Publications

For our code repositories
please visit our Github
2022
CMTr cap-adjacent 2'-O-ribose mRNA methyltransferases are required for reward learning and mRNA localization to synapses.
Irmgard U. Haussmann, Yanying Wu, Mohanakarthik P. Nallasivan, Nathan Archer, Zsuzsanna Bodi, Daniel Hebenstreit, Scott Waddell, Rupert Fray & Matthias Soller
Nature Communications
10.1038/s41467-022-28549-5.
2021
Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.
Sandip De, David M Edwards, Vibha Dwivedi, Jianming Wang, Wazeer Varsally, Hannah L Dixon, Anand K Singh, Precious O Owuamalam, Matthew T Wright, Reece P Summers, Md Nazmul Hossain, Emily M Price, Marcin W Wojewodzic, Francesco Falciani, Nikolas J Hodges, Marco Saponaro, Kayoko Tanaka, Claus M Azzalin, Peter Baumann, Daniel Hebenstreit, Saverio Brogna
Nucleic Acids Research
10.1093/nar/gkab1249
2021
Timing RNA polymerase pausing with TV-PRO-seq
Jie Zhang, Massimo Cavallaro, Daniel Hebenstreit
Cell Reports Methods
10.1016/j.crmeth.2021.100083
2021
Systemic and adipocyte transcriptional and metabolic dysregulation in idiopathic intracranial hypertension
Westgate CSJ, Botfield H, Alimajstorovic Z, Yiangou A, Walsh M, Smith G, Singhal R, Mitchell JL, Grech O, Markey KA, Hebenstreit D, Tennant DA, Tomlinson J, Mollan SP, Ludwig C, Akerman I, Lavery G, Sinclair A
JCI Insight
10.1172/jci.insight.145346
2021
Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision.
Jones M, Davies P, Liu J, Hebenstreit D
Briefings in Bioinformatics
10.1093/bib/bbab148
2021
3 '-5 ' crosstalk contributes to transcriptional bursting.
Massimo Cavallaro, Mark D Walsh, Matt Jones , James Teahan , Simone Tiberi, Bärbel Finkenstädt, Daniel Hebenstreit
Genome Biology
10.1186/s13059-020-02227-5
2020
Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells
Anand K Singh, Jie Zhang, Daniel Hebenstreit, Saverio Brogna
microPublication Biology
10.17912/micropub.biology.000319
2020
RNA editing contributes to epitranscriptome diversity in chronic lymphocytic leukemia.
Franz J Gassner , Nadja Zaborsky, Ilana Buchumenski, Erez Y Levanon, Matthias Gatterbauer, Maria Schubert, Stefanie Rauscher, Daniel Hebenstreit, Ferran Nadeu, Elias Campo, Alexander Egle , Richard Greil, Roland Geisberger
Leukemia
10.1038/s41375-020-0995-6
2020
Experience recruits MSK1 to expand the dynamic range of synapses and enhance cognition
Privitera, Lucia, Morè, Lorenzo, Cooper, Daniel D., Richardson, Philippa, Tsogka, Marianthi, Hebenstreit, Daniel, Arthur, J. Simon C. and Frenguelli, Bruno G.
The Journal of Neuroscience
10.1523/JNEUROSCI.2765-19.2020
2019
Exome sequencing of the TCL1 mouse model for CLL reveals genetic heterogeneity and dynamics during disease development
Nadja Zaborsky, Franz J. Gassner, Jan P. Höpner, Maria Schubert, Daniel Hebenstreit, Richard Stark, Daniela Asslaber, Markus Steiner, Roland Geisberger, Richard Greil & Alexander Egle
Leukemia
10.1038/s41375-018-0260-4
2019
The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci
Singh, Anand K., Choudhury, Subhendu Roy, De, Sandip, Zhang, Jie, Kissane, Stephen, Dwivedi, Vibha, Ramanathan, Preethi, Petric, Marija, Orsini, Luisa, Hebenstreit, Daniel and Brogna, Saverio
eLife
10.7554/eLife.41444
2019
LiBiNorm : an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
Nigel P. Dyer​, Vahid Shahrezaei, Daniel Hebenstreit
Peerj
10.7717/peerj.6222
2018
Bayesian inference on stochastic gene transcription from flow cytometry data
Tiberi, Simone, Walsh, Mark David, Cavallaro, Massimo, Hebenstreit, Daniel, Finkenstädt, Bärbel
Bioinformatics
10.1093/bioinformatics/bty568
2018
Nicotinamide nucleotide transhydrogenase as a novel treatment target in adrenocortical carcinoma
Chortis, Vasileios, Taylor, Angela E., Doig, Craig L., Walsh, Mark David, Meimaridou, Eirini, Jenkinson, Carl, Rodrigues-Blanco, Giovanny, Ronchi, Cristina L., Jafri, Alisha, Metherell, Louise A., Hebenstreit, Daniel, Dunn, Warwick B., Arlt, Wiebke, Foster, Paul A.
