-
1
-
-
79951475133
-
A decade's perspective on DNA sequencing technology
-
10.1038/nature09796, 21307932
-
Mardis ER. A decade's perspective on DNA sequencing technology. Nature 2011, 470:198-203. 10.1038/nature09796, 21307932.
-
(2011)
Nature
, vol.470
, pp. 198-203
-
-
Mardis, E.R.1
-
2
-
-
71049176982
-
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species
-
2877544, 19892720, Genome 10K Community of Scientists
-
Genome 10K Community of Scientists Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species. J Hered 2009, 100:659-674. 2877544, 19892720, Genome 10K Community of Scientists.
-
(2009)
J Hered
, vol.100
, pp. 659-674
-
-
-
3
-
-
79952781362
-
Creating a Buzz About Insect Genomes
-
10.1126/science.331.6023.1386, 21415334
-
Robinson GE, Hackett KJ, Purcell-Miramontes M, Brown SJ, Evans JD, Goldsmith MR, Lawson D, Okamuro J, Robertson HM, Schneider DJ. Creating a Buzz About Insect Genomes. Science 2011, 331:1386-1386. 10.1126/science.331.6023.1386, 21415334.
-
(2011)
Science
, vol.331
, pp. 1386-1386
-
-
Robinson, G.E.1
Hackett, K.J.2
Purcell-Miramontes, M.3
Brown, S.J.4
Evans, J.D.5
Goldsmith, M.R.6
Lawson, D.7
Okamuro, J.8
Robertson, H.M.9
Schneider, D.J.10
-
4
-
-
42949086676
-
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
-
10.1186/gb-2008-9-1-r7, 2395244, 18190707
-
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 2008, 9:R7. 10.1186/gb-2008-9-1-r7, 2395244, 18190707.
-
(2008)
Genome Biol
, vol.9
-
-
Haas, B.J.1
Salzberg, S.L.2
Zhu, W.3
Pertea, M.4
Allen, J.E.5
Orvis, J.6
White, O.7
Buell, C.R.8
Wortman, J.R.9
-
5
-
-
79956319465
-
Comparative Functional Genomics of the Fission Yeasts
-
10.1126/science.1203357, 3131103, 21511999
-
Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Muller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C. Comparative Functional Genomics of the Fission Yeasts. Science 2011, 332:930-936. 10.1126/science.1203357, 3131103, 21511999.
-
(2011)
Science
, vol.332
, pp. 930-936
-
-
Rhind, N.1
Chen, Z.2
Yassour, M.3
Thompson, D.A.4
Haas, B.J.5
Habib, N.6
Wapinski, I.7
Roy, S.8
Lin, M.F.9
Heiman, D.I.10
Young, S.K.11
Furuya, K.12
Guo, Y.13
Pidoux, A.14
Chen, H.M.15
Robbertse, B.16
Goldberg, J.M.17
Aoki, K.18
Bayne, E.H.19
Berlin, A.M.20
Desjardins, C.A.21
Dobbs, E.22
Dukaj, L.23
Fan, L.24
FitzGerald, M.G.25
French, C.26
Gujja, S.27
Hansen, K.28
Keifenheim, D.29
Levin, J.Z.30
Mosher, R.A.31
Muller, C.A.32
Pfiffner, J.33
Priest, M.34
Russ, C.35
Smialowska, A.36
Swoboda, P.37
Sykes, S.M.38
Vaughn, M.39
Vengrova, S.40
Yoder, R.41
Zeng, Q.42
Allshire, R.43
Baulcombe, D.44
Birren, B.W.45
Brown, W.46
Ekwall, K.47
Kellis, M.48
Leatherwood, J.49
Levin, H.50
Margalit, H.51
Martienssen, R.52
Nieduszynski, C.A.53
Spatafora, J.W.54
Friedman, N.55
Dalgaard, J.Z.56
Baumann, P.57
Niki, H.58
Regev, A.59
Nusbaum, C.60
more..
-
6
-
-
84858221706
-
Ensembl 2012
-
3245178, 22086963
-
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kahari AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernandez-Suarez XM, Harrow J, Herrero J, Hubbard TJP, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SMJ. Ensembl 2012. Nucleic Acids Res 2011, 40:D84-D90. 3245178, 22086963.
