Publications

• Home
• Research
• Publications
• People
• RNAi
• Links

2013

• Chen, R. A-J., Down, T.A., Stempor, P., Chen, Q.B., Egelhofer, T.A., Hillier, L.W., Jeffers, T.E. and Ahringer, J. (2013) The landscape of RNA polymerase II transcription initiation in C. elegans reveals enhancer and promoter architectures Genome Research in press

• Woods, S., Coghlan, A., Rivers, D., Warnecke, T., Jeffries, S.,J., Kwon, T., Rogers, A., Hurst, L., and Ahringer, J. (2013) Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses Plos Genetics in press

• Fievet, B.T.*, Rodriguez, J.*, Naganathan, S., Lee, C.., Zeiser, E., Ishidate, T., Shirayama, M., Grill, S., and Ahringer, J. (2013) Systematic genetic interaction screens uncover cell polarity regulators and functional redundancy Nature Cell Biology 15(1):103-12

2012

• Vielle, A. Lang, J., Dong, Y., Ercan, S., Kotwaliwale, C., Rechtsteiner, A., Appert, A., Chen, Q.B., Dose, A., Egelhofer, T., Stempor, P., Dernburg, A., Lieb, J., Strome,, S., and Ahringer, J. (2012) H4K20me1 contributes to downregulation of X-linked genes for C. elegans dosage compensation Nucleic Plos Genetics 8(9):e1002933

2011

• Cheung, M-S., Down, T.A., Latorre, I., and Ahringer, J. (2011) Systematic bias in deep sequencing data and its correction by BEADS Nucleic Acids Research 39(15):e103
• Zeiser, E., Frøkjær-Jensen, C., Jorgensen, E., and Ahringer, J. (2011) MosSCI and Gateway compatible plasmid toolkit for constitutive and inducible expression of transgenes in the C. elegans germline PlosOne 6(5):e20082
• Liu T, Rechtsteiner A, Egelhofer T a, et al (2011) Broad chromosomal domains of histone modification patterns in C. elegans. Genome research 2010:1775-1787

2010

• Gerstein MB, Lu ZJ, Van Nostrand EL, et al. (2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 330:1775-1787
• Egelhofer T, Minoda A, Ahringer J, et al. (2010) An assessment of histone-modification antibody quality. Nature structural and molecular biology. December 2010:8-11.
• Poulin GB, Ahringer J. (2010) The Caenorhabditis elegans CDT-2 ubiquitin ligase is required for attenuation of EGFR signalling in vulva precursor cells. BMC developmental biology. 10:109.
• St Johnston D, Ahringer J. (2010) Cell Polarity in Eggs and Epithelia: Parallels and Diversity. Cell. 141(5):757-774.

2009

• 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 Gen. 41(3):376-81.

2008

• Panbianco C, Weinkove D, Zanin E, Jones D, Divecha N, Gotta M, Ahringer J. (2008) A casein kinase 1 and PAR proteins regulate asymmetry of a PIP(2) synthesis enzyme for asymmetric spindle positioning. Dev Cell. 15(2):198-208.
• Rivers DM, Moreno S, Abraham M, Ahringer J. (2008) PAR proteins direct asymmetry of the cell cycle regulators Polo-like kinase and Cdc25. J Cell Biol. 180(5):877-85.
• Boutros M, Ahringer J. (2008) The art and design of genetic screens: RNA interference. Nat Rev Genet. 9(7):554-66.

2007

• Tsai MC, Ahringer J. (2007) Microtubules are involved in anterior-posterior axis formation in C. elegans embryos. J Cell Biol. 179(3):397-402.
• Welchman DP, Mathies LD, Ahringer J. (2007) Similar requirements for CDC-42 and the PAR-3/PAR-6/PKC-3 complex in diverse cell types. Dev Biol. 305(1):347-357.
• Dong Y, Bogdanova A, Habermann B, Zachariae W, Ahringer J. (2007) Free in PMC Identification of the C. elegans anaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast. BMC Dev. Biol. 207:19
• Miska EA, Ahringer J. (2007) RNA interference has second helpings. Nat Biotechnol. 25(3):302-3.
• Andrews R, Ahringer J. (2007) Asymmetry of Early Endosome Distribution in C. elegans Embryos PLoS One 2(6):e493

2006

• J Ahringer (ed.) (2006) Reverse genetics. In: Wormbook (Editor The C. elegans Research Community). 6 April 2006, http:www.wormbook.org. doi/10.1895/wormbook.1.47.1

2005

• Poulin, G., Dong, Y., Fraser, A.G., Hopper, N.A., and Ahringer, J. (2005) Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans. EMBO Journal, 24(51): 2613-2623.

