-
1
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
Alexa A, Rahnenführer J, Lengauer T. 2006. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22:1600-1607. doi: 10.1093/bioinformatics/btl140.
-
(2006)
Bioinformatics
, vol.22
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenführer, J.2
Lengauer, T.3
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
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. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25: 25-29. doi: 10.1038/75556.
-
(2000)
Nature Genetics
, 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..
-
3
-
-
80053375853
-
Induced pluripotent stem cells from highly endangered species
-
Ben-Nun IF, Montague SC, Houck ML, Tran HT, Garitaonandia I, Leonardo TR, Wang YC, Charter SJ, Laurent LC, Ryder OA, Loring JF. 2011. Induced pluripotent stem cells from highly endangered species. Nature Methods 8: 829-831. doi: 10.1038/nmeth.1706.
-
(2011)
Nature Methods
, vol.8
, pp. 829-831
-
-
Ben-Nun, I.F.1
Montague, S.C.2
Houck, M.L.3
Tran, H.T.4
Garitaonandia, I.5
Leonardo, T.R.6
Wang, Y.C.7
Charter, S.J.8
Laurent, L.C.9
Ryder, O.A.10
Loring, J.F.11
-
4
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to Multiple Testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to Multiple Testing. Journal of the Royal Statistical Society B 57:289-300.
-
(1995)
Journal of the Royal Statistical Society B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315-326. doi: 10.1016/j.cell.2006.02.041.
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
Mikkelsen, T.S.2
Xie, X.3
Kamal, M.4
Huebert, D.J.5
Cuff, J.6
Fry, B.7
Meissner, A.8
Wernig, M.9
Plath, K.10
Jaenisch, R.11
Wagschal, A.12
Feil, R.13
Schreiber, S.L.14
Lander, E.S.15
-
6
-
-
85042579925
-
A database of orthologous exons in primates for comparative analysis of RNA-seq data
-
Blekhman R. 2012. A database of orthologous exons in primates for comparative analysis of RNA-seq data. Nature Precedings.
-
(2012)
Nature Precedings
-
-
Blekhman, R.1
-
7
-
-
75649102520
-
Sex-specific and lineage-specific alternative splicing in primates
-
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. 2010. Sex-specific and lineage-specific alternative splicing in primates. Genome Research 20:180-189. doi: 10.1101/gr.099226.109.
-
(2010)
Genome Research
, vol.20
, pp. 180-189
-
-
Blekhman, R.1
Marioni, J.C.2
Zumbo, P.3
Stephens, M.4
Gilad, Y.5
-
8
-
-
57149084867
-
Gene regulation in primates evolves under tissuespecific selection pressures
-
Blekhman R, Oshlack A, Chabot AE, Smyth GK, Gilad Y. 2008. Gene regulation in primates evolves under tissuespecific selection pressures. PLOS Genetics 4:e1000271. doi: 10.1371/journal.pgen.1000271.
-
(2008)
PLOS Genetics
, vol.4
-
-
Blekhman, R.1
Oshlack, A.2
Chabot, A.E.3
Smyth, G.K.4
Gilad, Y.5
-
9
-
-
79551677421
-
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines
-
Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A. 2011. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 144:439-452. doi: 10.1016/j.cell.2010.12.032.
-
(2011)
Cell
, vol.144
, pp. 439-452
-
-
Bock, C.1
Kiskinis, E.2
Verstappen, G.3
Gu, H.4
Boulting, G.5
Smith, Z.D.6
Ziller, M.7
Croft, G.F.8
Amoroso, M.W.9
Oakley, D.H.10
Gnirke, A.11
Eggan, K.12
Meissner, A.13
-
10
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348. doi: 10.1038/nature10532.
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
Soumillon, M.2
Necsulea, A.3
Julien, P.4
Csárdi, G.5
Harrigan, P.6
Weier, M.7
Liechti, A.8
Aximu-Petri, A.9
Kircher, M.10
Albert, F.W.11
Zeller, U.12
Khaitovich, P.13
Grützner, F.14
Bergmann, S.15
Nielsen, R.16
Pääbo, S.17
Kaessmann, H.18
-
11
-
-
0015070886
-
Repetitive and non-repetitive DNA sequences and a specualation on the origins of evolutionary novelty
-
Britten RJ, Davidson EH. 1971. Repetitive and non-repetitive DNA sequences and a specualation on the origins of evolutionary novelty. The Quarterly Review of Biology 46:111-138. doi: 10.1086/406830.
-
(1971)
The Quarterly Review of Biology
, vol.46
, pp. 111-138
-
-
Britten, R.J.1
Davidson, E.H.2
-
12
-
-
0037993881
-
Stem cells. Setting standards for human embryonic stem cells
-
Brivanlou AH, Gage FH, Jaenisch R, Jessell T, Melton D, Rossant J. 2003. Stem cells. Setting standards for human embryonic stem cells. Science 300:913-916. doi: 10.1126/science.1082940.
-
(2003)
Science
, vol.300
, pp. 913-916
-
-
Brivanlou, A.H.1
Gage, F.H.2
Jaenisch, R.3
Jessell, T.4
Melton, D.5
Rossant, J.6
-
13
-
-
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, Plews JR, Abilez OJ, Cui B, Gold JD, Wu JC. 2014. Chemically defined generation of human cardiomyocytes. Nature Methods 11:855-860. doi: 10.1038/nmeth.2999.
-
(2014)
Nature 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
Plews, J.R.11
Abilez, O.J.12
Cui, B.13
Gold, J.D.14
Wu, J.C.15
-
14
-
-
79955403252
-
Gene expression differences among primates are associated with changes in a histone epigenetic modification
-
Cain CE, Blekhman R, Marioni JC, Gilad Y. 2011. Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics 187:1225-1234. doi: 10.1534/genetics.110.126177.
-
(2011)
Genetics
, vol.187
, pp. 1225-1234
-
-
Cain, C.E.1
Blekhman, R.2
Marioni, J.C.3
Gilad, Y.4
-
15
-
-
22744439568
-
Evolution at two levels: On genes and form
-
Carroll SB. 2005. Evolution at two levels: on genes and form. PLOS Biology 3:e245. doi: 10.1371/journal.pbio.0030245.
-
(2005)
PLOS Biology
, vol.3
-
-
Carroll, S.B.1
-
16
-
-
46149104377
-
Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution
-
Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25-36. doi: 10.1016/j.cell.2008.06.030.
