-
1
-
-
4544295425
-
Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR
-
Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE. 2004. Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science 305(5691): 1743-1746.
-
(2004)
Science
, vol.305
, Issue.5691
, pp. 1743-1746
-
-
Ao, W.1
Gaudet, J.2
Kent, W.J.3
Muttumu, S.4
Mango, S.E.5
-
2
-
-
84907420733
-
Regulatory analysis of the C. Elegans genome with spatiotemporal resolution
-
Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D et al. 2014. Regulatory analysis of the C. Elegans genome with spatiotemporal resolution. Nature 512(7515): 400-405.
-
(2014)
Nature
, vol.512
, Issue.7515
, pp. 400-405
-
-
Araya, C.L.1
Kawli, T.2
Kundaje, A.3
Jiang, L.4
Wu, B.5
Vafeados, D.6
Terrell, R.7
Weissdepp, P.8
Gevirtzman, L.9
Mace, D.10
-
3
-
-
77952262903
-
Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network
-
Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, Walhout AJ. 2010. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol 6: 367.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 367
-
-
Arda, H.E.1
Taubert, S.2
Macneil, L.T.3
Conine, C.C.4
Tsuda, B.5
Van Gilst, M.6
Sequerra, R.7
Doucette-Stamm, L.8
Yamamoto, K.R.9
Walhout, A.J.10
-
4
-
-
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 et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1): 25-29.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, 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
-
5
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X et al. 2009. Diversity and complexity in DNA recognition by transcription factors. Science 324(5935): 1720-1723.
-
(2009)
Science
, vol.324
, Issue.5935
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
6
-
-
84866937220
-
Inferring direct DNA binding from ChIP-seq
-
Bailey TL, Machanick P. 2012. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res 40(17): e128.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.17
-
-
Bailey, T.L.1
Machanick, P.2
-
7
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer MA, Tavazoie S. 2004. Predicting gene expression from sequence. Cell 117(2): 185-198.
-
(2004)
Cell
, vol.117
, Issue.2
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
8
-
-
42449084992
-
The magic of the hypoxia-signaling cascade
-
Benizri E, Ginouves A, Berra E. 2008. The magic of the hypoxia-signaling cascade. Cell Mol Life Sci 65(7-8): 1133-1149.
-
(2008)
Cell Mol Life Sci
, vol.65
, Issue.7-8
, pp. 1133-1149
-
-
Benizri, E.1
Ginouves, A.2
Berra, E.3
-
9
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
-
Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Pena-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET et al. 2008. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133(7): 1266-1276.
-
(2008)
Cell
, vol.133
, Issue.7
, pp. 1266-1276
-
-
Berger, M.F.1
Badis, G.2
Gehrke, A.R.3
Talukder, S.4
Philippakis, A.A.5
Pena-Castillo, L.6
Alleyne, T.M.7
Mnaimneh, S.8
Botvinnik, O.B.9
Chan, E.T.10
-
10
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, 3rd, Bulyk ML. 2006. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 24(11): 1429-1435.
-
(2006)
Nat Biotechnol
, vol.24
, Issue.11
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
He, F.S.4
Estep, P.W.5
Bulyk, M.L.6
-
11
-
-
80052507407
-
E2F transcription factor-1 regulates oxidative metabolism
-
Blanchet E, Annicotte JS, Lagarrigue S, Aguilar V, Clape C, Chavey C, Fritz V, Casas F, Apparailly F, Auwerx J et al. 2011. E2F transcription factor-1 regulates oxidative metabolism. Nature cell biology 13(9): 1146-1152.
-
(2011)
Nature Cell Biology
, vol.13
, Issue.9
, pp. 1146-1152
-
-
Blanchet, E.1
Annicotte, J.S.2
Lagarrigue, S.3
Aguilar, V.4
Clape, C.5
Chavey, C.6
Fritz, V.7
Casas, F.8
Apparailly, F.9
Auwerx, J.10
-
12
-
-
84907263788
-
Comparative analysis of regulatory information and circuits across distant species
-
Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L et al. 2014. Comparative analysis of regulatory information and circuits across distant species. Nature 512(7515): 453-456.
