-
1
-
-
79952266465
-
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.
-
10.1101/gr.112623.110, 3044858, 21106904
-
Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 2011, 21:447-455. 10.1101/gr.112623.110, 3044858, 21106904.
-
(2011)
Genome Res
, vol.21
, pp. 447-455
-
-
Pique-Regi, R.1
Degner, J.F.2
Pai, A.A.3
Gaffney, D.J.4
Gilad, Y.5
Pritchard, J.K.6
-
2
-
-
6944244084
-
A module map showing conditional activity of expression modules in cancer.
-
10.1038/ng1434, 15448693
-
Segal E, Friedman N, Koller D, Regev A. A module map showing conditional activity of expression modules in cancer. Nat Genet 2004, 36:1090-1098. 10.1038/ng1434, 15448693.
-
(2004)
Nat Genet
, vol.36
, pp. 1090-1098
-
-
Segal, E.1
Friedman, N.2
Koller, D.3
Regev, A.4
-
3
-
-
33947305781
-
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.
-
10.1186/1471-2105-7-S1-S7, 1764484, 17254312
-
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7(Suppl 1):S7. 10.1186/1471-2105-7-S1-S7, 1764484, 17254312.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 1
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Dalla Favera, R.6
Califano, A.7
-
4
-
-
62549145762
-
Toward accurate reconstruction of functional protein networks.
-
2671920, 19293828
-
Yosef N, Ungar L, Zalckvar E, Kimchi A, Kupiec M, Ruppin E, Sharan R. Toward accurate reconstruction of functional protein networks. Mol Syst Biol 2009, 5:248. 2671920, 19293828.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 248
-
-
Yosef, N.1
Ungar, L.2
Zalckvar, E.3
Kimchi, A.4
Kupiec, M.5
Ruppin, E.6
Sharan, R.7
-
5
-
-
33751327438
-
Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program.
-
10.1371/journal.pgen.0010039, 1239936, 16470937
-
Ihmels J, Bergmann S, Berman J, Barkai N. Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet 2005, 1:e39. 10.1371/journal.pgen.0010039, 1239936, 16470937.
-
(2005)
PLoS Genet
, vol.1
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
6
-
-
22844446947
-
An integrative genomics approach to infer causal associations between gene expression and disease.
-
10.1038/ng1589, 2841396, 15965475
-
Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, Lum PY, Leonardson A, Thieringer R, Metzger JM, Yang L, Castle J, Zhu H, Kash SF, Drake TA, Sachs A, Lusis AJ. An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 2005, 37:710-717. 10.1038/ng1589, 2841396, 15965475.
-
(2005)
Nat Genet
, vol.37
, pp. 710-717
-
-
Schadt, E.E.1
Lamb, J.2
Yang, X.3
Zhu, J.4
Edwards, S.5
Guhathakurta, D.6
Sieberts, S.K.7
Monks, S.8
Reitman, M.9
Zhang, C.10
Lum, P.Y.11
Leonardson, A.12
Thieringer, R.13
Metzger, J.M.14
Yang, L.15
Castle, J.16
Zhu, H.17
Kash, S.F.18
Drake, T.A.19
Sachs, A.20
Lusis, A.J.21
more..
-
7
-
-
45149108420
-
Mapping the genetic architecture of gene expression in human liver.
-
10.1371/journal.pbio.0060107, 2365981, 18462017
-
Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008, 6:e107. 10.1371/journal.pbio.0060107, 2365981, 18462017.
-
(2008)
PLoS Biol
, vol.6
-
-
Schadt, E.E.1
Molony, C.2
Chudin, E.3
Hao, K.4
Yang, X.5
Lum, P.Y.6
Kasarskis, A.7
Zhang, B.8
Wang, S.9
Suver, C.10
Zhu, J.11
Millstein, J.12
Sieberts, S.13
Lamb, J.14
GuhaThakurta, D.15
Derry, J.16
Storey, J.D.17
Avila-Campillo, I.18
Kruger, M.J.19
Johnson, J.M.20
Rohl, C.A.21
van Nas, A.22
Mehrabian, M.23
Drake, T.A.24
Lusis, A.J.25
Smith, R.C.26
Guengerich, F.P.27
Strom, S.C.28
Schuetz, E.29
Rushmore, T.H.30
more..