2004

• Poulin, G., Nandakumar, R., and Ahringer, J. (2004) Genome-wide RNAi screens in Caenorhabditis elegans: Impact on cancer research. Oncogene, 23(51): 8340-8345.
• Lettre, G., Kritikou, E.A., Jaeggi, M., Calixto, A., Fraser, A.G., Kamath, R.S., Ahringer, J., and Hengartner, M.O. (2004) Genome-wide RNAi identifies p53-dependent and -independent regulators of germ cell apoptosis in C. elegans. Cell Death Differ., 11(11): 1198-1203.
• Pocock, R., Ahringer, J., Mitsch, M., Maxwell, S., and Woollard, A. (2004) A regulatory network of T-box genes and the even-skipped homologue vab-7 controls patterning and morphogenesis in C. elegans. Development, 131(10): 2373-2385.
• Kemp, C.A., Kopish, K.R., Zipperlen, P., Ahringer, J., and O'Connell, K.F. (2004) Centrosome maturation and duplication in C. elegans require the coiled-coil protein SPD-2. Dev. Cell, 6(4): 511-523.

2003

• Malone, C., Misner, L., Le Bot, N., Tsai, M-C., Cambell, J.M., Ahringer, J., and White, J.G. (2003) The C. elegans Hook protein, ZYG-12, mediates the essential attachment between the centrosome and nucleus. Cell, 115(7): 825-836.
• Rappleye, C.A., Tagawa, A., Le Bot, N., Ahringer, J. and Aroian, R.V. (2003) Involvement of fatty acid pathways and cortical interaction of the pronuclear complex in Caenorhabditis elegans embryonic polarity. BMC Dev. Biol., 3(1): 8.
• Simmer, F., Moorman, C., van der Linden, A.M., Kuijk, E., van den Berghe, P.V.E., Kamath, R.S., Fraser, A.G., Ahringer, J., and Plasterk, R.H.A. (2003) Genome-wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions. PLoS Biology, 1(1): E12.
• Fraser, A.G., and Ahringer, J. (2003) Total interference : Genome-wide RNAi screens in C. elegans. In ìRNAi: A Guide to Gene Silencingî Ed. G. Hannon.
• Le Bot, N., Tsai, M-C., Andrews, R.K., and Ahringer, J. (2003) TAC-1, a regulator of microtubule length in the C.elegans embryo. Current Biology, 13(17): 1499-1505.
• Vastenhouw, N.L., Fischer, S.E.J., Robert, V.J.P., Thijssen, K.L., Fraser, A.G., Kamath, R.S., Ahringer, J., and Plasterk, R.H.A. (2003) A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Current Biology, 13(15): 1311-1316.
• Murphy, C.T., McCarroll, S.A., Bargmann, C.I., Fraser, A., Kamath, R.S., Ahringer, J., Li, H., and Kenyon, C. (2003) Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature, 424(6946): 277-283.
• Kamath, R.S., and Ahringer, J. (2003) Genome-wide RNAi screening in C. elegans. Methods, 30(4): 313-321.
• Gotta, M., Dong, Y., Peterson, Y.K., Lanier, S.M., and Ahringer, J. (2003) Asymmetrically distributed C. elegans homologues of AGS3/PINS control spindle position in the early embryo. Current Biology, 13(12): 1029-1037.
• Pothof, J., van Haaften, G., Thijssen, K., Kamath, R.S., Fraser, A.G., Ahringer, J., Plasterk, R.H.A., and Tijsterman, M. (2003) Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Genes Dev., 17(4): 443-448.
• Ahringer, J. (2003) Control of cell polarity and mitotic spindle positioning in animal cells. Curr. Opin. Cell Biol., 15(1): 73-81.
• Lee, S.S., Lee, R.Y.N., Fraser, A.G., Kamath, R.S., Ahringer, J., and Ruvkun, G. (2003) A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nature Genetics, 33(1): 40-48.
• Kamath, R.S., Fraser, A.G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D., Zipperlen, P., and Ahringer, J. (2003) Systematic Functional Analysis of the Caenorhabditis elegans Genome using RNAi. Nature, 421(6920): 231-237.
• Ashrafi, K., Chang, F., Watts, J.L., Fraser, A.G., Kamath, R.S., Ahringer, J., and Ruvkun, G. (2003) Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature, 421(6920): 268-272.