-
(2014)
Nature
, vol.512
, Issue.7515
, pp. 453-456
-
-
Boyle, A.P.1
Araya, C.L.2
Brdlik, C.3
Cayting, P.4
Cheng, C.5
Cheng, Y.6
Gardner, K.7
Hillier, L.W.8
Janette, J.9
Jiang, L.10
-
13
-
-
0032509302
-
Genome sequence of the nematode C. Elegans: A platform for investigating biology
-
C.elegans consortium. 1998. Genome sequence of the nematode C. Elegans: A platform for investigating biology. Science 282(5396): 2012-2018.
-
(1998)
Science
, vol.282
, Issue.5396
, pp. 2012-2018
-
-
-
14
-
-
0036120604
-
Structure of the DNA-bound T-box domain of human TBX3, a transcription factor responsible for ulnar-mammary syndrome
-
Coll M, Seidman JG, Muller CW. 2002. Structure of the DNA-bound T-box domain of human TBX3, a transcription factor responsible for ulnar-mammary syndrome. Structure 10(3): 343-356.
-
(2002)
Structure
, vol.10
, Issue.3
, pp. 343-356
-
-
Coll, M.1
Seidman, J.G.2
Muller, C.W.3
-
15
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: A sequence logo generator. Genome Res 14(6): 1188-1190.
-
(2004)
Genome Res
, vol.14
, Issue.6
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
16
-
-
84929194218
-
YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities
-
de Boer CG, Hughes TR. 2011. YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities. C.elegans consortium. 1998.
-
(2011)
C.Elegans Consortium.
, pp. 1998
-
-
De Boer, C.G.1
Hughes, T.R.2
-
17
-
-
33744972290
-
A gene-centered C. Elegans protein-DNA interaction network
-
Genome seqke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA et al. 2006. A gene-centered C. Elegans protein-DNA interaction network. Cell 125(6): 1193-1205.
-
(2006)
Cell
, vol.125
, Issue.6
, pp. 1193-1205
-
-
Genome Seqke, B.1
Mukhopadhyay, A.2
Ao, W.3
Elewa, A.M.4
Grove, C.A.5
Martinez, N.J.6
Sequerra, R.7
Doucette-Stamm, L.8
Reece-Hoyes, J.S.9
Hope, I.A.10
-
18
-
-
34547147926
-
Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae
-
Dobi KC, Winston F. 2007. Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Mol Cell Biol 27(15): 5575-5586.
-
(2007)
Mol Cell Biol
, vol.27
, Issue.15
, pp. 5575-5586
-
-
Dobi, K.C.1
Winston, F.2
-
19
-
-
7444256641
-
A first version of the Caenorhabditis elegans Promoterome
-
Dupuy D, Li QR, Deplancke B, Boxem M, Hao T, Lamesch P, Sequerra R, Bosak S, Doucette-Stamm L, Hope IA et al. 2004. A first version of the Caenorhabditis elegans Promoterome. Genome research 14(10B): 2169-2175.
-
(2004)
Genome Research
, vol.14
, Issue.10
, pp. 2169-2175
-
-
Dupuy, D.1
Li, Q.R.2
Deplancke, B.3
Boxem, M.4
Hao, T.5
Lamesch, P.6
Sequerra, R.7
Bosak, S.8
Doucette-Stamm, L.9
Hope, I.A.10
-
21
-
-
0035578168
-
Comparing nuclear receptors in worms, flies and humans
-
Enmark E, Gustafsson JA. 2001. Comparing nuclear receptors in worms, flies and humans. Trends in pharmacological sciences 22(12): 611-615.
-
(2001)
Trends in Pharmacological Sciences
, vol.22
, Issue.12
, pp. 611-615
-
-
Enmark, E.1
Gustafsson, J.A.2
-
22
-
-
0028782779
-
Integrated control of cell proliferation and cell death by the c-myc oncogene
-
Evan G, Harrington E, Fanidi A, Land H, Amati B, Bennett M. 1994. Integrated control of cell proliferation and cell death by the c-myc oncogene. Philosophical transactions of the Royal Society of London 345(1313): 269-275.