-
8
-
-
0037177625
-
Genetic dissection of transcriptional regulation in budding yeast.
-
10.1126/science.1069516, 11923494
-
Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 2002, 296:752-755. 10.1126/science.1069516, 11923494.
-
(2002)
Science
, vol.296
, pp. 752-755
-
-
Brem, R.B.1
Yvert, G.2
Clinton, R.3
Kruglyak, L.4
-
9
-
-
78049312702
-
Correction for hidden confounders in the genetic analysis of gene expression.
-
10.1073/pnas.1002425107, 2944732, 20810919
-
Listgarten J, Kadie C, Schadt EE, Heckerman D. Correction for hidden confounders in the genetic analysis of gene expression. Proc Natl Acad Sci USA 2010, 107:16465-16470. 10.1073/pnas.1002425107, 2944732, 20810919.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 16465-16470
-
-
Listgarten, J.1
Kadie, C.2
Schadt, E.E.3
Heckerman, D.4
-
10
-
-
67249117049
-
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
-
10.1073/pnas.0903103106, 2687147, 19474294
-
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106:9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 9362-9367
-
-
Hindorff, L.A.1
Sethupathy, P.2
Junkins, H.A.3
Ramos, E.M.4
Mehta, J.P.5
Collins, F.S.6
Manolio, T.A.7
-
11
-
-
0042856391
-
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors.
-
Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 2003, 35:57-64.
-
(2003)
Nat Genet
, vol.35
, pp. 57-64
-
-
Yvert, G.1
Brem, R.B.2
Whittle, J.3
Akey, J.M.4
Foss, E.5
Smith, E.N.6
Mackelprang, R.7
Kruglyak, L.8
-
12
-
-
47249142778
-
Revealing the architecture of gene regulation: the promise of eQTL studies.
-
10.1016/j.tig.2008.06.001, 2583071, 18597885
-
Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 2008, 24:408-415. 10.1016/j.tig.2008.06.001, 2583071, 18597885.
-
(2008)
Trends Genet
, vol.24
, pp. 408-415
-
-
Gilad, Y.1
Rifkin, S.A.2
Pritchard, J.K.3
-
13
-
-
84864437284
-
Inference of modules associated to eQTLs.
-
10.1093/nar/gks269, 3401454, 22447449
-
Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I. Inference of modules associated to eQTLs. Nucleic Acids Res 2012, 40:e98. 10.1093/nar/gks269, 3401454, 22447449.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kreimer, A.1
Litvin, O.2
Hao, K.3
Molony, C.4
Pe'er, D.5
Pe'er, I.6
-
14
-
-
77951439152
-
Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.
-
10.1371/journal.pgen.1000888, 2848547, 20369019
-
Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010, 6:e1000888. 10.1371/journal.pgen.1000888, 2848547, 20369019.
-
(2010)
PLoS Genet
, vol.6
-
-
Nicolae, D.L.1
Gamazon, E.2
Zhang, W.3
Duan, S.4
Dolan, M.E.5
Cox, N.J.6
-
15
-
-
34547216747
-
Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma.
-
10.1038/nature06014, 17611496
-
Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, Heath S, Depner M, von Berg A, Bufe A, Rietschel E, Heinzmann A, Simma B, Frischer T, Willis-Owen SA, Wong KC, Illig T, Vogelberg C, Weiland SK, von Mutius E, Abecasis GR, Farrall M, Gut IG, Lathrop GM, Cookson WO. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 2007, 448:470-473. 10.1038/nature06014, 17611496.
-
(2007)
Nature
, vol.448
, pp. 470-473
-
-
Moffatt, M.F.1
Kabesch, M.2
Liang, L.3
Dixon, A.L.4
Strachan, D.5
Heath, S.6
Depner, M.7
von Berg, A.8
Bufe, A.9
Rietschel, E.10
Heinzmann, A.11
Simma, B.12
Frischer, T.13
Willis-Owen, S.A.14
Wong, K.C.15
Illig, T.16
Vogelberg, C.17
Weiland, S.K.18
von Mutius, E.19
Abecasis, G.R.20
Farrall, M.21
Gut, I.G.22
Lathrop, G.M.23
Cookson, W.O.24
more..