2002

• Dillin, A., Hsu, A-L., Arantes-Oliveira, N., Lehrer-Graiwer, J., Hsin, H., Fraser, A.G., Kamath, R.S., Ahringer, J., and Kenyon, C. (2002) Rates of behavior and aging specified by mitochondrial function during development. Science, 298(5602): 2398-2401.
• Simmer, F., Tijsterman, M., Parrish, S., Koushika, S.P., Nonet, M.L., Fire, A., Ahringer, J., and Plasterk, R.H.A. (2002) Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Current Biology, 12(15): 1317-1319.
• Garigan, D., Hsu, A-L., Fraser, A.G., Kamath, R.S., Ahringer, J., and Kenyon, C. (2002) Genetic analysis of tissue aging in Caenorhabditis elegans: a role for heat-shock factor and bacterial proliferation. Genetics, 161(3): 1101-1112.
• Esmaeili, B., Ross, J., Neades, C., Miller, III, D.M., and Ahringer, J. (2002) The C. elegans even-skipped homolog, vab-7, specifies DB motoneurone identity and axon trajectory. Development, 129(4): 853-862.

2001

• Gotta, M., and Ahringer, J. (2001) Axis determination in C. elegans: initiating and transducing polarity. Curr. Opin. Genet. Dev., 11(4): 367-373.
• Zipperlen, P., Fraser, A.G., Kamath, R.S., Martinez-Campos, M., and Ahringer, J. (2001) Roles for 147 embryonic lethal genes on C. elegans chromosome I identified by RNA interference and video microscopy. EMBO Journal, 20(15): 3984-3992.
• Gotta, M., Abraham, M., and Ahringer, J. (2001) CDC-42 controls early cell polarity and spindle orientation in C. elegans. Current Biology, 11(7): 482-488.
• Gotta, M., and Ahringer, J. (2001) Distinct roles for Galpha and Gbetagamma in regulating spindle position and orientation in Caenorhabditis elegans embryos. Nature Cell Biology, 3(3): 297-300.
• Kamath, R.K., Martinez-Campos M., Zipperlen, P., Fraser, A., and Ahringer, J. (2001) Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biology, 2(1): research0002.1-10.

2000

• Fraser, A., Kamath, R.K., Zipperlen, P., Martinez-Campos M., Sohrmann, M. and Ahringer, J. (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature, 408(6810): 325-330.
• Ahringer, J. (2000) NuRD and SIN3 histone deacetylase complexes in development. Trends in Genetics, 16(8): 351-356.
• Solari, F., and Ahringer, J. (2000) NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans. Current Biology, 10(4): 223-226.

1999

• Solari, F., Bateman, A, and Ahringer, J. (1999) The Caenorhabditis elegans genes egl-27 and egr-1 are simliar to MTA1, a member of a chromatin regulatory complex, and are redundantly required for embryonic patterning. Development, 126(11): 2483-2494.

1998

• Gallegos, M., Ahringer, J., Crittenden, C., and Kimble, J. (1998) Repression by the 3' UTR of fem-3, a sex-determining gene, relies on a ubiquitous mog-dependent control in Caenorhabditis elegans. EMBO Journal 17(21): 6337-6347.

1997

• Ahringer, J. (1997) Maternal control of a zygotic patterning gene in C. elegans. Development, 124(19): 3865-3869.
• Ahringer, J. (1997) Turn to the worm! Curr. Opin. Genet. Dev., 7(3): 410-415.

1996

• Zwaal, R.*, Ahringer, J.*, van Luenen, H.G., Rushforth, A., Anderson, P., and Plasterk, R.H.A. (1996) G proteins are required for spatial orientation of early cell cleavages in C. elegans embryos. Cell, 86(4): 619-629. *equal contribution
• Ahringer, J. (1996) Posterior patterning by the Caenorhabditis elegans even-skipped homolog vab-7. Genes Dev., 10(9): 1120-1130.
• Goedert, M., Baur, C.P., Ahringer, J., Jakes, R., Hasegawa, M., Spillantini, M.G., Smith, M.J., and Hill, F. (1996) PTL-1, a microtubule-associated protein with tau-like repeats from the nematode Caenorhabditis elegans. J. Cell Science, 109(11): 2661-2672.

1995

• Ahringer, J. (1995) Embryonic tissue differentiation in Caenorhabditis elegans requires dif-1, a gene homologous to mitochondrial solute carriers. EMBO Journal, 14(10): 2307-2316.