-
(2011)
Nucleic Acids Res
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
Gil, L.11
Gordon, L.12
Hendrix, M.13
Hourlier, T.14
Johnson, N.15
Kahari, A.K.16
Keefe, D.17
Keenan, S.18
Kinsella, R.19
Komorowska, M.20
Koscielny, G.21
Kulesha, E.22
Larsson, P.23
Longden, I.24
McLaren, W.25
Muffato, M.26
Overduin, B.27
Pignatelli, M.28
Pritchard, B.29
Riat, H.S.30
Ritchie, G.R.S.31
Ruffier, M.32
Schuster, M.33
Sobral, D.34
Tang, Y.A.35
Taylor, K.36
Trevanion, S.37
Vandrovcova, J.38
White, S.39
Wilson, M.40
Wilder, S.P.41
Aken, B.L.42
Birney, E.43
Cunningham, F.44
Dunham, I.45
Durbin, R.46
Fernandez-Suarez, X.M.47
Harrow, J.48
Herrero, J.49
Hubbard, T.J.P.50
Parker, A.51
Proctor, G.52
Spudich, G.53
Vogel, J.54
Yates, A.55
Zadissa, A.56
Searle, S.M.J.57
more..
-
7
-
-
80053359585
-
The genome of the green anole lizard and a comparative analysis with birds and mammals
-
10.1038/nature10390, 3184186, 21881562
-
Alföldi J, di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, Hallers ten BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 2011, 477:587-591. 10.1038/nature10390, 3184186, 21881562.
-
(2011)
Nature
, vol.477
, pp. 587-591
-
-
Alföldi, J.1
di Palma, F.2
Grabherr, M.3
Williams, C.4
Kong, L.5
Mauceli, E.6
Russell, P.7
Lowe, C.B.8
Glor, R.E.9
Jaffe, J.D.10
Ray, D.A.11
Boissinot, S.12
Shedlock, A.M.13
Botka, C.14
Castoe, T.A.15
Colbourne, J.K.16
Fujita, M.K.17
Moreno, R.G.18
Hallers ten, B.F.19
Haussler, D.20
Heger, A.21
Heiman, D.22
Janes, D.E.23
Johnson, J.24
de Jong, P.J.25
Koriabine, M.Y.26
Lara, M.27
Novick, P.A.28
Organ, C.L.29
Peach, S.E.30
Poe, S.31
Pollock, D.D.32
de Queiroz, K.33
Sanger, T.34
Searle, S.35
Smith, J.D.36
Smith, Z.37
Swofford, R.38
Turner-Maier, J.39
Wade, J.40
Young, S.41
Zadissa, A.42
Edwards, S.V.43
Glenn, T.C.44
Schneider, C.J.45
Losos, J.B.46
Lander, E.S.47
Breen, M.48
Ponting, C.P.49
Lindblad-Toh, K.50
more..
-
8
-
-
79960891921
-
Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes
-
Castoe TA, de Koning JAP, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, Pollock DD. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biol 2011, 12:1-8.
-
(2011)
Genome Biol
, vol.12
, pp. 1-8
-
-
Castoe, T.A.1
de Koning, J.A.P.2
Hall, K.T.3
Yokoyama, K.D.4
Gu, W.5
Smith, E.N.6
Feschotte, C.7
Uetz, P.8
Ray, D.A.9
Dobry, J.10
Bogden, R.11
Mackessy, S.P.12
Bronikowski, A.M.13
Warren, W.C.14
Secor, S.M.15
Pollock, D.D.16
-
9
-
-
84865022771
-
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
-
3334581, 22293439
-
St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 2012, 13:415. 3334581, 22293439.
