-
1
-
-
84883788052
-
Mapping yeast transcriptional networks
-
Hughes TR, de Boer CG. 2013. Mapping yeast transcriptional networks. Genetics 195: 9-36. http://dx.doi.org/10.1534/genetics.113.153262.
-
(2013)
Genetics
, vol.195
, pp. 9-36
-
-
Hughes, T.R.1
de Boer, C.G.2
-
2
-
-
84961816668
-
The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network
-
Liu G, Marras A, Nielsen J. 2014. The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network. Quant Biol 2: 30-46.
-
(2014)
Quant Biol
, vol.2
, pp. 30-46
-
-
Liu, G.1
Marras, A.2
Nielsen, J.3
-
3
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309. http://dx.doi.org/10.1126/science.290.5500.2306.
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
4
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104. http://dx.doi.org/10.1038/nature02800.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gifford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
5
-
-
0034074199
-
Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress
-
Garcia-Gimeno MA, Struhl K. 2000. Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress. Mol Cell Biol 20: 4340-4349. http://dx.doi.org/10.1128/MCB.20.12.4340-4349.2000.
-
(2000)
Mol Cell Biol
, vol.20
, pp. 4340-4349
-
-
Garcia-Gimeno, M.A.1
Struhl, K.2
-
6
-
-
0036289351
-
Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress
-
Proft M, Struhl K. 2002. Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell 9: 1307-1317. http://dx.doi.org/10.1016/S1097-2765(02)00557-9.
-
(2002)
Mol Cell
, vol.9
, pp. 1307-1317
-
-
Proft, M.1
Struhl, K.2
-
7
-
-
23844449971
-
Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae
-
Proft M, Gibbons FD, Copeland M, Roth FP, Struhl K. 2005. Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. Eukaryot Cell 4: 1343-1352. http://dx.doi.org/10.1128/EC.4.8.1343-1352.2005.
-
(2005)
Eukaryot Cell
, vol.4
, pp. 1343-1352
-
-
Proft, M.1
Gibbons, F.D.2
Copeland, M.3
Roth, F.P.4
Struhl, K.5
-
8
-
-
84883186434
-
Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae
-
Cook KE, O’Shea EK. 2012. Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae. G3 (Bethesda) 2: 1129-1136. http://dx.doi.org/10.1534/g3.112.003251.
-
(2012)
G3 (Bethesda)
, vol.2
, pp. 1129-1136
-
-
Cook, K.E.1
O’Shea, E.K.2
-
9
-
-
77956513446
-
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction
-
Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD. 2010. Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics 9: 2076-2088. http://dx.doi.org/10.1074/mcp.M000116-MCP201.
-
(2010)
Mol Cell Proteomics
, vol.9
, pp. 2076-2088
-
-
Saleem, R.A.1
Rogers, R.S.2
Ratushny, A.V.3
Dilworth, D.J.4
Shannon, P.T.5
Shteynberg, D.6
Wan, Y.7
Moritz, R.L.8
Nesvizhskii, A.I.9
Rachubinski, R.A.10
Aitchison, J.D.11
-
10
-
-
0031784028
-
The 2 micrometer plasmid stability system: Analyses of the interactions among plasmid-and host-encoded components
-
Velmurugan S, Ahn YT, Yang XM, Wu XL, Jayaram M. 1998. The 2 micrometer plasmid stability system: analyses of the interactions among plasmid-and host-encoded components. Mol Cell Biol 18: 7466-7477. http://dx.doi.org/10.1128/MCB.18.12.7466.
-
(1998)
Mol Cell Biol
, vol.18
, pp. 7466-7477
-
-
Velmurugan, S.1
Ahn, Y.T.2
Yang, X.M.3
Wu, X.L.4
Jayaram, M.5
-
11
-
-
0033178880
-
New yeast genes important for chromosome integrity and segregation identified by dosage effects on genome stability
-
Ouspenski II, Elledge SJ, Brinkley BR. 1999. New yeast genes important for chromosome integrity and segregation identified by dosage effects on genome stability. Nucleic Acids Res 27: 3001-3008. http://dx.doi.org/10.1093/nar/27.15.3001.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3001-3008
-
-
Ouspenski, I.I.1
Elledge, S.J.2
Brinkley, B.R.3
-
12
-
-
84857473389
-
The bZIP transcription factor Rca1p is a central regulator of a novel CO2 sensing pathway in yeast
-
Cottier F, Raymond M, Kurzai O, Bolstad M, Leewattanapasuk W, Jiménez-López C, Lorenz MC, Sanglard D, Váchová L, Pavelka N, Palková Z, Mühlschlegel FA. 2012. The bZIP transcription factor Rca1p is a central regulator of a novel CO2 sensing pathway in yeast. PLoS Pathog 8: e1002485. http://dx.doi.org/10.1371/journal.ppat.1002485.
