-
1
-
-
84903179045
-
Macrophage models of Gaucher disease for evaluating disease pathogenesis and candidate drugs
-
Aflaki E, Stubblefield BK, Maniwang E, Lopez G, Moaven N, Goldin E, Marugan J, Patnaik S, Dutra A, Southall N, et al. 2014. Macrophage models of Gaucher disease for evaluating disease pathogenesis and candidate drugs. Sci Transl Med 6: 240ra73.
-
(2014)
Sci Transl Med
, vol.6
, pp. 240ra73
-
-
Aflaki, E.1
Stubblefield, B.K.2
Maniwang, E.3
Lopez, G.4
Moaven, N.5
Goldin, E.6
Marugan, J.7
Patnaik, S.8
Dutra, A.9
Southall, N.10
-
2
-
-
85027513769
-
-
bioRxiv
-
Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL, Kundu K, Consortium H, Hale C, Dougan G, Gaffney DJ, et al. 2017. Genetic effects on chromatin accessibility foreshadow gene expression changes in macrophage immune response. bioRxiv doi: 10.1101/102392.
-
(2017)
Genetic Effects on Chromatin Accessibility Foreshadow Gene Expression Changes in Macrophage Immune Response
-
-
Alasoo, K.1
Rodrigues, J.2
Mukhopadhyay, S.3
Knights, A.J.4
Mann, A.L.5
Kundu, K.6
Consortium, H.7
Hale, C.8
Dougan, G.9
Gaffney, D.J.10
-
3
-
-
84907584646
-
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
-
Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, Gilad Y. 2014. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet 10: e1004663.
-
(2014)
PLoS Genet
, vol.10
, pp. e1004663
-
-
Banovich, N.E.1
Lan, X.2
McVicker, G.3
van de Geijn, B.4
Degner, J.F.5
Blischak, J.D.6
Roux, J.7
Pritchard, J.K.8
Gilad, Y.9
-
4
-
-
84891685308
-
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
-
Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, et al. 2014. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res 24: 14–24.
-
(2014)
Genome Res
, vol.24
, pp. 14-24
-
-
Battle, A.1
Mostafavi, S.2
Zhu, X.3
Potash, J.B.4
Weissman, M.M.5
McCormick, C.6
Haudenschild, C.D.7
Beckman, K.B.8
Shi, J.9
Mei, R.10
-
5
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 1213–1218.
-
(2013)
Nat Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
6
-
-
84905242471
-
Chemically defined generation of human cardiomyocytes
-
Burridge PW, Matsa E, Shukla P, Lin ZC, Churko JM, Ebert AD, Lan F, Diecke S, Huber B, Mordwinkin NM, et al. 2014. Chemically defined generation of human cardiomyocytes. Nat Methods 11: 855–860.
-
(2014)
Nat Methods
, vol.11
, pp. 855-860
-
-
Burridge, P.W.1
Matsa, E.2
Shukla, P.3
Lin, Z.C.4
Churko, J.M.5
Ebert, A.D.6
Lan, F.7
Diecke, S.8
Huber, B.9
Mordwinkin, N.M.10
-
7
-
-
84964409142
-
Human induced pluripotent stem cell-derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity
-
Burridge PW, Li YF, Matsa E, Wu H, Ong SG, Sharma A, Holmstrom A, Chang AC, Coronado MJ, Ebert AD, et al. 2016. Human induced pluripotent stem cell-derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity. Nat Med 22: 547–556.
-
(2016)
Nat Med
, vol.22
, pp. 547-556
-
-
Burridge, P.W.1
Li, Y.F.2
Matsa, E.3
Wu, H.4
Ong, S.G.5
Sharma, A.6
Holmstrom, A.7
Chang, A.C.8
Coronado, M.J.9
Ebert, A.D.10
-
8
-
-
84958730029
-
Genetic variation, not cell type of origin, underlies the majority of identifiable regulatory differences in iPSCs
-
Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, Gilad Y. 2016. Genetic variation, not cell type of origin, underlies the majority of identifiable regulatory differences in iPSCs. PLoS Genet 12: e1005793.
