-
1
-
-
81155123590
-
Gene expression noise facilitates adaptation and drug resistance independently of mutation
-
Charlebois DA, Abdennur N, Kaern M (2011) Gene expression noise facilitates adaptation and drug resistance independently of mutation. Phys Rev Lett 107:218101
-
(2011)
Phys Rev Lett
, vol.107
, pp. 218101
-
-
Charlebois, D.A.1
Abdennur, N.2
Kaern, M.3
-
2
-
-
52949141845
-
Integrated detection and population-genetic analysis of SNPs and copy number variation
-
McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40:1166-1174
-
(2008)
Nat Genet
, vol.40
, pp. 1166-1174
-
-
McCarroll, S.A.1
Kuruvilla, F.G.2
Korn, J.M.3
Cawley, S.4
Nemesh, J.5
Wysoker, A.6
Shapero, M.H.7
De Bakker, P.I.8
Maller, J.B.9
Kirby, A.10
Elliott, A.L.11
Parkin, M.12
Hubbell, E.13
Webster, T.14
Mei, R.15
Veitch, J.16
Collins, P.J.17
Handsaker, R.18
Lincoln, S.19
Nizzari, M.20
Blume, J.21
Jones, K.W.22
Rava, R.23
Daly, M.J.24
Gabriel, S.B.25
Altshuler, D.26
more..
-
3
-
-
7244259100
-
Megabase deletions of gene deserts result in viable mice
-
Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM (2004) Megabase deletions of gene deserts result in viable mice. Nature 431:988-993
-
(2004)
Nature
, vol.431
, pp. 988-993
-
-
Nóbrega, M.A.1
Zhu, Y.2
Plajzer-Frick, I.3
Afzal, V.4
Rubin, E.M.5
-
4
-
-
70149105095
-
The population and evolutionary dynamics of homologous gene recombination in bacterial populations
-
Levin BR, Cornejo OE (2009) The population and evolutionary dynamics of homologous gene recombination in bacterial populations. PLoS Genet 5:e1000601
-
(2009)
PLoS Genet
, vol.5
-
-
Levin, B.R.1
Cornejo, O.E.2
-
5
-
-
84864208657
-
Systems analysis of eleven rodent disease models reveals an infl ammatome signature and key drivers
-
Wang IM, Zhang B, Yang X, Zhu J, Stepaniants S, Zhang C, Meng Q, Peters M, He Y, Ni C, Slipetz D, Crackower MA, Houshyar H, Tan CM, Asante-Appiah E, O'Neill G, Jane Luo M, Thieringer R, Yuan J, Chiu CS, Yee Lum P, Lamb J, Boie Y, Wilkinson HA, Schadt EE, Dai H, Roberts C (2012) Systems analysis of eleven rodent disease models reveals an infl ammatome signature and key drivers. Mol Syst Biol 8:594
-
(2012)
Mol Syst Biol
, vol.8
, pp. 594
-
-
Wang, I.M.1
Zhang, B.2
Yang, X.3
Zhu, J.4
Stepaniants, S.5
Zhang, C.6
Meng, Q.7
Peters, M.8
He, Y.9
Ni, C.10
Slipetz, D.11
Crackower, M.A.12
Houshyar, H.13
Tan, C.M.14
Asante-Appiah, E.15
O'Neill, G.16
Jane Luo, M.17
Thieringer, R.18
Yuan, J.19
Chiu, C.S.20
Yee Lum, P.21
Lamb, J.22
Boie, Y.23
Wilkinson, H.A.24
Schadt, E.E.25
Dai, H.26
Roberts, C.27
more..
