-
2
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
3
-
-
1542328960
-
Identification and distinct regulation of yeast tata box-containing genes
-
Basehoar AD, Zanton SJ, Pugh BF. 2004. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116: 699-709.
-
(2004)
Cell
, vol.116
, pp. 699-709
-
-
Basehoar, A.D.1
Zanton, S.J.2
Pugh, B.F.3
-
4
-
-
64249139132
-
Rna pol ii accumulates at promoters of growth genes during developmental arrest
-
Baugh LR, Demodena J, Sternberg PW. 2009. RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 324: 92-94.
-
(2009)
Science
, vol.324
, pp. 92-94
-
-
Baugh, L.R.1
Demodena, J.2
Sternberg, P.W.3
-
5
-
-
8444245244
-
Global nucleosome occupancy in yeast
-
Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. 2004. Global nucleosome occupancy in yeast. Genome Biol 5: R62.
-
(2004)
Genome Biol
, vol.5
-
-
Bernstein, B.E.1
Liu, C.L.2
Humphrey, E.L.3
Perlstein, E.O.4
Schreiber, S.L.5
-
6
-
-
20144380575
-
Functional genomics of the cilium, a sensory organelle
-
Blacque OE, Perens EA, Boroevich KA, Inglis PN, Li C, Warner A, Khattra J, Holt RA, Ou G, Mah AK, et al. 2005. Functional genomics of the cilium, a sensory organelle. Curr Biol 15: 935-941.
-
(2005)
Curr Biol
, vol.15
, pp. 935-941
-
-
Blacque, O.E.1
Perens, E.A.2
Boroevich, K.A.3
Inglis, P.N.4
Li, C.5
Warner, A.6
Khattra, J.7
Holt, R.A.8
Ou, G.9
Mah, A.K.10
-
8
-
-
38549105096
-
Trans-splicing and operons
-
(ed. The C. elegans Research Community)
-
Blumenthal T. 2005. Trans-splicing and operons. In WormBook (ed. The C. elegans Research Community), pp. 1-9. http://www.wormbook.org.
-
(2005)
WormBook
, pp. 1-9
-
-
Blumenthal, T.1
-
9
-
-
54949147307
-
F-seq: A feature density estimator for high-throughput sequence tags
-
Boyle AP, Guinney J, Crawford GE, Furey TS. 2008. F-Seq: A feature density estimator for high-throughput sequence tags. Bioinformatics 24: 2537-2538.
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
10
-
-
0029971668
-
Drosophila tfiid binds to a conserved downstream basal promoter element that is present inmany tata-boxdeficient promoters
-
Burke TW, Kadonaga JT. 1996. Drosophila TFIID binds to a conserved downstream basal promoter element that is present inmany TATA-boxdeficient promoters. Genes Dev 10: 711-724.
-
(1996)
Genes Dev
, vol.10
, pp. 711-724
-
-
Burke, T.W.1
Kadonaga, J.T.2
-
11
-
-
0032509302
-
Genome sequence of the nematode c. Elegans: A platform for investigating biology
-
The c. Elegans sequencing consortium
-
The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
-
(1998)
Science
, vol.282
, pp. 2012-2018
-
-
-
12
-
-
33744805985
-
Genomewide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, et al. 2006. Genomewide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635.
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
Semple, C.A.7
Taylor, M.S.8
Engstrom, P.G.9
Frith, M.C.10
-
13
-
-
79960043306
-
Ribosomal rna depletion for massively parallel bacterial rna-sequencing applications
-
Chen Z, Duan X. 2011. Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. Methods Mol Biol 733: 93-103.
-
(2011)
Methods Mol Biol
, vol.733
, pp. 93-103
-
-
Chen, Z.1
Duan, X.2
-
14
-
-
0026078472
-
Insertion of part of an intron into the 59 untranslated region of a caenorhabditis elegans gene converts it into a trans-spliced gene
-
Conrad R, Thomas J, Spieth J, Blumenthal T. 1991. Insertion of part of an intron into the 59 untranslated region of a Caenorhabditis elegans gene converts it into a trans-spliced gene. Mol Cell Biol 11: 1921-1926.