-
16
-
-
38649132270
-
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
-
10.1038/ng.75, 2682493, 18193044
-
Kathiresan S, Melander O, Guiducci C, Surti A, Burtt NP, Rieder MJ, Cooper GM, Roos C, Voight BF, Havulinna AS, Wahlstrand B, Hedner T, Corella D, Tai ES, Ordovas JM, Berglund G, Vartiainen E, Jousilahti P, Hedblad B, Taskinen MR, Newton-Cheh C, Salomaa V, Peltonen L, Groop L, Altshuler DM, Orho-Melander M. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 2008, 40:189-197. 10.1038/ng.75, 2682493, 18193044.
-
(2008)
Nat Genet
, vol.40
, pp. 189-197
-
-
Kathiresan, S.1
Melander, O.2
Guiducci, C.3
Surti, A.4
Burtt, N.P.5
Rieder, M.J.6
Cooper, G.M.7
Roos, C.8
Voight, B.F.9
Havulinna, A.S.10
Wahlstrand, B.11
Hedner, T.12
Corella, D.13
Tai, E.S.14
Ordovas, J.M.15
Berglund, G.16
Vartiainen, E.17
Jousilahti, P.18
Hedblad, B.19
Taskinen, M.R.20
Newton-Cheh, C.21
Salomaa, V.22
Peltonen, L.23
Groop, L.24
Altshuler, D.M.25
Orho-Melander, M.26
more..
-
17
-
-
33846978695
-
Relative impact of nucleotide and copy number variation on gene expression phenotypes.
-
10.1126/science.1136678, 2665772, 17289997
-
Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315:848-853. 10.1126/science.1136678, 2665772, 17289997.
-
(2007)
Science
, vol.315
, pp. 848-853
-
-
Stranger, B.E.1
Forrest, M.S.2
Dunning, M.3
Ingle, C.E.4
Beazley, C.5
Thorne, N.6
Redon, R.7
Bird, C.P.8
de Grassi, A.9
Lee, C.10
Tyler-Smith, C.11
Carter, N.12
Scherer, S.W.13
Tavare, S.14
Deloukas, P.15
Hurles, M.E.16
Dermitzakis, E.T.17
-
18
-
-
69949176863
-
Common regulatory variation impacts gene expression in a cell type-dependent manner.
-
10.1126/science.1174148, 2867218, 19644074
-
Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, Gagnebin M, Nisbett J, Deloukas P, Dermitzakis ET, Antonarakis SE. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 2009, 325:1246-1250. 10.1126/science.1174148, 2867218, 19644074.
-
(2009)
Science
, vol.325
, pp. 1246-1250
-
-
Dimas, A.S.1
Deutsch, S.2
Stranger, B.E.3
Montgomery, S.B.4
Borel, C.5
Attar-Cohen, H.6
Ingle, C.7
Beazley, C.8
Gutierrez Arcelus, M.9
Sekowska, M.10
Gagnebin, M.11
Nisbett, J.12
Deloukas, P.13
Dermitzakis, E.T.14
Antonarakis, S.E.15
-
19
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.
-
10.1038/35001009, 10688190
-
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627. 10.1038/35001009, 10688190.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
Qureshi-Emili, A.11
Li, Y.12
Godwin, B.13
Conover, D.14
Kalbfleisch, T.15
Vijayadamodar, G.16
Yang, M.17
Johnston, M.18
Fields, S.19
Rothberg, J.M.20
more..
-
20
-
-
0141484611
-
Evolutionary conservation of motif constituents in the yeast protein interaction network.
-
10.1038/ng1242, 12973352
-
Wuchty S, Oltvai ZN, Barabasi AL. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 2003, 35:176-179. 10.1038/ng1242, 12973352.
-
(2003)
Nat Genet
, vol.35
, pp. 176-179
-
-
Wuchty, S.1
Oltvai, Z.N.2
Barabasi, A.L.3
-
21
-
-
1842580761
-
Functional and topological characterization of protein interaction networks.
-
10.1002/pmic.200300636, 15048975
-
Yook SH, Oltvai ZN, Barabasi AL. Functional and topological characterization of protein interaction networks. Proteomics 2004, 4:928-942. 10.1002/pmic.200300636, 15048975.