-
(2012)
PLoS Pathog
, vol.8
-
-
Cottier, F.1
Raymond, M.2
Kurzai, O.3
Bolstad, M.4
Leewattanapasuk, W.5
Jiménez-López, C.6
Lorenz, M.C.7
Sanglard, D.8
Váchová, L.9
Pavelka, N.10
Palková, Z.11
Mühlschlegel, F.A.12
-
13
-
-
84863335386
-
Identification and functional characterization of Rca1, a transcription factor involved in both antifungal susceptibility and host response in Candida albicans
-
Vandeputte P, Pradervand S, Ischer F, Coste AT, Ferrari S, Harshman K, Sanglard D. 2012. Identification and functional characterization of Rca1, a transcription factor involved in both antifungal susceptibility and host response in Candida albicans. Eukaryot Cell 11: 916-931. http://dx.doi.org/10.1128/EC.00134-12.
-
(2012)
Eukaryot Cell
, vol.11
, pp. 916-931
-
-
Vandeputte, P.1
Pradervand, S.2
Ischer, F.3
Coste, A.T.4
Ferrari, S.5
Harshman, K.6
Sanglard, D.7
-
14
-
-
84861927480
-
New regulators of biofilm development in Candida glabrata
-
Riera M, Mogensen E, d’Enfert C, Janbon G. 2012. New regulators of biofilm development in Candida glabrata. Res Microbiol 163: 297-307. http://dx.doi.org/10.1016/j.resmic.2012.02.005.
-
(2012)
Res Microbiol
, vol.163
, pp. 297-307
-
-
Riera, M.1
Mogensen, E.2
d’Enfert, C.3
Janbon, G.4
-
15
-
-
83255164884
-
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
-
Rhee HS, Pugh BF. 2011. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147: 1408-1419. http://dx.doi.org/10.1016/j.cell.2011.11.013.
-
(2011)
Cell
, vol.147
, pp. 1408-1419
-
-
Rhee, H.S.1
Pugh, B.F.2
-
16
-
-
78649832864
-
Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast
-
Fendt SM, Oliveira AP, Christen S, Picotti P, Dechant RC, Sauer U. 2010. Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol Syst Biol 6: 432. http://dx.doi.org/10.1038/msb.2010.91.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 432
-
-
Fendt, S.M.1
Oliveira, A.P.2
Christen, S.3
Picotti, P.4
Dechant, R.C.5
Sauer, U.6
-
17
-
-
57749121616
-
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
-
Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR. 2008. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32: 878-887. http://dx.doi.org/10.1016/j.molcel.2008.11.020.
-
(2008)
Mol Cell
, vol.32
, pp. 878-887
-
-
Badis, G.1
Chan, E.T.2
van Bakel, H.3
Pena-Castillo, L.4
Tillo, D.5
Tsui, K.6
Carlson, C.D.7
Gossett, A.J.8
Hasinoff, M.J.9
Warren, C.L.10
Gebbia, M.11
Talukder, S.12
Yang, A.13
Mnaimneh, S.14
Terterov, D.15
Coburn, D.16
Li Yeo, A.17
Yeo, Z.X.18
Clarke, N.D.19
Lieb, J.D.20
Ansari, A.Z.21
Nislow, C.22
Hughes, T.R.23
more..
-
18
-
-
84862169505
-
YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities
-
De Boer CG, Hughes TR. 2012. YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res 40: D169-D179. http://dx.doi.org/10.1093/nar/gkr993.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
De Boer, C.G.1
Hughes, T.R.2
-
19
-
-
71549145607
-
Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi
-
Lavoie H, Hogues H, Whiteway M. 2009. Rearrangements of the transcriptional regulatory networks of metabolic pathways in fungi. Curr Opin Microbiol 12: 655-663. http://dx.doi.org/10.1016/j.mib.2009.09.015.