-
(2012)
Genome Biol
, vol.13
, pp. 415
-
-
St John, J.A.1
Braun, E.L.2
Isberg, S.R.3
Miles, L.G.4
Chong, A.Y.5
Gongora, J.6
Dalzell, P.7
Moran, C.8
Bed'hom, B.9
Abzhanov, A.10
Burgess, S.C.11
Cooksey, A.M.12
Castoe, T.A.13
Crawford, N.G.14
Densmore, L.D.15
Drew, J.C.16
Edwards, S.V.17
Faircloth, B.C.18
Fujita, M.K.19
Greenwold, M.J.20
Hoffmann, F.G.21
Howard, J.M.22
Iguchi, T.23
Janes, D.E.24
Khan, S.Y.25
Kohno, S.26
de Koning, A.J.27
Lance, S.L.28
McCarthy, F.M.29
McCormack, J.E.30
Merchant, M.E.31
Peterson, D.G.32
Pollock, D.D.33
Pourmand, N.34
Raney, B.J.35
Roessler, K.A.36
Sanford, J.R.37
Sawyer, R.H.38
Schmidt, C.J.39
Triplett, E.W.40
Tuberville, T.D.41
Venegas-Anaya, M.42
Howard, J.T.43
Jarvis, E.D.44
Guillette, L.J.45
Glenn, T.C.46
Green, R.E.47
Ray, D.A.48
more..
-
10
-
-
84862886541
-
The transposable element profile of the Anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure
-
10.4161/mge.1.2.17733, 3190321, 22016857
-
Tollis M, Boissinot S. The transposable element profile of the Anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure. Mobile genetic elements 2011, 1:107-111. 10.4161/mge.1.2.17733, 3190321, 22016857.
-
(2011)
Mobile genetic elements
, vol.1
, pp. 107-111
-
-
Tollis, M.1
Boissinot, S.2
-
11
-
-
79952274187
-
The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis carolinensis
-
10.1093/gbe/evq080, 3014272, 21127169
-
Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S. The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis carolinensis. Genome Biol Evol 2011, 3:1-14. 10.1093/gbe/evq080, 3014272, 21127169.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 1-14
-
-
Novick, P.A.1
Smith, J.D.2
Floumanhaft, M.3
Ray, D.A.4
Boissinot, S.5
-
12
-
-
79955043502
-
Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor
-
10.1093/gbe/evq087, 3035132, 21183607
-
Janes DE, Chapus C, Gondo Y, Clayton DF, Sinha S, Blatti CA, Organ CL, Fujita MK, Balakrishnan CN, Edwards SV. Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor. Genome Biol Evol 2011, 3:102-113. 10.1093/gbe/evq087, 3035132, 21183607.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 102-113
-
-
Janes, D.E.1
Chapus, C.2
Gondo, Y.3
Clayton, D.F.4
Sinha, S.5
Blatti, C.A.6
Organ, C.L.7
Fujita, M.K.8
Balakrishnan, C.N.9
Edwards, S.V.10
-
13
-
-
84856296604
-
The Anolis Lizard Genome: An Amniote Genome without Isochores
-
10.1093/gbe/evr072, 3184785, 21795750
-
Fujita MK, Edwards SV, Ponting CP. The Anolis Lizard Genome: An Amniote Genome without Isochores. Genome Biol Evol 2011, 3:974-984. 10.1093/gbe/evr072, 3184785, 21795750.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 974-984
-
-
Fujita, M.K.1
Edwards, S.V.2
Ponting, C.P.3
-
14
-
-
84879402049
-
Elevated Evolutionary Rates among Functionally Diverged Reproductive Genes across Deep Vertebrate Lineages
-
Grassa CJ, Kulathinal RJ. Elevated Evolutionary Rates among Functionally Diverged Reproductive Genes across Deep Vertebrate Lineages. International journal of evolutionary biology 2011, 2011:1-9.
-
(2011)
International journal of evolutionary biology
, vol.2011
, pp. 1-9
-
-
Grassa, C.J.1
Kulathinal, R.J.2
-
15
-
-
80051640492
-
Evolutionary genomics implies a specific function of Ant4 in mammalian and anole lizard male germ cells
-
10.1371/journal.pone.0023122, 3155547, 21858006
-
Lim CH, Hamazaki T, Braun EL, Wade J, Terada N. Evolutionary genomics implies a specific function of Ant4 in mammalian and anole lizard male germ cells. PLoS One 2011, 6:e23122. 10.1371/journal.pone.0023122, 3155547, 21858006.
