-
1
-
-
84895531783
-
Evolution at two levels of gene expression in yeast
-
Artieri CG, Fraser HB. 2014. Evolution at two levels of gene expression in yeast. Genome Res 24: 411-421.
-
(2014)
Genome Res
, vol.24
, pp. 411-421
-
-
Artieri, C.G.1
Fraser, H.B.2
-
2
-
-
84886822471
-
Hepatitis C virus 3′UTR regulates viral translation through direct interactions with the host translation machinery
-
Bai Y, Zhou K, Doudna JA. 2013. Hepatitis C virus 3′UTR regulates viral translation through direct interactions with the host translation machinery. Nucleic Acids Res 41: 7861-7874.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 7861-7874
-
-
Bai, Y.1
Zhou, K.2
Doudna, J.A.3
-
3
-
-
84884660617
-
Gene expression regulation by upstream open reading frames and human disease
-
Barbosa C, Peixeiro I, Romão L. 2013. Gene expression regulation by upstream open reading frames and human disease. PLoS Genet 9: e1003529.
-
(2013)
PLoS Genet
, vol.9
-
-
Barbosa, C.1
Peixeiro, I.2
Romão, L.3
-
4
-
-
0347513219
-
Characterizing gene sets with FuncAssociate
-
DOI 10.1093/bioinformatics/btg363
-
Berriz GF, King OD, Bryant B, Sander C, Roth FP. 2003. Characterizing gene sets with FuncAssociate. Bioinformatics 19: 2502-2504. (Pubitemid 38016661)
-
(2003)
Bioinformatics
, vol.19
, Issue.18
, pp. 2502-2504
-
-
Berriz, G.F.1
King, O.D.2
Bryant, B.3
Sander, C.4
Roth, F.P.5
-
5
-
-
84878013555
-
Ribosomal protein SA haploinsufficiency in humans with isolated congenital asplenia
-
Bolze A, Mahlaoui N, Byun M, Turner B, Trede N, Ellis SR, Abhyankar A, Itan Y, Patin E, Brebner S, et al. 2013. Ribosomal protein SA haploinsufficiency in humans with isolated congenital asplenia. Science 340: 976-978.
-
(2013)
Science
, vol.340
, pp. 976-978
-
-
Bolze, A.1
Mahlaoui, N.2
Byun, M.3
Turner, B.4
Trede, N.5
Ellis, S.R.6
Abhyankar, A.7
Itan, Y.8
Patin, E.9
Brebner, S.10
-
6
-
-
84856625798
-
High-resolution view of the yeast meiotic program revealed by ribosome profiling
-
Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. 2011. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science 335: 552-557.
-
(2011)
Science
, vol.335
, pp. 552-557
-
-
Brar, G.A.1
Yassour, M.2
Friedman, N.3
Regev, A.4
Ingolia, N.T.5
Weissman, J.S.6
-
7
-
-
0000640710
-
Modulation of chemical composition and other parameters of the cell by growth rate
-
ed. Neidhard FC, et al. ASM Press, Washington, DC
-
Bremer H, Dennis PP. 1996. Modulation of chemical composition and other parameters of the cell by growth rate. In Escherichia coli and Salmonella typhimurium: cellular and molecular biology (ed. Neidhard FC, et al.), Vol. 2, pp. 1553-1569. ASM Press, Washington, DC.
-
(1996)
Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology
, vol.2
, pp. 1553-1569
-
-
Bremer, H.1
Dennis, P.P.2
-
9
-
-
70849098603
-
Haploid genetic screens in human cells identify host factors used by pathogens
-
Carette JE, Guimaraes CP, Varadarajan M, Park AS, Wuethrich I, Godarova A, Kotecki M, Cochran BH, Spooner E, Ploegh HL, et al. 2009. Haploid genetic screens in human cells identify host factors used by pathogens. Science 326: 1231-1235.
-
(2009)
Science
, vol.326
, pp. 1231-1235
-
-
Carette, J.E.1
Guimaraes, C.P.2
Varadarajan, M.3
Park, A.S.4
Wuethrich, I.5
Godarova, A.6
Kotecki, M.7
Cochran, B.H.8
Spooner, E.9
Ploegh, H.L.10
-
10
-
-
84934434336
-
Investigating myc-dependent translational regulation in normal and cancer cells
-
Cunningham JT, Pourdehnad M, Stumpf CR, Ruggero D. 2013. Investigating myc-dependent translational regulation in normal and cancer cells. Methods Mol Biol 1012: 201-212.
