-
1
-
-
0030801002
-
Gapped BLAST and PaSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schffer AA, Zhang J, Zhang Z, MillerW, Lipman DJ. 1997. Gapped BLAST and PaSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
-
(2010)
Genome Biol
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
3
-
-
84902552747
-
HTSeq-a Python framework to work with high-throughput sequencing data
-
Anders S, Pyl PT, HuberW. 2014. HTSeq-a Python framework to work with high-throughput sequencing data. bioRxiv. http://biorxiv.org/content/ early/2014/02/20/002824.
-
(2014)
BioRxiv
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
4
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, et al. 2014. An atlas of active enhancers across human cell types and tissues. Nature 507: 455-461.
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
Gebhard, C.2
Miguel-Escalada, I.3
Hoof, I.4
Bornholdt, J.5
Boyd, M.6
Chen, Y.7
Zhao, X.8
Schmidl, C.9
Suzuki, T.10
-
5
-
-
0001677717
-
A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. A practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289-300.
-
(1995)
J R Stat Soc Ser B Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
6
-
-
84856937196
-
FOXA1: A transcription factor with parallel functions in development and cancer
-
Bernardo GM, Keri RA. 2012. FOXA1: a transcription factor with parallel functions in development and cancer. Biosci Rep 32: 113-130.
-
(2012)
Biosci Rep
, vol.32
, pp. 113-130
-
-
Bernardo, G.M.1
Keri, R.A.2
-
7
-
-
80054728495
-
Animal transcription networks as highly connected, quantitative continua
-
Biggin MD. 2011. Animal transcription networks as highly connected, quantitative continua. Dev Cell 21: 611-626.
-
(2011)
Dev Cell
, vol.21
, pp. 611-626
-
-
Biggin, M.D.1
-
8
-
-
84864041695
-
Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2
-
Bochkis IM, Schug J, Ye DZ, Kurinna S, Stratton SA, Barton MC, Kaestner KH. 2012. Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. PLoS Genet 8: e1002770.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002770
-
-
Bochkis, I.M.1
Schug, J.2
Ye, D.Z.3
Kurinna, S.4
Stratton, S.A.5
Barton, M.C.6
Kaestner, K.H.7
-
9
-
-
84863279150
-
Suppression of hepatocyte proliferation by hepatocyte nuclear factor 4a in adult mice
-
Bonzo JA, Ferry CH, Matsubara T, Kim JH, Gonzalez FJ. 2012. Suppression of hepatocyte proliferation by hepatocyte nuclear factor 4a in adult mice. J Biol Chem 287: 7345-7356.
-
(2012)
J Biol Chem
, vol.287
, pp. 7345-7356
-
-
Bonzo, J.A.1
Ferry, C.H.2
Matsubara, T.3
Kim, J.H.4
Gonzalez, F.J.5
-
10
-
-
34547874585
-
Divergence of transcription factor binding sites across related yeast species
-
Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. 2007. Divergence of transcription factor binding sites across related yeast species. Science 317: 815-819.
-
(2007)
Science
, vol.317
, pp. 815-819
-
-
Borneman, A.R.1
Gianoulis, T.A.2
Zhang, Z.D.3
Yu, H.4
Rozowsky, J.5
Seringhaus, M.R.6
Wang, L.Y.7
Gerstein, M.8
Snyder, M.9
-
11
-
-
77950566643
-
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
-
Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. 2010. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol 8: e1000343.
-
(2010)
PLoS Biol
, vol.8
, pp. e1000343
-
-
Bradley, R.K.1
Li, X.Y.2
Trapnell, C.3
Davidson, S.4
Pachter, L.5
Chu, H.C.6
Tonkin, L.A.7
Biggin, M.D.8
Eisen, M.B.9
-
12
-
-
84873512283
-
Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes
-
Caravaca JM, Donahue G, Becker JS, He X, Vinson C, Zaret KS. 2013. Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. Genes Dev 27: 251-260.
-
(2013)
Genes Dev
, vol.27
, pp. 251-260
-
-
Caravaca, J.M.1
Donahue, G.2
Becker, J.S.3
He, X.4
Vinson, C.5
Zaret, K.S.6
-
13
-
-
84897394513
-
The functional consequences of variation in transcription factor binding
-
Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. 2014. The functional consequences of variation in transcription factor binding. PLoS Genet 10: e1004226.
-
(2014)
PLoS Genet
, vol.10
, pp. e1004226
-
-
Cusanovich, D.A.1
Pavlovic, B.2
Pritchard, J.K.3
Gilad, Y.4
-
14
-
-
65349099931
-
Thirty years of Mus spretus: A promising future
-
Dejager L, Libert C, Montagutelli X. 2009. Thirty years of Mus spretus: a promising future. Trends Genet 25: 234-241.
