| Year |
Citation |
Score |
| 2024 |
Rice G, Gaitan-Escudero T, Charles-Obi K, Zeitlinger J, Rebeiz M. Gene regulatory network co-option is sufficient to induce a morphological novelty in . Biorxiv : the Preprint Server For Biology. PMID 38585823 DOI: 10.1101/2024.03.22.584840 |
0.326 |
|
| 2023 |
Maven BEJ, Gifford CA, Weilert M, Gonzalez-Teran B, Hüttenhain R, Pelonero A, Ivey KN, Samse-Knapp K, Kwong W, Gordon D, McGregor M, Nishino T, Okorie E, Rossman S, Costa MW, ... ... Zeitlinger J, et al. The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5. Stem Cell Reports. PMID 37863045 DOI: 10.1016/j.stemcr.2023.09.014 |
0.344 |
|
| 2023 |
Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J. Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development. Nature Communications. 14: 5862. PMID 37735176 DOI: 10.1038/s41467-023-41408-1 |
0.421 |
|
| 2023 |
Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science (New York, N.Y.). 381: eadd1250. PMID 37733848 DOI: 10.1126/science.add1250 |
0.489 |
|
| 2023 |
Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Developmental Cell. PMID 37557175 DOI: 10.1016/j.devcel.2023.07.007 |
0.394 |
|
| 2023 |
Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A. distillation of thermodynamic affinity from deep learning regulatory sequence models of protein-DNA binding. Biorxiv : the Preprint Server For Biology. PMID 37214836 DOI: 10.1101/2023.05.11.540401 |
0.339 |
|
| 2023 |
Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Emerging questions in transcriptional regulation. Cell Systems. 14: 247-251. PMID 37080160 DOI: 10.1016/j.cels.2023.03.005 |
0.429 |
|
| 2022 |
Raicu AM, Fay JC, Rohner N, Zeitlinger J, Arnosti DN. Off the deep end: what can deep learning do for the gene expression field? The Journal of Biological Chemistry. 102760. PMID 36462664 DOI: 10.1016/j.jbc.2022.102760 |
0.308 |
|
| 2021 |
Soffers JHM, Alcantara SG, Li X, Shao W, Seidel CW, Li H, Zeitlinger J, Abmayr SM, Workman JL. The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters. Plos Genetics. 17: e1009668. PMID 34807910 DOI: 10.1371/journal.pgen.1009668 |
0.401 |
|
| 2021 |
Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nature Genetics. PMID 33603233 DOI: 10.1038/s41588-021-00782-6 |
0.367 |
|
| 2021 |
Ramalingam V, Natarajan M, Johnston J, Zeitlinger J. TATA and paused promoters active in differentiated tissues have distinct expression characteristics. Molecular Systems Biology. 17: e9866. PMID 33543829 DOI: 10.15252/msb.20209866 |
0.331 |
|
| 2020 |
Zeitlinger J. Seven myths of how transcription factors read the cis-regulatory code. Current Opinion in Systems Biology. 23: 22-31. PMID 33134611 DOI: 10.1016/j.coisb.2020.08.002 |
0.419 |
|
| 2019 |
Vincent BJ, Rice GR, Wong GM, Glassford WJ, Downs KI, Shastay JL, Charles-Obi K, Natarajan M, Gogol M, Zeitlinger J, Rebeiz M. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of . G3 (Bethesda, Md.). PMID 31619460 DOI: 10.1534/G3.119.400788 |
0.502 |
|
| 2019 |
Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Reports. 27: 3770-3779.e7. PMID 31242411 DOI: 10.1016/J.Celrep.2019.05.099 |
0.354 |
|
| 2018 |
Papagianni A, Forés M, Shao W, He S, Koenecke N, Andreu MJ, Samper N, Paroush Z, González-Crespo S, Zeitlinger J, Jiménez G. Capicua controls Toll/IL-1 signaling targets independently of RTK regulation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29432195 DOI: 10.1073/Pnas.1713930115 |
0.345 |
|
| 2017 |
De Kumar B, Parker HJ, Paulson A, Parrish ME, Zeitlinger J, Krumlauf R. Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis. Developmental Biology. PMID 28982536 DOI: 10.1016/J.Ydbio.2017.09.033 |
0.377 |
|
| 2017 |
De Kumar B, Parker HJ, Paulson A, Parrish ME, Pushel I, Singh NP, Zhang Y, Slaughter BD, Unruh JR, Florens L, Zeitlinger J, Krumlauf R. HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. Genome Research. PMID 28784834 DOI: 10.1101/Gr.219386.116 |
0.421 |
|
| 2017 |
Shao W, Zeitlinger J. Paused RNA polymerase II inhibits new transcriptional initiation. Nature Genetics. PMID 28504701 DOI: 10.1038/ng.3867 |