-
(2008)
Cell
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
17
-
-
77957916358
-
Reprogramming huntington monkey skin cells into pluripotent stem cells
-
Chan AWS, Cheng PH, Neumann A, Yang JJ. 2010. Reprogramming huntington monkey skin cells into pluripotent stem cells. Cellular Reprogramming 12:509-517. doi: 10.1089/cell.2010.0019.
-
(2010)
Cellular Reprogramming
, vol.12
, pp. 509-517
-
-
Chan, A.1
Cheng, P.H.2
Neumann, A.3
Yang, J.J.4
-
18
-
-
79955611823
-
Chemically defined conditions for human iPSC derivation and culture
-
Chen G, Gulbranson DR, Hou Z, Bolin JM, Ruotti V, Probasco MD, Smuga-Otto K, Howden SE, Diol NR, Propson NE, Wagner R, Lee GO, Antosiewicz-Bourget J, Teng JM, Thomson JA. 2011. Chemically defined conditions for human iPSC derivation and culture. Nature Methods 8:424-429. doi: 10.1038/nmeth.1593.
-
(2011)
Nature Methods
, vol.8
, pp. 424-429
-
-
Chen, G.1
Gulbranson, D.R.2
Hou, Z.3
Bolin, J.M.4
Ruotti, V.5
Probasco, M.D.6
Smuga-Otto, K.7
Howden, S.E.8
Diol, N.R.9
Propson, N.E.10
Wagner, R.11
Lee, G.O.12
Antosiewicz-Bourget, J.13
Teng, J.M.14
Thomson, J.A.15
-
19
-
-
84865049791
-
Non-colony type monolayer culture of human embryonic stem cells
-
Chen KG, Mallon BS, Hamilton RS, Kozhich OA, Park K, Hoeppner DJ, Robey PG, McKay RD. 2012. Non-colony type monolayer culture of human embryonic stem cells. Stem Cell Research 9:237-248. doi: 10.1016/j.scr.2012.06.003.
-
(2012)
Stem Cell Research
, vol.9
, pp. 237-248
-
-
Chen, K.G.1
Mallon, B.S.2
Hamilton, R.S.3
Kozhich, O.A.4
Park, K.5
Hoeppner, D.J.6
Robey, P.G.7
McKay, R.D.8
-
20
-
-
84859527233
-
Self-renewing endodermal progenitor lines generated from human pluripotent stem cells
-
Cheng X, Ying L, Lu L, Galvão AM, Mills JA, Lin HC, Kotton DN, Shen SS, Nostro MC, Choi JK, Weiss MJ, French DL, Gadue P. 2012. Self-renewing endodermal progenitor lines generated from human pluripotent stem cells. Cell Stem Cell 10:371-384. doi: 10.1016/j.stem.2012.02.024.
-
(2012)
Cell Stem Cell
, vol.10
, pp. 371-384
-
-
Cheng, X.1
Ying, L.2
Lu, L.3
Galvão, A.M.4
Mills, J.A.5
Lin, H.C.6
Kotton, D.N.7
Shen, S.S.8
Nostro, M.C.9
Choi, J.K.10
Weiss, M.J.11
French, D.L.12
Gadue, P.13
-
21
-
-
79952900560
-
Turning straw into gold: Directing cell fate for regenerative medicine. Nature Reviews
-
Cohen DE, Melton D. 2011. Turning straw into gold: directing cell fate for regenerative medicine. Nature Reviews. Genetics 12:243-252. doi: 10.1038/nrg2938.
-
(2011)
Genetics
, vol.12
, pp. 243-252
-
-
Cohen, D.E.1
Melton, D.2
-
22
-
-
84879911829
-
The evolution of lineage-specific regulatory activities in the human embryonic limb
-
Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. 2013. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154:185-196. doi: 10.1016/j.cell.2013.05.056.
-
(2013)
Cell
, vol.154
, pp. 185-196
-
-
Cotney, J.1
Leng, J.2
Yin, J.3
Reilly, S.K.4
Demare, L.E.5
Emera, D.6
Ayoub, A.E.7
Rakic, P.8
Noonan, J.P.9
-
23
-
-
79960083404
-
Development of histocompatible primate-induced pluripotent stem cells for neural transplantation
-
Deleidi M, Hargus G, Hallett P, Osborn T, Isacson O. 2011. Development of histocompatible primate-induced pluripotent stem cells for neural transplantation. Stem cells 29:1052-1063. doi: 10.1002/stem.662.
-
(2011)
Stem Cells
, vol.29
, pp. 1052-1063
-
-
Deleidi, M.1
Hargus, G.2
Hallett, P.3
Osborn, T.4
Isacson, O.5
-
24
-
-
46249088370
-
Lumi: A pipeline for processing Illumina microarray
-
Du P, Kibbe WA, Lin SM. 2008. Lumi: a pipeline for processing Illumina microarray. Bioinformatics 24:1547-1548. doi: 10.1093/bioinformatics/btn224.
-
(2008)
Bioinformatics
, vol.24
, pp. 1547-1548
-
-
Du, P.1
Kibbe, W.A.2
Lin, S.M.3
-
25
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797. doi: 10.1093/nar/gkh340.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
26
-
-
65849256049
-
A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice
-
Enard W, Gehre S, Hammerschmidt K, Hölter SM, Blass T, Somel M, Brückner MK, Schreiweis C, Winter C, Sohr R, Becker L, Wiebe V, Nickel B, Giger T, Müller U, Groszer M, Adler T, Aguilar A, Bolle I, Calzada-Wack J, Dalke C, Ehrhardt N, Favor J, Fuchs H, Gailus-Durner V, Hans W, Hölzlwimmer G, Javaheri A, Kalaydjiev S, Kallnik M, Kling E, Kunder S, Mossbrugger I, Naton B, Racz I, Rathkolb B, Rozman J, Schrewe A, Busch DH, Graw J, Ivandic B, Klingenspor M, Klopstock T, Ollert M, Quintanilla-Martinez L, Schulz H, Wolf E, Wurst W, Zimmer A, Fisher SE, Morgenstern R, Arendt T, de Angelis MH, Fischer J, Schwarz J, Pääbo S. 2009. A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell 137:961-971. doi: 10.1016/j.cell.2009.03.041.
