-
1
-
-
2942572926
-
Quantifying the relationship between co-expression, co-regulation and gene function
-
D.J. Allocco, I.S. Kohane, and A.J. Butte Quantifying the relationship between co-expression, co-regulation and gene function BMC Bioinformatics 5 2004 18
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 18
-
-
Allocco, D.J.1
Kohane, I.S.2
Butte, A.J.3
-
2
-
-
25844433114
-
Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels
-
M. Bengtsson, A. Ståhlberg, P. Rorsman, and M. Kubista Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels Genome Res. 15 2005 1388 1392
-
(2005)
Genome Res.
, vol.15
, pp. 1388-1392
-
-
Bengtsson, M.1
Ståhlberg, A.2
Rorsman, P.3
Kubista, M.4
-
3
-
-
84874913500
-
Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology
-
J.A. Briggs, J. Sun, J. Shepherd, D.A. Ovchinnikov, T.L. Chung, S.P. Nayler, L.P. Kao, C.A. Morrow, N.Y. Thakar, and S.Y. Soo et al. Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology Stem Cells 31 2013 467 478
-
(2013)
Stem Cells
, vol.31
, pp. 467-478
-
-
Briggs, J.A.1
Sun, J.2
Shepherd, J.3
Ovchinnikov, D.A.4
Chung, T.L.5
Nayler, S.P.6
Kao, L.P.7
Morrow, C.A.8
Thakar, N.Y.9
Soo, S.Y.10
-
4
-
-
37549002155
-
Nanog safeguards pluripotency and mediates germline development
-
I. Chambers, J. Silva, D. Colby, J. Nichols, B. Nijmeijer, M. Robertson, J. Vrana, K. Jones, L. Grotewold, and A. Smith Nanog safeguards pluripotency and mediates germline development Nature 450 2007 1230 1234
-
(2007)
Nature
, vol.450
, pp. 1230-1234
-
-
Chambers, I.1
Silva, J.2
Colby, D.3
Nichols, J.4
Nijmeijer, B.5
Robertson, M.6
Vrana, J.7
Jones, K.8
Grotewold, L.9
Smith, A.10
-
5
-
-
46249088370
-
Lumi: A pipeline for processing Illumina microarray
-
P. Du, W.A. Kibbe, and S.M. Lin lumi: a pipeline for processing Illumina microarray Bioinformatics 24 2008 1547 1548
-
(2008)
Bioinformatics
, vol.24
, pp. 1547-1548
-
-
Du, P.1
Kibbe, W.A.2
Lin, S.M.3
-
6
-
-
0035799309
-
Establishment of human embryonic stem cell-transfected clones carrying a marker for undifferentiated cells
-
R. Eiges, M. Schuldiner, M. Drukker, O. Yanuka, J. Itskovitz-Eldor, and N. Benvenisty Establishment of human embryonic stem cell-transfected clones carrying a marker for undifferentiated cells Curr. Biol. 11 2001 514 518
-
(2001)
Curr. Biol.
, vol.11
, pp. 514-518
-
-
Eiges, R.1
Schuldiner, M.2
Drukker, M.3
Yanuka, O.4
Itskovitz-Eldor, J.5
Benvenisty, N.6
-
7
-
-
84876515907
-
STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
-
A. Francheschini, D. Szklarczyk, S. Frankild, M. Kuhn, M. Simonovic, A. Roth, J. Lin, P. Minguez, P. Bork, and C. von Mering et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration Nucleic Acids Res. 41 2012 1 8
-
(2012)
Nucleic Acids Res.
, vol.41
, pp. 1-8
-
-
Francheschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
Lin, J.7
Minguez, P.8
Bork, P.9
Von Mering, C.10
-
8
-
-
84861968321
-
RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation
-
G. Fuchs, E. Shema, R. Vesterman, E. Kotler, Z. Wolchinsky, S. Wilder, L. Golomb, A. Pribluda, F. Zhang, and M. Haj-Yahya et al. RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation Mol. Cell 46 2012 662 673
-
(2012)
Mol. Cell
, vol.46
, pp. 662-673
-
-
Fuchs, G.1
Shema, E.2
Vesterman, R.3
Kotler, E.4
Wolchinsky, Z.5
Wilder, S.6
Golomb, L.7
Pribluda, A.8
Zhang, F.9
Haj-Yahya, M.10
-
9
-
-
84886615682
-
The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network
-
D.A. Garfield, D.E. Runcie, C.C. Babbitt, R. Haygood, W.J. Nielsen, and G.A. Wray The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network PLoS Biol. 11 2013 e1001696
-
(2013)
PLoS Biol.