Endocrinology
10.1210/en.2018-00014
2017
AKR1C3-mediated adipose androgen generation drives lipotoxicity in women with polycystic ovary syndrome
O'Reilly, Michael W., Kempegowda, Punith, Walsh, Mark David, Taylor, Angela E., Manolopoulos, Konstantinos N., Allwood, J. William, Semple, Robert K., Hebenstreit, Daniel, Dunn, Warwick B., Tomlinson, Jeremy W., Arlt, Wiebke
The Journal of Clinical Endocrinology & Metabolism
10.1210/jc.2017-00947
2017
Imprecision and DNA break repair biased towards incompatible end joining in leukemia
Gassner, Franz, Schubert, Maria, Rebhandl, Stefan, Spandl, Karina, Zaborsky, Nadja, Catakovic, Kemal, Blaimer, Stephanie, Hebenstreit, Daniel, Griel, Richard, Geisberger, Roland
Molecular Cancer Research
10.1158/1541-7786.MCR-17-0373
2016
Modeling enzyme processivity reveals that RNA-Seq libraries are biased in characteristic and correctable ways
Archer, Nathan, Walsh, Mark, Shahrezaei, Vahid, Hebenstreit, Daniel
Cell Systems
10.1016/j.cels.2016.10.012
2015
The regulatory T Cell lineage factor Foxp3 regulates gene expression through several distinct mechanisms mostly independent of direct DNA binding
Xie, Xin, Stubbington, Michael J. T., Nissen, Jesper K., Andersen, Kristian G., Hebenstreit, Daniel, Teichmann, Sarah A., Betz, Alexander G
PLoS Genetics
10.1371/journal.pgen.1005251
2014
AID induces intraclonal diversity and genomic damage in CD86(+) chronic lymphocytic leukemia cells
Huemer, Michael, Rebhandl, Stefan, Zaborsky, Nadja, Gassner, Franz, Hainzl, Stefan, Weiss, Lukas, Hebenstreit, Daniel, Greil, Richard, Geisberger, Roland
European Journal of Immunology
10.1002/eji.201344421
2014
APOBEC3 signature mutations in chronic lymphocytic leukemia
Rebhandl, S., Huemer, M., Gassner, F. J., Zaborsky, N., Hebenstreit, Daniel, Catakovic, K., Grössinger, E. M., Greil, R., Geisberger, R
Leukemia
doi:10.1038/leu.2014.160
2014
Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis
Mahata, Bidesh, Zhang, Xiuwei, Kolodziejczyk, Aleksandra A., Proserpio, Valentina, Haim-Vilmovsky, Liora, Taylor, Angela E., Hebenstreit, Daniel, Dingler, Felix A., Moignard, Victoria, Göttgens, Berthold, Arlt, Wiebke, McKenzie, Andrew N. J., Teichmann, Sarah A.
Cell Reports
10.1016/j.celrep.2014.04.011
2014
Supply and demand : apply market forces to peer review
Ott, Sascha, Hebenstreit, Daniel
Nature
10.1038/506295b
2013
Are gene loops the cause of transcriptional noise?