-
(2009)
Cell
, vol.137
, pp. 961-971
-
-
Enard, W.1
Gehre, S.2
Hammerschmidt, K.3
Hölter, S.M.4
Blass, T.5
Somel, M.6
Brückner, M.K.7
Schreiweis, C.8
Winter, C.9
Sohr, R.10
Becker, L.11
Wiebe, V.12
Nickel, B.13
Giger, T.14
Müller, U.15
Groszer, M.16
Adler, T.17
Aguilar, A.18
Bolle, I.19
Calzada-Wack, J.20
Dalke, C.21
Ehrhardt, N.22
Favor, J.23
Fuchs, H.24
Gailus-Durner, V.25
Hans, W.26
Hölzlwimmer, G.27
Javaheri, A.28
Kalaydjiev, S.29
Kallnik, M.30
Kling, E.31
Kunder, S.32
Mossbrugger, I.33
Naton, B.34
Racz, I.35
Rathkolb, B.36
Rozman, J.37
Schrewe, A.38
Busch, D.H.39
Graw, J.40
Ivandic, B.41
Klingenspor, M.42
Klopstock, T.43
Ollert, M.44
Quintanilla-Martinez, L.45
Schulz, H.46
Wolf, E.47
Wurst, W.48
Zimmer, A.49
Fisher, S.E.50
Morgenstern, R.51
Arendt, T.52
De Angelis, M.H.53
Fischer, J.54
Schwarz, J.55
Pääbo, S.56
more..
-
27
-
-
67650485688
-
Derivation of induced pluripotent stem cells from pig somatic cells
-
Ezashi T, Telugu BP, Alexenko AP, Sachdev S, Sinha S, Roberts RM. 2009. Derivation of induced pluripotent stem cells from pig somatic cells. Proceedings of the National Academy of Sciences of USA 106:10993-10998. doi: 10.1073/pnas.0905284106.
-
(2009)
Proceedings of the National Academy of Sciences of USA
, vol.106
, pp. 10993-10998
-
-
Ezashi, T.1
Telugu, B.P.2
Alexenko, A.P.3
Sachdev, S.4
Sinha, S.5
Roberts, R.M.6
-
28
-
-
84863885448
-
Comparative studies of gene expression and the evolution of gene regulation
-
Gallego Romero I, Ruvinsky I, Gilad Y. 2012. Comparative studies of gene expression and the evolution of gene regulation. Nature Reviews Genetics 13:505-516. doi: 10.1038/nrg3229.
-
(2012)
Nature Reviews Genetics
, vol.13
, pp. 505-516
-
-
Gallego Romero, I.1
Ruvinsky, I.2
Gilad, Y.3
-
29
-
-
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 Biology 5:R80. doi: 10.1186/gb-2004-5-10-r80.
-
(2004)
Genome Biology
, 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..
-
30
-
-
19844365733
-
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
-
Gilad Y, Rifkin Sa, Bertone P, Gerstein M, White KP. 2005. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Research 15:674-680. doi: 10.1101/gr.3335705.
-
(2005)
Genome Research
, vol.15
, pp. 674-680
-
-
Gilad, Y.1
Sa, R.2
Bertone, P.3
Gerstein, M.4
White, K.P.5
-
31
-
-
84884678913
-
Dynamics of DNA methylation in recent human and great ape evolution
-
Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, Navarro A, Esteller M, Sharp AJ, Marques-Bonet T. 2013. Dynamics of DNA methylation in recent human and great ape evolution. PLOS Genetics 9:e1003763. doi: 10.1371/journal.pgen.1003763.
-
(2013)
PLOS Genetics
, vol.9
-
-
Hernando-Herraez, I.1
Prado-Martinez, J.2
Garg, P.3
Fernandez-Callejo, M.4
Heyn, H.5
Hvilsom, C.6
Navarro, A.7
Esteller, M.8
Sharp, A.J.9
Marques-Bonet, T.10
-
32
-
-
84901272219
-
Path to the clinic: Assessment of iPSC-based cell therapies in vivo in a nonhuman primate model
-
Hong SG, Winkler T, Wu C, Guo V, Pittaluga S, Nicolae A, Donahue RE, Metzger ME, Price SD, Uchida N, Kuznetsov SA, Kilts T, Li L, Robey PG, Dunbar CE. 2014. Path to the clinic: assessment of iPSC-based cell therapies in vivo in a nonhuman primate model. Cell Reports 7:1298-1309. doi: 10.1016/j.celrep.2014.04.019.
-
(2014)
Cell Reports
, vol.7
, pp. 1298-1309
-
-
Hong, S.G.1
Winkler, T.2
Wu, C.3
Guo, V.4
Pittaluga, S.5
Nicolae, A.6
Donahue, R.E.7
Metzger, M.E.8
Price, S.D.9
Uchida, N.10
Kuznetsov, S.A.11
Kilts, T.12
Li, L.13
Robey, P.G.14
Dunbar, C.E.15
-
33
-
-
33750598248
-
Chromatin-binding regions of EBNA1 protein facilitate the enhanced transfection of Epstein-Barr virus-based vectors
-
Howden SE, Wardan H, Voullaire L, McLenachan S, Williamson R, Ioannou P, Vadolas J. 2006. Chromatin-binding regions of EBNA1 protein facilitate the enhanced transfection of Epstein-Barr virus-based vectors. Human Gene Therapy 17:833-844. doi: 10.1089/hum.2006.17.833.
-
(2006)
Human Gene Therapy
, vol.17
, pp. 833-844
-
-
Howden, S.E.1
Wardan, H.2
Voullaire, L.3
McLenachan, S.4
Williamson, R.5
Ioannou, P.6
Vadolas, J.7
-
34
-
-
84856956771
-
Probing sporadic and familial Alzheimer’s disease using induced pluripotent stem cells
-
Israel MA, Yuan SH, Bardy C, Reyna SM, Mu Y, Herrera C, Hefferan MP, Van Gorp S, Nazor KL, Boscolo FS, Carson CT, Laurent LC, Marsala M, Gage FH, Remes AM, Koo EH, Goldstein LS. 2012. Probing sporadic and familial Alzheimer’s disease using induced pluripotent stem cells. Nature 482:216-220. doi: 10.1038/nature10821.
-
(2012)
Nature
, vol.482
, pp. 216-220
-
-
Israel, M.A.1
Yuan, S.H.2
Bardy, C.3
Reyna, S.M.4
Mu, Y.5
Herrera, C.6
Hefferan, M.P.7
Van Gorp, S.8
Nazor, K.L.9
Boscolo, F.S.10
Carson, C.T.11
Laurent, L.C.12
Marsala, M.13
Gage, F.H.14
Remes, A.M.15
Koo, E.H.16
Goldstein, L.S.17
-
35
-
-
0017771466
-
Evolution and tinkering
-
Jacob F. 1977. Evolution and tinkering. Science 196:1161-1166. doi: 10.1126/science.860134.