, vol.11
, pp. 1001696
-
-
Garfield, D.A.1
Runcie, D.E.2
Babbitt, C.C.3
Haygood, R.4
Nielsen, W.J.5
Wray, G.A.6
-
10
-
-
53049092465
-
Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states
-
K. Hayashi, S.M. Lopes, F. Tang, and M.A. Surani Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states Cell Stem Cell 3 2008 391 401
-
(2008)
Cell Stem Cell
, vol.3
, pp. 391-401
-
-
Hayashi, K.1
Lopes, S.M.2
Tang, F.3
Surani, M.A.4
-
11
-
-
70450193138
-
A continuum of cell states spans pluripotency and lineage commitment in human embryonic stem cells
-
S.R. Hough, A.L. Laslett, S.B. Grimmond, G. Kolle, and M.F. Pera A continuum of cell states spans pluripotency and lineage commitment in human embryonic stem cells PLoS ONE 4 2009 e7708
-
(2009)
PLoS ONE
, vol.4
, pp. 7708
-
-
Hough, S.R.1
Laslett, A.L.2
Grimmond, S.B.3
Kolle, G.4
Pera, M.F.5
-
12
-
-
34248199004
-
Bifurcation dynamics in lineage-commitment in bipotent progenitor cells
-
S. Huang, Y.P. Guo, G. May, and T. Enver Bifurcation dynamics in lineage-commitment in bipotent progenitor cells Dev. Biol. 305 2007 695 713
-
(2007)
Dev. Biol.
, vol.305
, pp. 695-713
-
-
Huang, S.1
Guo, Y.P.2
May, G.3
Enver, T.4
-
13
-
-
62549089350
-
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
-
A.C. Huang, L. Hu, S.A. Kauffman, W. Zhang, and I. Shmulevich Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation BMC Syst. Biol. 3 2009 20
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 20
-
-
Huang, A.C.1
Hu, L.2
Kauffman, S.A.3
Zhang, W.4
Shmulevich, I.5
-
15
-
-
0037805576
-
The KEGG database
-
discussion 101-103, 119-128, 244-252
-
M. Kanehisa The KEGG database Novartis Found. Symp. 247 2002 91 101 discussion 101-103, 119-128, 244-252
-
(2002)
Novartis Found. Symp.
, vol.247
, pp. 91-101
-
-
Kanehisa, M.1
-
16
-
-
84877297850
-
Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and Nanog
-
V. Karwacki-Neisius, J. Göke, R. Osorno, F. Halbritter, J.H. Ng, A.Y. Weiße, F.C. Wong, A. Gagliardi, N.P. Mullin, and N. Festuccia et al. Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and Nanog Cell Stem Cell 12 2013 531 545
-
(2013)
Cell Stem Cell
, vol.12
, pp. 531-545
-
-
Karwacki-Neisius, V.1
Göke, J.2
Osorno, R.3
Halbritter, F.4
Ng, J.H.5
Weiße, A.Y.6
Wong, F.C.7
Gagliardi, A.8
Mullin, N.P.9
Festuccia, N.10
-
17
-
-
7644238181
-
Biological robustness
-
H. Kitano Biological robustness Nat. Rev. Genet. 5 2004 826 837
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 826-837
-
-
Kitano, H.1
-
18
-
-
70350241660
-
Identification of human embryonic stem cell surface markers by combined membrane-polysome translation state array analysis and immunotranscriptional profiling
-
G. Kolle, M. Ho, Q. Zhou, H.S. Chy, K. Krishnan, N. Cloonan, I. Bertoncello, A.L. Laslett, and S.M. Grimmond Identification of human embryonic stem cell surface markers by combined membrane-polysome translation state array analysis and immunotranscriptional profiling Stem Cells 27 2009 2446 2456
-
(2009)
Stem Cells
, vol.27
, pp. 2446-2456
-
-
Kolle, G.1
Ho, M.2
Zhou, Q.3
Chy, H.S.4
Krishnan, K.5
Cloonan, N.6
Bertoncello, I.7
Laslett, A.L.8
Grimmond, S.M.9
-
19
-
-
83055182013
-
Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
-
G. Kolle, J.L. Shepherd, B. Gardiner, K.S. Kassahn, N. Cloonan, D.L.A. Wood, E. Nourbakhsh, D.F. Taylor, S. Wani, and H.S. Chy et al. Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells Genome Res. 21 2011 2014 2025
-
(2011)
Genome Res.