-
(2004)
Proteomics
, vol.4
, pp. 928-942
-
-
Yook, S.H.1
Oltvai, Z.N.2
Barabasi, A.L.3
-
22
-
-
0035799707
-
Lethality and centrality in protein networks.
-
10.1038/35075138, 11333967
-
Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
23
-
-
22844450110
-
Systematic interpretation of genetic interactions using protein networks.
-
10.1038/nbt1096, 2814446, 15877074
-
Kelley R, Ideker T. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 2005, 23:561-566. 10.1038/nbt1096, 2814446, 15877074.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 561-566
-
-
Kelley, R.1
Ideker, T.2
-
24
-
-
79851502150
-
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology.
-
10.1371/journal.pgen.1001273, 3020935, 21249183
-
Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, Cotsapas C, Daly MJ. Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet 2011, 7:e1001273. 10.1371/journal.pgen.1001273, 3020935, 21249183.
-
(2011)
PLoS Genet
, vol.7
-
-
Rossin, E.J.1
Lage, K.2
Raychaudhuri, S.3
Xavier, R.J.4
Tatar, D.5
Benita, Y.6
Cotsapas, C.7
Daly, M.J.8
-
25
-
-
41949118715
-
Network properties of genes harboring inherited disease mutations.
-
10.1073/pnas.0701722105, 2393821, 18326631
-
Feldman I, Rzhetsky A, Vitkup D. Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci USA 2008, 105:4323-4328. 10.1073/pnas.0701722105, 2393821, 18326631.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 4323-4328
-
-
Feldman, I.1
Rzhetsky, A.2
Vitkup, D.3
-
26
-
-
80052493684
-
A network-based approach to prioritize results from genome-wide association studies.
-
10.1371/journal.pone.0024220, 3168369, 21915301
-
Akula N, Baranova A, Seto D, Solka J, Nalls MA, Singleton A, Ferrucci L, Tanaka T, Bandinelli S, Cho YS, Kim YJ, Lee JY, Han BG, McMahon FJ. A network-based approach to prioritize results from genome-wide association studies. PLoS One 2011, 6:e24220. 10.1371/journal.pone.0024220, 3168369, 21915301.
-
(2011)
PLoS One
, vol.6
-
-
Akula, N.1
Baranova, A.2
Seto, D.3
Solka, J.4
Nalls, M.A.5
Singleton, A.6
Ferrucci, L.7
Tanaka, T.8
Bandinelli, S.9
Cho, Y.S.10
Kim, Y.J.11
Lee, J.Y.12
Han, B.G.13
McMahon, F.J.14
-
27
-
-
84864590971
-
Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia.
-
10.1371/journal.pcbi.1002587, 3390381, 22792057
-
Jia P, Wang L, Fanous AH, Pato CN, Edwards TL, Zhao Z. Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia. PLoS Comput Biol 2012, 8:e1002587. 10.1371/journal.pcbi.1002587, 3390381, 22792057.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Jia, P.1
Wang, L.2
Fanous, A.H.3
Pato, C.N.4
Edwards, T.L.5
Zhao, Z.6
-
28
-
-
78650562728
-
DmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.
-
10.1093/bioinformatics/btq615, 3008643, 21045073
-
Jia P, Zheng S, Long J, Zheng W, Zhao Z. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics 2011, 27:95-102. 10.1093/bioinformatics/btq615, 3008643, 21045073.
-
(2011)
Bioinformatics
, vol.27
, pp. 95-102
-
-
Jia, P.1
Zheng, S.2
Long, J.3
Zheng, W.4
Zhao, Z.5
-
29
-
-
0003684449
-
-
New York: Springer, 2
-
Hastie T, Tibshirani R, Friedman JH. The elements of statistical learning: data mining, inference, and prediction 2009, New York: Springer, 2.
-
(2009)
The elements of statistical learning: data mining, inference, and prediction
-
-
Hastie, T.1
Tibshirani, R.2
Friedman, J.H.3
-
30
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing.
-
10.1038/nature08872, 3089435, 20220758
-
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010, 464:768-772. 10.1038/nature08872, 3089435, 20220758.