-
(2009)
Curr Opin Microbiol
, vol.12
, pp. 655-663
-
-
Lavoie, H.1
Hogues, H.2
Whiteway, M.3
-
20
-
-
84930417233
-
ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors
-
Starick SR, Ibn-Salem J, Jurk M, Hernandez C, Love MI, Chung HR, Vingron M, Thomas-Chollier M, Meijsing SH. 2015. ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Res 25: 825-835. http://dx.doi.org/10.1101/gr.185157.114.
-
(2015)
Genome Res
, vol.25
, pp. 825-835
-
-
Starick, S.R.1
Ibn-Salem, J.2
Jurk, M.3
Hernandez, C.4
Love, M.I.5
Chung, H.R.6
Vingron, M.7
Thomas-Chollier, M.8
Meijsing, S.H.9
-
21
-
-
27444438834
-
Carbonic anhydrase (Nce103p): An essential biosynthetic enzyme for growth of Saccharomyces cerevisiae at atmospheric carbon dioxide pressure
-
Aguilera J, Van Dijken JP, De Winde JH, Pronk JT. 2005. Carbonic anhydrase (Nce103p): an essential biosynthetic enzyme for growth of Saccharomyces cerevisiae at atmospheric carbon dioxide pressure. Biochem J 391: 311-316. http://dx.doi.org/10.1042/BJ20050556.
-
(2005)
Biochem J
, vol.391
, pp. 311-316
-
-
Aguilera, J.1
Van Dijken, J.P.2
De Winde, J.H.3
Pronk, J.T.4
-
22
-
-
0034971791
-
The Saccharomyces cerevisiae Sko1p transcription factor mediates HOG pathway-dependent osmotic regulation of a set of genes encoding enzymes implicated in protection from oxidative damage
-
Rep M, Proft M, Remize F, Tamás M, Serrano R, Thevelein JM, Hohmann S. 2001. The Saccharomyces cerevisiae Sko1p transcription factor mediates HOG pathway-dependent osmotic regulation of a set of genes encoding enzymes implicated in protection from oxidative damage. Mol Microbiol 40: 1067-1083. http://dx.doi.org/10.1046/j.1365-2958.2001.02384.x.
-
(2001)
Mol Microbiol
, vol.40
, pp. 1067-1083
-
-
Rep, M.1
Proft, M.2
Remize, F.3
Tamás, M.4
Serrano, R.5
Thevelein, J.M.6
Hohmann, S.7
-
23
-
-
39849087243
-
A systematic approach to detecting transcription factors in response to environmental stresses
-
Lin LH, Lee HC, Li WH, Chen BS. 2007. A systematic approach to detecting transcription factors in response to environmental stresses. BMC Bioinformatics 8: 473. http://dx.doi.org/10.1186/1471-2105-8-473.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 473
-
-
Lin, L.H.1
Lee, H.C.2
Li, W.H.3
Chen, B.S.4
-
24
-
-
84873392956
-
Linking the signaling cascades and dynamic regulatory networks controlling stress responses
-
Gitter A, Carmi M, Barkai N, Bar-Joseph Z. 2013. Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res 23: 365-376. http://dx.doi.org/10.1101/gr.138628.112.
-
(2013)
Genome Res
, vol.23
, pp. 365-376
-
-
Gitter, A.1
Carmi, M.2
Barkai, N.3
Bar-Joseph, Z.4
-
25
-
-
13944278132
-
Mitochondria, oxidants, and aging
-
Balaban RS, Nemoto S, Finkel T. 2005. Mitochondria, oxidants, and aging. Cell 120: 483-495. http://dx.doi.org/10.1016/j.cell.2005.02.001.
-
(2005)
Cell
, vol.120
, pp. 483-495
-
-
Balaban, R.S.1
Nemoto, S.2
Finkel, T.3
-
26
-
-
84938936390
-
Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli
-
Seo SW, Kim D, O’Brien EJ, Szubin R, Palsson BO. 2015. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun 6: 7970.