-
(1994)
Philosophical Transactions of the Royal Society of London
, vol.345
, Issue.1313
, pp. 269-275
-
-
Evan, G.1
Harrington, E.2
Fanidi, A.3
Land, H.4
Amati, B.5
Bennett, M.6
-
23
-
-
75549090603
-
The Pfam protein families database
-
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K et al. 2010. The Pfam protein families database. Nucleic Acids Res 38(Database issue): D211-222.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D211-D222
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
Pollington, J.E.6
Gavin, O.L.7
Gunasekaran, P.8
Ceric, G.9
Forslund, K.10
-
24
-
-
33845691406
-
Defining the transcriptional redundancy of early bodywall muscle development in C. Elegans: Evidence for a unified theory of animal muscle development
-
Fukushige T, Brodigan TM, Schriefer LA, Waterston RH, Krause M. 2006. Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development. Genes Dev 20(24): 3395-3406.
-
(2006)
Genes Dev
, vol.20
, Issue.24
, pp. 3395-3406
-
-
Fukushige, T.1
Brodigan, T.M.2
Schriefer, L.A.3
Waterston, R.H.4
Krause, M.5
-
26
-
-
0036468361
-
Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4
-
Gaudet J, Mango SE. 2002. Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295(5556): 821-825.
-
(2002)
Science
, vol.295
, Issue.5556
, pp. 821-825
-
-
Gaudet, J.1
Mango, S.E.2
-
27
-
-
77951612492
-
Recent advances in understanding the molecular mechanisms regulating C. Elegans transcription
-
Gaudet J, McGhee JD. 2010. Recent advances in understanding the molecular mechanisms regulating C. Elegans transcription. Dev Dyn 239(5): 1388-1404.
-
(2010)
Dev Dyn
, vol.239
, Issue.5
, pp. 1388-1404
-
-
Gaudet, J.1
McGhee, J.D.2
-
28
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
-
Gerstein MB, Lu ZJ Van, Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K et al. 2010. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330(6012): 1775-1787.
-
(2010)
Science
, vol.330
, Issue.6012
, pp. 1775-1787
-
-
Gerstein, M.B.1
Zj Van, L.2
Nostrand, E.L.3
Cheng, C.4
Arshinoff, B.I.5
Liu, T.6
Yip, K.Y.7
Robilotto, R.8
Rechtsteiner, A.9
Ikegami, K.10
-
29
-
-
79953300078
-
FIMO: Scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS. 2011. FIMO: Scanning for occurrences of a given motif. Bioinformatics 27(7): 1017-1018.
-
(2011)
Bioinformatics
, vol.27
, Issue.7
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
30
-
-
67650594823
-
A multiparameter network reveals extensive divergence between C. Elegans bHLH transcription factors
-
Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ. 2009. A multiparameter network reveals extensive divergence between C. Elegans bHLH transcription factors. Cell 138(2): 314-327.
-
(2009)
Cell
, vol.138
, Issue.2
, pp. 314-327
-
-
Grove, C.A.1
De Masi, F.2
Barrasa, M.I.3
Newburger, D.E.4
Alkema, M.J.5
Bulyk, M.L.6
Walhout, A.J.7
-
31
-
-
51349094325
-
Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution
-
Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP. 2008. Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution. BMC genomics 9: 399.
-
(2008)
BMC Genomics
, vol.9
, pp. 399
-
-
Haerty, W.1
Artieri, C.2
Khezri, N.3
Singh, R.S.4
Gupta, B.P.5
-
32
-
-
79960937846
-
DAF-12 regulates a connected network of genes to ensure robust developmental decisions
-
Hochbaum D, Zhang Y, Stuckenholz C, Labhart P, Alexiadis V, Martin R, Knolker HJ, Fisher AL. 2011. DAF-12 regulates a connected network of genes to ensure robust developmental decisions. PLoS genetics 7(7): e1002179.
