Biology Reference
In-Depth Information
[122] Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, Bounoutas A,
et al. Identification of genes expressed in C. elegans touch
receptor neurons. Nature 2002;418:331
e
5.
[123] Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL,
McWhirter RD, et al. A spatial and temporal map of C. elegans
gene expression. Genome Res 2011;21:325
e
41.
[124] Gaudet J, Muttumu S, Horner M, Mango SE. Whole-genome
analysis of temporal gene expression during foregut development.
PLoS Biol 2004;2:e352.
[125] Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS,
Claggett JM, et al. Pairing of competitive and topologically
distinct regulatory modules enhances patterned gene expression.
Mol Syst Biol 2008;4:163.
[126] Baugh LR, Hunter CP. MyoD, modularity, and myogenesis:
conservation of regulators and redundancy in C. elegans. Genes
Dev 2006;20:3342
e
6.
[127] Long F, Peng H, Liu X, Kim SK, Myers E. A 3D digital atlas of C.
elegans and its application to single-cell analyses. Nat Methods
2009;6:667
e
72.
[128] Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sanchez-Blanco A,
et al. Analysis of cell fate from single-cell gene expression
profiles in C. elegans. Cell 2009;139:623
e
33.
[129] Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH.
Automated cell lineage tracing in Caenorhabditis elegans. Proc
Natl Acad Sci U S A 2006;103:2707
divergence between C. elegans bHLH transcription factors. Cell
2009;138:314
27.
[140] Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, et al.
Diverse transcription factor binding features revealed by genome-
wide ChIP-seq in C. elegans. Genome Res 2011;21:245
e
54.
[141] Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A,
Delhomme N, et al. Tissue-specific analysis of chromatin state
identifies temporal signatures of enhancer activity during
embryonic development. Nat Genet 2012;44:148
e
56.
[142] Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I,
Cheung MS, et al. Broad chromosomal domains of histone modi-
fication patterns in C. elegans. Genome Res 2011;21:227
e
36.
[143] Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD,
Kelly WG, et al. The genomic distribution and function of histone
variant HTZ-1 during C. elegans embryogenesis. PLoS Genet
2008;4:e1000187.
[144] Ercan S, Giresi PG, Whittle CM, Zhang X, Green RD, Lieb JD. X
chromosome repression by localization of the C. elegans dosage
compensation machinery to sites of transcription initiation. Nat
Genet 2007;39:403
e
8.
[145] Ercan S, Dick LL, Lieb JD. The C. elegans dosage compensation
complex propagates dynamically and independently of X chro-
mosome sequence. Curr Biol 2009;19:1777
e
87.
[146] Rechtsteiner A, Ercan S, Takasaki T, Phippen TM, Egelhofer TA,
Wang W, et al. The histone H3K36 methyltransferase MES-4 acts
epigenetically to transmit the memory of germline gene expres-
sion to progeny. PLoS Genet 2010;6.
[147] Gu SG, Pak J, Guang S, Maniar JM, Kennedy S, Fire A.
Amplification of siRNA in Caenorhabditis elegans generates
a transgenerational sequence-targeted histone H3 lysine 9 meth-
ylation footprint. Nat Genet 2012;44:157
e
64.
[148] Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP,
et al. Transgenerational epigenetic inheritance of longevity in
Caenorhabditis elegans. Nature 2011;479:365
e
71.
[149] Casanueva MO, Burga A, Lehner B. Fitness trade-offs and envi-
ronmentally induced mutation buffering in isogenic C. elegans.
Science 2012;335:82
e
5.
[150] Pincus Z, Smith-Vikos T, Slack FJ. MicroRNA predictors of
longevity in Caenorhabditis elegans. PLoS Genet 2011;7:e1002306.
[151] Rea SL, Wu D, Cypser JR, Vaupel JW, Johnson TE. A stress-
sensitive reporter predicts longevity in isogenic populations of
Caenorhabditis elegans. Nat Genet 2005;37:894
e
8.
[152] Sanchez-Blanco A, Kim SK. Variable pathogenicity determines
individual lifespan in Caenorhabditis elegans. PLoS Genet
2011;7:e1002047.
[153] Herndon LA, Schmeissner PJ, Dudaronek JM, Brown PA,
Listner KM, Sakano Y, et al. Stochastic and genetic factors
influence tissue-specific decline in ageing C. elegans. Nature
2002;419:808
e
12.
[130] Murray JI, Bao Z, Boyle TJ, Boeck ME, Mericle BL,
Nicholas TJ, et al. Automated analysis of embryonic gene
expression with cellular resolution in C. elegans. Nat Methods
2008;5:703
e
9.
[131] Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, et al.
Genome-scale analysis of in vivo spatiotemporal promoter activity
in Caenorhabditis elegans. Nat biotechnol 2007;25:663
e
8.
[132] Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A,
Tyagi S. Imaging individual mRNA molecules using multiple
singly labeled probes. Nat Methods 2008;5:877
e
9.
[133] Burga A, Casanueva MO, Lehner B. Predicting mutation outcome
from early stochastic variation in genetic interaction partners.
Nature 2011;480:250
e
3.
[134] Raj A, Rifkin SA, Andersen E, van Oudenaarden A. Variability in
gene expression underlies incomplete penetrance. Nature 2010;
463:913
e
8.
[135] Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA,
Martinez NJ, et al. A gene-centered C. elegans protein-DNA
interaction network. Cell 2006;125:1193
e
205.
[136] Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van
Gilst M, et al. Functional modularity of nuclear hormone recep-
tors in a Caenorhabditis elegans metabolic gene regulatory
network. Mol syst biol 2010;6:367.
[137] Vermeirssen V, Barrasa MI, Hidalgo CA, Babon JA, Sequerra R,
Doucette-Stamm L, et al. Transcription factor modularity in
a gene-centered C. elegans core neuronal protein
e
14.
[154] Raviv TR, Ljosa V, Conery AL, Ausubel FM, Carpenter AE,
Golland P, et al. Morphology-guided graph search for untangling
objects: C. elegans analysis. Medical image computing and
computer-assisted intervention: MICCAI International Confer-
ence on Medical Image Computing and Computer-Assisted
Intervention 2010;13:634
e
41.
[155] Rockman MV, Kruglyak L. Recombinational landscape and
population genomics of Caenorhabditis elegans. PLoS Genet
2009;5:e1000419.
e
DNA interac-
e
71.
[138] Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R,
Doucette-Stamm L, et al. A C. elegans genome-scale microRNA
network contains composite feedback motifs with high flux
capacity. Genes Dev 2008;22:2535
e
49.
[139] Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ,
Bulyk ML, et al. A multiparameter network reveals extensive
tion network. Genome Res 2007;17:1061
e