-
6
-
-
84864761135
-
Systems biology Modular biological complexity
-
Koch C (2012) Systems biology. Modular biological complexity. Science 337:531-532
-
(2012)
Science
, vol.337
, pp. 531-532
-
-
Koch, C.1
-
7
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS,
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Dunham, I.1
Kundaje, A.2
Aldred, S.F.3
Collins, P.J.4
Davis, C.A.5
Doyle, F.6
Epstein, C.B.7
Frietze, S.8
Harrow, J.9
Kaul, R.10
Khatun, J.11
Lajoie, B.R.12
Landt, S.G.13
Lee, B.K.14
Pauli, F.15
Rosenbloom, K.R.16
Sabo, P.17
Safi, A.18
Sanyal, A.19
Shoresh, N.20
Simon, J.M.21
Song, L.22
Trinklein, N.D.23
Altshuler, R.C.24
Birney, E.25
Brown, J.B.26
Cheng, C.27
Djebali, S.28
Dong, X.29
Dunham, I.30
Ernst, J.31
Furey, T.S.32
Gerstein, M.33
Giardine, B.34
Greven, M.35
Hardison, R.C.36
Harris, R.S.37
Herrero, J.38
Hoffman, M.M.39
Iyer, S.40
Kelllis, M.41
Khatun, J.42
Kheradpour, P.43
Kundaje, A.44
Lassman, T.45
Li, Q.46
Lin, X.47
Marinov, G.K.48
Merkel, A.49
Mortazavi, A.50
Parker, S.C.51
Reddy, T.E.52
Rozowsky, J.53
Schlesinger, F.54
Thurman, R.E.55
Wang, J.56
Ward57
more..
-
8
-
-
79953137435
-
Human gut microbiome: The second genome of human body
-
Zhu B, Wang X, Li L (2010) Human gut microbiome: The second genome of human body. Protein Cell 1:718-725
-
(2010)
Protein Cell
, vol.1
, pp. 718-725
-
-
Zhu, B.1
Wang, X.2
Li, L.3
-
9
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
Mende, D.R.11
Li, J.12
Xu, J.13
Li, S.14
Li, D.15
Cao, J.16
Wang, B.17
Liang, H.18
Zheng, H.19
Xie, Y.20
Tap, J.21
Lepage, P.22
Bertalan, M.23
Batto, J.M.24
Hansen, T.25
Le Paslier, D.26
Linneberg, A.27
Nielsen, H.B.28
Pelletier, E.29
Renault, P.30
Sicheritz-Ponten, T.31
Turner, K.32
Zhu, H.33
Yu, C.34
Li, S.35
Jian, M.36
Zhou, Y.37
Li, Y.38
Zhang, X.39
Li, S.40
Qin, N.41
Yang, H.42
Wang, J.43
Brunak, S.44
Doré, J.45
Guarner, F.46
Kristiansen, K.47
Pedersen, O.48
Parkhill, J.49
Weissenbach, J.50
Bork, P.51
Ehrlich, S.D.52
Wang, J.53
more..
-
10
-
-
84858439578
-
The human microbiome: At the interface of health and disease
-
Cho I, Blaser MJ (2012) The human microbiome: At the interface of health and disease. Nat Rev Genet 13:260-270
-
(2012)
Nat Rev Genet
, vol.13
, pp. 260-270
-
-
Cho, I.1
Blaser, M.J.2
-
11
-
-
84864614787
-
Host remodeling of the gut microbiome and metabolic changes during pregnancy
-
Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Kling Bäckhed H, Gonzalez A, Werner JJ, Angenent LT, Knight R, Bäckhed F, Isolauri E, Salminen S, Ley RE (2012) Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150:470-480
-
(2012)
Cell
, vol.150
, pp. 470-480
-
-
Koren, O.1
Goodrich, J.K.2
Cullender, T.C.3
Spor, A.4
Laitinen, K.5
Kling Bäckhed, H.6
Gonzalez, A.7
Werner, J.J.8
Angenent, L.T.9
Knight, R.10
Bäckhed, F.11
Isolauri, E.12
Salminen, S.13
Ley, R.E.14
-
12
-
-
84864366225
-
Infl ammation drives dysbiosis and bacterial invasion in murine models of ileal Crohn's disease
-
Craven M, Egan CE, Dowd SE, McDonough SP, Dogan B, Denkers EY, Bowman D, Scherl EJ, Simpson KW (2012) Infl ammation drives dysbiosis and bacterial invasion in murine models of ileal Crohn's disease. PLoS One 7:e41594
-
(2012)
PLoS One
, vol.7
-