-
(2013)
Methods Mol Biol
, vol.1012
, pp. 201-212
-
-
Cunningham, J.T.1
Pourdehnad, M.2
Stumpf, C.R.3
Ruggero, D.4
-
11
-
-
84859256941
-
Critical evaluation of imprinted gene expression by RNA-Seq: A new perspective
-
DeVeale B, van der Kooy D, Babak T. 2012. Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet 8: e1002600.
-
(2012)
PLoS Genet
, vol.8
-
-
DeVeale, B.1
Van Der Kooy, D.2
Babak, T.3
-
12
-
-
84880652281
-
Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast
-
Dvir S, Velten L, Sharon E, Zeevi D, Carey LB, Weinberger A, Segal E. 2013 Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci 110: E2792-E2801.
-
(2013)
Proc Natl Acad Sci
, vol.110
-
-
Dvir, S.1
Velten, L.2
Sharon, E.3
Zeevi, D.4
Carey, L.B.5
Weinberger, A.6
Segal, E.7
-
14
-
-
70350651269
-
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis
-
Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KCL, Gagné V, et al. 2009. Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet 41: 1216-1222.
-
(2009)
Nat Genet
, vol.41
, pp. 1216-1222
-
-
Ge, B.1
Pokholok, D.K.2
Kwan, T.3
Grundberg, E.4
Morcos, L.5
Verlaan, D.J.6
Le, J.7
Koka, V.8
Lam, K.C.L.9
Gagné, V.10
-
15
-
-
5044229348
-
Molecular mechanisms of translational control
-
DOI 10.1038/nrm1488
-
Gebauer F, Hentze MW. 2004. Molecular mechanisms of translational control. Nat Rev Mol Cell Biol 5: 827-835. (Pubitemid 39336276)
-
(2004)
Nature Reviews Molecular Cell Biology
, vol.5
, Issue.10
, pp. 827-835
-
-
Gebauer, F.1
Hentze, M.W.2
-
16
-
-
79954456859
-
Determinants of translation efficiency and accuracy
-
Gingold H, Pilpel Y. 2011. Determinants of translation efficiency and accuracy. Mol Syst Biol 7: 481.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 481
-
-
Gingold, H.1
Pilpel, Y.2
-
17
-
-
77955299096
-
High-resolution analysis of parent-of-origin allelic expression in the mouse brain
-
Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C. 2010. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329: 643-648.
-
(2010)
Science
, vol.329
, pp. 643-648
-
-
Gregg, C.1
Zhang, J.2
Weissbourd, B.3
Luo, S.4
Schroth, G.P.5
Haig, D.6
Dulac, C.7
-
18
-
-
84874707325
-
The "obligate diploid" Candida albicans forms mating-competent haploids
-
Hickman MA, Zeng G, Forche A, Hirakawa MP, Abbey D, Harrison BD, Wang Y-M, Su C-H, Bennett RJ, Wang Y, et al. 2013. The "obligate diploid" Candida albicans forms mating-competent haploids. Nature 494: 55-59.
-
(2013)
Nature
, vol.494
, pp. 55-59
-
-
Hickman, M.A.1
Zeng, G.2
Forche, A.3
Hirakawa, M.P.4
Abbey, D.5
Harrison, B.D.6
Wang, Y.-M.7
Su, C.-H.8
Bennett, R.J.9
Wang, Y.10
-
19
-
-
84862777192
-
The translational landscape of mTOR signalling steers cancer initiation and metastasis
-
Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi EY, Stumpf CR, Christensen C, Bonham MJ, et al. 2012. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485: 55-61.
-
(2012)
Nature
, vol.485
, pp. 55-61
-
-
Hsieh, A.C.1
Liu, Y.2
Edlind, M.P.3
Ingolia, N.T.4
Janes, M.R.5
Sher, A.6
Shi, E.Y.7
Stumpf, C.R.8
Christensen, C.9
Bonham, M.J.10
-
20
-
-
0032535452
-
A newly identified N-terminal amino acid sequence of human eIF4G binds poly(A)-binding protein and functions in poly(A)-dependent translation
-
DOI 10.1093/emboj/17.24.7480
-
Imataka H, Gradi A, Sonenberg N. 1998. A newly identified N-terminal amino acid sequence of human eIF4G binds poly(A)-binding protein and functions in poly(A)-dependent translation. EMBO J 17: 7480-7489. (Pubitemid 29002714)
-
(1998)
EMBO Journal
, vol.17
, Issue.24
, pp. 7480-7489
-
-
Imataka, H.1
Gradi, A.2
Sonenberg, N.3
-
21
-
-
84862232618
-
The Candida genome database incorporates multiple Candida species: Multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata
-
Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G. 2012. The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Nucleic Acids Res 40: D667-D674.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Inglis, D.O.1
Arnaud, M.B.2
Binkley, J.3
Shah, P.4
Skrzypek, M.S.5
Wymore, F.6
Binkley, G.7
Miyasato, S.R.8
Simison, M.9
Sherlock, G.10
-
22
-
-
62549134121
-
Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. 2009. Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223.