-
(2011)
Plos Genetics
, vol.7
, Issue.7
-
-
Hochbaum, D.1
Zhang, Y.2
Stuckenholz, C.3
Labhart, P.4
Alexiadis, V.5
Martin, R.6
Knolker, H.J.7
Fisher, A.L.8
-
33
-
-
84898957996
-
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation
-
Jiang P, Singh M. 2014. CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic acids research 42(5): 2833-2847.
-
(2014)
Nucleic Acids Research
, vol.42
, Issue.5
, pp. 2833-2847
-
-
Jiang, P.1
Singh, M.2
-
34
-
-
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(1-2): 327-339.
-
(2013)
Cell
, vol.152
, Issue.1-2
, 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
-
35
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in KEGG
-
(Database issue)
-
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42(Database issue): D199-205.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
Furumichi, M.5
Tanabe, M.6
-
36
-
-
79959459272
-
Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays
-
Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR. 2011. Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Res 39(11): 4680-4690.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.11
, pp. 4680-4690
-
-
Lam, K.N.1
Van Bakel, H.2
Cote, A.G.3
Van Der Ven, A.4
Hughes, T.R.5
-
37
-
-
84865777819
-
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
-
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P et al. 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22(9): 1813-1831.
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1813-1831
-
-
Landt, S.G.1
Marinov, G.K.2
Kundaje, A.3
Kheradpour, P.4
Pauli, F.5
Batzoglou, S.6
Bernstein, B.E.7
Bickel, P.8
Brown, J.B.9
Cayting, P.10
-
38
-
-
33749325080
-
Genomic evolution of Hox gene clusters
-
Lemons D, McGinnis W. 2006. Genomic evolution of Hox gene clusters. Science 313(5795): 1918-1922.
-
(2006)
Science
, vol.313
, Issue.5795
, pp. 1918-1922
-
-
Lemons, D.1
McGinnis, W.2
-
39
-
-
59949083141
-
Transcriptional regulation and stabilization of left-right neuronal identity in C. Elegans
-
Lesch BJ, Gehrke AR, Bulyk ML, Bargmann CI. 2009. Transcriptional regulation and stabilization of left-right neuronal identity in C. Elegans. Genes Dev 23(3): 345-358.
-
(2009)
Genes Dev
, vol.23
, Issue.3
, pp. 345-358
-
-
Lesch, B.J.1
Gehrke, A.R.2
Bulyk, M.L.3
Bargmann, C.I.4
-
40
-
-
84862221167
-
SMART 7: Recent updates to the protein domain annotation resource
-
(Database issue)
-
Letunic I, Doerks T, Bork P. 2012. SMART 7: Recent updates to the protein domain annotation resource. Nucleic acids research 40(Database issue): D302-305.
-
(2012)
Nucleic Acids Research
, vol.40
, pp. D302-D305
-
-
Letunic, I.1
Doerks, T.2
Bork, P.3
-
41
-
-
84865146725
-
C. Elegans PAT-9 is a nuclear zinc finger protein critical for the assembly of muscle attachments
-
Liu Q, Jones TI, Bachmann RA, Meghpara M, Rogowski L, Williams BD, Jones PL. 2012. C. elegans PAT-9 is a nuclear zinc finger protein critical for the assembly of muscle attachments. Cell and bioscience 2(1): 18.
-
(2012)
Cell and Bioscience
, vol.2
, Issue.1
, pp. 18
-
-
Liu, Q.1
Jones, T.I.2
Bachmann, R.A.3
Meghpara, M.4
Rogowski, L.5
Williams, B.D.6
Jones, P.L.7
-
42
-
-
33749381311
-
Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
-
Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. 2006. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res 16(12): 1517-1528.
-
(2006)
Genome Res
, vol.16
, Issue.12
, pp. 1517-1528
-
-
Liu, X.1
Lee, C.K.2
Granek, J.A.3
Clarke, N.D.4
Lieb, J.D.5
-
43
-
-
84891808382
-
JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles
-
(Database issue)
-
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H et al. 2014. JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42(Database issue): D142-147.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
Buchman, S.7
Chen, C.Y.8
Chou, A.9
Ienasescu, H.10
-
44
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
(Database issue)
-
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(Database issue): D108-110.