Hebenstreit, Daniel
Trends in Genetics
10.1016/j.tig.2013.04.001
2012
Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells
Hebenstreit, Daniel, Deonarine, Andrew, Babu, M. Madan, Teichmann, Sarah A
Current Opinion in Cell Biology
10.1016/j.ceb.2012.03.007
2012
Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs
Brookes, Emily, de Santiago, Inês, Hebenstreit, Daniel, Morris, Kelly J., Carroll, Tom, Xie, Sheila Q., Stock, Julie K., Heidemann, Martin, Eick, Dirk, Nozaki, Naohito, Kimura, Hiroshi, Ragoussis, Jiannis, Teichmann, Sarah A., Pombo, Ana
Cell Stem Cell
10.1016/j.stem.2011.12.017
2011
RNA sequencing reveals two major classes of gene expression levels in metazoan cells
Hebenstreit, Daniel, Fang, Miaoqing, Gu, Muxin, Charoensawan, Varodom, van Oudenaarden, Alexander, Teichmann, Sarah A.
Molecular Systems Biology
10.1038/msb.2011.28
2011
Analysis and simulation of gene expression profiles in pure and mixed cell populations
Hebenstreit, Daniel, Teichmann, Sarah A.
Physical Biology
10.1088/1478-3975/8/3/035013
2010
EpiChIP : gene-by-gene quantification of epigenetic modification levels
Hebenstreit, Daniel, Gu, M., Haider, S., Turner, D. J., Lio, P., Teichmann, Sarah A.
Nucleic Acids Research
10.1093/nar/gkq1226
2010
Inhibition of Suppressive T Cell Factor 1 (TCF-1) Isoforms in Naive CD4+ T Cells Is Mediated by IL-4/STAT6 Signaling
Maier, E., Hebenstreit, Daniel, Posselt, G., Hammerl, P., Duschl, A., Horejs-Hoeck, J.
Journal of Biological Chemistry
10.1074/jbc.M110.144949
2008
LEF-1 negatively controls interleukin-4 expression through a proximal promoter regulatory element
Hebenstreit, Daniel, Giaisi, M., Treiber, M. K., Zhang, X.-B., Mi, H.-F., Horejs-Hoeck, J., Andersen, Kristian G., Krammer, P. H., Duschl, A., Li-Weber, M.
Journal of Biological Chemistry
10.1074/jbc.M804096200
2007
Identification of a distal tandem STAT6 element within the CCL17 locus
Maier, Elisabeth, Wirnsberger, Gerald, Horejs-Hoeck, Jutta, Duschl, Albert, Hebenstreit, Daniel
Human Immunology
10.1016/j.humimm.2007.10.012
2006
IL-4 induces expression of TARC/CCL17 via two STAT6 binding sites
Wirnsberger, Gerald, Hebenstreit, Daniel, Posselt, Gernot, Horejs-Hoeck, Jutta, Duschl, Albert
European Journal of Immunology
10.1002/eji.200635972
2006
Signaling mechanisms, interaction partners, and target genes of STAT6
Hebenstreit, Daniel, Wirnsberger, Gerald, Horejs-Hoeck, Jutta, Duschl, Albert
Cytokine & Growth Factor Reviews
10.1016/j.cytogfr.2006.01.004
2005
Structural changes in calcium-binding allergens : use of circular dichroism to study binding characteristics
Hebenstreit, Daniel, Ferreira, F.
Allergy
10.1111/j.1398-9995.2005.00907.x
2005
JAK/STAT-dependent gene regulation by cytokines
Hebenstreit, Daniel, Horejs-Hoeck, J., Duschl, A.
Drug news & perspectives
10.1358/dnp.2005.18.4.908658
2004
SOCS-1 and SOCS-3 inhibit IL-4 and IL-13 induced activation of Eotaxin-3/CCL26 gene expression in HEK293 cells
Hebenstreit, Daniel, Luft, P., Schmiedlechner, A., Duschl, A., Horejshoeck, J.
Molecular Immunology
10.1016/j.molimm.2004.09.004
2003
IL-4 and IL-13 induce SOCS-1 gene expression in A549 cells by three functional STAT6-binding motifs located upstream of the transcription initiation site
Hebenstreit, Daniel, Luft, P., Schmiedlechner, A., Regl, G., Frischauf, A.-M., Aberger, F., Duschl, A., Horejs-Hoeck, J.
The Journal of Immunology
10.4049/jimmunol.171.11.5901
2002
Molecular and immunological characterization of profilin from mugwort pollen
Wopfner, N., Willeroider, M., Hebenstreit, Daniel, Ree, R. van, Aalbers, M., Briza, P., Thalhamer, J., Ebner, C., Richter, K., Ferreira, F.
Biological Chemistry
10.1515/BC.2002.199