-
(2016)
PLoS Genet
, vol.12
, pp. e1005793
-
-
Burrows, C.K.1
Banovich, N.E.2
Pavlovic, B.J.3
Patterson, K.4
Gallego Romero, I.5
Pritchard, J.K.6
Gilad, Y.7
-
9
-
-
85032582887
-
Inferring relevant cell types for complex traits by using single-cell gene expression
-
Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK. 2017. Inferring relevant cell types for complex traits by using single-cell gene expression. Am J Hum Genet 101: 686–699.
-
(2017)
Am J Hum Genet
, vol.101
, pp. 686-699
-
-
Calderon, D.1
Bhaskar, A.2
Knowles, D.A.3
Golan, D.4
Raj, T.5
Fu, A.Q.6
Pritchard, J.K.7
-
10
-
-
85017175121
-
A drug screen using human iPSC-derived hepatocyte-like cells reveals cardiac glycosides as a potential treatment for hypercholesterolemia
-
Cayo MA, Mallanna SK, Di Furio F, Jing R, Tolliver LB, Bures M, Urick A, Noto FK, Pashos EE, Greseth MD, et al. 2017. A drug screen using human iPSC-derived hepatocyte-like cells reveals cardiac glycosides as a potential treatment for hypercholesterolemia. Cell Stem Cell 20: 478–489.
-
(2017)
Cell Stem Cell
, vol.20
, pp. 478-489
-
-
Cayo, M.A.1
Mallanna, S.K.2
Di Furio, F.3
Jing, R.4
Tolliver, L.B.5
Bures, M.6
Urick, A.7
Noto, F.K.8
Pashos, E.E.9
Greseth, M.D.10
-
11
-
-
85020704801
-
-
bioRxiv
-
Cheng CS, Gate RE, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Subramaniam M, Shammim M, Hougen KL, et al. 2016. Genetic determinants of chromatin accessibility and gene regulation in t cell activation across human individuals. bioRxiv doi: 10.1101/090241.
-
(2016)
Genetic Determinants of Chromatin Accessibility and Gene Regulation in T Cell Activation Across Human Individuals
-
-
Cheng, C.S.1
Gate, R.E.2
Aiden, A.P.3
Siba, A.4
Tabaka, M.5
Lituiev, D.6
Machol, I.7
Subramaniam, M.8
Shammim, M.9
Hougen, K.L.10
-
12
-
-
84879116702
-
Efficient drug screening and gene correction for treating liver disease using patient-specific stem cells
-
Choi SM, Kim Y, Shim JS, Park JT, Wang RH, Leach SD, Liu JO, Deng C, Ye Z, Jang YY, et al. 2013. Efficient drug screening and gene correction for treating liver disease using patient-specific stem cells. Hepatology 57: 2458–2468.
-
(2013)
Hepatology
, vol.57
, pp. 2458-2468
-
-
Choi, S.M.1
Kim, Y.2
Shim, J.S.3
Park, J.T.4
Wang, R.H.5
Leach, S.D.6
Liu, J.O.7
Deng, C.8
Ye, Z.9
Jang, Y.Y.10
-
13
-
-
84947252379
-
A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs
-
Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, et al. 2015. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol 33: 1173–1181.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 1173-1181
-
-
Choi, J.1
Lee, S.2
Mallard, W.3
Clement, K.4
Tagliazucchi, G.M.5
Lim, H.6
Choi, I.Y.7
Ferrari, F.8
Tsankov, A.M.9
Pop, R.10
-
14
-
-
84859260926
-
The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes
-
Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, Gilad Y. 2012. The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Hum Mol Genet 21: 2111–2123.
-
(2012)
Hum Mol Genet
, vol.21
, pp. 2111-2123
-
-
Cusanovich, D.A.1
Billstrand, C.2
Zhou, X.3
Chavarria, C.4
De Leon, S.5
Michelini, K.6
Pai, A.A.7
Ober, C.8
Gilad, Y.9
-
15
-
-
84928333932
-
Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation
-
D’Aiuto L, Zhi Y, Kumar Das D, Wilcox MR, Johnson JW, McClain L, MacDonald ML, Di Maio R, Schurdak ME, Piazza P, et al. 2014. Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation. Organogenesis 10: 365–377.