-
Craven, M.1
Egan, C.E.2
Dowd, S.E.3
McDonough, S.P.4
Dogan, B.5
Denkers, E.Y.6
Bowman, D.7
Scherl, E.J.8
Simpson, K.W.9
-
13
-
-
0023651349
-
A thousand and one protein kinases
-
Hunter T (1987) A thousand and one protein kinases. Cell 50:823-829
-
(1987)
Cell
, vol.50
, pp. 823-829
-
-
Hunter, T.1
-
15
-
-
79959829720
-
Widespread RNA and DNA sequence differences in the human transcriptome
-
Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG (2011) Widespread RNA and DNA sequence differences in the human transcriptome. Science 333:53-58
-
(2011)
Science
, vol.333
, pp. 53-58
-
-
Li, M.1
Wang, I.X.2
Li, Y.3
Bruzel, A.4
Richards, A.L.5
Toung, J.M.6
Cheung, V.G.7
-
16
-
-
84862979818
-
Distinct DNA methylomes of newborns and centenarians
-
Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, Diez J, Sanchez-Mut JV, Setien F, Carmona FJ, Puca AA, Sayols S, Pujana MA, Serra-Musach J, Iglesias-Platas I, Formiga F, Fernandez AF, Fraga MF, Heath SC, Valencia A, Gut IG, Wang J, Esteller M (2012) Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A 109:10522-10527
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 10522-10527
-
-
Heyn, H.1
Li, N.2
Ferreira, H.J.3
Moran, S.4
Pisano, D.G.5
Gomez, A.6
Diez, J.7
Sanchez-Mut, J.V.8
Setien, F.9
Carmona, F.J.10
Puca, A.A.11
Sayols, S.12
Pujana, M.A.13
Serra-Musach, J.14
Iglesias-Platas, I.15
Formiga, F.16
Fernandez, A.F.17
Fraga, M.F.18
Heath, S.C.19
Valencia, A.20
Gut, I.G.21
Wang, J.22
Esteller, M.23
more..
-
17
-
-
84864031521
-
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia
-
Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME (2012) Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet 8:e1002781
-
(2012)
PLoS Genet
, vol.8
-
-
Akalin, A.1
Garrett-Bakelman, F.E.2
Kormaksson, M.3
Busuttil, J.4
Zhang, L.5
Khrebtukova, I.6
Milne, T.A.7
Huang, Y.8
Biswas, D.9
Hess, J.L.10
Allis, C.D.11
Roeder, R.G.12
Valk, P.J.13
Löwenberg, B.14
Delwel, R.15
Fernandez, H.F.16
Paietta, E.17
Tallman, M.S.18
Schroth, G.P.19
Mason, C.E.20
Melnick, A.21
Figueroa, M.E.22
more..
-
18
-
-
84856555311
-
A DNA methylation fi ngerprint of 1628 human samples
-
Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, Yamamoto H, Hidalgo M, Tan AC, Galm O, Ferrer I, Sanchez-Cespedes M, Villanueva A, Carmona J, Sanchez-Mut JV, Berdasco M, Moreno V, Capella G, Monk D, Ballestar E, Ropero S, Martinez R, Sanchez-Carbayo M, Prosper F, Agirre X, Fraga MF, Graña O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M (2012) A DNA methylation fi ngerprint of 1628 human samples. Genome Res 22:407-419
-
(2012)
Genome Res
, vol.22
, pp. 407-419
-
-
Fernandez, A.F.1
Assenov, Y.2
Martin-Subero, J.I.3
Balint, B.4
Siebert, R.5
Taniguchi, H.6
Yamamoto, H.7
Hidalgo, M.8
Tan, A.C.9
Galm, O.10
Ferrer, I.11
Sanchez-Cespedes, M.12
Villanueva, A.13
Carmona, J.14
Sanchez-Mut, J.V.15
Berdasco, M.16
Moreno, V.17
Capella, G.18
Monk, D.19
Ballestar, E.20
Ropero, S.21
Martinez, R.22
Sanchez-Carbayo, M.23
Prosper, F.24
Agirre, X.25
Fraga, M.F.26
Graña, O.27
Perez-Jurado, L.28
Mora, J.29
Puig, S.30
Prat, J.31
Badimon, L.32
Puca, A.A.33
Meltzer, S.J.34
Lengauer, T.35
Bridgewater, J.36
Bock, C.37
Esteller, M.38
more..