-
(1977)
Science
, vol.196
, pp. 1161-1166
-
-
Jacob, F.1
-
36
-
-
39149130361
-
Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming
-
Jaenisch R, Young R. 2008. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132:567-582. doi: 10.1016/j.cell.2008.01.015.
-
(2008)
Cell
, vol.132
, pp. 567-582
-
-
Jaenisch, R.1
Young, R.2
-
37
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson A. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116. doi: 10.1126/science.1090005.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.2
-
38
-
-
0024382879
-
Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers
-
Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX, Wilson AC. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of USA 86:6196-6200. doi: 10.1073/pnas.86.16.6196.
-
(1989)
Proceedings of the National Academy of Sciences of USA
, vol.86
, pp. 6196-6200
-
-
Kocher, T.D.1
Thomas, W.K.2
Meyer, A.3
Edwards, S.V.4
Paabo, S.5
Villablanca, F.X.6
Wilson, A.C.7
-
39
-
-
84896735766
-
Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
-
Law CW, Chen Y, Shi W, Smyth GK. 2014. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 15:R29. doi: 10.1186/gb-2014-15-2-r29.
-
(2014)
Genome Biology
, vol.15
-
-
Law, C.W.1
Chen, Y.2
Shi, W.3
Smyth, G.K.4
-
40
-
-
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. doi: 10.1093/bioinformatics/btp324.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
41
-
-
84885912865
-
-
Database, bat057
-
Li Q, Lian S, Dai Z, Xiang Q, Dai X. 2013. BGDB: a database of bivalent genes. Database 2013:bat057. doi: 10.1093/database/bat057.
-
(2013)
BGDB: A Database of Bivalent Genes
-
-
Li, Q.1
Lian, S.2
Dai, Z.3
Xiang, Q.4
Dai, X.5
-
42
-
-
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. Nature Protocols 8:162-175. doi: 10.1038/nprot.2012.150.
-
(2013)
Nature Protocols
, 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
-
43
-
-
84897397058
-
FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
-
Liao Y, Smyth GK, Shi W. 2013. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923-930. doi: 10.1093/bioinformatics/btt656.
-
(2013)
Bioinformatics
, vol.30
, pp. 923-930
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
44
-
-
56549121405
-
Generation of induced pluripotent stem cells from adult rhesus monkey fibroblasts
-
Liu H, Zhu F, Yong J, Zhang P, Hou P, Li H, Jiang W, Cai J, Liu M, Cui K, Qu X, Xiang T, Lu D, Chi X, Gao G, Ji W, Ding M, Deng H. 2008. Generation of induced pluripotent stem cells from adult rhesus monkey fibroblasts. Cell Stem Cell 3:587-590. doi: 10.1016/j.stem.2008.10.014.
-
(2008)
Cell Stem Cell
, vol.3
, pp. 587-590
-
-
Liu, H.1
Zhu, F.2
Yong, J.3
Zhang, P.4
Hou, P.5
Li, H.6
Jiang, W.7
Cai, J.8
Liu, M.9
Cui, K.10
Qu, X.11
Xiang, T.12
Lu, D.13
Chi, X.14
Gao, G.15
Ji, W.16
Ding, M.17
Deng, H.18
-
45
-
-
84865064735
-
Signaling defects in iPSC-derived fragile X premutation neurons
-
Liu J, Koscielska KA, Cao Z, Hulsizer S, Grace N, Mitchell G, Nacey C, Githinji J, McGee J, Garcia-Arocena D, Hagerman RJ, Nolta J, Pessah IN, Hagerman PJ. 2012. Signaling defects in iPSC-derived fragile X premutation neurons. Human Molecular Genetics 21:3795-3805. doi: 10.1093/hmg/dds207.
-
(2012)
Human Molecular Genetics
, vol.21
, pp. 3795-3805
-
-
Liu, J.1
Koscielska, K.A.2
Cao, Z.3
Hulsizer, S.4
Grace, N.5
Mitchell, G.6
Nacey, C.7
Githinji, J.8
McGee, J.9
Garcia-Arocena, D.10
Hagerman, R.J.11
Nolta, J.12
Pessah, I.N.13
Hagerman, P.J.14
-
46
-
-
84882245890
-
Genetic and epigenetic stability of human pluripotent stem cells. Nature Reviews
-
Lund RJ, Närvä E, Lahesmaa R. 2012. Genetic and epigenetic stability of human pluripotent stem cells. Nature Reviews. Genetics 13:732-744. doi: 10.1038/nrg3271.
-
(2012)
Genetics
, vol.13
, pp. 732-744
-
-
Lund, R.J.1
Närvä, E.2
Lahesmaa, R.3
-
47
-
-
84904214305
-
Abnormalities in human pluripotent cells due to reprogramming mechanisms
-
Ma H, Morey R, O’Neil RC, He Y, Daughtry B, Schultz MD, Hariharan M, Nery JR, Castanon R, Sabatini K, Thiagarajan RD, Tachibana M, Kang E, Tippner-Hedges R, Ahmed R, Gutierrez NM, Van Dyken C, Polat A, Sugawara A, Sparman M, Gokhale S, Amato P, Wolf DP, Ecker JR, Laurent LC, Mitalipov S. 2014. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511:177-183. doi: 10.1038/nature13551.
-
(2014)
Nature
, vol.511
, pp. 177-183
-
-
Ma, H.1
Morey, R.2
O’neil, R.C.3
He, Y.4
Daughtry, B.5
Schultz, M.D.6
Hariharan, M.7
Nery, J.R.8
Castanon, R.9
Sabatini, K.10
Thiagarajan, R.D.11
Tachibana, M.12
Kang, E.13
Tippner-Hedges, R.14
Ahmed, R.15
Gutierrez, N.M.16
Van Dyken, C.17
Polat, A.18
Sugawara, A.19
Sparman, M.20
Gokhale, S.21
Amato, P.22
Wolf, D.P.23
Ecker, J.R.24
Laurent, L.C.25
Mitalipov, S.26
more..
-
48
-
-
84901460449
-
Proposing a model for studying primate development using induced pluripotent stem cells
-
Gage FH, Christen Y, editors, Berlin, Heidelberg: Springer Berlin Heidelberg
-
Marchetto MC, Muotri AR, Gage FH. 2013a. Proposing a model for studying primate development using induced pluripotent stem cells. In: Gage FH, Christen Y, editors. Programmed cells from basic neuroscience to therapy. Berlin, Heidelberg: Springer Berlin Heidelberg. p. 31-39.
