77952308587
-
Different requirements for conserved post-transcriptional regulators in planarian regeneration and stem cell maintenance
-
Rouhana L, Shibata N, Nishimura O, Agata K. 2010. Different requirements for conserved post-transcriptional regulators in planarian regeneration and stem cell maintenance. Developmental Biology 341: 429-443. doi: 10. 1016/j.ydbio.2010.02.037
-
(2010)
Developmental Biology
, vol.341
, pp. 429-443
-
-
Rouhana, L.1
Shibata, N.2
Nishimura, O.3
Agata, K.4
-
54
-
-
84857320620
-
PRMT5 and the role of symmetrical dimethylarginine in chromatoid bodies of planarian stem cells
-
Rouhana L, Vieira AP, Roberts-Galbraith RH, Newmark PA. 2012. PRMT5 and the role of symmetrical dimethylarginine in chromatoid bodies of planarian stem cells. Development 139: 1083-1094. doi: 10.1242/dev. 076182
-
(2012)
Development
, vol.139
, pp. 1083-1094
-
-
Rouhana, L.1
Vieira, A.P.2
Roberts-Galbraith, R.H.3
Newmark, P.A.4
-
55
-
-
84897125705
-
Rethinking differentiation: Stem cells, regeneration, and plasticity
-
Sánchez Alvarado A, Yamanaka S. 2014. Rethinking differentiation: stem cells, regeneration, and plasticity. Cell 157: 110-119. doi: 10.1016/j.cell.2014.02.041
-
(2014)
Cell
, vol.157
, pp. 110-119
-
-
Sánchez Alvarado, A.1
Yamanaka, S.2
-
56
-
-
84898431583
-
On the origin and evolutionary history of NANOG
-
Scerbo P, Markov GV, Vivien C, Kodjabachian L, Demeneix B, Coen L, Girardot F. 2014. On the origin and evolutionary history of NANOG. PLoS One 9: e85104. doi: 10.1371/journal.pone.0085104
-
(2014)
PLoS One
, vol.9
-
-
Scerbo, P.1
Markov, G.V.2
Vivien, C.3
Kodjabachian, L.4
Demeneix, B.5
Coen, L.6
Girardot, F.7
-
57
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3: 1-25. doi: 10.2202/1544-6115.1027
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
, pp. 1-25
-
-
Smyth, G.K.1
-
58
-
-
84892741340
-
The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation
-
Solana J, Gamberi C, Mihaylova Y, Grosswendt S, Chen C, Lasko P, Rajewsky N, Aboobaker AA. 2013. The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation. PLoS Genetics 9: e1004003. doi: 10.1371/journal.pgen.1004003
-
(2013)
PLoS Genetics
, vol.9
-
-
Solana, J.1
Gamberi, C.2
Mihaylova, Y.3
Grosswendt, S.4
Chen, C.5
Lasko, P.6
Rajewsky, N.7
Aboobaker, A.A.8
-
59
-
-
84858724123
-
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach
-
Solana J, Kao D, Mihaylova Y, Jaber-Hijazi F, Malla S, Wilson R, Aboobaker A. 2012. Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biology 13: R19. doi: 10.1186/gb-2012-13-3-r19
-
(2012)
Genome Biology
, vol.13
, pp. 19
-
-
Solana, J.1
Kao, D.2
Mihaylova, Y.3
Jaber-Hijazi, F.4
Malla, S.5
Wilson, R.6
Aboobaker, A.7
-
60
-
-
84874980486
-
Closing the circle of germline and stem cells: The Primordial Stem Cell hypothesis
-
Solana J. 2013. Closing the circle of germline and stem cells: the Primordial Stem Cell hypothesis. EvoDevo 4: 2. doi: 10.1186/2041-9139-4-2
-
(2013)
EvoDevo
, vol.4
, pp. 2
-
-
Solana, J.1
-
61
-
-
79960286977
-
The cellular basis for animal regeneration
-
Tanaka EM, Reddien PW. 2011. The cellular basis for animal regeneration. Developmental Cell 21: 172-185. doi: 10.1016/j.devcel.2011.06.016
-
(2011)
Developmental Cell
, vol.21
, pp. 172-185
-
-
Tanaka, E.M.1
Reddien, P.W.2
-
62
-
-
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, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28: 511-515. doi: 10.1038/nbt.1621.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
63
-
-
84946069451
-
UniProt: A hub for protein information
-
UniProt Consortium. 2015. UniProt: a hub for protein information. Nucleic Acids Research 43: D204-D212. doi: 10.1093/nar/gku989
-
(2015)
Nucleic Acids Research
, vol.43
, pp. D204-D212
-
-
-
64
-
-
84909590292
-
Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment
-
van Wolfswinkel JC, Wagner DE, Reddien PW. 2014. Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment. Cell Stem Cell 15: 326-339. doi: 10.1016/j.stem.2014.06.007
-
(2014)
Cell Stem Cell
, vol.15
, pp. 326-339
-
-
van Wolfswinkel, J.C.1
Wagner, D.E.2
Reddien, P.W.3
-
65
-
-
84899044116
-