-
(2014)
Organogenesis
, vol.10
, pp. 365-377
-
-
D’Aiuto, L.1
Zhi, Y.2
Kumar Das, D.3
Wilcox, M.R.4
Johnson, J.W.5
McClain, L.6
MacDonald, M.L.7
Di Maio, R.8
Schurdak, M.E.9
Piazza, P.10
-
16
-
-
84940565386
-
Stem cell-derived liver cells for drug testing and disease modeling
-
Davidson MD, Ware BR, Khetani SR. 2015. Stem cell-derived liver cells for drug testing and disease modeling. Discov Med 19: 349–358.
-
(2015)
Discov Med
, vol.19
, pp. 349-358
-
-
Davidson, M.D.1
Ware, B.R.2
Khetani, S.R.3
-
17
-
-
85017100835
-
Large-scale profiling reveals the influence of genetic variation on gene expression in human induced pluripotent stem cells
-
DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D’Antonio M, et al. 2017. Large-scale profiling reveals the influence of genetic variation on gene expression in human induced pluripotent stem cells. Cell Stem Cell 20: 533–546.
-
(2017)
Cell Stem Cell
, vol.20
, pp. 533-546
-
-
DeBoever, C.1
Li, H.2
Jakubosky, D.3
Benaglio, P.4
Reyna, J.5
Olson, K.M.6
Huang, H.7
Biggs, W.8
Sandoval, E.9
D’Antonio, M.10
-
18
-
-
84857111200
-
DNase I sensitivity QTLs are a major determinant of human expression variation
-
Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, et al. 2012. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390–394.
-
(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
-
19
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15–21.
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
20
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57–74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
21
-
-
84923326765
-
Genetic and epigenetic fine mapping of causal autoimmune disease variants
-
Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, et al. 2015. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518: 337–343.
-
(2015)
Nature
, vol.518
, pp. 337-343
-
-
Farh, K.K.1
Marson, A.2
Zhu, J.3
Kleinewietfeld, M.4
Housley, W.J.5
Beik, S.6
Shoresh, N.7
Whitton, H.8
Ryan, R.J.9
Shishkin, A.A.10
-
22
-
-
84944453625
-
Suboptimization of developmental enhancers
-
Farley EK, Olson KM, Zhang W, Brandt AJ, Rokhsar DS, Levine MS. 2015. Suboptimization of developmental enhancers. Science 350: 325–328.
-
(2015)
Science
, vol.350
, pp. 325-328
-
-
Farley, E.K.1
Olson, K.M.2
Zhang, W.3
Brandt, A.J.4
Rokhsar, D.S.5
Levine, M.S.6
-
23
-
-
85000443086
-
Partitioning heritability by functional annotation using genome-wide association summary statistics
-
Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, Anttila V, Xu H, Zang C, Farh K, et al. 2015. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat Genet 47: 1228–1235.
-
(2015)
Nat Genet
, vol.47
, pp. 1228-1235
-
-
Finucane, H.K.1
Bulik-Sullivan, B.2
Gusev, A.3
Trynka, G.4
Reshef, Y.5
Loh, P.R.6
Anttila, V.7
Xu, H.8
Zang, C.9
Farh, K.10
-
24
-
-
77953223693
-
Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain
-
Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, Arepalli S, Dillman A, Rafferty IP, Troncoso J, et al. 2010. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6: e1000952.
-
(2010)
PLoS Genet
, vol.6
, pp. e1000952
-
-
Gibbs, J.R.1
van der Brug, M.P.2
Hernandez, D.G.3
Traynor, B.J.4
Nalls, M.A.5
Lai, S.L.6
Arepalli, S.7
Dillman, A.8
Rafferty, I.P.9
Troncoso, J.10
-
25
-
-
84878682420
-
The Genotype-Tissue Expression (GTEx) project
-
The GTEx Consortium
-
The GTEx Consortium. 2013. The Genotype-Tissue Expression (GTEx) project. Nat Genet 45: 580–585.