-
(1991)
Mol Cell Biol
, vol.11
, pp. 1921-1926
-
-
Conrad, R.1
Thomas, J.2
Spieth, J.3
Blumenthal, T.4
-
15
-
-
0033618267
-
Structure and promoter activity of the 59 flanking region of ace-1, the gene encoding acetylcholinesterase of class a in caenorhabditis elegans
-
Culetto E, Combes D, Fedon Y, Roig A, Toutant JP, Arpagaus M. 1999. Structure and promoter activity of the 59 flanking region of ace-1, the gene encoding acetylcholinesterase of class A in Caenorhabditis elegans. J Mol Biol 290: 951-966.
-
(1999)
J Mol Biol
, vol.290
, pp. 951-966
-
-
Culetto, E.1
Combes, D.2
Fedon, Y.3
Roig, A.4
Toutant, J.P.5
Arpagaus, M.6
-
16
-
-
0024961717
-
Sequence analysis of the complete caenorhabditis elegans myosin heavy chain gene family
-
Dibb NJ, Maruyama IN, Krause M, Karn J. 1989. Sequence analysis of the complete Caenorhabditis elegans myosin heavy chain gene family. J Mol Biol 205: 603-613.
-
(1989)
J Mol Biol
, vol.205
, pp. 603-613
-
-
Dibb, N.J.1
Maruyama, I.N.2
Krause, M.3
Karn, J.4
-
17
-
-
57149119464
-
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
-
Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. 2008. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol 4: E1000216.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Field, Y.1
Kaplan, N.2
Fondufe-Mittendorf, Y.3
Moore, I.K.4
Sharon, E.5
Lubling, Y.6
Widom, J.7
Segal, E.8
-
18
-
-
33744824906
-
Evolutionary turnover of mammalian transcription start sites
-
Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A. 2006. Evolutionary turnover of mammalian transcription start sites. Genome Res 16: 713-722.
-
(2006)
Genome Res
, vol.16
, pp. 713-722
-
-
Frith, M.C.1
Ponjavic, J.2
Fredman, D.3
Kai, C.4
Kawai, J.5
Carninci, P.6
Hayashizaki, Y.7
Sandelin, A.8
-
19
-
-
78651320424
-
The ucsc genome browser database: Update 2011
-
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, ClineMS, Goldman M, Barber GP, Clawson H, Coelho A, et al. 2011. The UCSC Genome Browser database: Update 2011. Nucleic Acids Res 39: D876-D882.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Fujita, P.A.1
Rhead, B.2
Zweig, A.S.3
Hinrichs, A.S.4
Karolchik, D.5
Cline, M.S.6
Goldman, M.7
Barber, G.P.8
Clawson, H.9
Coelho, A.10
-
20
-
-
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: 1775-1787.
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
Gerstein, M.B.1
Lu, Z.J.2
Van 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
-
22
-
-
79955567707
-
Core promoter t-blocks correlate with gene expression levels in c elegans
-
Grishkevich V, Hashimshony T, Yanai I. 2011. Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Res 21: 707-717.
-
(2011)
Genome Res
, vol.21
, pp. 707-717
-
-
Grishkevich, V.1
Hashimshony, T.2
Yanai, I.3
-
23
-
-
74149094362
-
Partitioning the c. Elegans genome by nucleosome modification, occupancy, and positioning
-
Gu SG, Fire A. 2010. Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning. Chromosoma 119: 73-87.
-
(2010)
Chromosoma
, vol.119
, pp. 73-87
-
-
Gu, S.G.1
Fire, A.2
-
24
-
-
75549084124
-
Wormbase: A comprehensive resource for nematode research
-
Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, et al. 2010. WormBase: A comprehensive resource for nematode research. Nucleic Acids Res 38: D463-D467.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Harris, T.W.1
Antoshechkin, I.2
Bieri, T.3
Blasiar, D.4
Chan, J.5
Chen, W.J.6
De La Cruz, N.7
Davis, P.8
Duesbury, M.9
Fang, R.10
-
25
-
-
58149463224
-
High-resolution analysis of the 59-end transcriptome using a next generation dna sequencer
-
Hashimoto S, QuW, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, et al. 2009. High-resolution analysis of the 59-end transcriptome using a next generation DNA sequencer. PLoS ONE 4: E4108.