MBNL1 and RBFOX2 cooperate to establish a splicing programme involved in pluripotent stem cell differentiation
-
Venables JP, Lapasset L, Gadea G, Fort P, Klinck R, Irimia M, Vignal E, Thibault P, Prinos P, Chabot B, Abou Elela S, Roux P, Lemaitre JM, Tazi J. 2013. MBNL1 and RBFOX2 cooperate to establish a splicing programme involved in pluripotent stem cell differentiation. Nature Communications 4: 2480. doi: 10.1038/ncomms3480
-
(2013)
Nature Communications
, vol.4
, pp. 2480
-
-
Venables, J.P.1
Lapasset, L.2
Gadea, G.3
Fort, P.4
Klinck, R.5
Irimia, M.6
Vignal, E.7
Thibault, P.8
Prinos, P.9
Chabot, B.10
Abou Elela, S.11
Roux, P.12
Lemaitre, J.M.13
Tazi, J.14
-
66
-
-
79955985703
-
Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration
-
Wagner DE, Wang IE, Reddien PW. 2011. Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science 332: 811-816. doi: 10.1126/science.1203983
-
(2011)
Science
, vol.332
, pp. 811-816
-
-
Wagner, D.E.1
Wang, I.E.2
Reddien, P.W.3
-
67
-
-
84865201988
-
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins
-
Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB. 2012. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150: 710-724. doi: 10.1016/j.cell.2012.06.041
-
(2012)
Cell
, vol.150
, pp. 710-724
-
-
Wang, E.T.1
Cody, N.A.2
Jog, S.3
Biancolella, M.4
Wang, T.T.5
Treacy, D.J.6
Luo, S.7
Schroth, G.P.8
Housman, D.E.9
Reddy, S.10
Lécuyer, E.11
Burge, C.B.12
-
68
-
-
84931829028
-
Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins
-
Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, Cooper TA, Burge CB. 2015. Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins. Genome Research 25: 858-871. doi: 10.1101/gr.184390.114
-
(2015)
Genome Research
, vol.25
, pp. 858-871
-
-
Wang, E.T.1
Ward, A.J.2
Cherone, J.M.3
Giudice, J.4
Wang, T.T.5
Treacy, D.J.6
Lambert, N.J.7
Freese, P.8
Saxena, T.9
Cooper, T.A.10
Burge, C.B.11
-
69
-
-
77956108781
-
CUGBP1 overexpression in mouse skeletal muscle reproduces features of myotonic dystrophy type 1
-
Ward AJ, Rimer M, Killian JM, Dowling JJ, Cooper TA. 2010. CUGBP1 overexpression in mouse skeletal muscle reproduces features of myotonic dystrophy type 1. Human Molecular Genetics 19: 3614-3622. doi: 10.1093/hmg/ddq277
-
(2010)
Human Molecular Genetics
, vol.19
, pp. 3614-3622
-
-
Ward, A.J.1
Rimer, M.2
Killian, J.M.3
Dowling, J.J.4
Cooper, T.A.5
-
70
-
-
1542358787
-
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
-
Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. Journal of Molecular Biology 337: 635-645. doi: 10.1016/j.jmb. 2004.02.002
-
(2004)
Journal of Molecular Biology
, vol.337
, pp. 635-645
-
-
Ward, J.J.1
Sodhi, J.S.2
McGuffin, L.J.3
Buxton, B.F.4
Jones, D.T.5
-
71
-
-
84961620215
-
A generic and cell-type-specific wound response precedes regeneration in planarians
-
Wurtzel O, Cote LE, Poirier A, Satija R, Regev A, Reddien PW. 2015. A generic and cell-type-specific wound response precedes regeneration in planarians. Developmental Cell 35: 632-645. doi: 10.1016/j.devcel.2015.11. 004
-
(2015)
Developmental Cell
, vol.35
, pp. 632-645
-
-
Wurtzel, O.1
Cote, L.E.2
Poirier, A.3
Satija, R.4
Regev, A.5
Reddien, P.W.6
-
72
-
-
84925010163
-
Regulation of pluripotency by RNA binding proteins
-
Ye J, Blelloch R. 2014. Regulation of pluripotency by RNA binding proteins. Cell Stem Cell 15: 271-280. doi: 10. 1016/j.stem.2014.08.010
-
(2014)
Cell Stem Cell
, vol.15
, pp. 271-280
-
-
Ye, J.1
Blelloch, R.2
-
73
-
-
0034800374
-
InterProScan-an integration platform for the signature-recognition methods in InterPro
-
Zdobnov EM, Apweiler R. 2001. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 17: 847-848. doi: 10.1093/bioinformatics/17.9.847
-
(2001)
Bioinformatics.
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
74
-
-
84937434095
-
A mex3 homolog is required for differentiation during planarian stem cell lineage development
-
Zhu SJ, Hallows SE, Currie KW, Xu C, Pearson BJ. 2015. A mex3 homolog is required for differentiation during planarian stem cell lineage development. eLife 4: e07025. doi: 10.7554/eLife.07025
-
(2015)
eLife
, vol.4
-
-
Zhu, S.J.1
Hallows, S.E.2
Currie, K.W.3
Xu, C.4
Pearson, B.J.5
|