-
19
-
-
84862649489
-
Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons
-
Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR (2012) Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 149:1635-1646
-
(2012)
Cell
, vol.149
, pp. 1635-1646
-
-
Meyer, K.D.1
Saletore, Y.2
Zumbo, P.3
Elemento, O.4
Mason, C.E.5
Jaffrey, S.R.6
-
20
-
-
84864258618
-
A whole-cell computational model predicts phenotype from genotype
-
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401
-
(2012)
Cell
, vol.150
, pp. 389-401
-
-
Karr, J.R.1
Sanghvi, J.C.2
Macklin, D.N.3
Gutschow, M.V.4
Jacobs, J.M.5
Bolival, B.6
Assad-Garcia, N.7
Glass, J.I.8
Covert, M.W.9
-
21
-
-
84864402194
-
Leveraging models of cell regulation and GWAS data in integrative network-based association studies
-
Califano A, Butte AJ, Friend S, Ideker T, Schadt E (2012) Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet 44:841-847
-
(2012)
Nat Genet
, vol.44
, pp. 841-847
-
-
Califano, A.1
Butte, A.J.2
Friend, S.3
Ideker, T.4
Schadt, E.5
-
23
-
-
72849144434
-
Sequencing technologies - The next generation
-
Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11:31-46
-
(2010)
Nat Rev Genet
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
24
-
-
84862590549
-
Going beyond fi ve bases in DNA sequencing
-
Korlach J, Turner SW (2012) Going beyond fi ve bases in DNA sequencing. Curr Opin Struct Biol 22(3):251-261
-
(2012)
Curr Opin Struct Biol
, vol.22
, Issue.3
, pp. 251-261
-
-
Korlach, J.1
Turner, S.W.2
-
25
-
-
77953623282
-
Designing deep sequencing experiments: Detecting structural variation and estimating transcript abundance
-
Bashir A, Bansal V, Bafna V (2010) Designing deep sequencing experiments: Detecting structural variation and estimating transcript abundance. BMC Genomics 11:385
-
(2010)
BMC Genomics
, vol.11
, pp. 385
-
-
Bashir, A.1
Bansal, V.2
Bafna, V.3
-
26
-
-
84856453032
-
Sensitive and specifi c single-molecule sequencing of 5-hydroxymethylcytosine
-
Song CX, Clark TA, Lu XY, Kislyuk A, Dai Q, Turner SW, He C, Korlach J (2012) Sensitive and specifi c single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods 9:75-77
-
(2012)
Nat Methods
, vol.9
, pp. 75-77
-
-
Song, C.X.1
Clark, T.A.2
Lu, X.Y.3
Kislyuk, A.4
Dai, Q.5
Turner, S.W.6
He, C.7
Korlach, J.8
-
28
-
-
84860779086
-
Topology of the human and mouse m6a RNA methylomes revealed by m6a-seq
-
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G (2012) Topology of the human and mouse m6a RNA methylomes revealed by m6a-seq. Nature 485:201-206
-
(2012)
Nature
, vol.485
, pp. 201-206
-
-
Dominissini, D.1
Moshitch-Moshkovitz, S.2
Schwartz, S.3
Salmon-Divon, M.4
Ungar, L.5
Osenberg, S.6
Cesarkas, K.7
Jacob-Hirsch, J.8
Amariglio, N.9
Kupiec, M.10
Sorek, R.11
Rechavi, G.12
-
29
-
-
84874958804
-
Novel RNA regulatory mechanisms revealed in the epitranscriptome
-
Saletore Y, Chen-Kiang S, Mason CE (2013) Novel RNA regulatory mechanisms revealed in the epitranscriptome. RNA Biol 10(3):342-346
-
(2013)
RNA Biol
, vol.10
, Issue.3
, pp. 342-346
-
-
Saletore, Y.1
Chen-Kiang, S.2
Mason, C.E.3
-
30
-
-
85027958937
-
The birth of the Epitranscriptome: Deciphering the function of RNA modifi cations
-
Saletore Y, Meyer K, Korlach J, Vilfan I, Jaffrey S, Mason CE (2012) The birth of the Epitranscriptome: Deciphering the function of RNA modifi cations. Genome Biol 13(10):175
-
(2012)
Genome Biol
, vol.13
, Issue.10
, pp. 175
-
-
Saletore, Y.1
Meyer, K.2
Korlach, J.3
Vilfan, I.4
Jaffrey, S.5
Mason, C.E.6
-
31
-
-
84863986007
-
Heterogeneous pathways and timing of factor departure during translation initiation
-
Tsai A, Petrov A, Marshall RA, Korlach J, Uemura S, Puglisi JD (2012) Heterogeneous pathways and timing of factor departure during translation initiation. Nature 487:390-393