-
(2009)
PLoS ONE
, vol.4
-
-
Hashimoto, S.1
QuW Ahsan, B.2
Ogoshi, K.3
Sasaki, A.4
Nakatani, Y.5
Lee, Y.6
Ogawa, M.7
Ametani, A.8
Suzuki, Y.9
-
26
-
-
63849342015
-
Massively parallel sequencing of the polyadenylated transcriptome of c. Elegans
-
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. 2009. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 19: 657-666.
-
(2009)
Genome Res
, vol.19
, pp. 657-666
-
-
Hillier, L.W.1
Reinke, V.2
Green, P.3
Hirst, M.4
Marra, M.A.5
Waterston, R.H.6
-
27
-
-
0032479501
-
Multiple sp1 sites efficiently drive transcription of the tata-less promoter of the human glypican 3 (gpc3) gene
-
Huber R, Schlessinger D, Pilia G. 1998. Multiple Sp1 sites efficiently drive transcription of the TATA-less promoter of the human glypican 3 (GPC3) gene. Gene 214: 35-44.
-
(1998)
Gene
, vol.214
, pp. 35-44
-
-
Huber, R.1
Schlessinger, D.2
Pilia, G.3
-
28
-
-
74949115966
-
Chromatin 'programming' by sequence - Is there more to the nucleosome code than %gc?
-
Hughes A, Rando OJ. 2009. Chromatin 'programming' by sequence - is there more to the nucleosome code than %GC? J Biol 8: 96.
-
(2009)
J Biol
, vol.8
, pp. 96
-
-
Hughes, A.1
Rando, O.J.2
-
29
-
-
34548690553
-
High-throughput in vivo analysis of gene expression in caenorhabditis elegans
-
Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, et al. 2007. High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol 5: E237.
-
(2007)
PLoS Biol
, vol.5
-
-
Hunt-Newbury, R.1
Viveiros, R.2
Johnsen, R.3
Mah, A.4
Anastas, D.5
Fang, L.6
Halfnight, E.7
Lee, D.8
Lin, J.9
Lorch, A.10
-
30
-
-
0034892172
-
Changes in gene expression associated with developmental arrest and longevity in caenorhabditis elegans
-
Jones SJ, Riddle DL, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA. 2001. Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res 11: 1346-1352.
-
(2001)
Genome Res
, vol.11
, pp. 1346-1352
-
-
Jones, S.J.1
Riddle, D.L.2
Pouzyrev, A.T.3
Velculescu, V.E.4
Hillier, L.5
Eddy, S.R.6
Stricklin, S.L.7
Baillie, D.L.8
Waterston, R.9
Marra, M.A.10
-
31
-
-
62649085538
-
The dnaencoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNAencoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
Field, Y.6
LeProust, E.M.7
Hughes, T.R.8
Lieb, J.D.9
Widom, J.10
-
32
-
-
33846000624
-
Large-scale production of sage libraries from microdissected tissues, flow-sorted cells, and cell lines
-
Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, et al. 2007. Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res 17: 108-116.
-
(2007)
Genome Res
, vol.17
, pp. 108-116
-
-
Khattra, J.1
Delaney, A.D.2
Zhao, Y.3
Siddiqui, A.4
Asano, J.5
McDonald, H.6
Pandoh, P.7
Dhalla, N.8
Prabhu, A.L.9
Ma, K.10
-
33
-
-
61349098460
-
Differential chromatin marking of introns and expressed exons by h3k36me3
-
Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. 2009. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41: 376-381.
-
(2009)
Nat Genet
, vol.41
, pp. 376-381
-
-
Kolasinska-Zwierz, P.1
Down, T.2
Latorre, I.3
Liu, T.4
Liu, X.S.5
Ahringer, J.6
-
34
-
-
0023659440
-
A trans-spliced leader sequence on actin mrna in c. Elegans
-
Krause M, Hirsh D. 1987. A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 49: 753-761.
-
(1987)
Cell
, vol.49
, pp. 753-761
-
-
Krause, M.1
Hirsh, D.2
-
35
-
-
0031882652
-
New core promoter element in rna polymerase ii-dependent transcription: Sequence-specific dna binding by transcription factor iib
-
Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH. 1998. New core promoter element in RNA polymerase II-dependent transcription: Sequence-specific DNA binding by transcription factor IIB. Genes Dev 12: 34-44.