-
(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
-
46
-
-
84907485371
-
Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module
-
McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW. 2014. Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module. Cell 159(1): 58-68.
-
(2014)
Cell
, vol.159
, Issue.1
, pp. 58-68
-
-
McKeown, A.N.1
Bridgham, J.T.2
Erson, D.W.3
Murphy, M.N.4
Ortlund, E.A.5
Thornton, J.W.6
-
48
-
-
33750930653
-
Design of a combinatorial DNA microarray for protein-DNA interaction studies
-
Mintseris J, Eisen MB. 2006. Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics 7: 429.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 429
-
-
Mintseris, J.1
Eisen, M.B.2
-
49
-
-
0039706410
-
Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor
-
Muller CW, Herrmann BG. 1997. Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. Nature 389(6653): 884-888.
-
(1997)
Nature
, vol.389
, Issue.6653
, pp. 884-888
-
-
Muller, C.W.1
Herrmann, B.G.2
-
50
-
-
84929152789
-
C2H2 zinc finger proteins greatly expand the human regulatory lexicon
-
Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM et al. 2015. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol.
-
(2015)
Nat Biotechnol
-
-
Najafabadi, H.S.1
Mnaimneh, S.2
Schmitges, F.W.3
Garton, M.4
Lam, K.N.5
Yang, A.6
Albu, M.7
Weirauch, M.T.8
Radovani, E.9
Kim, P.M.10
-
51
-
-
84880681583
-
DNA-binding specificity changes in the evolution of forkhead transcription factors
-
Nakagawa S, Gisselbrecht SS, Rogers JM, Hartl DL, Bulyk ML. 2013. DNA-binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci U S A 110(30): 12349-12354.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.30
, pp. 12349-12354
-
-
Nakagawa, S.1
Gisselbrecht, S.S.2
Rogers, J.M.3
Hartl, D.L.4
Bulyk, M.L.5
-
52
-
-
0037044839
-
Sex-specific gene regulation. The Doublesex DM motif is a bipartite DNA-binding domain
-
Narendra U, Zhu L, Li B, Wilken J, Weiss MA. 2002. Sex-specific gene regulation. The Doublesex DM motif is a bipartite DNA-binding domain. J Biol Chem 277(45): 43463-43473.
-
(2002)
J Biol Chem
, vol.277
, Issue.45
, pp. 43463-43473
-
-
Narendra, U.1
Zhu, L.2
Li, B.3
Wilken, J.4
Weiss, M.A.5
-
53
-
-
79551614016
-
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. Elegans
-
Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E et al. 2011. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. Elegans.Genome research 21(2): 245-254.
-
(2011)
Genome Research
, vol.21
, Issue.2
, pp. 245-254
-
-
Niu, W.1
Lu, Z.J.2
Zhong, M.3
Sarov, M.4
Murray, J.I.5
Brdlik, C.M.6
Janette, J.7
Chen, C.8
Alves, P.9
Preston, E.10
-
54
-
-
32244446124
-
Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. Elegans
-
Pauli F, Liu Y, Kim YA, Chen PJ, Kim SK. 2006. Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. Elegans. Development 133(2): 287-295.
-
(2006)
Development
, vol.133
, Issue.2
, pp. 287-295
-
-
Pauli, F.1
Liu, Y.2
Kim, Y.A.3
Chen, P.J.4
Kim, S.K.5
-
55
-
-
84880427394
-
A compendium of RNA-binding motifs for decoding gene regulation
-
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A et al. 2013. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499(7457): 172-177.
-
(2013)
Nature
, vol.499
, Issue.7457
, pp. 172-177
-
-
Ray, D.1
Kazan, H.2
Cook, K.B.3
Weirauch, M.T.4
Najafabadi, H.S.5
Li, X.6
Gueroussov, S.7
Albu, M.8
Zheng, H.9
Yang, A.10
-
56
-
-
67649892615
-
The C. Elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
-
Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJ. 2009. The C. Elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res 37(11): 3689-3698.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.11
, pp. 3689-3698
-
-
Reece-Hoyes, J.S.1
Deplancke, B.2
Barrasa, M.I.3
Hatzold, J.4
Smit, R.B.5
Arda, H.E.6
Pope, P.A.7
Gaudet, J.8
Conradt, B.9
Walhout, A.J.10
-
57
-
-
33744976395
-
A compendium of Caenorhabditis elegans regulatory transcription factors: A resource for mapping transcription regulatory networks
-
R110
-
Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ. 2005. A compendium of Caenorhabditis elegans regulatory transcription factors: A resource for mapping transcription regulatory networks. Genome Biol 6(13): R110.