-
(2011)
PLoS One
, vol.6
-
-
Lim, C.H.1
Hamazaki, T.2
Braun, E.L.3
Wade, J.4
Terada, N.5
-
16
-
-
79959857887
-
Relationships among reproductive morphology, behavior, and testosterone in a natural population of green anole lizards
-
10.1016/j.physbeh.2011.05.004, 21600228
-
Johnson MA, Cohen RE, Vandecar JR, Wade J. Relationships among reproductive morphology, behavior, and testosterone in a natural population of green anole lizards. Physiol Behav 2011, 104:437-445. 10.1016/j.physbeh.2011.05.004, 21600228.
-
(2011)
Physiol Behav
, vol.104
, pp. 437-445
-
-
Johnson, M.A.1
Cohen, R.E.2
Vandecar, J.R.3
Wade, J.4
-
17
-
-
77953494523
-
Behavioural display systems across nine Anolis lizard species: sexual dimorphisms in structure and function
-
10.1098/rspb.2009.2323, 2871862, 20129985
-
Johnson MA, Wade J. Behavioural display systems across nine Anolis lizard species: sexual dimorphisms in structure and function. Proceedings of the Royal Society B: Biological Sciences 2010, 277:1711-1719. 10.1098/rspb.2009.2323, 2871862, 20129985.
-
(2010)
Proceedings of the Royal Society B: Biological Sciences
, vol.277
, pp. 1711-1719
-
-
Johnson, M.A.1
Wade, J.2
-
18
-
-
84855658200
-
Repeated modification of early limb morphogenesis programmes underlies the convergence of relative limb length in Anolis lizards
-
10.1098/rspb.2011.0840, 21849319
-
Sanger TJ, Revell LJ, Gibson-Brown JJ, Losos JB. Repeated modification of early limb morphogenesis programmes underlies the convergence of relative limb length in Anolis lizards. Proceedings of the Royal Society B: Biological Sciences 2012, 279:739-748. 10.1098/rspb.2011.0840, 21849319.
-
(2012)
Proceedings of the Royal Society B: Biological Sciences
, vol.279
, pp. 739-748
-
-
Sanger, T.J.1
Revell, L.J.2
Gibson-Brown, J.J.3
Losos, J.B.4
-
19
-
-
82755189551
-
Convergent evolution of phenotypic integration and its alignment with morphological diversification in Caribbean Anolis ecomorphs
-
10.1111/j.1558-5646.2011.01416.x, 23362474
-
Kolbe JJ, Revell LJ, Szekely B, Brodie ED, Losos JB. Convergent evolution of phenotypic integration and its alignment with morphological diversification in Caribbean Anolis ecomorphs. Evolution; international journal of organic evolution 2011, 65:3608-3624. 10.1111/j.1558-5646.2011.01416.x, 23362474.
-
(2011)
Evolution; international journal of organic evolution
, vol.65
, pp. 3608-3624
-
-
Kolbe, J.J.1
Revell, L.J.2
Szekely, B.3
Brodie, E.D.4
Losos, J.B.5
-
20
-
-
69949094996
-
Reptilian heart development and the molecular basis of cardiac chamber evolution
-
10.1038/nature08324, 2753965, 19727199
-
Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG. Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature 2009, 461:95-98. 10.1038/nature08324, 2753965, 19727199.
-
(2009)
Nature
, vol.461
, pp. 95-98
-
-
Koshiba-Takeuchi, K.1
Mori, A.D.2
Kaynak, B.L.3
Cebra-Thomas, J.4
Sukonnik, T.5
Georges, R.O.6
Latham, S.7
Beck, L.8
Henkelman, R.M.9
Black, B.L.10
Olson, E.N.11
Wade, J.12
Takeuchi, J.K.13
Nemer, M.14
Gilbert, S.F.15
Bruneau, B.G.16
-
21
-
-
84857029629
-
Somitogenesis in the anole lizard and alligator reveals evolutionary convergence and divergence in the amniote segmentation clock
-
10.1016/j.ydbio.2011.11.021, 22178152
-
Eckalbar WL, Lasku E, Infante CR, Elsey RM, Markov GJ, Allen AN, Corneveaux JJ, Losos JB, DeNardo DF, Huentelman MJ, Wilson-Rawls J, Rawls A, Kusumi K. Somitogenesis in the anole lizard and alligator reveals evolutionary convergence and divergence in the amniote segmentation clock. Dev Biol 2012, 363:308-319. 10.1016/j.ydbio.2011.11.021, 22178152.