-
(2009)
Trends Genet
, vol.25
, pp. 234-241
-
-
Dejager, L.1
Libert, C.2
Montagutelli, X.3
-
15
-
-
0022203256
-
Phylogenies and the comparative method
-
Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat 125: 1-15.
-
(1985)
Am Nat
, vol.125
, pp. 1-15
-
-
Felsenstein, J.1
-
16
-
-
84875391572
-
Ensembl 2013
-
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, et al. 2013. Ensembl 2013. Nucleic Acids Res 41: D48-D55.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D48-D55
-
-
Flicek, P.1
Ahmed, I.2
Amode, M.R.3
Barrell, D.4
Beal, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fairley, S.10
-
17
-
-
84870538799
-
Extensive compensatory cistrans regulation in the evolution of mouse gene expression
-
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC. 2012. Extensive compensatory cistrans regulation in the evolution of mouse gene expression. Genome Res 22: 2376-2384.
-
(2012)
Genome Res
, vol.22
, pp. 2376-2384
-
-
Goncalves, A.1
Leigh-Brown, S.2
Thybert, D.3
Stefflova, K.4
Turro, E.5
Flicek, P.6
Brazma, A.7
Odom, D.T.8
Marioni, J.C.9
-
18
-
-
37549027209
-
GEIGER: Investigating evolutionary radiations
-
Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24: 129-131.
-
(2008)
Bioinformatics
, vol.24
, pp. 129-131
-
-
Harmon, L.J.1
Weir, J.T.2
Brock, C.D.3
Glor, R.E.4
Challenger, W.5
-
19
-
-
0035141324
-
Hepatocyte nuclear factor 4a (nuclear receptor 2A1) is essential for maintenance of hepatic gene expression and lipid homeostasis
-
Hayhurst GP, Lee YH, Lambert G, Ward JM, Gonzalez FJ. 2001. Hepatocyte nuclear factor 4a (nuclear receptor 2A1) is essential for maintenance of hepatic gene expression and lipid homeostasis. Mol Cell Biol 21: 1393-1403.
-
(2001)
Mol Cell Biol
, vol.21
, pp. 1393-1403
-
-
Hayhurst, G.P.1
Lee, Y.H.2
Lambert, G.3
Ward, J.M.4
Gonzalez, F.J.5
-
20
-
-
79955471381
-
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
-
He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. 2011. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet 43: 414-420.
-
(2011)
Nat Genet
, vol.43
, pp. 414-420
-
-
He, Q.1
Bardet, A.F.2
Patton, B.3
Purvis, J.4
Johnston, J.5
Paulson, A.6
Gogol, M.7
Stark, A.8
Zeitlinger, J.9
-
21
-
-
80052851950
-
Mouse genomic variation and its effect on phenotypes and gene regulation
-
Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, et al. 2011. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289-294.
-
(2011)
Nature
, vol.477
, pp. 289-294
-
-
Keane, T.M.1
Goodstadt, L.2
Danecek, P.3
White, M.A.4
Wong, K.5
Yalcin, B.6
Heger, A.7
Agam, A.8
Slater, G.9
Goodson, M.10
-
22
-
-
84864629645
-
Rapid turnover of long noncoding RNAs and the evolution of gene expression
-
Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT, Marques AC. 2012. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet 8: e1002841.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002841
-
-
Kutter, C.1
Watt, S.2
Stefflova, K.3
Wilson, M.D.4
Goncalves, A.5
Ponting, C.P.6
Odom, D.T.7
Marques, A.C.8
-
23
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
24
-
-
84864483625
-
RobiNA: A user-friendly, integrated software solution for RNA-seq-based transcriptomics
-
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. 2012.RobiNA: a user-friendly, integrated software solution for RNA-seq-based transcriptomics. Nucleic Acids Res 40: W622-W627.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W622-W627
-
-
Lohse, M.1
Bolger, A.M.2
Nagel, A.3
Fernie, A.R.4
Lunn, J.E.5
Stitt, M.6
Usadel, B.7
-
25
-
-
34547396004
-
The frailty of adaptive hypotheses for the origins of organismal complexity
-
Lynch M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci 104: 8597-8604.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 8597-8604
-
-
Lynch, M.1
-
26
-
-
68849103482
-
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
-
MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SVE, et al. 2009. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions.Genome Biol 10: R80.