-
(2012)
Nature
, vol.487
, pp. 390-393
-
-
Tsai, A.1
Petrov, A.2
Marshall, R.A.3
Korlach, J.4
Uemura, S.5
Puglisi, J.D.6
-
33
-
-
46249130709
-
The beginning of the end for microarrays
-
Shendure J (2008) The beginning of the end for microarrays Nat Methods 5:585-587
-
(2008)
Nat Methods
, vol.5
, pp. 585-587
-
-
Shendure, J.1
-
34
-
-
84869457261
-
The expanding scope of DNA sequencing
-
Shendure J, Lieberman Aiden E (2012) The expanding scope of DNA sequencing. Nat Biotechnol 30:1084-1094
-
(2012)
Nat Biotechnol
, vol.30
, pp. 1084-1094
-
-
Shendure, J.1
Lieberman Aiden, E.2
-
35
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509-1517
-
(2008)
Genome Res
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
36
-
-
84863385039
-
Comment on "widespread RNA and DNA sequence differences in the human transcriptome"
-
author reply 1302
-
Kleinman CL, Majewski J (2012) Comment on "widespread RNA and DNA sequence differences in the human transcriptome". Science 335:1302, author reply 1302
-
(2012)
Science
, vol.335
, pp. 1302
-
-
Kleinman, C.L.1
Majewski, J.2
-
37
-
-
84863385039
-
Comment on "widespread RNA and DNA sequence differences in the human transcriptome"
-
author reply 1302
-
Pickrell JK, Gilad Y, Pritchard JK (2012) Comment on "widespread RNA and DNA sequence differences in the human transcriptome". Science 335:1302, author reply 1302
-
(2012)
Science
, vol.335
, pp. 1302
-
-
Pickrell, J.K.1
Gilad, Y.2
Pritchard, J.K.3
-
38
-
-
34250330777
-
What is a gene, post-encode History and updated defi nition
-
Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) What is a gene, post-encode History and updated defi nition. Genome Res 17:669-681
-
(2007)
Genome Res
, vol.17
, pp. 669-681
-
-
Gerstein, M.B.1
Bruce, C.2
Rozowsky, J.S.3
Zheng, D.4
Du, J.5
Korbel, J.O.6
Emanuelsson, O.7
Zhang, Z.D.8
Weissman, S.9
Snyder, M.10
-
39
-
-
77955975125
-
Strand-specifi c RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
-
Yassour M, Pfi ffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A (2010) Strand-specifi c RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 11:R87
-
(2010)
Genome Biol
, vol.11
-
-
Yassour, M.1
Pfiffner, J.2
Levin, J.Z.3
Adiconis, X.4
Gnirke, A.5
Nusbaum, C.6
Thompson, D.A.7
Friedman, N.8
Regev, A.9
-
40
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
41
-
-
0025879424
-
Complementary DNA sequencing: Expressed sequence tags and human genome project
-
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF (1991) Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 252:1651-1656
-
(1991)
Science
, vol.252
, pp. 1651-1656
-
-
Adams, M.D.1
Kelley, J.M.2
Gocayne, J.D.3
Dubnick, M.4
Polymeropoulos, M.H.5
Xiao, H.6
Merril, C.R.7
Wu, A.8
Olde, B.9
Moreno, R.F.10
-
43
-
-
0032545933
-
Potent and specifi c genetic interference by double-stranded RNA in Caenorhabditis elegans
-
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specifi c genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-811
-
(1998)
Nature
, vol.391
, pp. 806-811
-
-
Fire, A.1
Xu, S.2
Montgomery, M.K.3
Kostas, S.A.4
Driver, S.E.5
Mello, C.C.6
-
44
-
-
70349956497
-
Direct RNA sequencing
-
Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF, Bowers J, Jarosz M, Milos PM (2009) Direct RNA sequencing. Nature 461:814-818
-
(2009)
Nature
, vol.461
, pp. 814-818
-
-
Ozsolak, F.1
Platt, A.R.2
Jones, D.R.3
Reifenberger, J.G.4
Sass, L.E.5
McInerney, P.6
Thompson, J.F.7
Bowers, J.8
Jarosz, M.9
Milos, P.M.10
-
45
-
-
77954526823
-
The case for cloud computing in genome informatics
-
Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11:207
-
(2010)
Genome Biol
, vol.11
, pp. 207
-
-
Stein, L.D.1
-
46
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11:473-483
-
(2010)
Brief Bioinform