-
(2015)
Nat Commun
, vol.6
, pp. 7970
-
-
Seo, S.W.1
Kim, D.2
O’Brien, E.J.3
Szubin, R.4
Palsson, B.O.5
-
27
-
-
84858588614
-
Saccharomyces Genome Database: The genomics resource of budding yeast
-
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED. 2012. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40: D700-D705. http://dx.doi.org/10.1093/nar/gkr1029.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
Fisk, D.G.11
Hirschman, J.E.12
Hitz, B.C.13
Karra, K.14
Krieger, C.J.15
Miyasato, S.R.16
Nash, R.S.17
Park, J.18
Skrzypek, M.S.19
Simison, M.20
Weng, S.21
Wong, E.D.22
more..
-
28
-
-
0028265881
-
Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development
-
Gimeno CJ, Fink GR. 1994. Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development. Mol Cell Biol 14: 2100-2112. http://dx.doi.org/10.1128/MCB.14.3.2100.
-
(1994)
Mol Cell Biol
, vol.14
, pp. 2100-2112
-
-
Gimeno, C.J.1
Fink, G.R.2
-
29
-
-
27844459081
-
Fungal adenylyl cyclase integrates CO2 sensing with cAMP signaling and virulence
-
Klengel T, Liang WJ, Chaloupka J, Ruoff C, Schröppel K, Naglik JR, Eckert SE, Mogensen EG, Haynes K, Tuite MF, Levin LR, Buck J, Mühlschlegel FA. 2005. Fungal adenylyl cyclase integrates CO2 sensing with cAMP signaling and virulence. Curr Biol 15: 2021-2026. http://dx.doi.org/10.1016/j.cub.2005.10.040.
-
(2005)
Curr Biol
, vol.15
, pp. 2021-2026
-
-
Klengel, T.1
Liang, W.J.2
Chaloupka, J.3
Ruoff, C.4
Schröppel, K.5
Naglik, J.R.6
Eckert, S.E.7
Mogensen, E.G.8
Haynes, K.9
Tuite, M.F.10
Levin, L.R.11
Buck, J.12
Mühlschlegel, F.A.13
-
30
-
-
0034214335
-
An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains
-
Van Dijken JP, Bauer J, Brambilla L, Duboc P, Francois JM, Gancedo C, Giuseppin ML, Heijnen JJ, Hoare M, Lange HC, Madden EA, Niederberger P, Nielsen J, Parrou JL, Petit T, Porro D, Reuss M, van Riel N, Rizzi M, Steensma HY, Verrips CT, Vindelov J, Pronk JT. 2000. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26: 706-714. http://dx.doi.org/10.1016/S0141-0229(00)00162-9.
-
(2000)
Enzyme Microb Technol
, vol.26
, pp. 706-714
-
-
Van Dijken, J.P.1
Bauer, J.2
Brambilla, L.3
Duboc, P.4
Francois, J.M.5
Gancedo, C.6
Giuseppin, M.L.7
Heijnen, J.J.8
Hoare, M.9
Lange, H.C.10
Madden, E.A.11
Niederberger, P.12
Nielsen, J.13
Parrou, J.L.14
Petit, T.15
Porro, D.16
Reuss, M.17
van Riel, N.18
Rizzi, M.19
Steensma, H.Y.20
Verrips, C.T.21
Vindelov, J.22
Pronk, J.T.23
more..
-
31
-
-
0037087284
-
Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers
-
Reid RJ, Sunjevaric I, Keddache M, Rothstein R, Kedacche M. 2002. Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers. Yeast 19: 319-328. http://dx.doi.org/10.1002/yea.817.
-
(2002)
Yeast
, vol.19
, pp. 319-328
-
-
Reid, R.J.1
Sunjevaric, I.2
Keddache, M.3
Rothstein, R.4
Kedacche, M.5
-
32
-
-
0034841844
-
The tandem affinity purification (TAP) method: A general procedure of protein complex purification
-
Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, Bragado-Nilsson E, Wilm M, Séraphin B. 2001. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24: 218-229. http://dx.doi.org/10.1006/meth.2001.1183.