-
(2012)
Dev Biol
, vol.363
, pp. 308-319
-
-
Eckalbar, W.L.1
Lasku, E.2
Infante, C.R.3
Elsey, R.M.4
Markov, G.J.5
Allen, A.N.6
Corneveaux, J.J.7
Losos, J.B.8
DeNardo, D.F.9
Huentelman, M.J.10
Wilson-Rawls, J.11
Rawls, A.12
Kusumi, K.13
-
22
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
10.1093/nar/gkg770, 206470, 14500829
-
Haas BJ. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 2003, 31:5654-5666. 10.1093/nar/gkg770, 206470, 14500829.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5654-5666
-
-
Haas, B.J.1
-
23
-
-
27244444905
-
Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures
-
10.1104/pp.105.060541, 1176417, 15965016
-
Loke JC. Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures. Plant Physiol 2005, 138:1457-1468. 10.1104/pp.105.060541, 1176417, 15965016.
-
(2005)
Plant Physiol
, vol.138
, pp. 1457-1468
-
-
Loke, J.C.1
-
24
-
-
44349130371
-
Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation
-
10.1093/nar/gkn158, 2396415, 18411206
-
Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ. Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. Nucleic Acids Res 2008, 36:3150-3161. 10.1093/nar/gkn158, 2396415, 18411206.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3150-3161
-
-
Shen, Y.1
Ji, G.2
Haas, B.J.3
Wu, X.4
Zheng, J.5
Reese, G.J.6
Li, Q.Q.7
-
25
-
-
38049057159
-
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
-
10.1101/gr.6743907, 2134774, 18025269
-
Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M. MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 2007, 18:188-196. 10.1101/gr.6743907, 2134774, 18025269.
-
(2007)
Genome Res
, vol.18
, pp. 188-196
-
-
Cantarel, B.L.1
Korf, I.2
Robb, S.M.C.3
Parra, G.4
Ross, E.5
Moore, B.6
Holt, C.7
Alvarado, A.S.8
Yandell, M.9
-
26
-
-
84055178433
-
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
-
10.1186/1471-2105-12-491, 3280279, 22192575
-
Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011, 12:491. 10.1186/1471-2105-12-491, 3280279, 22192575.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 491
-
-
Holt, C.1
Yandell, M.2
-
27
-
-
2942544417
-
Gene finding in novel genomes
-
10.1186/1471-2105-5-59, 421630, 15144565
-
Korf I. Gene finding in novel genomes. BMC Bioinformatics 2004, 5:59. 10.1186/1471-2105-5-59, 421630, 15144565.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 59
-
-
Korf, I.1
-
28
-
-
2942527473
-
Gene prediction with a hidden Markov model and a new intron submodel
-
10.1093/bioinformatics/btg1080, 14534192
-
Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003, 19:ii215-ii225. 10.1093/bioinformatics/btg1080, 14534192.
-
(2003)
Bioinformatics
, vol.19
-
-
Stanke, M.1
Waack, S.2
-
29
-
-
33645161645
-
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
-
10.1186/1471-2105-7-62, 1409804, 16469098
-
Stanke M, Schöffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 2006, 7:62. 10.1186/1471-2105-7-62, 1409804, 16469098.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 62
-
-
Stanke, M.1
Schöffmann, O.2
Morgenstern, B.3
Waack, S.4
-
30
-
-
84866171318
-
The Gross Anatomy of the Original and Regenerated Tail in the Green Anole (Anolis carolinensis)
-
Ritzman TB, Stroik LK, Julik E, Hutchins ED, Lasku E, Denardo DF, Wilson-Rawls J, Rawls JA, Kusumi K, Fisher RE. The Gross Anatomy of the Original and Regenerated Tail in the Green Anole (Anolis carolinensis). Anat Rec 2012, 295:1596-1608.
