Miller, D.E., Staber, C., Zeitlinger, J., and Hawley, R.S. (2018) GENOME REPORT: Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing. G3. Oct 3;8(10):3131-3141. PAPER
Li, Z., Qian, P., Shao, W., Shi, H., He, X.C., Gogal, M., Yu, Z., Wang, Y., Qi, M., Zhu, Y., Perry, J.M., Zhang, K., Tao, F., Zhou, K., Hu, D., Han, Y., Zhao, C., Alexander, R., Xu, H., Chen, S., Peak, A., Hall, K., Peterson, M., Perera, A., Haug, J.S., Parmely, T., Li, H., Shen, B., Zeitlinger, J., He, C., and Li, L. (2018) Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion. Cell Research. Sep;28(9):904-917. PAPER
Papagianni, A., Forés, M., Shao, W., He, S., Koenecke, N., José Andreu, M., Samper, N., Paroush, Z., González-Crespo, S., Zeitlinger, J., and Jiménez, G. (2018) Capicua controls ToII/IL-1 signaling targets independently of RTK regulation. PNAS, Feb 20;115(8):1807-1812. PAPER
De Kumar, B., Parker, H.J., Paulson, A., Parrish M.E., Zeitlinger, J., and Krumlauf, R. (2017) Hoxa1 targets signaling pathways during neural differentation of ES cells and mouse embryogenesis. Developmental Biology, Dec 1;432(1):151-164. PAPER
De Kumar, B., Parker, H.J., Paulson, A., Parrish M.E., Pushel, I., Singh, N.P., Zhang, Y., Slaughter, B.D., Unruh, J.R., Florens, L., Zeitlinger, J., and Krumlauf, R. (2017) HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. Genome Research, Sep; 27(9):1501-1512. PAPER
Pascual, J., Jacobs, J., Sansores-Garcia, L., Natarajan, M., Zeitlinger, J., Aerts, S., Halder, G. and Hamaratoglu, F. (2017) Hippo Reprograms the Transcriptional Response to Ras Signaling.
Developmental Cell, Sep 25;42(6):667-680.e4. Data | PAPER
Shao, W., and Zeitlinger, J. (2017) Paused RNA polymerase II inhibits new transcriptional initiation. Nature Genetics, July:49(7): 1045-1051. Data | PAPER
Koenecke, N., Johnston, J., He, Q., Meier, S., and Zeitlinger, J. (2017) Drosophila poised enhancers are generated during tissue patterning with the help of repression. Genome Research, Jan; 27(1):64-74. Data | PAPER
Koenecke, N., Johnston, J., Gaertner, B., Natarajan, M., and Zeitlinger, J. (2016) Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. Genome Biology, Sep 27;17(1):196. Data | PAPER
Sun, Y., Nien, C.Y., Chen, K., Liu, H.Y., Johnston, J., Zeitlinger, J., and Rushlow, C. (2015) Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.
Genome Research, Nov;25(11):1703-14. PAPER
He Q, Johnston J, Zeitlinger J. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat Biotechnol.2015;33:395-401. Abstract | Original Data
Ikmi A, Gaertner B, Seidel C, Srivastava M, Zeitlinger J, Gibson MC. Molecular Evolution of the Yap/Yorkie Proto-oncogene and Elucidation of its Core Transcriptional Program. Mol Biol Evol.2014;31:1375-1390. Abstract | Original Data
Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev.2014;28:1550-1555.Abstract | Original Data
Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics.2013;29:2705-2713. Abstract
Chen K, Johnston J, Shao W, Meier S, Staber C, Zeitlinger J. A global change in RNA polymerase II pausing during the Drosophila midblastula transition. eLife.2013;2:e00861. Abstract | Original Data
Lagha M, Bothma JP, Esposito E, Ng S, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour DS, Zeitlinger J, Levine MS. Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell. 2013;153:976-987. Abstract
Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression. Cell Rep. 2012;2:1670-1683. Abstract | Original Data
He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet.2011;43:414-420. Abstract
Zeitlinger J. Book review of Evolution, Development, and the Predictable Genome by David L. Stern. Am J Hum Biol.2011;43:414-420. Abstract
Zeitlinger J, Stark A. Developmental gene regulation in the era of genomics. Dev Biol.2010;339:230-239. Abstract
Hendrix D, Hong J-W, Zeitlinger J, Rokhsar DS, Levine M. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci. 2008;105(22):7762-7767. Abstract
Zeitlinger J, Stark A, Kellis M, Hong J-W, Nechaev S, Adelman K, Levine M, Young RA. RNA polymerase stalling at developmental control genes in the Drosophila embryo. Nat Genet. 2007;39(12):1512-1516. Abstract
Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev.2007;21:385-390. Abstract
Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch R. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature.2006;441:349-353. Abstract
Pokholok DK, Zeitlinger J, Hannett NM, Reynolds DB, Young RA. Activated signal transduction kinases frequently occupy target genes. Science.2006;313:533-536. Abstract
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature.2004;431:99-104. Abstract
Zeitlinger J, Simon I, Harbison CT, Hannett NM, Volkert TL, Fink GR, Young RA. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell.2003;113:395-404. Abstract
Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA. Genome-wide location and function of DNA binding proteins. Science.2000;290:2306-2309. Abstract
Zeitlinger J, Bohmann D. Thorax closure in Drosophila: involvement of Fos and the JNK pathway. Development.1999;126:3947-3956. Abstract
Zeitlinger J, Kockel L, Peverali FA, Jackson DB, Mlodzik M, Bohmann D. Defective dorsal closure and loss of epidermal decapentaplegic expression in Drosophila fos mutants. EMBO J.1997;16:7393-7401. Abstract