0.336 |
|
| 2016 |
Koenecke N, Johnston J, Gaertner B, Natarajan M, Zeitlinger J. Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. Genome Biology. 17: 196. PMID 27678375 DOI: 10.1186/S13059-016-1057-2 |
0.391 |
|
| 2015 |
Arnosti DN, Fay JC, Zeitlinger J. Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis: A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 37: 1042-4. PMID 26354485 DOI: 10.1002/bies.201500106 |
0.366 |
|
| 2015 |
Sun Y, Nien CY, Chen K, Liu HY, Johnston J, Zeitlinger J, Rushlow C. Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Research. PMID 26335633 DOI: 10.1101/Gr.192542.115 |
0.384 |
|
| 2015 |
He Q, Johnston J, Zeitlinger J. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nature Biotechnology. 33: 395-401. PMID 25751057 DOI: 10.1038/nbt.3121 |
0.386 |
|
| 2014 |
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 & Development. 28: 1550-5. PMID 24958592 DOI: 10.1101/Gad.245662.114 |
0.472 |
|
| 2014 |
Gaertner B, Zeitlinger J. RNA polymerase II pausing during development. Development (Cambridge, England). 141: 1179-83. PMID 24595285 DOI: 10.1242/dev.088492 |
0.364 |
|
| 2014 |
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. Molecular Biology and Evolution. 31: 1375-90. PMID 24509725 DOI: 10.1093/Molbev/Msu071 |
0.359 |
|
| 2013 |
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 (Oxford, England). 29: 2705-13. PMID 23980024 DOI: 10.1093/Bioinformatics/Btt470 |
0.363 |
|
| 2013 |
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. 2: e00861. PMID 23951546 DOI: 10.7554/eLife.00861 |
0.347 |
|
| 2013 |
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. 153: 976-87. PMID 23706736 DOI: 10.1016/J.Cell.2013.04.045 |
0.333 |
|
| 2011 |
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. Nature Genetics. 43: 414-20. PMID 21478888 DOI: 10.1038/ng.808 |
0.349 |
|
| 2010 |
Zeitlinger J, Stark A. Developmental gene regulation in the era of genomics. Developmental Biology. 339: 230-9. PMID 20045679 DOI: 10.1016/j.ydbio.2009.12.039 |
0.483 |
|
| 2008 |
Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America. 105: 7762-7. PMID 18505835 DOI: 10.1073/Pnas.0802406105 |
0.365 |
|
| 2007 |
Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K. RNA polymerase is poised for activation across the genome. Nature Genetics. 39: 1507-11. PMID 17994021 DOI: 10.1038/Ng.2007.21 |
0.503 |
|
| 2007 |
Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genetics. 39: 1512-6. PMID 17994019 DOI: 10.1038/Ng.2007.26 |
0.515 |
|
| 2007 |
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 & Development. 21: 385-90. PMID 17322397 DOI: 10.1101/Gad.1509607 |
0.575 |
|
| 2006 |
Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. High-resolution computational models of genome binding events. Nature Biotechnology. 24: 963-70. PMID 16900145 DOI: 10.1038/Nbt1233 |
0.563 |
|
| 2006 |
Pokholok DK, Zeitlinger J, Hannett NM, Reynolds DB, Young RA. Activated signal transduction kinases frequently occupy target genes. Science (New York, N.Y.). 313: 533-6. PMID 16873666 DOI: 10.1126/science.1127677 |
0.53 |
|
| 2006 |
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, et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature. 441: 349-53. PMID 16625203 DOI: 10.1038/Nature04733 |
0.758 |
|
| 2005 |
Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, Young RA. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell. 122: 517-27. PMID 16122420 DOI: 10.1016/J.Cell.2005.06.026 |
0.757 |
|
| 2004 |
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, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 431: 99-104. PMID 15343339 DOI: 10.1038/Nature02800 |
0.604 |
|
| 2003 |
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. 113: 395-404. PMID 12732146 DOI: 10.1016/S0092-8674(03)00301-5 |
0.613 |
|
| 2002 |
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (New York, N.Y.). 298: 799-804. PMID 12399584 DOI: 10.1126/Science.1075090 |
0.507 |
|
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