-
(2012)
Anat Rec
, vol.295
, pp. 1596-1608
-
-
Ritzman, T.B.1
Stroik, L.K.2
Julik, E.3
Hutchins, E.D.4
Lasku, E.5
Denardo, D.F.6
Wilson-Rawls, J.7
Rawls, J.A.8
Kusumi, K.9
Fisher, R.E.10
-
31
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
10.1038/nbt.1883, 21572440
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29:644-652. 10.1038/nbt.1883, 21572440.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
Chen, Z.11
Mauceli, E.12
Hacohen, N.13
Gnirke, A.14
Rhind, N.15
di Palma, F.16
Birren, B.W.17
Nusbaum, C.18
Lindblad-Toh, K.19
Friedman, N.20
Regev, A.21
more..
-
32
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
10.1101/gr.089532.108, 2694472, 19251739
-
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: A parallel assembler for short read sequence data. Genome Res 2009, 19:1117-23. 10.1101/gr.089532.108, 2694472, 19251739.
-
(2009)
Genome Res
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.M.5
Birol, I.6
-
33
-
-
70350664649
-
De novo transcriptome assembly with ABySS
-
10.1093/bioinformatics/btp367, 19528083
-
Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJM. De novo transcriptome assembly with ABySS. Bioinformatics 2009, 25:2872-2877. 10.1093/bioinformatics/btp367, 19528083.
-
(2009)
Bioinformatics
, vol.25
, pp. 2872-2877
-
-
Birol, I.1
Jackman, S.D.2
Nielsen, C.B.3
Qian, J.Q.4
Varhol, R.5
Stazyk, G.6
Morin, R.D.7
Zhao, Y.8
Hirst, M.9
Schein, J.E.10
Horsman, D.E.11
Connors, J.M.12
Gascoyne, R.D.13
Marra, M.A.14
Jones, S.J.M.15
-
34
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
10.1038/nmeth.1517, 20935650
-
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu A-L, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nat Methods 2010, 7:909-912. 10.1038/nmeth.1517, 20935650.
-
(2010)
Nat Methods
, vol.7
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
Corbett, R.4
Field, M.5
Jackman, S.D.6
Mungall, K.7
Lee, S.8
Okada, H.M.9
Qian, J.Q.10
Griffith, M.11
Raymond, A.12
Thiessen, N.13
Cezard, T.14
Butterfield, Y.S.15
Newsome, R.16
Chan, S.K.17
She, R.18
Varhol, R.19
Kamoh, B.20
Prabhu, A.-L.21
Tam, A.22
Zhao, Y.23
Moore, R.A.24
Hirst, M.25
Marra, M.A.26
Jones, S.J.M.27
Hoodless, P.A.28
Birol, I.29
more..
-
35
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
10.1093/bioinformatics/btl158, 16731699
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
36
-
-
81055148251
-
Developing a community-based genetic nomenclature for anole lizards
-
10.1186/1471-2164-12-554, 3248570, 22077994
-
Kusumi K, Kulathinal RJ, Abzhanov A, Boissinot S, Crawford NG, Faircloth BC, Glenn TC, Janes DE, Losos JB, Menke DB, Poe S, Sanger TJ, Schneider CJ, Stapley J, Wade J, Wilson-Rawls J. Developing a community-based genetic nomenclature for anole lizards. BMC Genomics 2011, 12:554. 10.1186/1471-2164-12-554, 3248570, 22077994.
-
(2011)
BMC Genomics
, vol.12
, pp. 554
-
-
Kusumi, K.1
Kulathinal, R.J.2
Abzhanov, A.3
Boissinot, S.4
Crawford, N.G.5
Faircloth, B.C.6
Glenn, T.C.7
Janes, D.E.8
Losos, J.B.9
Menke, D.B.10
Poe, S.11
Sanger, T.J.12
Schneider, C.J.13
Stapley, J.14
Wade, J.15
Wilson-Rawls, J.16
-
37
-
-
24644503098
-
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
-
10.1093/bioinformatics/bti610, 16081474
-
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676. 10.1093/bioinformatics/bti610, 16081474.
