Stempor, P., Ahringer, J. (2016)
SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics Wellcome Open Research 2016, 1:14, doi: 10.12688/wellcomeopenres.10004.1

Heppert, J.K., Dickinson, D.J., Pani, A.M., Higgins, C.D., Steward, A., Ahringer, J., Kuhn, J.R., Goldstein, B. (2016)
Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system Molecular Biology of the Cell 27(22), 3385-3394 | PDF

Evans, K.J., Huang, N., Stempor, P., Chesney, M.A., Down, T.A., and Ahringer, J. (2016)
Stable C. elegans chromatin domains separate broadly expressed and developmentally regulated genes PNAS 113, E7020–E7029, doi: 10.1073 | PDF


Latorre, I., Chesney, M.A., Garrigues, J.M., Stempor, P., Appert, A., Francesconi, M., Strome, S., and Ahringer, J. (2015)
The DREAM complex promotes gene body H2A.Z for target repression Genes Dev 29(5), 495-500 | PDF


Ho, J.W., Jung, Y.L., Liu, T., Alver, B.H. Lee, S., Ikegami, K., Sohn, K.A., Minoda, A., Tolstorukov, M.Y., Appert, A., Parker, S.C., Gu, T., Kundaje, A., Riddle, N.C., Bishop, E., Egelhofer, T.A., Hu, S.S., Alekseyenko, A.A., Rechtsteiner, A., Asker, D., Belsky, J.A., Bowman, S.K., Chen, Q.B., Chen, R.A., Day, D.S., Dong, Y., Dose, A.C., Duan, X., Epstein, C.B., Ercan, S., Feingold, E.A., Ferrari, F., Garrigues, J.M., Gehlenborg, N., Good, P.J., Haseley, P., He, D., Herrmann, M., Hoffman, M.M., Jeffers, T.E., Kharchenko, P.V., Kolasinska-Zwierz, P., Kotwaliwale, C.V., Kumar, N., Langley, SA, Larschan, EN, Latorre, I., Libbrecht, M.W., Lin, X., Park, R., Pazin, M.J., Pham, H.N., Plachetka, A., Qin, B., Schwartz, YB, Shoresh, N., Stempor, P., Vielle, A., Wang, C., Whittle, C.M., Xue, H., Kingston, R.E., Kim, J.H., Bernstein, B.E., Dernburg, A.F., Pirrotta, V., Kuroda, M.I., Noble, WS.., Tullius, T.D., Kellis, M., MacAlpine, D.M.^, Strome, S.^, Elgin, S.C.^, Liu, X.S.^, Lieb, J.D.^, Ahringer, J.^, Karpen, G.H.^, Park, P.J.^ (2014)
Comparative analysis of metazoan chromatin architecture Nature 512, 449-452 (^corresponding authors) | PDF

Weick, E-M.^, Sarkies, P.^, Silva, N., Chen, A.-J.1, Moss, S.M.M., Cording, A.C., Ahringer, J., Martinez-Perez, E. and Miska, E.A.
PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif- dependent piRNAs in C. elegans Genes Dev 28, 783-96 (^corresponding authors) | PDF

Chen, A.-J., Stempor, P., Down, T.A., Zeiser, E., Feuer, S., and Ahringer, J. (2014)
Extreme HOT regions are CpG dense promoters in C. elegans and human Genome Research 24(7):1138-46 | PDF

Gaggioli, V., Zeiser, E., Rivers, D., Bradshaw, C.R., Ahringer, J^., and Zegerman, P.^ (2014)
CDK phosphorylation of SLD-2 is essential for replication initiation and germ line development in C. elegans Journal of Cell Biology 204, 507–522 (^corresponding authors) | PDF


Stamper, E.L., Rodenbusch, S.E., Rosu, S., Ahringer, J., Villeneuve, A.M., and Dernburg, A.F. (2013)
Identification of DSB-1, a protein required for initiation of meiotic recombination in Caenorhabditis elegans, illuminates a crossover assurance checkpoint Plos Genetics 9(8):e1003679 | PDF

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 9(5):e1003330 | PDF

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 23(8):1339-47 | PDF

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 | PDF


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 Plos Genetics 8(9):e1002933 | PDF


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 | PDF

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 | PDF

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 | PDF


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. | PDF

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. | PDF

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. | PDF

St Johnston D, Ahringer J. (2010)
Cell Polarity in Eggs and Epithelia: Parallels and Diversity. Cell. 141(5):757-774. | PDF


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. | PDF


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. | PDF

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. | PDF

Boutros M, Ahringer J. (2008)
The art and design of genetic screens: RNA interference. Nat Rev Genet. 9(7):554-66. | PDF


Tsai MC, Ahringer J. (2007)
Microtubules are involved in anterior-posterior axis formation in C. elegans embryos. J Cell Biol. 179(3):397-402. | PDF

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. | PDF

Dong Y, Bogdanova A, Habermann B, Zachariae W, Ahringer J. (2007)
Identification of the C. elegans anaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast. BMC Dev. Biol. 207:19 | PDF

Miska EA, Ahringer J. (2007)
RNA interference has second helpings. Nat Biotechnol. 25(3):302-3. | PDF

Andrews R, Ahringer J. (2007)
Asymmetry of Early Endosome Distribution in C. elegans Embryos PLoSOne 2(6):e493| PDF


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


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.| PDF


Poulin, G., Nandakumar, R., and Ahringer, J. (2004)
Genome-wide RNAi screens in Caenorhabditis elegans: Impact on cancer research. Oncogene, 23(51): 8340-8345. | PDF

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. | PDF

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.| PDF


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. PDF

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. | PDF

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. | PDF

Fraser, A.G., and Ahringer, J. (2003)
Total interference : Genome-wide RNAi screens in C. elegans. In RNAi: A Guide to Gene Silencing 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. | PDF

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. | PDF

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. | PDF

Kamath, R.S., and Ahringer, J. (2003)
Genome-wide RNAi screening in C. elegans. Methods, 30(4): 313-321. | PDF

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. | PDF

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. | PDF

Ahringer, J. (2003)
Control of cell polarity and mitotic spindle positioning in animal cells. Curr. Opin. Cell Biol., 15(1): 73-81. | PDF

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. | PDF PDF

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. | PDF

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. | PDF


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. PDF

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. | PDF

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. | PDF PDF

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. | PDF


Gotta, M., and Ahringer, J. (2001)
Axis determination in C. elegans: initiating and transducing polarity. Curr. Opin. Genet. Dev., 11(4): 367-373. | PDF

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. | PDF

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. | PDF

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. | PDF

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. | PDF


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. | PDF

Ahringer, J. (2000)
NuRD and SIN3 histone deacetylase complexes in development. Trends in Genetics, 16(8): 351-356. | PDF

Solari, F., and Ahringer, J. (2000)
NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans. Current Biology, 10(4): 223-226. | PDF


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. | PDF


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. | PDF


Ahringer, J. (1997)
Maternal control of a zygotic patterning gene in C. elegans. Development, 124(19): 3865-3869. | PDF

Ahringer, J. (1997)
Turn to the worm! Curr. Opin. Genet. Dev., 7(3): 410-415. | PDF


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 | PDF

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. | PDF


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.