-
(2001)
Methods
, vol.24
, pp. 218-229
-
-
Puig, O.1
Caspary, F.2
Rigaut, G.3
Rutz, B.4
Bouveret, E.5
Bragado-Nilsson, E.6
Wilm, M.7
Séraphin, B.8
-
33
-
-
0024669291
-
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae
-
Sikorski RS, Hieter P. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
-
(1989)
Genetics
, vol.122
, pp. 19-27
-
-
Sikorski, R.S.1
Hieter, P.2
-
34
-
-
0026710123
-
Effect of benzoic acid on metabolic fluxes in yeasts: A continuous-culture study on the regulation of respiration and alcoholic fermentation
-
Verduyn C, Postma E, Scheffers WA, Van Dijken JP. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517. http://dx.doi.org/10.1002/yea.320080703.
-
(1992)
Yeast
, vol.8
, pp. 501-517
-
-
Verduyn, C.1
Postma, E.2
Scheffers, W.A.3
Van Dijken, J.P.4
-
35
-
-
84873020117
-
ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy
-
Rhee HS, Pugh BF. 2012. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr Protoc Mol Biol 100: 21.24.1-21.24.14.
-
(2012)
Curr Protoc Mol Biol
, vol.100
-
-
Rhee, H.S.1
Pugh, B.F.2
-
36
-
-
84920906247
-
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
-
Seo SW, Kim D, Latif H, O’Brien EJ, Szubin R, Palsson BO. 2014. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun 5: 4910.
-
(2014)
Nat Commun
, vol.5
, pp. 4910
-
-
Seo, S.W.1
Kim, D.2
Latif, H.3
O’Brien, E.J.4
Szubin, R.5
Palsson, B.O.6
-
37
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. http://dx.doi.org/10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
38
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
39
-
-
84866086842
-
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
-
Guo Y, Mahony S, Gifford DK. 2012. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput Biol 8: e1002638. http://dx.doi.org/10.1371/journal.pcbi.1002638.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Guo, Y.1
Mahony, S.2
Gifford, D.K.3
-
40
-
-
84875634162
-
Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
-
Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192. http://dx.doi.org/10.1093/bib/bbs017.
-
(2013)
Brief Bioinform
, vol.14
, pp. 178-192
-
-
Thorvaldsdóttir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
41
-
-
79952334870
-
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
-
Rye MB, Sætrom P, Drabløs F. 2011. A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. Nucleic Acids Res 39: e25. http://dx.doi.org/10.1093/nar/gkq1187.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Rye, M.B.1
Sætrom, P.2
Drabløs, F.3
-
42
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842. http://dx.doi.org/10.1093/bioinformatics/btq033.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
43
-
-
79958117256
-
MEME-ChIP: Motif analysis of large DNA datasets
-
Machanick P, Bailey TL. 2011. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27: 1696-1697. http://dx.doi.org/10.1093/bioinformatics/btr189.
-
(2011)
Bioinformatics
, vol.27
, pp. 1696-1697
-
-
Machanick, P.1
Bailey, T.L.2
-
44
-
-
84891806965
-
The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
-
Teixeira MC, Monteiro PT, Guerreiro JF, Gonçalves JP, Mira NP, dos Santos SC, Cabrito TR, Palma M, Costa C, Francisco AP, Madeira SC, Oliveira AL, Freitas AT, Sá-Correia I. 2014. The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res 42: D161-D166. http://dx.doi.org/10.1093/nar/gkt1015.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Teixeira, M.C.1
Monteiro, P.T.2
Guerreiro, J.F.3
Gonçalves, J.P.4
Mira, N.P.5
dos Santos, S.C.6
Cabrito, T.R.7
Palma, M.8
Costa, C.9
Francisco, A.P.10
Madeira, S.C.11
Oliveira, A.L.12
Freitas, A.T.13
Sá-Correia, I.14
-
45
-
-
0035710746
-
Analysis of relative gene expression data using real-time quantitative PCR and the 2___CT method
-
Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2___CT method. Methods 25: 402-408. http://dx.doi.org/10.1006/meth.2001.1262.
-
(2001)
Methods
, vol.25
, pp. 402-408
-
-
Livak, K.J.1
Schmittgen, T.D.2
-
46
-
-
70349739736
-
The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets
-
Nicol JW, Helt GA, Blanchard SG, Jr, Raja A, Loraine AE. 2009. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25: 2730-2731. http://dx.doi.org/10.1093/bioinformatics/btp472.
-
(2009)
Bioinformatics
, vol.25
, pp. 2730-2731
-
-
Nicol, J.W.1
Helt, G.A.2
Blanchard, S.G.3
Raja, A.4
Loraine, A.E.5
|