, vol.11
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
47
-
-
67649884743
-
Fast and accurate short read alignment with burrows-wheeler transform
-
Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25:1754-1760
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
48
-
-
84859210032
-
Fast gapped-read alignment with bowtie
-
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie Nat Methods 9:357-359
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
49
-
-
84874194145
-
Sequence assembly demystifi ed
-
Nagarajan N, Pop M (2013) Sequence assembly demystifi ed. Nat Rev Genet 14:157-167
-
(2013)
Nat Rev Genet
, vol.14
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
50
-
-
77952886150
-
Assembly algorithms for next-generation sequencing data
-
Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315-327
-
(2010)
Genomics
, vol.95
, pp. 315-327
-
-
Miller, J.R.1
Koren, S.2
Sutton, G.3
-
51
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30(7):693-700
-
(2012)
Nat Biotechnol
, vol.30
, Issue.7
, pp. 693-700
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
Ganapathy, G.6
Wang, Z.7
Rasko, D.A.8
McCombie, W.R.9
Jarvis, E.D.10
Phillippy, A.M.11
-
53
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5:R80
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
Hornik, K.11
Hothorn, T.12
Huber, W.13
Iacus, S.14
Irizarry, R.15
Leisch, F.16
Li, C.17
Maechler, M.18
Rossini, A.J.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.Y.24
Zhang, J.25
more..
-
54
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cuffl inks
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cuffl inks. Nat Protoc 7:562-578
-
(2012)
Nat Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
55
-
-
84865527768
-
Detecting differential usage of exons from RNA-seq data
-
Anders S, Reyes A, Huber W (2012) Detecting differential usage of exons from RNA-seq data. Genome Res 22:2008-2017
-
(2012)
Genome Res
, vol.22
, pp. 2008-2017
-
-
Anders, S.1
Reyes, A.2
Huber, W.3
-
56
-
-
77956295988
-
The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data
-
McKenna AH, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, Depristo M (2010) The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297-1303
-
(2010)
Genome Res
, vol.20
, pp. 1297-1303
-
-
McKenna, A.H.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
Depristo, M.11
-
57
-
-
84975742565
-
A map of human genome variation from populationscale sequencing
-
1000 Genomes Project Consortium
-
57. 1000 Genomes Project Consortium (2010) A map of human genome variation from populationscale sequencing. Nature 467:1061-1073
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
58
-
-
84864929478
-
Computational inference of mRNA stability from histone modifi cation and transcriptome profi les
-
Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS (2012) Computational inference of mRNA stability from histone modifi cation and transcriptome profi les. Nucleic Acids Res 40:6414-6423
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 6414-6423
-
-
Wang, C.1
Tian, R.2
Zhao, Q.3
Xu, H.4
Meyer, C.A.5
Li, C.6
Zhang, Y.7
Liu, X.S.8
-
59
-
-
78049440479
-
High resolution models of transcription factor-DNA affi nities improve in vitro and in vivo binding predictions
-
Agius P, Arvey A, Chang W, Noble WS, Leslie C (2010) High resolution models of transcription factor-DNA affi nities improve in vitro and in vivo binding predictions. PLoS Comput Biol 6:e1000916
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Agius, P.1
Arvey, A.2
Chang, W.3
Noble, W.S.4
Leslie, C.5
-
60
-
-
62649160355
-
Identifi cation of DNA-binding proteins using structural, electrostatic and evolutionary features
-