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
Marioni, J.C.2
Pai, A.A.3
Degner, J.F.4
Engelhardt, B.E.5
Nkadori, E.6
Veyrieras, J.B.7
Stephens, M.8
Gilad, Y.9
Pritchard, J.K.10
-
31
-
-
84857131934
-
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
-
10.1371/journal.pone.0030629, 3281037, 22359548
-
Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, Pritchard JK. Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One 2012, 7:e30629. 10.1371/journal.pone.0030629, 3281037, 22359548.
-
(2012)
PLoS One
, vol.7
-
-
Veyrieras, J.B.1
Gaffney, D.J.2
Pickrell, J.K.3
Gilad, Y.4
Stephens, M.5
Pritchard, J.K.6
-
32
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population.
-
10.1038/nature08903, 20220756
-
Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 2010, 464:773-777. 10.1038/nature08903, 20220756.
-
(2010)
Nature
, vol.464
, pp. 773-777
-
-
Montgomery, S.B.1
Sammeth, M.2
Gutierrez-Arcelus, M.3
Lach, R.P.4
Ingle, C.5
Nisbett, J.6
Guigo, R.7
Dermitzakis, E.T.8
-
33
-
-
80052322958
-
Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.
-
10.1371/journal.pgen.1002197, 3150446, 21829388
-
Fehrmann RS, Jansen RC, Veldink JH, Westra HJ, Arends D, Bonder MJ, Fu J, Deelen P, Groen HJ, Smolonska A, Weersma RK, Hofstra RM, Buurman WA, Rensen S, Wolfs MG, Platteel M, Zhernakova A, Elbers CC, Festen EM, Trynka G, Hofker MH, Saris CG, Ophoff RA, van den Berg LH, van Heel DA, Wijmenga C, Te Meerman GJ, Franke L. Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet 2011, 7:e1002197. 10.1371/journal.pgen.1002197, 3150446, 21829388.
-
(2011)
PLoS Genet
, vol.7
-
-
Fehrmann, R.S.1
Jansen, R.C.2
Veldink, J.H.3
Westra, H.J.4
Arends, D.5
Bonder, M.J.6
Fu, J.7
Deelen, P.8
Groen, H.J.9
Smolonska, A.10
Weersma, R.K.11
Hofstra, R.M.12
Buurman, W.A.13
Rensen, S.14
Wolfs, M.G.15
Platteel, M.16
Zhernakova, A.17
Elbers, C.C.18
Festen, E.M.19
Trynka, G.20
Hofker, M.H.21
Saris, C.G.22
Ophoff, R.A.23
van den Berg, L.H.24
van Heel, D.A.25
Wijmenga, C.26
Te Meerman, G.J.27
Franke, L.28
more..
-
34
-
-
84877730113
-
Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs.
-
3631766, 23603706
-
Chang X, Xu T, Li Y, Wang K. Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs. Sci Rep 2013, 3:1691. 3631766, 23603706.
-
(2013)
Sci Rep
, vol.3
, pp. 1691
-
-
Chang, X.1
Xu, T.2
Li, Y.3
Wang, K.4
-
35
-
-
75249089572
-
SCAN: SNP and copy number annotation.
-
10.1093/bioinformatics/btp644, 2852202, 19933162
-
Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, Dolan ME, Cox NJ. SCAN: SNP and copy number annotation. Bioinformatics 2010, 26:259-262. 10.1093/bioinformatics/btp644, 2852202, 19933162.
-
(2010)
Bioinformatics
, vol.26
, pp. 259-262
-
-
Gamazon, E.R.1
Zhang, W.2
Konkashbaev, A.3
Duan, S.4
Kistner, E.O.5
Nicolae, D.L.6
Dolan, M.E.7
Cox, N.J.8
-
36
-
-
66149119826
-
Modularity and interactions in the genetics of gene expression.
-
10.1073/pnas.0810208106, 2672504, 19223586
-
Litvin O, Causton HC, Chen BJ, Pe'er D. Modularity and interactions in the genetics of gene expression. Proc Natl Acad Sci USA 2009, 106:6441-6446. 10.1073/pnas.0810208106, 2672504, 19223586.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 6441-6446
-
-
Litvin, O.1
Causton, H.C.2
Chen, B.J.3
Pe'er, D.4
-
37
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes.