-
(2013)
Programmed Cells from Basic Neuroscience to Therapy
, pp. 31-39
-
-
Marchetto, M.C.1
Muotri, A.R.2
Gage, F.H.3
-
49
-
-
84888642291
-
Differential L1 regulation in pluripotent stem cells of humans and apes
-
Marchetto MC, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola AC, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, Gage FH. 2013b. Differential L1 regulation in pluripotent stem cells of humans and apes. Nature 503:525-529. doi: 10.1038/nature12686.
-
(2013)
Nature
, vol.503
, pp. 525-529
-
-
Marchetto, M.C.1
Narvaiza, I.2
Denli, A.M.3
Benner, C.4
Lazzarini, T.A.5
Nathanson, J.L.6
Paquola, A.C.7
Desai, K.N.8
Herai, R.H.9
Weitzman, M.D.10
Yeo, G.W.11
Muotri, A.R.12
Gage, F.H.13
-
50
-
-
44049089423
-
Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells
-
Masui S, Ohtsuka S, Yagi R, Takahashi K, Ko MS, Niwa H. 2008. Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells. BMC Developmental Biology 8:45. doi: 10.1186/1471-213X-8-45.
-
(2008)
BMC Developmental Biology
, vol.8
-
-
Masui, S.1
Ohtsuka, S.2
Yagi, R.3
Takahashi, K.4
Ko, M.S.5
Niwa, H.6
-
51
-
-
79952386187
-
Human-specific loss of regulatory DNA and the evolution of human-specific traits
-
McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM. 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471:216-219. doi: 10.1038/nature09774.
-
(2011)
Nature
, vol.471
, pp. 216-219
-
-
McLean, C.Y.1
Reno, P.L.2
Pollen, A.A.3
Bassan, A.I.4
Capellini, T.D.5
Guenther, C.6
Indjeian, V.B.7
Lim, X.8
Menke, D.B.9
Schaar, B.T.10
Wenger, A.M.11
Bejerano, G.12
Kingsley, D.M.13
-
52
-
-
45849151146
-
Protocols for cytogenetic studies of human embryonic stem cells
-
Meisner LF, Johnson JA. 2008. Protocols for cytogenetic studies of human embryonic stem cells. Methods 45: 133-141. doi: 10.1016/j.ymeth.2008.03.005.
-
(2008)
Methods
, vol.45
, pp. 133-141
-
-
Meisner, L.F.1
Johnson, J.A.2
-
53
-
-
84878852415
-
Modeling human disease with pluripotent stem cells: From genome association to function
-
Merkle FT, Eggan K. 2013. Modeling human disease with pluripotent stem cells: from genome association to function. Cell Stem Cell 12:656-668. doi: 10.1016/j.stem.2013.05.016.
-
(2013)
Cell Stem Cell
, vol.12
, pp. 656-668
-
-
Merkle, F.T.1
Eggan, K.2
-
54
-
-
79953267538
-
A bioinformatic assay for pluripotency in human cells
-
Müller FJ, Schuldt BM, Williams R, Mason D, Altun G, Papapetrou EP, Danner S, Goldmann JE, Herbst A, Schmidt NO, Aldenhoff JB, Laurent LC, Loring JF. 2011. A bioinformatic assay for pluripotency in human cells. Nature Methods 8:315-317. doi: 10.1038/nmeth.1580.
-
(2011)
Nature Methods
, vol.8
, pp. 315-317
-
-
Müller, 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
Aldenhoff, J.B.11
Laurent, L.C.12
Loring, J.F.13
-
55
-
-
79960290466
-
Induced pluripotent stem cell lines derived from equine fibroblasts
-
Nagy K, Sung HK, Zhang P, Laflamme S, Vincent P, Agha-Mohammadi S, Woltjen K, Monetti C, Michael IP, Smith LC, Nagy A. 2011. Induced pluripotent stem cell lines derived from equine fibroblasts. Stem Cell Reviews 7: 693-702. doi: 10.1007/s12015-011-9239-5.
-
(2011)
Stem Cell Reviews
, vol.7
, pp. 693-702
-
-
Nagy, K.1
Sung, H.K.2
Zhang, P.3
Laflamme, S.4
Vincent, P.5
Agha-Mohammadi, S.6
Woltjen, K.7
Monetti, C.8
Michael, I.P.9
Smith, L.C.10
Nagy, A.11
-
56
-
-
84860643156
-
Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives
-
Nazor KL, Altun G, Lynch C, Tran H, Harness JV, Slavin I, Garitaonandia I, Mu¨ ller FJ, Wang YC, Boscolo FS, Fakunle E, Dumevska B, Lee S, Park HS, Olee T, D’Lima DD, Semechkin R, Parast MM, Galat V, Laslett AL, Schmidt U, Keirstead HS, Loring JF, Laurent LC. 2012. Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives. Cell Stem Cell 10:620-634. doi: 10.1016/j.stem.2012.02.013.
-
(2012)
Cell Stem Cell
, vol.10
, pp. 620-634
-
-
Nazor, K.L.1
Altun, G.2
Lynch, C.3
Tran, H.4
Harness, J.V.5
Slavin, I.6
Garitaonandia, I.7
Ller, M.8
Fj, W.Y.9
Boscolo, F.S.10
Fakunle, E.11
Dumevska, B.12
Lee, S.13
Park, H.S.14
Olee, T.15
D’lima, D.D.16
Semechkin, R.17
Parast, M.M.18
Galat, V.19
Laslett, A.L.20
Schmidt, U.21
Keirstead, H.S.22
Loring, J.F.23
Laurent, L.C.24
more..
-
57
-
-
79955615662
-
The transcriptional and signalling networks of pluripotency
-
Ng HH, Surani MA. 2011. The transcriptional and signalling networks of pluripotency. Nature Cell Biology 13: 490-496. doi: 10.1038/ncb0511-490.
-
(2011)
Nature Cell Biology
, vol.13
, pp. 490-496
-
-
Ng, H.H.1
Surani, M.A.2
-
58
-
-
84855387733
-
Induction of retinal pigment epithelial cells from monkey iPS cells
-
Okamoto S, Takahashi M. 2011. Induction of retinal pigment epithelial cells from monkey iPS cells. Investigative Ophthalmology & Visual Science 52:8785-8790. doi: 10.1167/iovs.11-8129.