Nimrod G, Szilágyi A, Leslie C, Ben-Tal N (2009) Identifi cation of DNA-binding proteins using structural, electrostatic and evolutionary features. J Mol Biol 387:1040-1053
-
(2009)
J Mol Biol
, vol.387
, pp. 1040-1053
-
-
Nimrod, G.1
Szilágyi, A.2
Leslie, C.3
Ben-Tal, N.4
-
61
-
-
70149083249
-
Analyzing gene expression data from microarray and next-generation DNA sequencing transcriptome profi ling assays using GeneSifter analysis edition
-
Porter S, Olson NE, Smith T (2009) Analyzing gene expression data from microarray and next-generation DNA sequencing transcriptome profi ling assays using GeneSifter analysis edition. Curr Protoc Bioinformatics 7(14):1-35
-
(2009)
Curr Protoc Bioinformatics
, vol.7
, Issue.14
, pp. 1-35
-
-
Porter, S.1
Olson, N.E.2
Smith, T.3
-
62
-
-
0036126302
-
GENEHUNTER: Your 'one-stop shop' for statistical genetic analysis
-
Nyholt DR (2002) GENEHUNTER: Your 'one-stop shop' for statistical genetic analysis Hum Hered 53:2-7
-
(2002)
Hum Hered
, vol.53
, pp. 2-7
-
-
Nyholt, D.R.1
-
63
-
-
84860846775
-
The 2012 nucleic acids research database issue and the online molecular biology database collection
-
Galperin MY, Fernández-Suárez XM (2012) The 2012 nucleic acids research database issue and the online molecular biology database collection. Nucleic Acids Res 40:D1-D8
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Galperin, M.Y.1
Fernández-Suárez, X.M.2
-
64
-
-
84863895244
-
Gene data to hit milestone
-
Baker M (2012) Gene data to hit milestone. Nature 487:282-283
-
(2012)
Nature
, vol.487
, pp. 282-283
-
-
Baker, M.1
-
65
-
-
55549115654
-
Genes mirror geography within Europe
-
Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD (2008) Genes mirror geography within Europe. Nature 456:98-101
-
(2008)
Nature
, vol.456
, pp. 98-101
-
-
Novembre, J.1
Johnson, T.2
Bryc, K.3
Kutalik, Z.4
Boyko, A.R.5
Auton, A.6
Indap, A.7
King, K.S.8
Bergmann, S.9
Nelson, M.R.10
Stephens, M.11
Bustamante, C.D.12
-
66
-
-
50849101381
-
Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays
-
Homer N, Szelinger S, Redman M, Duggan D, Tembe W, Muehling J, Pearson JV, Stephan DA, Nelson SF, Craig DW (2008) Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet 4:e1000167
-
(2008)
PLoS Genet
, vol.4
-
-
Homer, N.1
Szelinger, S.2
Redman, M.3
Duggan, D.4
Tembe, W.5
Muehling, J.6
Pearson, J.V.7
Stephan, D.A.8
Nelson, S.F.9
Craig, D.W.10
-
67
-
-
84868614968
-
One-stop shop for disease genes
-
Baker M (2012) One-stop shop for disease genes. Nature 491:171
-
(2012)
Nature
, vol.491
, pp. 171
-
-
Baker, M.1
-
68
-
-
77955491294
-
Predicting protein structures with a multiplayer online game
-
Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popovi Z, Players F (2010) Predicting protein structures with a multiplayer online game. Nature 466:756-760
-
(2010)
Nature
, vol.466
, pp. 756-760
-
-
Cooper, S.1
Khatib, F.2
Treuille, A.3
Barbero, J.4
Lee, J.5
Beenen, M.6
Leaver-Fay, A.7
Baker, D.8
Popovi, Z.9
Players, F.10
-
69
-
-
84872236997
-
Pharmacogenomics of warfarin in populations of african descent
-
Suarez-Kurtz G, Botton MR (2013) Pharmacogenomics of warfarin in populations of african descent. Br J Clin Pharmacol 75:334-346
-
(2013)
Br J Clin Pharmacol
, vol.75
, pp. 334-346
-
-
Suarez-Kurtz, G.1
Botton, M.R.2
-
71
-
-
84865323065
-
Tracking a hospital outbreak of carbapenemresistant klebsiella pneumoniae with whole-genome sequencing
-
Snitkin E, Zelazny AM, Thomas PJ, Stock F, NISC Comparative Sequencing Program, Henderson DK, Palmore TN, Segre JA (2012) Tracking a hospital outbreak of carbapenemresistant klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4:148ra116
-
(2012)
Sci Transl Med
, vol.4
-
-
Snitkin, E.1
Zelazny, A.M.2
Thomas, P.J.3
Stock, F.4
Nisc Comparative Sequencing Program Henderson, D.K.5
Palmore, T.N.6
Segre, J.A.7
|