-
(1998)
Genes Dev
, vol.12
, pp. 34-44
-
-
Lagrange, T.1
Kapanidis, A.N.2
Tang, H.3
Reinberg, D.4
Ebright, R.H.5
-
36
-
-
34250785284
-
Genetic properties influencing the evolvability of gene expression
-
Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. 2007. Genetic properties influencing the evolvability of gene expression. Science 317: 118-121.
-
(2007)
Science
, vol.317
, pp. 118-121
-
-
Landry, C.R.1
Lemos, B.2
Rifkin, S.A.3
Dickinson, W.J.4
Hartl, D.L.5
-
38
-
-
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
-
39
-
-
0017584322
-
The organization of the histone genes in drosophila melanogaster: Functional and evolutionary implications
-
Lifton RP, Goldberg ML, Karp RW, Hogness DS. 1978. The organization of the histone genes in Drosophila melanogaster: Functional and evolutionary implications. Cold Spring Harb Symp Quant Biol 42: 1047-1051.
-
(1978)
Cold Spring Harb Symp Quant Biol
, vol.42
, pp. 1047-1051
-
-
Lifton, R.P.1
Goldberg, M.L.2
Karp, R.W.3
Hogness, D.S.4
-
40
-
-
3042784063
-
The mte, a new core promoter element for transcription by rna polymerase ii
-
Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga JT. 2004. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev 18: 1606-1617.
-
(2004)
Genes Dev
, vol.18
, pp. 1606-1617
-
-
Lim, C.Y.1
Santoso, B.2
Boulay, T.3
Dong, E.4
Ohler, U.5
Kadonaga, J.T.6
-
41
-
-
33947732940
-
A novel family of c. Elegans snrnps contains proteins associated with trans-splicing
-
MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T. 2007. A novel family of C. elegans snRNPs contains proteins associated with trans-splicing. RNA 13: 511-520.
-
(2007)
RNA
, vol.13
, pp. 511-520
-
-
MacMorris, M.1
Kumar, M.2
Lasda, E.3
Larsen, A.4
Kraemer, B.5
Blumenthal, T.6
-
42
-
-
0028213438
-
Oligo-capping: A simple method to replace the cap structure of eukaryotic mrnas with oligoribonucleotides
-
Maruyama K, Sugano S. 1994. Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138: 171-174.
-
(1994)
Gene
, vol.138
, pp. 171-174
-
-
Maruyama, K.1
Sugano, S.2
-
43
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083.
-
(2008)
Genome Res
, vol.18
, pp. 1073-1083
-
-
Mavrich, T.N.1
Ioshikhes, I.P.2
Venters, B.J.3
Jiang, C.4
Tomsho, L.P.5
Qi, J.6
Schuster, S.C.7
Albert, I.8
Pugh, B.F.9
-
44
-
-
33846818720
-
The elt-2 gata-factor and the global regulation of transcription in the c. Elegans intestine
-
McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, et al. 2007. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol 302: 627-645.
-
(2007)
Dev Biol
, vol.302
, pp. 627-645
-
-
McGhee, J.D.1
Sleumer, M.C.2
Bilenky, M.3
Wong, K.4
McKay, S.J.5
Goszczynski, B.6
Tian, H.7
Krich, N.D.8
Khattra, J.9
Holt, R.A.10
-
45
-
-
3242683216
-
Gene expression profiling of cells, tissues, and developmental stages of the nematode c. Elegans
-
McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, et al. 2003. Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb Symp Quant Biol 68: 159-169.
-
(2003)
Cold Spring Harb Symp Quant Biol
, vol.68
, pp. 159-169
-
-
McKay, S.J.1
Johnsen, R.2
Khattra, J.3
Asano, J.4
Baillie, D.L.5
Chan, S.6
Dube, N.7
Fang, L.8
Goszczynski, B.9
Ha, E.10
-
46
-
-
67651238706
-
An integrated strategy to study muscle development and myofilament structure in caenorhabditis elegans
-
Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, et al. 2009. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet 5: E1000537.