-
(2005)
Bioinformatics
, vol.21
, pp. 3674-3676
-
-
Conesa, A.1
Gotz, S.2
Garcia-Gomez, J.M.3
Terol, J.4
Talon, M.5
Robles, M.6
-
38
-
-
43949138227
-
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
-
Conesa A, Götz S. Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. International journal of plant genomics 2008, 2008:1-12.
-
(2008)
International journal of plant genomics
, vol.2008
, pp. 1-12
-
-
Conesa, A.1
Götz, S.2
-
39
-
-
45549089420
-
High-throughput functional annotation and data mining with the Blast2GO suite
-
10.1093/nar/gkn176, 2425479, 18445632
-
Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008, 36:3420-3435. 10.1093/nar/gkn176, 2425479, 18445632.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3420-3435
-
-
Gotz, S.1
Garcia-Gomez, J.M.2
Terol, J.3
Williams, T.D.4
Nagaraj, S.H.5
Nueda, M.J.6
Robles, M.7
Talon, M.8
Dopazo, J.9
Conesa, A.10
-
40
-
-
77949601825
-
CD-HIT Suite: a web server for clustering and comparing biological sequences
-
10.1093/bioinformatics/btq003, 2828112, 20053844
-
Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010, 26:680-682. 10.1093/bioinformatics/btq003, 2828112, 20053844.
-
(2010)
Bioinformatics
, vol.26
, pp. 680-682
-
-
Huang, Y.1
Niu, B.2
Gao, Y.3
Fu, L.4
Li, W.5
-
41
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
10.1186/1471-2105-6-31, 553969, 15713233
-
Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31. 10.1186/1471-2105-6-31, 553969, 15713233.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.C.1
Birney, E.2
-
42
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
10.1038/nmeth.1923, 22388286
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359. 10.1038/nmeth.1923, 22388286.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
43
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
10.1038/nbt.1621, 3146043, 20436464
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515. 10.1038/nbt.1621, 3146043, 20436464.
-
(2010)
Nat Biotechnol
, 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
-
44
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
10.1093/bioinformatics/btp120, 2672628, 19289445
-
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
45
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
10.1186/gb-2009-10-3-r25, 2690996, 19261174
-
Langmead B, Trapnell C, Pop M. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
-
46
-
-
80051941094
-
Identification of novel transcripts in annotated genomes using RNA-Seq
-
10.1093/bioinformatics/btr355, 21697122
-
Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011, 27:2325-2329. 10.1093/bioinformatics/btr355, 21697122.
-
(2011)
Bioinformatics
, vol.27
, pp. 2325-2329
-
-
Roberts, A.1
Pimentel, H.2
Trapnell, C.3
Pachter, L.4
-
47
-
-
79952709611
-
Improving RNA-Seq expression estimates by correcting for fragment bias
-
10.1186/gb-2011-12-3-r22, 3129672, 21410973
-
Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 2011, 12:R22. 10.1186/gb-2011-12-3-r22, 3129672, 21410973.
-
(2011)
Genome Biol
, vol.12
-
-
Roberts, A.1
Trapnell, C.2
Donaghey, J.3
Rinn, J.L.4
Pachter, L.5
-
48
-
-
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, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 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
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
49
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
10.1101/gr.9.9.868, 310812, 10508846
-
Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
-
(1999)
Genome Res
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
50
-
-
77950298955
-
-
Hoboken, NJ, USA: John Wiley & Sons, Inc
-
Tarailo-Graovac M, Chen N. Current Protocols in Bioinformatics 2002, Hoboken, NJ, USA: John Wiley & Sons, Inc.
-
(2002)
Current Protocols in Bioinformatics
-
-
Tarailo-Graovac, M.1
Chen, N.2
-
51
-
-
0036226603
-
BLAT--The BLAST-Like Alignment Tool
-
187518, 11932250
-
Kent WJ. BLAT--The BLAST-Like Alignment Tool. Genome Res 2002, 12:656-664. 187518, 11932250.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
|