-
(2013)
Nat Genet
, vol.45
, pp. 580-585
-
-
-
26
-
-
84929001104
-
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
-
The GTEx Consortium
-
The GTEx Consortium. 2015. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348: 648–660.
-
(2015)
Science
, vol.348
, pp. 648-660
-
-
-
27
-
-
84879055641
-
Passive and active DNA methylation and the interplay with genetic variation in gene regulation
-
Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T, Romano L, Planchon A, et al. 2013. Passive and active DNA methylation and the interplay with genetic variation in gene regulation. eLife 2: e00523.
-
(2013)
eLife
, vol.2
, pp. e00523
-
-
Gutierrez-Arcelus, M.1
Lappalainen, T.2
Montgomery, S.B.3
Buil, A.4
Ongen, H.5
Yurovsky, A.6
Bryois, J.7
Giger, T.8
Romano, L.9
Planchon, A.10
-
28
-
-
84989849276
-
A synergistic DNA logic predicts genome-wide chromatin accessibility
-
Hashimoto T, Sherwood RI, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJ, Srinivasan S, Jaakkola T, Gifford DK, et al. 2016. A synergistic DNA logic predicts genome-wide chromatin accessibility. Genome Res 26: 1430–1440.
-
(2016)
Genome Res
, vol.26
, pp. 1430-1440
-
-
Hashimoto, T.1
Sherwood, R.I.2
Kang, D.D.3
Rajagopal, N.4
Barkal, A.A.5
Zeng, H.6
Emons, B.J.7
Srinivasan, S.8
Jaakkola, T.9
Gifford, D.K.10
-
29
-
-
84872540994
-
DNA-binding specificities of human transcription factors
-
Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, et al. 2013. DNA-binding specificities of human transcription factors. Cell 152: 327–339.
-
(2013)
Cell
, vol.152
, pp. 327-339
-
-
Jolma, A.1
Yan, J.2
Whitington, T.3
Toivonen, J.4
Nitta, K.R.5
Rastas, P.6
Morgunova, E.7
Enge, M.8
Taipale, M.9
Wei, G.10
-
30
-
-
84976908652
-
Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks
-
Kelley DR, Snoek J, Rinn JL. 2016. Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res 26: 990–999.
-
(2016)
Genome Res
, vol.26
, pp. 990-999
-
-
Kelley, D.R.1
Snoek, J.2
Rinn, J.L.3
-
31
-
-
84887320563
-
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription
-
Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, et al. 2013. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342: 744–747.
-
(2013)
Science
, vol.342
, pp. 744-747
-
-
Kilpinen, H.1
Waszak, S.M.2
Gschwind, A.R.3
Raghav, S.K.4
Witwicki, R.M.5
Orioli, A.6
Migliavacca, E.7
Wiederkehr, M.8
Gutierrez-Arcelus, M.9
Panousis, N.I.10
-
32
-
-
85020793872
-
Common genetic variation drives molecular heterogeneity in human iPSCs
-
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, et al. 2017. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 546: 370–375.
-
(2017)
Nature
, vol.546
, pp. 370-375
-
-
Kilpinen, H.1
Goncalves, A.2
Leha, A.3
Afzal, V.4
Alasoo, K.5
Ashford, S.6
Bala, S.7
Bensaddek, D.8
Casale, F.P.9
Culley, O.J.10
-
33
-
-
77954100084
-
Transposable elements have rewired the core regulatory network of human embryonic stem cells
-
Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng HH, Bourque G. 2010. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42: 631–634.
-
(2010)
Nat Genet
, vol.42
, pp. 631-634
-
-
Kunarso, G.1
Chia, N.Y.2
Jeyakani, J.3
Hwang, C.4
Lu, X.5
Chan, Y.S.6
Ng, H.H.7
Bourque, G.8
-
34
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
35
-
-
84885645853
-
Transcriptome and genome sequencing uncovers functional variation in humans
-
’t
-
Lappalainen T, Sammeth M, Friedlander MR,’t Hoen PA, Monlong J, Rivas MA, Gonzalez-Porta M, Kurbatova N, Griebel T, Ferreira PG, et al. 2013. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501: 506–511.