, vol.21
, pp. 2014-2025
-
-
Kolle, G.1
Shepherd, J.L.2
Gardiner, B.3
Kassahn, K.S.4
Cloonan, N.5
Wood, D.L.A.6
Nourbakhsh, E.7
Taylor, D.F.8
Wani, S.9
Chy, H.S.10
-
20
-
-
42949131308
-
Selection to minimise noise in living systems and its implications for the evolution of gene expression
-
B. Lehner Selection to minimise noise in living systems and its implications for the evolution of gene expression Mol. Syst. Biol. 4 2008 170
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 170
-
-
Lehner, B.1
-
21
-
-
84881171093
-
Statistical mechanics of pluripotency
-
B.D. MacArthur, and I.R. Lemischka Statistical mechanics of pluripotency Cell 154 2013 484 489
-
(2013)
Cell
, vol.154
, pp. 484-489
-
-
Macarthur, B.D.1
Lemischka, I.R.2
-
22
-
-
80054119877
-
Attract: A method for identifying core pathways that define cellular phenotypes
-
J.C. Mar, N.A. Matigian, J. Quackenbush, and C.A. Wells attract: a method for identifying core pathways that define cellular phenotypes PLoS ONE 6 2011 e25445
-
(2011)
PLoS ONE
, vol.6
, pp. 25445
-
-
Mar, J.C.1
Matigian, N.A.2
Quackenbush, J.3
Wells, C.A.4
-
23
-
-
79954521574
-
Defining an informativeness metric for clustering gene expression data
-
J.C. Mar, C.A. Wells, and J. Quackenbush Defining an informativeness metric for clustering gene expression data Bioinformatics 27 2011 1094 1100
-
(2011)
Bioinformatics
, vol.27
, pp. 1094-1100
-
-
Mar, J.C.1
Wells, C.A.2
Quackenbush, J.3
-
24
-
-
80052308980
-
Variance of gene expression identifies altered network constraints in neurological disease
-
J.C. Mar, N.A. Matigian, A. Mackay-Sim, G.D. Mellick, C.M. Sue, P.A. Silburn, J.J. McGrath, J. Quackenbush, and C.A. Wells Variance of gene expression identifies altered network constraints in neurological disease PLoS Genet. 7 2011 e1002207
-
(2011)
PLoS Genet.
, vol.7
, pp. 1002207
-
-
Mar, J.C.1
Matigian, N.A.2
Mackay-Sim, A.3
Mellick, G.D.4
Sue, C.M.5
Silburn, P.A.6
McGrath, J.J.7
Quackenbush, J.8
Wells, C.A.9
-
25
-
-
77949504985
-
BisoGenet: A new tool for gene network building, visualisation and analysis
-
A. Martin, M. Ochagavia, L. Rabasa, J. Miranda, J. Fernandez-de-Cossio, and R. Bringas BisoGenet: a new tool for gene network building, visualisation and analysis BMC Bioinformatics 11 2010 1 9
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 1-9
-
-
Martin, A.1
Ochagavia, M.2
Rabasa, L.3
Miranda, J.4
Fernandez-De-Cossio, J.5
Bringas, R.6
-
26
-
-
33846845067
-
Secreted frizzled related protein 2 (Sfrp2) is the key Akt-mesenchymal stem cell-released paracrine factor mediating myocardial survival and repair
-
M. Mirotsou, Z. Zhang, A. Deb, L. Zhang, M. Gnecchi, N. Noiseux, H. Mu, A. Pachori, and V. Dzau Secreted frizzled related protein 2 (Sfrp2) is the key Akt-mesenchymal stem cell-released paracrine factor mediating myocardial survival and repair Proc. Natl. Acad. Sci. USA 104 2007 1643 1648
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 1643-1648
-
-
Mirotsou, M.1
Zhang, Z.2
Deb, A.3
Zhang, L.4
Gnecchi, M.5
Noiseux, N.6
Mu, H.7
Pachori, A.8
Dzau, V.9
-
27
-
-
79953267538
-
A bioinformatic assay for pluripotency in human cells
-
F.-J. Müller, B.M. Schuldt, R. Williams, D. Mason, G. Altun, E.P. Papapetrou, S. Danner, J.E. Goldmann, A. Herbst, and N.O. Schmidt et al. A bioinformatic assay for pluripotency in human cells Nat. Methods 8 2011 315 317
-
(2011)
Nat. 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
-
28
-
-
77952858910
-
Culture of human pluripotent stem cells using completely defined conditions on a recombinant E-cadherin substratum
-
M. Nagaoka, K. Si-Tayeb, T. Akaike, and S.A. Duncan Culture of human pluripotent stem cells using completely defined conditions on a recombinant E-cadherin substratum BMC Dev. Biol. 10 2010 60
-
(2010)
BMC Dev. Biol.