-
(2005)
Genome Biol
, vol.6
, Issue.13
-
-
Reece-Hoyes, J.S.1
Deplancke, B.2
Shingles, J.3
Grove, C.A.4
Hope, I.A.5
Walhout, A.J.6
-
58
-
-
82355175168
-
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
-
Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, Pesyna C, Dekker J, Myers CL, Walhout AJ. 2011. Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat Methods 8(12): 1059-1064.
-
(2011)
Nat Methods
, vol.8
, Issue.12
, pp. 1059-1064
-
-
Reece-Hoyes, J.S.1
Diallo, A.2
Lajoie, B.3
Kent, A.4
Shrestha, S.5
Kadreppa, S.6
Pesyna, C.7
Dekker, J.8
Myers, C.L.9
Walhout, A.J.10
-
59
-
-
84891668199
-
Extensive rewiring and complex evolutionary dynamics in a C. Elegans multiparameter transcription factor network
-
Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR et al. 2013. Extensive rewiring and complex evolutionary dynamics in a C. Elegans multiparameter transcription factor network. Mol Cell 51(1): 116-127.
-
(2013)
Mol Cell
, vol.51
, Issue.1
, pp. 116-127
-
-
Reece-Hoyes, J.S.1
Pons, C.2
Diallo, A.3
Mori, A.4
Shrestha, S.5
Kadreppa, S.6
Nelson, J.7
Diprima, S.8
Dricot, A.9
Lajoie, B.R.10
-
61
-
-
21244454411
-
Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes
-
Robinson-Rechavi M, Maina CV, Gissendanner CR, Laudet V, Sluder A. 2005. Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes. Journal of molecular evolution 60(5): 577-586.
-
(2005)
Journal of Molecular Evolution
, vol.60
, Issue.5
, pp. 577-586
-
-
Robinson-Rechavi, M.1
Maina, C.V.2
Gissendanner, C.R.3
Laudet, V.4
Sluder, A.5
-
62
-
-
84865266808
-
A genome-scale resource for in vivo tag-based protein function exploration in C. Elegans
-
Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M et al. 2012. A genome-scale resource for in vivo tag-based protein function exploration in C. Elegans. Cell 150(4): 855-866.
-
(2012)
Cell
, vol.150
, Issue.4
, pp. 855-866
-
-
Sarov, M.1
Murray, J.I.2
Schanze, K.3
Pozniakovski, A.4
Niu, W.5
Angermann, K.6
Hasse, S.7
Rupprecht, M.8
Vinis, E.9
Tinney, M.10
-
63
-
-
84885058074
-
Early evolution of the T-box transcription factor family
-
Sebe-Pedros A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gomez-Skarmeta JL et al. 2013. Early evolution of the T-box transcription factor family. Proceedings of the National Academy of Sciences of the United States of America 110(40): 16050-16055.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, Issue.40
, pp. 16050-16055
-
-
Sebe-Pedros, A.1
Ariza-Cosano, A.2
Weirauch, M.T.3
Leininger, S.4
Yang, A.5
Torruella, G.6
Adamski, M.7
Adamska, M.8
Hughes, T.R.9
Gomez-Skarmeta, J.L.10
-
64
-
-
84893863046
-
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
-
Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK. 2014. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol 32(2): 171-178.
-
(2014)
Nat Biotechnol
, vol.32
, Issue.2
, pp. 171-178
-
-
Sherwood, R.I.1
Hashimoto, T.2
O'donnell, C.W.3
Lewis, S.4
Barkal, A.A.5
Van Hoff, J.P.6
Karun, V.7
Jaakkola, T.8
Gifford, D.K.9
-
65
-
-
84906790368
-
Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding
-
Siggers T, Reddy J, Barron B, Bulyk ML. 2014. Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Mol Cell 55(4): 640-648.