-
(2013)
Nature
, vol.501
, pp. 506-511
-
-
Lappalainen, T.1
Sammeth, M.2
Friedlander, M.R.3
Hoen, P.A.4
Monlong, J.5
Rivas, M.A.6
Gonzalez-Porta, M.7
Kurbatova, N.8
Griebel, T.9
Ferreira, P.G.10
-
36
-
-
84968732934
-
RNA splicing is a primary link between genetic variation and disease
-
Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK. 2016. RNA splicing is a primary link between genetic variation and disease. Science 352: 600–604.
-
(2016)
Science
, vol.352
, pp. 600-604
-
-
Li, Y.I.1
van de Geijn, B.2
Raj, A.3
Knowles, D.A.4
Petti, A.A.5
Golan, D.6
Gilad, Y.7
Pritchard, J.K.8
-
37
-
-
84872016692
-
Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions
-
Lian X, Zhang J, Azarin SM, Zhu K, Hazeltine LB, Bao X, Hsiao C, Kamp TJ, Palecek SP. 2013. Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions. Nat Protoc 8: 162–175.
-
(2013)
Nat Protoc
, vol.8
, pp. 162-175
-
-
Lian, X.1
Zhang, J.2
Azarin, S.M.3
Zhu, K.4
Hazeltine, L.B.5
Bao, X.6
Hsiao, C.7
Kamp, T.J.8
Palecek, S.P.9
-
38
-
-
84876526111
-
Drug screening using a library of human induced pluripotent stem cell–derived cardiomyocytes reveals disease-specific patterns of cardiotoxicity
-
Liang P, Lan F, Lee AS, Gong T, Sanchez-Freire V, Wang Y, Diecke S, Sallam K, Knowles JW, Wang PJ, et al. 2013. Drug screening using a library of human induced pluripotent stem cell–derived cardiomyocytes reveals disease-specific patterns of cardiotoxicity. Circulation 127: 1677–1691.
-
(2013)
Circulation
, vol.127
, pp. 1677-1691
-
-
Liang, P.1
Lan, F.2
Lee, A.S.3
Gong, T.4
Sanchez-Freire, V.5
Wang, Y.6
Diecke, S.7
Sallam, K.8
Knowles, J.W.9
Wang, P.J.10
-
39
-
-
84878580738
-
The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote
-
Liao Y, Smyth GK, Shi W. 2013. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 41: e108.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. e108
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
40
-
-
84929510967
-
Machine learning applications in genetics and genomics
-
Libbrecht MW, Noble WS. 2015. Machine learning applications in genetics and genomics. Nat Rev Genet 16: 321–332.
-
(2015)
Nat Rev Genet
, vol.16
, pp. 321-332
-
-
Libbrecht, M.W.1
Noble, W.S.2
-
41
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, et al. 2006. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34: D108–D110.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D108-D110
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
-
42
-
-
84949091882
-
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo
-
Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA. 2015. Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Nat Genet 47: 1393–1401.
-
(2015)
Nat Genet
, vol.47
, pp. 1393-1401
-
-
Maurano, M.T.1
Haugen, E.2
Sandstrom, R.3
Vierstra, J.4
Shafer, A.5
Kaul, R.6
Stamatoyannopoulos, J.A.7
-
43
-
-
84890109489
-
Human iPSC-based modeling of late-onset disease via progerin-induced aging
-
Miller JD, Ganat YM, Kishinevsky S, Bowman RL, Liu B, Tu EY, Mandal PK, Vera E, Shim JW, Kriks S, et al. 2013. Human iPSC-based modeling of late-onset disease via progerin-induced aging. Cell Stem Cell 13: 691–705.