-
(2009)
PLoS Genet
, vol.5
-
-
Meissner, B.1
Warner, A.2
Wong, K.3
Dube, N.4
Lorch, A.5
McKay, S.J.6
Khattra, J.7
Rogalski, T.8
Somasiri, A.9
Chaudhry, I.10
-
47
-
-
78751535249
-
Identification of transcription start sites of trans-spliced genes: Uncovering unusual operon arrangements
-
Morton JJ, Blumenthal T. 2011. Identification of transcription start sites of trans-spliced genes: Uncovering unusual operon arrangements. RNA 17: 327-337.
-
(2011)
RNA
, vol.17
, pp. 327-337
-
-
Morton, J.J.1
Blumenthal, T.2
-
48
-
-
77954716355
-
A paired-end sequencing strategy to map the complex landscape of transcription initiation
-
Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, Ohler U, Zhu J. 2010. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods 7: 521-527.
-
(2010)
Nat Methods
, vol.7
, pp. 521-527
-
-
Ni, T.1
Corcoran, D.L.2
Rach, E.A.3
Song, S.4
Spana, E.P.5
Gao, Y.6
Ohler, U.7
Zhu, J.8
-
49
-
-
0012253746
-
Computational analysis of core promoters in the drosophila genome
-
Ohler U, Liao GC, Niemann H, Rubin GM. 2002. Computational analysis of core promoters in the Drosophila genome. Genome Biol 3: RESEARCH0087.
-
(2002)
Genome Biol
, vol.3
-
-
Ohler, U.1
Liao, G.C.2
Niemann, H.3
Rubin, G.M.4
-
50
-
-
0027451263
-
Sequence requirements for myosin gene expression and regulation in caenorhabditis elegans
-
Okkema PG, Harrison SW, Plunger V, Aryana A, Fire A. 1993. Sequence requirements for myosin gene expression and regulation in Caenorhabditis elegans. Genetics 135: 385-404.
-
(1993)
Genetics
, vol.135
, pp. 385-404
-
-
Okkema, P.G.1
Harrison, S.W.2
Plunger, V.3
Aryana, A.4
Fire, A.5
-
51
-
-
0025034642
-
Tandemly duplicated caenorhabditis elegans collagen genes differ in their modes of splicing
-
Park YS, Kramer JM. 1990. Tandemly duplicated Caenorhabditis elegans collagen genes differ in their modes of splicing. J Mol Biol 211: 395-406.
-
(1990)
J Mol Biol
, vol.211
, pp. 395-406
-
-
Park, Y.S.1
Kramer, J.M.2
-
52
-
-
0028206062
-
The c. Elegans sqt-1 and rol-6 collagen genes are coordinately expressed during development, but not at all stages that display mutant phenotypes
-
Park YS, Kramer JM. 1994. The C. elegans sqt-1 and rol-6 collagen genes are coordinately expressed during development, but not at all stages that display mutant phenotypes. Dev Biol 163: 112-124.
-
(1994)
Dev Biol
, vol.163
, pp. 112-124
-
-
Park, Y.S.1
Kramer, J.M.2
-
53
-
-
0001820920
-
X-means: Extended k-means with efficient estimation of the number of clusters
-
Stanford, CA Morgan Kaufmann, Stanford, CA.
-
Pelleg D, Moore A. 2000. X-means: Extended k-means with efficient estimation of the number of clusters. In 17th International Conference on Machine Learning, Stanford, CA, pp. 727-734. Morgan Kaufmann, Stanford, CA.
-
(2000)
17th International Conference on Machine Learning
, pp. 727-734
-
-
Pelleg, D.1
Moore, A.2
-
54
-
-
79851485916
-
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
-
Rach EA,Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U. 2011. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet 7: E1001274.
-
(2011)
PLoS Genet
, vol.7
-
-
Rach, E.A.1
Winter, D.R.2
Benjamin, A.M.3
Corcoran, D.L.4
Ni, T.5
Zhu, J.6
Ohler, U.7
-
55
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
Raser JM, O'Shea EK. 2004. Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814.
-
(2004)
Science
, vol.304
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
57
-
-
58449116917
-
Chromatinassociated periodicity in genetic variation downstream of transcriptional start sites
-
Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto S, Ogawa M, Matsushima K, Gu SG, Kasahara M, Ahsan B, et al. 2009. Chromatinassociated periodicity in genetic variation downstream of transcriptional start sites. Science 323: 401-404.