-
10.1093/nar/28.1.27, 102409, 10592173
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
38
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
-
10.1038/75556, 3037419, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
39
-
-
77957243164
-
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
-
10.1093/bioinformatics/btq466, 2944209, 20709693
-
Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 2010, 26:2438-2444. 10.1093/bioinformatics/btq466, 2944209, 20709693.
-
(2010)
Bioinformatics
, vol.26
, pp. 2438-2444
-
-
Lachmann, A.1
Xu, H.2
Krishnan, J.3
Berger, S.I.4
Mazloom, A.R.5
Ma'ayan, A.6
-
40
-
-
84857111200
-
DNase I sensitivity QTLs are a major determinant of human expression variation.
-
10.1038/nature10808, 3501342, 22307276
-
Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 2012, 482:390-394. 10.1038/nature10808, 3501342, 22307276.
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.F.1
Pai, A.A.2
Pique-Regi, R.3
Veyrieras, J.B.4
Gaffney, D.J.5
Pickrell, J.K.6
De Leon, S.7
Michelini, K.8
Lewellen, N.9
Crawford, G.E.10
Stephens, M.11
Gilad, Y.12
Pritchard, J.K.13
-
41
-
-
33745012299
-
Modularity and community structure in networks.
-
10.1073/pnas.0601602103, 1482622, 16723398
-
Newman ME. Modularity and community structure in networks. Proc Natl Acad Sci USA 2006, 103:8577-8582. 10.1073/pnas.0601602103, 1482622, 16723398.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 8577-8582
-
-
Newman, M.E.1
-
42
-
-
34249079154
-
Network motifs: theory and experimental approaches.
-
10.1038/nrg2102, 17510665
-
Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet 2007, 8:450-461. 10.1038/nrg2102, 17510665.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
43
-
-
77954143522
-
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
-
10.1038/ng.609, 3080658, 20581827
-
Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segre AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, et al. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2010, 42:579-589. 10.1038/ng.609, 3080658, 20581827.
-
(2010)
Nat Genet
, vol.42
, pp. 579-589
-
-
Voight, B.F.1
Scott, L.J.2
Steinthorsdottir, V.3
Morris, A.P.4
Dina, C.5
Welch, R.P.6
Zeggini, E.7
Huth, C.8
Aulchenko, Y.S.9
Thorleifsson, G.10
McCulloch, L.J.11
Ferreira, T.12
Grallert, H.13
Amin, N.14
Wu, G.15
Willer, C.J.16
Raychaudhuri, S.17
McCarroll, S.A.18
Langenberg, C.19
Hofmann, O.M.20
Dupuis, J.21
Qi, L.22
Segre, A.V.23
van Hoek, M.24
Navarro, P.25
Ardlie, K.26
Balkau, B.27
Benediktsson, R.28
Bennett, A.J.29
Blagieva, R.30
more..
-
44
-
-
0035312290
-
All Tcf HMG box transcription factors interact with Groucho-related co-repressors.
-
10.1093/nar/29.7.1410, 31284, 11266540
-
Brantjes H, Roose J, van De Wetering M, Clevers H. All Tcf HMG box transcription factors interact with Groucho-related co-repressors. Nucleic Acids Res 2001, 29:1410-1419. 10.1093/nar/29.7.1410, 31284, 11266540.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 1410-1419
-
-
Brantjes, H.1
Roose, J.2
van De Wetering, M.3
Clevers, H.4
-
45
-
-
1942469444
-
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.
-
10.1073/pnas.0306752101, 395901, 15079056
-
Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA 2004, 101:5934-5939. 10.1073/pnas.0306752101, 395901, 15079056.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 5934-5939
-
-
Yeger-Lotem, E.1
Sattath, S.2
Kashtan, N.3
Itzkovitz, S.4
Milo, R.5
Pinter, R.Y.6
Alon, U.7
Margalit, H.8
-
46
-
-
0037174670
-
Network motifs: simple building blocks of complex networks.
-
10.1126/science.298.5594.824, 12399590
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827. 10.1126/science.298.5594.824, 12399590.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
47
-
-
2442706422
-
An overview of Ensembl.