-
(2011)
Investigative Ophthalmology & Visual Science
, vol.52
, pp. 8785-8790
-
-
Okamoto, S.1
Takahashi, M.2
-
59
-
-
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, Shibata T, Kunisada T, Takahashi M, Takahashi J, Saji H, Yamanaka S. 2011. A more efficient method to generate integration-free human iPS cells. Nature Methods 8:409-412. doi: 10.1038/nmeth.1591.
-
(2011)
Nature 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
Shibata, T.11
Kunisada, T.12
Takahashi, M.13
Takahashi, J.14
Saji, H.15
Yamanaka, S.16
-
60
-
-
79958252915
-
Chromatin connections to pluripotency and cellular reprogramming
-
Orkin SH, Hochedlinger K. 2011. Chromatin connections to pluripotency and cellular reprogramming. Cell 145: 835-850. doi: 10.1016/j.cell.2011.05.019.
-
(2011)
Cell
, vol.145
, pp. 835-850
-
-
Orkin, S.H.1
Hochedlinger, K.2
-
61
-
-
84867095528
-
A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development
-
Paige SL, Thomas S, Stoick-Cooper CL, Wang H, Maves L, Sandstrom R, Pabon L, Reinecke H, Pratt G, Keller G, Moon RT, Stamatoyannopoulos J, Murry CE. 2012. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell 151:221-232. doi: 10.1016/j.cell.2012.08.027.
-
(2012)
Cell
, vol.151
, pp. 221-232
-
-
Paige, S.L.1
Thomas, S.2
Stoick-Cooper, C.L.3
Wang, H.4
Maves, L.5
Sandstrom, R.6
Pabon, L.7
Reinecke, H.8
Pratt, G.9
Keller, G.10
Moon, R.T.11
Stamatoyannopoulos, J.12
Murry, C.E.13
-
62
-
-
1042304216
-
APE: Analyses of phylogenetics and evolution in R language
-
Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290. doi: 10.1093/bioinformatics/btg412.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
63
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:167-172. doi: 10.1038/nature05113.
-
(2006)
Nature
, vol.443
, pp. 167-172
-
-
Pollard, K.S.1
Salama, S.R.2
Lambert, N.3
Lambot, M.A.4
Coppens, S.5
Pedersen, J.S.6
Katzman, S.7
King, B.8
Onodera, C.9
Siepel, A.10
Kern, A.D.11
Dehay, C.12
Igel, H.13
Ares, M.14
Vanderhaeghen, P.15
Haussler, D.16
-
64
-
-
51149097366
-
Human-specific gain of function in a developmental enhancer
-
Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, Fitzpatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP. 2008. Human-specific gain of function in a developmental enhancer. Science 321:1346-1350. doi: 10.1126/science.1159974.
-
(2008)
Science
, vol.321
, pp. 1346-1350
-
-
Prabhakar, S.1
Visel, A.2
Akiyama, J.A.3
Shoukry, M.4
Lewis, K.D.5
Holt, A.6
Plajzer-Frick, I.7
Morrison, H.8
Fitzpatrick, D.R.9
Afzal, V.10
Pennacchio, L.A.11
Rubin, E.M.12
Noonan, J.P.13
-
66
-
-
84868484735
-
Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
-
Rada-Iglesias A, Bajpai R, Prescott S, Brugmann Sa, Swigut T, Wysocka J. 2012. Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell 11:633-648. doi: 10.1016/j.stem.2012.07.006.
-
(2012)
Cell Stem Cell
, vol.11
, pp. 633-648
-
-
Rada-Iglesias, A.1
Bajpai, R.2
Prescott, S.3
Sa, B.4
Swigut, T.5
Wysocka, J.6
-
67
-
-
84867772337
-
Characterization of human-induced pluripotent stem cell-derived cardiomyocytes: Bioenergetics and utilization in safety screening
-
Rana P, Anson B, Engle S, Will Y. 2012. Characterization of human-induced pluripotent stem cell-derived cardiomyocytes: bioenergetics and utilization in safety screening. Toxicological Sciences 130:117-131. doi: 10.1093/toxsci/kfs233.
-
(2012)
Toxicological Sciences
, vol.130
, pp. 117-131
-
-
Rana, P.1
Anson, B.2
Engle, S.3
Will, Y.4
-
69
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium
-
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. 2015. Integrative analysis of 111 reference human epigenomes. Nature 518:317-330. doi: 10.1038/nature14248.
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Kundaje, A.1
Meuleman, W.2
Ernst, J.3
Bilenky, M.4
Yen, A.5
Heravi-Moussavi, A.6
Kheradpour, P.7
Zhang, Z.8
Wang, J.9
Ziller, M.J.10
Amin, V.11
Whitaker, J.W.12
Schultz, M.D.13
Ward, L.D.14
Sarkar, A.15
Quon, G.16
Sandstrom, R.S.17
Eaton, M.L.18
Wu, Y.C.19
Pfenning, A.R.20
Wang, X.21
Claussnitzer, M.22
Liu, Y.23
Coarfa, C.24
Harris, R.A.25
Shoresh, N.26
Epstein, C.B.27
Gjoneska, E.28
Leung, D.29
Xie, W.30
Hawkins, R.D.31
Lister, R.32
Hong, C.33
Gascard, P.34
Mungall, A.J.35
Moore, R.36
Chuah, E.37
Tam, A.38
Canfield, T.K.39
Hansen, R.S.40
Kaul, R.41
Sabo, P.J.42
Bansal, M.S.43
Carles, A.44
Dixon, J.R.45
Farh, K.H.46
Feizi, S.47
Karlic, R.48
Kim, A.R.49
Kulkarni, A.50
Li, D.51
Lowdon, R.52
Elliott, G.53
Mercer, T.R.54
Neph, S.J.55
Onuchic, V.56
Polak, P.57
Rajagopal, N.58
Ray, P.59
Sallari, R.C.60
Siebenthall, K.T.61
Sinnott-Armstrong, N.A.62
Stevens, M.63
Thurman, R.E.64
Wu, J.65
Zhang, B.66
Zhou, X.67
Beaudet, A.E.68
Boyer, L.A.69
De Jager, P.L.70
Farnham, P.J.71
Fisher, S.J.72
Haussler, D.73
Jones, S.J.74
Li, W.75
Marra, M.A.76
McManus, M.T.77
Sunyaev, S.78
Thomson, J.A.79
Tlsty, T.D.80
Tsai, L.H.81
Wang, W.82
Waterland, R.A.83
Zhang, M.Q.84
Chadwick, L.H.85
Bernstein, B.E.86
Costello, J.F.87
Ecker, J.R.88
Hirst, M.89
Meissner, A.90
Milosavljevic, A.91
Ren, B.92
Stamatoyannopoulos, J.A.93
Wang, T.94
Kellis, M.95
more..