-
(2009)
Science
, vol.323
, pp. 401-404
-
-
Sasaki, S.1
Mello, C.C.2
Shimada, A.3
Nakatani, Y.4
Hashimoto, S.5
Ogawa, M.6
Matsushima, K.7
Gu, S.G.8
Kasahara, M.9
Ahsan, B.10
-
58
-
-
31944432339
-
A genome-wide analysis of cpg dinucleotides in the human genome distinguishes two distinct classes of promoters
-
Saxonov S, Berg P, Brutlag DL. 2006. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci 103: 1412-1417.
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 1412-1417
-
-
Saxonov, S.1
Berg, P.2
Brutlag, D.L.3
-
59
-
-
32044442759
-
Promoter features related to tissue specificity as measured by shannon entropy
-
Schug J, SchullerWP, Kappen C, Salbaum JM, BucanM, Stoeckert CJ Jr. 2005. Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol 6: R33.
-
(2005)
Genome Biol
, vol.6
-
-
Schug, J.1
Schuller, W.P.2
Kappen, C.3
Salbaum, J.M.4
Bucan, M.5
Stoeckert Jr., C.J.6
-
60
-
-
60349115060
-
Poly(dA:dT) tracts: Major determinants of nucleosome organization
-
Segal E, Widom J. 2009. Poly(dA:dT) tracts: Major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 65-71
-
-
Segal, E.1
Widom, J.2
-
61
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
62
-
-
84865315273
-
Regulatory elements of caenorhabditis elegans ribosomal protein genes
-
Sleumer MC, Wei G, Wang Y, Chang H, Xu T, Chen R, Zhang MQ. 2012. Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BMC Genomics 13: 433.
-
(2012)
BMC Genomics
, vol.13
, pp. 433
-
-
Sleumer, M.C.1
Wei, G.2
Wang, Y.3
Chang, H.4
Xu, T.5
Chen, R.6
Zhang, M.Q.7
-
63
-
-
0024557039
-
The ''initiator'' as a transcription control element
-
Smale ST, Baltimore D. 1989. The ''initiator'' as a transcription control element. Cell 57: 103-113.
-
(1989)
Cell
, vol.57
, pp. 103-113
-
-
Smale, S.T.1
Baltimore, D.2
-
64
-
-
0027166660
-
Operons in c. Elegans: Polycistronicmrna precursors are processed by trans-splicing of sl2 to downstream coding regions
-
Spieth J, Brooke G, Kuersten S, Lea K, Blumenthal T. 1993. Operons in C. elegans: PolycistronicmRNA precursors are processed by trans-splicing of SL2 to downstream coding regions. Cell 73: 521-532.
-
(1993)
Cell
, vol.73
, pp. 521-532
-
-
Spieth, J.1
Brooke, G.2
Kuersten, S.3
Lea, K.4
Blumenthal, T.5
-
65
-
-
4243088097
-
The genome sequence of caenorhabditis briggsae: A platform for comparative genomics
-
Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, et al. 2003. The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biol 1: E45.
-
(2003)
PLoS Biol
, vol.1
-
-
Stein, L.D.1
Bao, Z.2
Blasiar, D.3
Blumenthal, T.4
Brent, M.R.5
Chen, N.6
Chinwalla, A.7
Clarke, L.8
Clee, C.9
Coghlan, A.10
-
66
-
-
0025860028
-
A cold-sensitive mrna splicing mutant is a member of the rna helicase gene family
-
Strauss EJ, Guthrie C. 1991. A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family. Genes Dev 5: 629-641.
-
(1991)
Genes Dev
, vol.5
, pp. 629-641
-
-
Strauss, E.J.1
Guthrie, C.2
-
67
-
-
0022981733
-
Evidence for trans splicing in trypanosomes
-
Sutton RE, Boothroyd JC. 1986. Evidence for trans splicing in trypanosomes. Cell 47: 527-535.
-
(1986)
Cell
, vol.47
, pp. 527-535
-
-
Sutton, R.E.1
Boothroyd, J.C.2
-
68
-
-
0034991911
-
Diverse transcriptional initiation revealed by fine, large-scale mapping of mrna start sites
-
Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, Hata H, Ota T, Isogai T, Tanaka T, Morishita S, et al. 2001. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep 2: 388-393.