, vol.10
, pp. 60
-
-
Nagaoka, M.1
Si-Tayeb, K.2
Akaike, T.3
Duncan, S.A.4
-
29
-
-
0037472928
-
Genomic function: Rate of evolution and gene dispensability
-
discussion 497-498
-
C. Pál, B. Papp, and L.D. Hurst Genomic function: rate of evolution and gene dispensability Nature 421 2003 496 497 discussion 497-498
-
(2003)
Nature
, vol.421
, pp. 496-497
-
-
Pál, C.1
Papp, B.2
Hurst, L.D.3
-
30
-
-
77952018749
-
Functional analysis of the Cdk7.cyclin H.Mat1 complex in mouse embryonic stem cells and embryos
-
S.A. Patel, and M.C. Simon Functional analysis of the Cdk7.cyclin H.Mat1 complex in mouse embryonic stem cells and embryos J. Biol. Chem. 285 2010 15587 15598
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 15587-15598
-
-
Patel, S.A.1
Simon, M.C.2
-
31
-
-
77249114260
-
Variability in gene expression underlies incomplete penetrance
-
A. Raj, S.A. Rifkin, E. Andersen, and A. van Oudenaarden Variability in gene expression underlies incomplete penetrance Nature 463 2010 913 918
-
(2010)
Nature
, vol.463
, pp. 913-918
-
-
Raj, A.1
Rifkin, S.A.2
Andersen, E.3
Van Oudenaarden, A.4
-
32
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13 2003 2498 2504
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
33
-
-
84890984246
-
Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells
-
A.M. Singh, J. Chappell, R. Trost, L. Lin, T. Wang, J. Tang, B.K. Matlock, K.P. Weller, H. Wu, and S. Zhao et al. Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells Stem Cell Rev. 1 2013 532 544
-
(2013)
Stem Cell Rev.
, vol.1
, pp. 532-544
-
-
Singh, A.M.1
Chappell, J.2
Trost, R.3
Lin, L.4
Wang, T.5
Tang, J.6
Matlock, B.K.7
Weller, K.P.8
Wu, H.9
Zhao, S.10
-
34
-
-
84893023300
-
Nanog heterogeneity: Tilting at windmills?
-
A. Smith Nanog heterogeneity: tilting at windmills? Cell Stem Cell 13 2013 6 7
-
(2013)
Cell Stem Cell
, vol.13
, pp. 6-7
-
-
Smith, A.1
-
35
-
-
33745000256
-
Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification
-
G. Swiers, R. Patient, and M. Loose Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification Dev. Biol. 294 2006 525 540
-
(2006)
Dev. Biol.
, vol.294
, pp. 525-540
-
-
Swiers, G.1
Patient, R.2
Loose, M.3
-
36
-
-
84873025549
-
Variability in the generation of induced pluripotent stem cells: Importance for disease modeling
-
A.M. Vitale, N.A. Matigian, S. Ravishankar, B. Bellette, S.A. Wood, E.J. Wolvetang, and A. Mackay-Sim Variability in the generation of induced pluripotent stem cells: importance for disease modeling Stem Cells Transl. Med. 1 2012 641 650
-
(2012)
Stem Cells Transl. Med.
, vol.1
, pp. 641-650
-
-
Vitale, A.M.1
Matigian, N.A.2
Ravishankar, S.3
Bellette, B.4
Wood, S.A.5
Wolvetang, E.J.6
Mackay-Sim, A.7
-
38
-
-
77952360137
-
Revealing a core signaling regulatory mechanism for pluripotent stem cell survival and self-renewal by small molecules
-
Y. Xu, X. Zhu, H.S. Hahm, W. Wei, E. Hao, A. Hayek, and S. Ding Revealing a core signaling regulatory mechanism for pluripotent stem cell survival and self-renewal by small molecules Proc. Natl. Acad. Sci. USA 107 2010 8129 8134
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 8129-8134
-
-
Xu, Y.1
Zhu, X.2
Hahm, H.S.3
Wei, W.4
Hao, E.5
Hayek, A.6
Ding, S.7
-
39
-
-
84874788156
-
The zinc finger transcription factor Ovol2 acts downstream of the bone morphogenetic protein pathway to regulate the cell fate decision between neuroectoderm and mesendoderm
-
T. Zhang, Q. Zhu, Z. Xie, Y. Chen, Y. Qiao, L. Li, and N. Jing The zinc finger transcription factor Ovol2 acts downstream of the bone morphogenetic protein pathway to regulate the cell fate decision between neuroectoderm and mesendoderm J. Biol. Chem. 288 2013 6166 6177
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 6166-6177
-
-
Zhang, T.1
Zhu, Q.2
Xie, Z.3
Chen, Y.4
Qiao, Y.5
Li, L.6
Jing, N.7
|