-
(2009)
Genome Biol
, vol.10
, pp. R80
-
-
MacArthur, S.1
Li, X.Y.2
Li, J.3
Brown, J.B.4
Chu, H.C.5
Zeng, L.6
Grondona, B.P.7
Hechmer, A.8
Simirenko, L.9
Keränen, S.V.E.10
-
27
-
-
76049125511
-
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
-
Ouyang Z, Zhou Q, Wong WH. 2009. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci 106: 21521-21526.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 21521-21526
-
-
Ouyang, Z.1
Zhou, Q.2
Wong, W.H.3
-
28
-
-
84884698724
-
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression
-
Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB. 2013. Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet 9: e1003748.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003748
-
-
Paris, M.1
Kaplan, T.2
Li, X.Y.3
Villalta, J.E.4
Lott, S.E.5
Eisen, M.B.6
-
29
-
-
70350653808
-
Transcriptome analysis by strand-specific sequencing of complementary DNA
-
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. 2009. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. e123
-
-
Parkhomchuk, D.1
Borodina, T.2
Amstislavskiy, V.3
Banaru, M.4
Hallen, L.5
Krobitsch, S.6
Lehrach, H.7
Soldatov, A.8
-
30
-
-
84855199947
-
-
R Foundation for Statistical Computing, Vienna, Austria.
-
R Core Team. 2014. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.Rproject. org/.
-
(2014)
A Language and Environment for Statistical Computing
-
-
-
31
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
32
-
-
77953062527
-
Fivevertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, et al. 2010. Fivevertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328: 1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
Kutter, C.7
Watt, S.8
Martinez-Jimenez, C.P.9
Mackay, S.10
-
33
-
-
79953319002
-
Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers
-
Sérandour AA, Avner S, Percevault F, Demay F, Bizot M, Lucchetti-Miganeh C, Barloy-Hubler F, Brown M, Lupien M, Métivier R, et al. 2011.Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers. Genome Res 21: 555-565.
-
(2011)
Genome Res
, vol.21
, pp. 555-565
-
-
Sérandour, A.A.1
Avner, S.2
Percevault, F.3
Demay, F.4
Bizot, M.5
Lucchetti-Miganeh, C.6
Barloy-Hubler, F.7
Brown, M.8
Lupien, M.9
Métivier, R.10
-
34
-
-
76249102739
-
Organogenesis and development of the liver
-
Si-Tayeb K, Lemaigre FP, Duncan SA. 2010. Organogenesis and development of the liver. Dev Cell 18: 175-189.
-
(2010)
Dev Cell
, vol.18
, pp. 175-189
-
-
Si-Tayeb, K.1
Lemaigre, F.P.2
Duncan, S.A.3
-
36
-
-
84881141882
-
Cooperativity and rapid evolution of cobound transcription factors in closely related mammals
-
Stefflova K, Thybert D,Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, et al. 2013. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell 154: 530-540.
-
(2013)
Cell
, vol.154
, pp. 530-540
-
-
Stefflova, K.1
Thybert, D.2
Wilson, M.D.3
Streeter, I.4
Aleksic, J.5
Karagianni, P.6
Brazma, A.7
Adams, D.J.8
Talianidis, I.9
Marioni, J.C.10
-
37
-
-
84878882810
-
TherMos: Estimating protein-DNA binding energies from in vivo binding profiles
-
Sun W, Hu X, Lim MHK, Ng CKL, Choo SH, Castro DS, Drechsel D, Guillemot F, Kolatkar PR, Jauch R, et al. 2013. TherMos: estimating protein-DNA binding energies from in vivo binding profiles. Nucleic Acids Res 41: 5555-5568.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 5555-5568
-
-
Sun, W.1
Hu, X.2
Lim, M.H.K.3
Ng, C.K.L.4
Choo, S.H.5
Castro, D.S.6
Drechsel, D.7
Guillemot, F.8
Kolatkar, P.R.9
Jauch, R.10
-
38
-
-
0036242296
-
A tamoxifen-inducible chimeric Cre recombinase specifically effective in the fetal and adult mouse liver
-
Tannour-Louet M, Porteu A, Vaulont S, Kahn A, Vasseur-Cognet M. 2002. A tamoxifen-inducible chimeric Cre recombinase specifically effective in the fetal and adult mouse liver. Hepatology 35: 1072-1081.
-
(2002)
Hepatology
, vol.35
, pp. 1072-1081
-
-
Tannour-Louet, M.1
Porteu, A.2
Vaulont, S.3
Kahn, A.4
Vasseur-Cognet, M.5
-
39
-
-
38349018723
-
On the relation between promoter divergence and gene expression evolution
-
Tirosh I, Weinberger A, Bezalel D, Kaganovich M, Barkai N. 2008. On the relation between promoter divergence and gene expression evolution. Mol Syst Biol 4: 159.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 159
-
-
Tirosh, I.1
Weinberger, A.2
Bezalel, D.3
Kaganovich, M.4
Barkai, N.5
-
40
-
-
77951820899
-
Fast and SNP-tolerant detection of complex variants and splicing in short reads
-
Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
-
(2010)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
|