-
(2013)
Cell Stem Cell
, vol.13
, pp. 691-705
-
-
Miller, J.D.1
Ganat, Y.M.2
Kishinevsky, S.3
Bowman, R.L.4
Liu, B.5
Tu, E.Y.6
Mandal, P.K.7
Vera, E.8
Shim, J.W.9
Kriks, S.10
-
44
-
-
79953267538
-
A bioinfor-matic assay for pluripotency in human cells
-
Muller FJ, Schuldt BM, Williams R, Mason D, Altun G, Papapetrou EP, Danner S, Goldmann JE, Herbst A, Schmidt NO, et al. 2011. A bioinfor-matic assay for pluripotency in human cells. Nat Methods 8: 315–317.
-
(2011)
Nat Methods
, vol.8
, pp. 315-317
-
-
Muller, F.J.1
Schuldt, B.M.2
Williams, R.3
Mason, D.4
Altun, G.5
Papapetrou, E.P.6
Danner, S.7
Goldmann, J.E.8
Herbst, A.9
Schmidt, N.O.10
-
45
-
-
79955634826
-
A more efficient method to generate integration-free human iPS cells
-
Okita K, Matsumura Y, Sato Y, Okada A, Morizane A, Okamoto S, Hong H, Nakagawa M, Tanabe K, Tezuka K, et al. 2011. A more efficient method to generate integration-free human iPS cells. Nat Methods 8: 409–412.
-
(2011)
Nat Methods
, vol.8
, pp. 409-412
-
-
Okita, K.1
Matsumura, Y.2
Sato, Y.3
Okada, A.4
Morizane, A.5
Okamoto, S.6
Hong, H.7
Nakagawa, M.8
Tanabe, K.9
Tezuka, K.10
-
46
-
-
84969945169
-
Fast and efficient QTL mapper for thousands of molecular phenotypes
-
Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O. 2016. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics 32: 1479–1485.
-
(2016)
Bioinformatics
, vol.32
, pp. 1479-1485
-
-
Ongen, H.1
Buil, A.2
Brown, A.A.3
Dermitzakis, E.T.4
Delaneau, O.5
-
47
-
-
84910673362
-
Generation of functional human pancreatic β cells in vitro
-
Pagliuca FW, Millman JR, Gurtler M, Segel M, Van Dervort A, Ryu JH, Peterson QP, Greiner D, Melton DA. 2014. Generation of functional human pancreatic β cells in vitro. Cell 159: 428–439.
-
(2014)
Cell
, vol.159
, pp. 428-439
-
-
Pagliuca, F.W.1
Millman, J.R.2
Gurtler, M.3
Segel, M.4
Van Dervort, A.5
Ryu, J.H.6
Peterson, Q.P.7
Greiner, D.8
Melton, D.A.9
-
48
-
-
85017182988
-
Large, diverse population cohorts of hiPSCs and derived hepatocyte-like cells reveal functional genetic variation at blood lipid-associated loci
-
Pashos EE, Park Y, Wang X, Raghavan A, Yang W, Abbey D, Peters DT, Arbelaez J, Hernandez M, Kuperwasser N, et al. 2017. Large, diverse population cohorts of hiPSCs and derived hepatocyte-like cells reveal functional genetic variation at blood lipid-associated loci. Cell Stem Cell 20: 558–570.
-
(2017)
Cell Stem Cell
, vol.20
, pp. 558-570
-
-
Pashos, E.E.1
Park, Y.2
Wang, X.3
Raghavan, A.4
Yang, W.5
Abbey, D.6
Peters, D.T.7
Arbelaez, J.8
Hernandez, M.9
Kuperwasser, N.10
-
49
-
-
84903452732
-
Genetic background drives transcriptional variation in human induced pluripotent stem cells
-
Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L, Gaffney D. 2014. Genetic background drives transcriptional variation in human induced pluripotent stem cells. PLoS Genet 10: e1004432.
-
(2014)
PLoS Genet
, vol.10
, pp. e1004432
-
-
Rouhani, F.1
Kumasaka, N.2
De Brito, M.C.3
Bradley, A.4
Vallier, L.5
Gaffney, D.6
-
51
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci 100: 9440–9445.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
52
-
-
33747195353
-
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
-
Takahashi K, Yamanaka S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663–676.