-
10.1101/gr.1860604, 479121, 15078858
-
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, et al. An overview of Ensembl. Genome Res 2004, 14:925-928. 10.1101/gr.1860604, 479121, 15078858.
-
(2004)
Genome Res
, vol.14
, pp. 925-928
-
-
Birney, E.1
Andrews, T.D.2
Bevan, P.3
Caccamo, M.4
Chen, Y.5
Clarke, L.6
Coates, G.7
Cuff, J.8
Curwen, V.9
Cutts, T.10
Down, T.11
Eyras, E.12
Fernandez-Suarez, X.M.13
Gane, P.14
Gibbins, B.15
Gilbert, J.16
Hammond, M.17
Hotz, H.R.18
Iyer, V.19
Jekosch, K.20
Kahari, A.21
Kasprzyk, A.22
Keefe, D.23
Keenan, S.24
Lehvaslaiho, H.25
McVicker, G.26
Melsopp, C.27
Meidl, P.28
Mongin, E.29
Pettett, R.30
more..
-
48
-
-
50449088836
-
A wiki for the life sciences where authorship matters.
-
10.1038/ng.f.217, 18728691
-
Hoffmann R. A wiki for the life sciences where authorship matters. Nat Genet 2008, 40:1047-1051. 10.1038/ng.f.217, 18728691.
-
(2008)
Nat Genet
, vol.40
, pp. 1047-1051
-
-
Hoffmann, R.1
-
49
-
-
58149193222
-
Human Protein Reference Database--2009 update.
-
10.1093/nar/gkn892, 2686490, 18988627
-
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database--2009 update. Nucleic Acids Res 2009, 37:D767-772. 10.1093/nar/gkn892, 2686490, 18988627.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
Balakrishnan, L.11
Marimuthu, A.12
Banerjee, S.13
Somanathan, D.S.14
Sebastian, A.15
Rani, S.16
Ray, S.17
Harrys Kishore, C.J.18
Kanth, S.19
Ahmed, M.20
Kashyap, M.K.21
Mohmood, R.22
Ramachandra, Y.L.23
Krishna, V.24
Rahiman, B.A.25
Mohan, S.26
Ranganathan, P.27
Ramabadran, S.28
Chaerkady, R.29
Pandey, A.30
more..
-
50
-
-
75649122259
-
A high-resolution association mapping panel for the dissection of complex traits in mice.
-
10.1101/gr.099234.109, 2813484, 20054062
-
Bennett BJ, Farber CR, Orozco L, Kang HM, Ghazalpour A, Siemers N, Neubauer M, Neuhaus I, Yordanova R, Guan B, Truong A, Yang WP, He A, Kayne P, Gargalovic P, Kirchgessner T, Pan C, Castellani LW, Kostem E, Furlotte N, Drake TA, Eskin E, Lusis AJ. A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 2010, 20:281-290. 10.1101/gr.099234.109, 2813484, 20054062.
-
(2010)
Genome Res
, vol.20
, pp. 281-290
-
-
Bennett, B.J.1
Farber, C.R.2
Orozco, L.3
Kang, H.M.4
Ghazalpour, A.5
Siemers, N.6
Neubauer, M.7
Neuhaus, I.8
Yordanova, R.9
Guan, B.10
Truong, A.11
Yang, W.P.12
He, A.13
Kayne, P.14
Gargalovic, P.15
Kirchgessner, T.16
Pan, C.17
Castellani, L.W.18
Kostem, E.19
Furlotte, N.20
Drake, T.A.21
Eskin, E.22
Lusis, A.J.23
more..
-
51
-
-
80052851950
-
Mouse genomic variation and its effect on phenotypes and gene regulation.
-
10.1038/nature10413, 3276836, 21921910
-
Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellaker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 2011, 477:289-294. 10.1038/nature10413, 3276836, 21921910.