-
70
-
-
29144492108
-
Ancient and recent positive selection transformed opioid cis-regulation in humans
-
Rockman MV, Hahn MW, Soranzo N, Zimprich F, Goldstein DB, Wray GA. 2005. Ancient and recent positive selection transformed opioid cis-regulation in humans. PLOS Biology 3:e387. doi: 10.1371/journal.pbio.0030387.
-
(2005)
PLOS Biology
, vol.3
-
-
Rockman, M.V.1
Hahn, M.W.2
Soranzo, N.3
Zimprich, F.4
Goldstein, D.B.5
Wray, G.A.6
-
71
-
-
67649834440
-
ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions
-
Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. 2009. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48:240-248. doi: 10.1016/j.ymeth.2009.03.001.
-
(2009)
Methods
, vol.48
, pp. 240-248
-
-
Schmidt, D.1
Wilson, M.D.2
Spyrou, C.3
Brown, G.D.4
Hadfield, J.5
Odom, D.T.6
-
72
-
-
67650841125
-
Analysis of Rex1 (Zfp42) function in embryonic stem cell differentiation
-
Scotland KB, Chen S, Sylvester R, Gudas LJ. 2009. Analysis of Rex1 (zfp42) function in embryonic stem cell differentiation. Developmental Dynamics 238:1863-1877. doi: 10.1002/dvdy.22037.
-
(2009)
Developmental Dynamics
, vol.238
, pp. 1863-1877
-
-
Scotland, K.B.1
Chen, S.2
Sylvester, R.3
Gudas, L.J.4
-
73
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3:Article3. doi: 10.2202/1544-6115.1027.
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
-
-
Smyth, G.K.1
-
74
-
-
84871339130
-
Residual expression of reprogramming factors affects the transcriptional program and epigenetic signatures of induced pluripotent stem cells
-
Sommer CA, Christodoulou C, Gianotti-Sommer A, Shen SS, Sailaja BS, Hezroni H, Spira A, Meshorer E, Kotton DN, Mostoslavsky G. 2012. Residual expression of reprogramming factors affects the transcriptional program and epigenetic signatures of induced pluripotent stem cells. PLOS ONE 7:e51711. doi: 10.1371/journal.pone.0051711.
-
(2012)
PLOS ONE
, vol.7
-
-
Sommer, C.A.1
Christodoulou, C.2
Gianotti-Sommer, A.3
Shen, S.S.4
Sailaja, B.S.5
Hezroni, H.6
Spira, A.7
Meshorer, E.8
Kotton, D.N.9
Mostoslavsky, G.10
-
75
-
-
84887987260
-
Unveiling the critical role of REX1 in the regulation of human stem cell pluripotency
-
Son MY, Choi H, Han YM, Cho YS. 2013. Unveiling the critical role of REX1 in the regulation of human stem cell pluripotency. Stem Cells 31:2374-2387. doi: 10.1002/stem.1509.
-
(2013)
Stem Cells
, vol.31
, pp. 2374-2387
-
-
Son, M.Y.1
Choi, H.2
Han, Y.M.3
Cho, Y.S.4
-
76
-
-
79952598545
-
Identifying dispersed epigenomic domains from ChIP-Seq data
-
Song Q, Smith AD. 2011. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27: 870-871. doi: 10.1093/bioinformatics/btr030.
-
(2011)
Bioinformatics
, vol.27
, pp. 870-871
-
-
Song, Q.1
Smith, A.D.2
-
77
-
-
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. doi: 10.1016/j.cell.2007.11.019.
-
(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
-
78
-
-
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. doi: 10.1016/j.cell.2006.07.024.
-
(2006)
Cell
, vol.126
, pp. 663-676
-
-
Takahashi, K.1
Yamanaka, S.2
-
79
-
-
84872564830
-
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
-
Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S. 2013. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 29:189-196. doi: 10.1093/bioinformatics/bts680.
-
(2013)
Bioinformatics
, vol.29
, pp. 189-196
-
-
Teschendorff, A.E.1
Marabita, F.2
Lechner, M.3
Bartlett, T.4
Tegner, J.5
Gomez-Cabrero, D.6
Beck, S.7
-
80
-
-
84872048038
-
Distinct metabolic flow enables large-scale purification of mouse and human pluripotent stem cell-derived cardiomyocytes
-
Tohyama S, Hattori F, Sano M, Hishiki T, Nagahata Y, Matsuura T, Hashimoto H, Suzuki T, Yamashita H, Satoh Y, Egashira T, Seki T, Muraoka N, Yamakawa H, Ohgino Y, Tanaka T, Yoichi M, Yuasa S, Murata M, Suematsu M, Fukuda K. 2013. Distinct metabolic flow enables large-scale purification of mouse and human pluripotent stem cell-derived cardiomyocytes. Cell Stem Cell 12:127-137. doi: 10.1016/j.stem.2012.09.013.
-
(2013)
Cell Stem Cell
, vol.12
, pp. 127-137
-
-
Tohyama, S.1
Hattori, F.2
Sano, M.3
Hishiki, T.4
Nagahata, Y.5
Matsuura, T.6
Hashimoto, H.7
Suzuki, T.8
Yamashita, H.9
Satoh, Y.10
Egashira, T.11
Seki, T.12
Muraoka, N.13
Yamakawa, H.14
Ohgino, Y.15
Tanaka, T.16
Yoichi, M.17
Yuasa, S.18
Murata, M.19
Suematsu, M.20
Fukuda, K.21
more..
-
81
-
-
77955931659
-
Generating induced pluripotent stem cells from common marmoset (Callithrix jacchus) fetal liver cells using defined factors, including Lin28
-
Tomioka I, Maeda T, Shimada H, Kawai K, Okada Y, Igarashi H, Oiwa R, Iwasaki T, Aoki M, Kimura T, Shiozawa S, Shinohara H, Suemizu H, Sasaki E, Okano H. 2010. Generating induced pluripotent stem cells from common marmoset (Callithrix jacchus) fetal liver cells using defined factors, including Lin28. Genes to Cells 15:959-969. doi: 10.1111/j.1365-2443.2010.01437.x.