-
(2006)
Cell
, vol.126
, pp. 663-676
-
-
Takahashi, K.1
Yamanaka, S.2
-
53
-
-
36248966518
-
Induction of pluripotent stem cells from adult human fibroblasts by defined factors
-
Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S. 2007. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131: 861–872.
-
(2007)
Cell
, vol.131
, pp. 861-872
-
-
Takahashi, K.1
Tanabe, K.2
Ohnuki, M.3
Narita, M.4
Ichisaka, T.5
Tomoda, K.6
Yamanaka, S.7
-
54
-
-
84930810293
-
Reprogramming LCLs to iPSCs results in recovery of donor-specific gene expression signature
-
Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. 2015. Reprogramming LCLs to iPSCs results in recovery of donor-specific gene expression signature. PLoS Genet 11: e1005216.
-
(2015)
PLoS Genet
, vol.11
, pp. e1005216
-
-
Thomas, S.M.1
Kagan, C.2
Pavlovic, B.J.3
Burnett, J.4
Patterson, K.5
Pritchard, J.K.6
Gilad, Y.7
-
55
-
-
84946481204
-
WASP: Allele-specific software for robust molecular quantitative trait locus discovery
-
van de Geijn B, McVicker G, Gilad Y, Pritchard JK. 2015. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods 12: 1061–1063.
-
(2015)
Nat Methods
, vol.12
, pp. 1061-1063
-
-
van de Geijn, B.1
McVicker, G.2
Gilad, Y.3
Pritchard, J.K.4
-
56
-
-
0001579865
-
Canalization of development and genetic assimilation of acquired characters
-
Waddington CH. 1959. Canalization of development and genetic assimilation of acquired characters. Nature 183: 1654–1655.
-
(1959)
Nature
, vol.183
, pp. 1654-1655
-
-
Waddington, C.H.1
-
57
-
-
81255169342
-
Modeling familial Alzheimer’s disease with induced pluripotent stem cells
-
Yagi T, Ito D, Okada Y, Akamatsu W, Nihei Y, Yoshizaki T, Yamanaka S, Okano H, Suzuki N. 2011. Modeling familial Alzheimer’s disease with induced pluripotent stem cells. Hum Mol Genet 20: 4530–4539.
-
(2011)
Hum Mol Genet
, vol.20
, pp. 4530-4539
-
-
Yagi, T.1
Ito, D.2
Okada, Y.3
Akamatsu, W.4
Nihei, Y.5
Yoshizaki, T.6
Yamanaka, S.7
Okano, H.8
Suzuki, N.9
-
58
-
-
36749043230
-
Induced pluripotent stem cell lines derived from human somatic cells
-
Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, et al. 2007. Induced pluripotent stem cell lines derived from human somatic cells. Science 318: 1917–1920.
-
(2007)
Science
, vol.318
, pp. 1917-1920
-
-
Yu, J.1
Vodyanik, M.A.2
Smuga-Otto, K.3
Antosiewicz-Bourget, J.4
Frane, J.L.5
Tian, S.6
Nie, J.7
Jonsdottir, G.A.8
Ruotti, V.9
Stewart, R.10
-
60
-
-
84976520648
-
Convolutional neural network architectures for predicting DNA-protein binding
-
Zeng H, Edwards MD, Liu G, Gifford DK. 2016. Convolutional neural network architectures for predicting DNA-protein binding. Bioinformatics 32: i121–i127.
-
(2016)
Bioinformatics
, vol.32
, pp. i121-i127
-
-
Zeng, H.1
Edwards, M.D.2
Liu, G.3
Gifford, D.K.4
-
61
-
-
53849146020
-
Model-based Analysis of ChIP-Seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
-
(2008)
Genome Biol
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
-
62
-
-
84958257565
-
Predicting effects of noncoding variants with deep learning-based sequence model
-
Zhou J, Troyanskaya OG. 2015. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods 12: 931–934.
-
(2015)
Nat Methods
, vol.12
, pp. 931-934
-
-
Zhou, J.1
Troyanskaya, O.G.2
|