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.S.3
Weissman, J.S.4
-
23
-
-
18844421908
-
A graves' disease-associated Kozak sequence single-nucleotide polymorphism enhances the efficiency of CD40 gene translation: A case for translational pathophysiology
-
DOI 10.1210/en.2004-1617
-
Jacobson EM, Concepcion E, Oashi T, Tomer Y. 2005. A Graves' disease-associated Kozak sequence single-nucleotide polymorphism enhances the efficiency of CD40 gene translation: a case for translational pathophysiology. Endocrinology 146: 2684-2691. (Pubitemid 40695571)
-
(2005)
Endocrinology
, vol.146
, Issue.6
, pp. 2684-2691
-
-
Jacobson, E.M.1
Concepcion, E.2
Oashi, T.3
Tomer, Y.4
-
24
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
DOI 10.1038/nature01644
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254. (Pubitemid 40852689)
-
(2003)
Nature
, vol.423
, Issue.6937
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
25
-
-
84859232053
-
Imprinted genes... And the number is?
-
Kelsey G, Bartolomei MS. 2012. Imprinted genes ... and the number is? PLoS Genet 8: e1002601.
-
(2012)
PLoS Genet
, vol.8
-
-
Kelsey, G.1
Bartolomei, M.S.2
-
26
-
-
84868275675
-
Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS
-
Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L. 2012 Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Mol Syst Biol 8: 602.
-
(2012)
Mol Syst Biol
, vol.8
, pp. 602
-
-
Khan, Z.1
Bloom, J.S.2
Amini, S.3
Singh, M.4
Perlman, D.H.5
Caudy, A.A.6
Kruglyak, L.7
-
27
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla G, Murray AW, Tollervey D, Plotkin JB. 2009. Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255-258.
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
28
-
-
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.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
29
-
-
84898990515
-
AUF1 contributes to Cryptochrome1 mRNA degradation and rhythmic translation
-
Lee K-H, Kim S-H, Kim H-J, Kim W, Lee H-R, Jung Y, Choi J-H, Hong KY, Jang SK, Kim K-T. 2014. AUF1 contributes to Cryptochrome1 mRNA degradation and rhythmic translation. Nucleic Acids Res 42: 3590-3606.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 3590-3606
-
-
Lee, K.-H.1
Kim, S.-H.2
Kim, H.-J.3
Kim, W.4
Lee, H.-R.5
Jung, Y.6
Choi, J.-H.7
Hong, K.Y.8
Jang, S.K.9
Kim, K.-T.10
-
30
-
-
84862017684
-
Genotype-based test in mapping cis-regulatory variants from allele-specific expression data
-
Lefebvre JF, Vello E, Ge B, Montgomery SB, Dermitzakis ET, Pastinen T, Labuda D. 2012. Genotype-based test in mapping cis-regulatory variants from allele-specific expression data. PLoS ONE 7: e38667.
-
(2012)
PLoS ONE
, vol.7
-
-
Lefebvre, J.F.1
Vello, E.2
Ge, B.3
Montgomery, S.B.4
Dermitzakis, E.T.5
Pastinen, T.6
Labuda, D.7
-
31
-
-
77951652022
-
Direct determination of molecular haplotypes by chromosome microdissection
-
Ma L, Xiao Y, Huang H, Wang Q, Rao W, Feng Y, Zhang K, Song Q. 2010. Direct determination of molecular haplotypes by chromosome microdissection. Nat Methods 7: 299-301.
-
(2010)
Nat Methods
, vol.7
, pp. 299-301
-
-
Ma, L.1
Xiao, Y.2
Huang, H.3
Wang, Q.4
Rao, W.5
Feng, Y.6
Zhang, K.7
Song, Q.8
-
32
-
-
0038487811
-
Poly(A)-binding proteins: Multifunctional scaffolds for the post-transcriptional control of gene expression
-
Mangus DA, Evans MC, Jacobson A. 2003. Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol 4: 223.
-
(2003)
Genome Biol
, vol.4
, pp. 223
-
-
Mangus, D.A.1
Evans, M.C.2
Jacobson, A.3
-
33
-
-
84895525650
-
Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
-
McManus J, May GE, Spealman P, Shteyman A. 2014. Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Res 24: 422-430.