-
(2010)
Genes to Cells
, vol.15
, pp. 959-969
-
-
Tomioka, I.1
Maeda, T.2
Shimada, H.3
Kawai, K.4
Okada, Y.5
Igarashi, H.6
Oiwa, R.7
Iwasaki, T.8
Aoki, M.9
Kimura, T.10
Shiozawa, S.11
Shinohara, H.12
Suemizu, H.13
Sasaki, E.14
Okano, H.15
-
82
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111. doi: 10.1093/bioinformatics/btp120.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
83
-
-
84867073340
-
Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage
-
Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG. 2012. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 151: 206-220. doi: 10.1016/j.cell.2012.07.035.
-
(2012)
Cell
, vol.151
, pp. 206-220
-
-
Wamstad, J.A.1
Alexander, J.M.2
Truty, R.M.3
Shrikumar, A.4
Li, F.5
Eilertson, K.E.6
Ding, H.7
Wylie, J.N.8
Pico, A.R.9
Capra, J.A.10
Erwin, G.11
Kattman, S.J.12
Keller, G.M.13
Srivastava, D.14
Levine, S.S.15
Pollard, K.S.16
Holloway, A.K.17
Boyer, L.A.18
Bruneau, B.G.19
-
84
-
-
84902087268
-
Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies
-
Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang DZ, Li K, Wang J, Wanders RJ, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK, Pu WT. 2014. Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nature Medicine 20:616-623. doi: 10.1038/nm.3545.
-
(2014)
Nature Medicine
, vol.20
, pp. 616-623
-
-
Wang, G.1
McCain, M.L.2
Yang, L.3
He, A.4
Pasqualini, F.S.5
Agarwal, A.6
Yuan, H.7
Jiang, D.8
Zhang, D.9
Zangi, L.10
Geva, J.11
Roberts, A.E.12
Ma, Q.13
Ding, J.14
Chen, J.15
Wang, D.Z.16
Li, K.17
Wang, J.18
Wanders, R.J.19
Kulik, W.20
Vaz, F.M.21
Laflamme, M.A.22
Murry, C.E.23
Chien, K.R.24
Kelley, R.I.25
Church, G.M.26
Parker, K.K.27
Pu, W.T.28
more..
-
85
-
-
84861083159
-
Nonhuman primate induced pluripotent stem cells in regenerative medicine
-
Wu Y, Mishra A, Qiu Z, Farnsworth S, Tardif SD, Hornsby PJ. 2012. Nonhuman primate induced pluripotent stem cells in regenerative medicine. Stem Cells International 2012:767195. doi: 10.1155/2012/767195.
-
(2012)
Stem Cells International
, vol.2012
-
-
Wu, Y.1
Mishra, A.2
Qiu, Z.3
Farnsworth, S.4
Tardif, S.D.5
Hornsby, P.J.6
-
86
-
-
77952290826
-
Generation of induced pluripotent stem cells from newborn marmoset skin fibroblasts
-
Wu Y, Zhang Y, Mishra A, Tardif SD, Hornsby PJ. 2010. Generation of induced pluripotent stem cells from newborn marmoset skin fibroblasts. Stem Cell Research 4:180-188. doi: 10.1016/j.scr.2010.02.003.
-
(2010)
Stem Cell Research
, vol.4
, pp. 180-188
-
-
Wu, Y.1
Zhang, Y.2
Mishra, A.3
Tardif, S.D.4
Hornsby, P.J.5
-
87
-
-
84896051735
-
Primate iPS cells as tools for evolutionary analyses
-
Wunderlich S, Kircher M, Vieth B, Haase A, Merkert S, Beier J, Göhring G, Glage S, Schambach A, Curnow EC, Pääbo S, Martin U, Enard W. 2014. Primate iPS cells as tools for evolutionary analyses. Stem Cell Research 12: 622-629. doi: 10.1016/j.scr.2014.02.001.
-
(2014)
Stem Cell Research
, vol.12
, pp. 622-629
-
-
Wunderlich, S.1
Kircher, M.2
Vieth, B.3
Haase, A.4
Merkert, S.5
Beier, J.6
Göhring, G.7
Glage, S.8
Schambach, A.9
Curnow, E.C.10
Pääbo, S.11
Martin, U.12
Enard, W.13
-
88
-
-
84878282421
-
Epigenomic analysis of multilineage differentiation of human embryonic stem cells
-
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. 2013. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153:1134-1148. doi: 10.1016/j.cell.2013.04.022.
-
(2013)
Cell
, vol.153
, pp. 1134-1148
-
-
Xie, W.1
Schultz, M.D.2
Lister, R.3
Hou, Z.4
Rajagopal, N.5
Ray, P.6
Whitaker, J.W.7
Tian, S.8
Hawkins, R.D.9
Leung, D.10
Yang, H.11
Wang, T.12
Lee, A.Y.13
Swanson, S.A.14
Zhang, J.15
Zhu, Y.16
Kim, A.17
Nery, J.R.18
Urich, M.A.19
Kuan, S.20
Yen, C.A.21
Klugman, S.22
Yu, P.23
Suknuntha, K.24
Propson, N.E.25
Chen, H.26
Edsall, L.E.27
Wagner, U.28
Li, Y.29
Ye, Z.30
Kulkarni, A.31
Xuan, Z.32
Chung, W.Y.33
Chi, N.C.34
Antosiewicz-Bourget, J.E.35
Slukvin, I.36
Stewart, R.37
Zhang, M.Q.38
Wang, W.39
Thomson, J.A.40
Ecker, J.R.41
Ren, B.42
more..
-
89
-
-
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, Liu XS. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biology 9:R137. doi: 10.1186/gb-2008-9-9-r137.
-
(2008)
Genome Biology
, vol.9
-
-
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
Liu, X.S.11
-
90
-
-
84937492151
-
Epigenetic modifications are associated with inter-species gene expression variation in primates
-
Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y. 2014. Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biology 15:547. doi: 10.1186/s13059-014-0547-3.
-
(2014)
Genome Biology
, vol.15
-
-
Zhou, X.1
Cain, C.E.2
Myrthil, M.3
Lewellen, N.4
Michelini, K.5
Davenport, E.R.6
Stephens, M.7
Pritchard, J.K.8
Gilad, Y.9
-
91
-
-
84855281409
-
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
-
Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A. 2011. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLOS Genetics 7:e1002389. doi: 10.1371/journal.pgen.1002389.
-
(2011)
PLOS Genetics
, vol.7
-
-
Ziller, M.J.1
Müller, F.2
Liao, J.3
Zhang, Y.4
Gu, H.5
Bock, C.6
Boyle, P.7
Epstein, C.B.8
Bernstein, B.E.9
Lengauer, T.10
Gnirke, A.11
Meissner, A.12
|