-
(2011)
Nature
, vol.477
, pp. 289-294
-
-
Keane, T.M.1
Goodstadt, L.2
Danecek, P.3
White, M.A.4
Wong, K.5
Yalcin, B.6
Heger, A.7
Agam, A.8
Slater, G.9
Goodson, M.10
Furlotte, N.A.11
Eskin, E.12
Nellaker, C.13
Whitley, H.14
Cleak, J.15
Janowitz, D.16
Hernandez-Pliego, P.17
Edwards, A.18
Belgard, T.G.19
Oliver, P.L.20
McIntyre, R.E.21
Bhomra, A.22
Nicod, J.23
Gan, X.24
Yuan, W.25
van der Weyden, L.26
Steward, C.A.27
Bala, S.28
Stalker, J.29
Mott, R.30
more..
-
53
-
-
34548292504
-
PLINK: a tool set for whole-genome association and population-based linkage analyses.
-
10.1086/519795, 1950838, 17701901
-
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.
-
(2007)
Am J Hum Genet
, vol.81
, pp. 559-575
-
-
Purcell, S.1
Neale, B.2
Todd-Brown, K.3
Thomas, L.4
Ferreira, M.A.5
Bender, D.6
Maller, J.7
Sklar, P.8
de Bakker, P.I.9
Daly, M.J.10
Sham, P.C.11
-
54
-
-
78651320424
-
The UCSC Genome Browser database: update 2011.
-
10.1093/nar/gkq963, 3242726, 20959295
-
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2011, 39:D876-882. 10.1093/nar/gkq963, 3242726, 20959295.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Fujita, P.A.1
Rhead, B.2
Zweig, A.S.3
Hinrichs, A.S.4
Karolchik, D.5
Cline, M.S.6
Goldman, M.7
Barber, G.P.8
Clawson, H.9
Coelho, A.10
Diekhans, M.11
Dreszer, T.R.12
Giardine, B.M.13
Harte, R.A.14
Hillman-Jackson, J.15
Hsu, F.16
Kirkup, V.17
Kuhn, R.M.18
Learned, K.19
Li, C.H.20
Meyer, L.R.21
Pohl, A.22
Raney, B.J.23
Rosenbloom, K.R.24
Smith, K.E.25
Haussler, D.26
Kent, W.J.27
more..
-
56
-
-
78049480691
-
GeneCards Version 3: the human gene integrator.
-
Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, Sirota-Madi A, Olender T, Golan Y, Stelzer G, Harel A, Lancet D. GeneCards Version 3: the human gene integrator. Database (Oxford) 2010, 2010:baq020.
-
(2010)
Database (Oxford)
, vol.2010
, pp. 20
-
-
Safran, M.1
Dalah, I.2
Alexander, J.3
Rosen, N.4
Iny Stein, T.5
Shmoish, M.6
Nativ, N.7
Bahir, I.8
Doniger, T.9
Krug, H.10
Sirota-Madi, A.11
Olender, T.12
Golan, Y.13
Stelzer, G.14
Harel, A.15
Lancet, D.16
-
58
-
-
77954565730
-
Efficient physical embedding of topologically complex information processing networks in brains and computer circuits.
-
10.1371/journal.pcbi.1000748, 2858671, 20421990
-
Bassett DS, Greenfield DL, Meyer-Lindenberg A, Weinberger DR, Moore SW, Bullmore ET. Efficient physical embedding of topologically complex information processing networks in brains and computer circuits. PLoS Comput Biol 2010, 6:e1000748. 10.1371/journal.pcbi.1000748, 2858671, 20421990.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Bassett, D.S.1
Greenfield, D.L.2
Meyer-Lindenberg, A.3
Weinberger, D.R.4
Moore, S.W.5
Bullmore, E.T.6
-
59
-
-
80053149227
-
Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification.
-
10.1371/journal.pone.0024503, 3180289, 21966361
-
Stokes A, Drozdov I, Guerra E, Ouzounis CA, Warnakulasuriya S, Gleeson MJ, McGurk M, Tavassoli M, Odell EW. Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification. PLoS One 2011, 6:e24503. 10.1371/journal.pone.0024503, 3180289, 21966361.
-
(2011)
PLoS One
, vol.6
-
-
Stokes, A.1
Drozdov, I.2
Guerra, E.3
Ouzounis, C.A.4
Warnakulasuriya, S.5
Gleeson, M.J.6
McGurk, M.7
Tavassoli, M.8
Odell, E.W.9
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