-
(2014)
Genome Res
, vol.24
, pp. 422-430
-
-
McManus, J.1
May, G.E.2
Spealman, P.3
Shteyman, A.4
-
34
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population
-
Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. 2010. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
-
(2010)
Nature
, vol.464
, pp. 773-777
-
-
Montgomery, S.B.1
Sammeth, M.2
Gutierrez-Arcelus, M.3
Lach, R.P.4
Ingle, C.5
Nisbett, J.6
Guigo, R.7
Dermitzakis, E.T.8
-
35
-
-
84883626672
-
Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure
-
Muzzey D, Schwartz K, Weissman JS, Sherlock G. 2013. Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure. Genome Biol 14: R97.
-
(2013)
Genome Biol
, vol.14
-
-
Muzzey, D.1
Schwartz, K.2
Weissman, J.S.3
Sherlock, G.4
-
36
-
-
77954763156
-
Genome-wide allele-specific analysis: Insights into regulatory variation
-
Pastinen T. 2010. Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet 11: 533-538.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 533-538
-
-
Pastinen, T.1
-
37
-
-
84863637922
-
Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells
-
Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, et al. 2012. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 487: 190-195.
-
(2012)
Nature
, vol.487
, pp. 190-195
-
-
Peters, B.A.1
Kermani, B.G.2
Sparks, A.B.3
Alferov, O.4
Hong, P.5
Alexeev, A.6
Jiang, Y.7
Dahl, F.8
Tang, Y.T.9
Haas, J.10
-
38
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK. 2010. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
Marioni, J.C.2
Pai, A.A.3
Degner, J.F.4
Engelhardt, B.E.5
Nkadori, E.6
Veyrieras, J.-B.7
Stephens, M.8
Gilad, Y.9
Pritchard, J.K.10
-
39
-
-
0032858414
-
From factors to mechanisms: Translation and translational control in eukaryotes
-
DOI 10.1016/S0959-437X(99)00005-2
-
Preiss T, Hentze MW. 1999. From factors to mechanisms: translation and translational control in eukaryotes. Curr Opin Genet Dev 9: 515-521. (Pubitemid 29484043)
-
(1999)
Current Opinion in Genetics and Development
, vol.9
, Issue.5
, pp. 515-521
-
-
Preiss, T.1
Hentze, M.W.2
-
40
-
-
84893351549
-
Genomewide probing of RNA structure reveals active unfolding of mRNA structures in vivo
-
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. 2014. Genomewide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505: 701-705.
-
(2014)
Nature
, vol.505
, pp. 701-705
-
-
Rouskin, S.1
Zubradt, M.2
Washietl, S.3
Kellis, M.4
Weissman, J.S.5
-
41
-
-
84879345901
-
Rate-limiting steps in yeast protein translation
-
Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. 2013. Rate-limiting steps in yeast protein translation. Cell 153: 1589-1601.
-
(2013)
Cell
, vol.153
, pp. 1589-1601
-
-
Shah, P.1
Ding, Y.2
Niemczyk, M.3
Kudla, G.4
Plotkin, J.B.5
-
42
-
-
0023650543
-
The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li WH. 1987. The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15: 1281-1295.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
43
-
-
79960925156
-
The cancerous translation apparatus
-
Stumpf CR, Ruggero D. 2011. The cancerous translation apparatus. Curr Opin Genet Dev 21: 474-483.
-
(2011)
Curr Opin Genet Dev
, vol.21
, pp. 474-483
-
-
Stumpf, C.R.1
Ruggero, D.2
-
44
-
-
84893358533
-
Landscape and variation of RNA secondary structure across the human transcriptome
-
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, et al. 2014. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505: 706-709.
-
(2014)
Nature
, vol.505
, pp. 706-709
-
-
Wan, Y.1
Qu, K.2
Zhang, Q.C.3
Flynn, R.A.4
Manor, O.5
Ouyang, Z.6
Zhang, J.7
Spitale, R.C.8
Snyder, M.P.9
Segal, E.10
-
45
-
-
0033229970
-
The economics of ribosome biosynthesis in yeast
-
DOI 10.1016/S0968-0004(99)01460-7, PII S0968000499014607
-
Warner JR. 1999. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24: 437-440. (Pubitemid 29528205)
-
(1999)
Trends in Biochemical Sciences
, vol.24
, Issue.11
, pp. 437-440
-
-
Warner, J.R.1
-
46
-
-
84907130989
-
In vitro and in vivo protein synthesis in Candida albicans. 3. Protein synthesis and inhibition
-
Yamaguchi H, Iwata K. 1970. In vitro and in vivo protein synthesis in Candida albicans. 3. Protein synthesis and inhibition. Sabouraudia 8: 201-211.
-
(1970)
Sabouraudia
, vol.8
, pp. 201-211
-
-
Yamaguchi, H.1
Iwata, K.2
-
47
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
DOI 10.1093/nar/gkg595
-
Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3406-3415
-
-
Zuker, M.1
|