-
(2014)
Mol Cell
, vol.55
, Issue.4
, pp. 640-648
-
-
Siggers, T.1
Reddy, J.2
Barron, B.3
Bulyk, M.L.4
-
66
-
-
58149218155
-
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
-
Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F et al. 2009. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods 6(1): 47-54.
-
(2009)
Nat Methods
, vol.6
, Issue.1
, pp. 47-54
-
-
Simonis, N.1
Rual, J.F.2
Carvunis, A.R.3
Tasan, M.4
Lemmens, I.5
Hirozane-Kishikawa, T.6
Hao, T.7
Sahalie, J.M.8
Venkatesan, K.9
Gebreab, F.10
-
67
-
-
62549085647
-
Caenorhabditis elegans cisRED: A catalogue of conserved genomic elements
-
Sleumer MC, Bilenky M, He A, Robertson G, Thiessen N, Jones SJ. 2009. Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. Nucleic acids research 37(4): 1323-1334.
-
(2009)
Nucleic Acids Research
, vol.37
, Issue.4
, pp. 1323-1334
-
-
Sleumer, M.C.1
Bilenky, M.2
He, A.3
Robertson, G.4
Thiessen, N.5
Jones, S.J.6
-
68
-
-
80053539409
-
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
-
Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Graf S, Huss M, Keefe D et al. 2011. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome research 21(10): 1757-1767.
-
(2011)
Genome Research
, vol.21
, Issue.10
, pp. 1757-1767
-
-
Song, L.1
Zhang, Z.2
Grasfeder, L.L.3
Boyle, A.P.4
Giresi, P.G.5
Lee, B.K.6
Sheffield, N.C.7
Graf, S.8
Huss, M.9
Keefe, D.10
-
69
-
-
37349114118
-
Nuclear receptors: Decoding metabolic disease
-
Sonoda J, Pei L, Evans RM. 2008. Nuclear receptors: Decoding metabolic disease. FEBS Lett 582(1): 2-9.
-
(2008)
FEBS Lett
, vol.582
, Issue.1
, pp. 2-9
-
-
Sonoda, J.1
Pei, L.2
Evans, R.M.3
-
70
-
-
79551613376
-
A spatial and temporal map of C. Elegans gene expression
-
Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J et al. 2010. A spatial and temporal map of C. Elegans gene expression. Genome Res 21(2): 325-341.
-
(2010)
Genome Res
, vol.21
, Issue.2
, pp. 325-341
-
-
Spencer, W.C.1
Zeller, G.2
Watson, J.D.3
Henz, S.R.4
Watkins, K.L.5
McWhirter, R.D.6
Petersen, S.7
Sreedharan, V.T.8
Widmer, C.9
Jo, J.10
-
71
-
-
77953689090
-
Structural basis of TBX5-DNA recognition: The T-box domain in its DNA-bound and -unbound form
-
Stirnimann CU, Ptchelkine D, Grimm C, Muller CW. 2002. Structural basis of TBX5-DNA recognition: the T-box domain in its DNA-bound and -unbound form. Journal of molecular biology 400(1): 71-81.
-
(2002)
Journal of Molecular Biology
, vol.400
, Issue.1
, pp. 71-81
-
-
Stirnimann, C.U.1
Ptchelkine, D.2
Grimm, C.3
Muller, C.W.4
-
72
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo GD. 2000. DNA binding sites: Representation and discovery. Bioinformatics 16(1): 16-23.
-
(2000)
Bioinformatics
, vol.16
, Issue.1
, pp. 16-23
-
-
Stormo, G.D.1
-
73
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart JM, Segal E, Koller D, Kim SK. 2003. A gene-coexpression network for global discovery of conserved genetic modules. Science 302(5643): 249-255.