-
(2001)
EMBO Rep
, vol.2
, pp. 388-393
-
-
Suzuki, Y.1
Taira, H.2
Tsunoda, T.3
Mizushima-Sugano, J.4
Sese, J.5
Hata, H.6
Ota, T.7
Isogai, T.8
Tanaka, T.9
Morishita, S.10
-
70
-
-
77949393272
-
High nucleosome occupancy is encoded at human regulatory sequences
-
Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR. 2010. High nucleosome occupancy is encoded at human regulatory sequences. PLoS ONE 5: E9129.
-
(2010)
PLoS ONE
, vol.5
-
-
Tillo, D.1
Kaplan, N.2
Moore, I.K.3
Fondufe-Mittendorf, Y.4
Gossett, A.J.5
Field, Y.6
Lieb, J.D.7
Widom, J.8
Segal, E.9
Hughes, T.R.10
-
71
-
-
46449103738
-
A high-resolution, nucleosome position map of c. Elegans reveals a lack of universal sequence-dictated positioning
-
Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, et al. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051-1063.
-
(2008)
Genome Res
, vol.18
, pp. 1051-1063
-
-
Valouev, A.1
Ichikawa, J.2
Tonthat, T.3
Stuart, J.4
Ranade, S.5
Peckham, H.6
Zeng, K.7
Malek, J.A.8
Costa, G.9
McKernan, K.10
-
72
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 2011. Determinants of nucleosome organization in primary human cells. Nature 474: 516-520.
-
(2011)
Nature
, vol.474
, pp. 516-520
-
-
Valouev, A.1
Johnson, S.M.2
Boyd, S.D.3
Smith, C.L.4
Fire, A.Z.5
Sidow, A.6
-
73
-
-
66349103355
-
Identification of genes expressed in the hermaphrodite germ line of c. Elegans using
-
Wang X, Zhao Y, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D. 2009. Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics 10: 213.
-
(2009)
SAGE. BMC Genomics
, vol.10
, pp. 213
-
-
Wang, X.1
Zhao, Y.2
Wong, K.3
Ehlers, P.4
Kohara, Y.5
Jones, S.J.6
Marra, M.A.7
Holt, R.A.8
Moerman, D.G.9
Hansen, D.10
-
74
-
-
74949110964
-
Highresolution nucleosome mapping reveals transcription-dependent promoter packaging
-
Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N. 2010. Highresolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 20: 90-100.
-
(2010)
Genome Res
, vol.20
, pp. 90-100
-
-
Weiner, A.1
Hughes, A.2
Yassour, M.3
Rando, O.J.4
Friedman, N.5
-
75
-
-
52949083577
-
The genomic distribution and function of histone variant htz-1 during c. Elegans embryogenesis
-
Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD. 2008. The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genet 4: E1000187.
-
(2008)
PLoS Genet
, vol.4
-
-
Whittle, C.M.1
McClinic, K.N.2
Ercan, S.3
Zhang, X.4
Green, R.D.5
Kelly, W.G.6
Lieb, J.D.7
-
76
-
-
34250364559
-
Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of yy1
-
Xi H, Yu Y, Fu Y, Foley J, Halees A,Weng Z. 2007. Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res 17: 798-806.
-
(2007)
Genome Res
, vol.17
, pp. 798-806
-
-
Xi, H.1
Yu, Y.2
Fu, Y.3
Foley, J.4
Halees, A.5
Weng, Z.6
-
77
-
-
33846214719
-
Prevalence of the initiator over the tata box in human and yeast genes and identification of dna motifs enriched in human tata-less core promoters
-
Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E. 2007. Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389: 52-65.
-
(2007)
Gene
, vol.389
, pp. 52-65
-
-
Yang, C.1
Bolotin, E.2
Jiang, T.3
Sladek, F.M.4
Martinez, E.5
-
78
-
-
52949138674
-
On the nature of human housekeeping genes
-
Zhu J, He F, Hu S, Yu J. 2008. On the nature of human housekeeping genes. Trends Genet 24: 481-484.
-
(2008)
Trends Genet
, vol.24
, pp. 481-484
-
-
Zhu, J.1
He, F.2
Hu, S.3
Yu, J.4
|