-
(2003)
Science
, vol.302
, Issue.5643
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
75
-
-
0033713259
-
The RFX-type transcription factor DAF-19 regulates sensory neuron cilium formation in C. Elegans
-
Swoboda P, Adler HT, Thomas JH. 2000. The RFX-type transcription factor DAF-19 regulates sensory neuron cilium formation in C. Elegans. Mol Cell 5(3): 411-421.
-
(2000)
Mol Cell
, vol.5
, Issue.3
, pp. 411-421
-
-
Swoboda, P.1
Adler, H.T.2
Thomas, J.H.3
-
76
-
-
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(4): 663-676.
-
(2006)
Cell
, vol.126
, Issue.4
, pp. 663-676
-
-
Takahashi, K.1
Yamanaka, S.2
-
77
-
-
84887478181
-
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
-
Teytelman L, Thurtle DM, Rine J, van Oudenaarden A. 2013. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A 110(46): 18602-18607.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.46
, pp. 18602-18607
-
-
Teytelman, L.1
Thurtle, D.M.2
Rine, J.3
Van Oudenaarden, A.4
-
79
-
-
84873594686
-
Evaluation of methods for modeling transcription factor sequence specificity
-
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S et al. 2013. Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol 31(2): 126-134.
-
(2013)
Nat Biotechnol
, vol.31
, Issue.2
, pp. 126-134
-
-
Weirauch, M.T.1
Cote, A.2
Norel, R.3
Annala, M.4
Zhao, Y.5
Riley, T.R.6
Saez-Rodriguez, J.7
Cokelaer, T.8
Vedenko, A.9
Talukder, S.10
-
80
-
-
84856660311
-
A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution
-
Weirauch MT, Hughes TR. 2011. A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Subcell Biochem 52: 25-73.
-
(2011)
Subcell Biochem
, vol.52
, pp. 25-73
-
-
Weirauch, M.T.1
Hughes, T.R.2
-
81
-
-
84907413210
-
Determination and inference of eukaryotic transcription factor sequence specificity
-
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K et al. 2014. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158(6): 1431-1443.
-
(2014)
Cell
, vol.158
, Issue.6
, pp. 1431-1443
-
-
Weirauch, M.T.1
Yang, A.2
Albu, M.3
Cote, A.G.4
Montenegro-Montero, A.5
Drewe, P.6
Najafabadi, H.S.7
Lambert, S.A.8
Mann, I.9
Cook, K.10
-
83
-
-
84875985531
-
Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans
-
Zhao G, Ihuegbu N, Lee M, Schriefer L, Wang T, Stormo GD. 2012. Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. G3 (Bethesda) 2(4): 469-481.
-
(2012)
G3 (Bethesda)
, vol.2
, Issue.4
, pp. 469-481
-
-
Zhao, G.1
Ihuegbu, N.2
Lee, M.3
Schriefer, L.4
Wang, T.5
Stormo, G.D.6
-
84
-
-
33847727867
-
Identification of muscle-specific regulatory modules in Caenorhabditis elegans
-
Zhao G, Schriefer LA, Stormo GD. 2007. Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome research 17(3): 348-357.
-
(2007)
Genome Research
, vol.17
, Issue.3
, pp. 348-357
-
-
Zhao, G.1
Schriefer, L.A.2
Stormo, G.D.3
-
86
-
-
79958115193
-
Quantitative analysis demonstrates most transcription factors require only simple models of specificity
-
Zhao Y, Stormo GD. 2011. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol 29(6): 480-483.
-
(2011)
Nat Biotechnol
, vol.29
, Issue.6
, pp. 480-483
-
-
Zhao, Y.1
Stormo, G.D.2
-
87
-
-
0034661247
-
Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers
-
Zhu L, Wilken J, Phillips NB, Narendra U, Chan G, Stratton SM, Kent SB, Weiss MA. 2000. Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers. Genes Dev 14(14): 1750-1764.
-
(2000)
Genes Dev
, vol.14
, Issue.14
, pp. 1750-1764
-
-
Zhu, L.1
Wilken, J.2
Phillips, N.B.3
Narendra, U.4
Chan, G.5
Stratton, S.M.6
Kent, S.B.7
Weiss, M.A.8
|