Job Title
Reader
Department
Life Sciences
Phone
024 765 74457
Web Link
Research Interests
My group is working on the mechanisms of transcriptional regulation in metazoan cells. We are interested in several aspects of this, including the interplay of epigenetics and transcription, the role of 'noise' in gene and protein expression, and the reorganization of transcriptional networks upon differentiation. To study these subjects, we are employing a systems-biology approach based on accurate experimental quantification with next-generation sequencing technologies such as mRNA-seq and ChIP-seq, studying cell population diversity with flow cytometry, and statistical and mathematical analysis of the data. We focus on the system of murine T helper cells, particularly the Th2 subtype, which provides a valuable model for mammalian cell differentiation and is experimentally accessible.
If you are interested in joining my group, please contact me per email and send me your CV. Molecular biologists, bioinformaticians, physicists, and mathematicians welcome.
Biography
Reader / Associate Professor at University of Warwick, Coventry, UK, 2020 - present
Associate Professor at University of Warwick, Coventry, UK, 2017 - 2020
Assistant Professor at University of Warwick, Coventry, UK, 2012 - 2017
MRC Career Development Fellow at MRC Laboratory of Molecular Biology, Cambridge, UK, 2009 - 2012
Post-doctoral fellow at the MRC Laboratory of Molecular Biology, Cambridge, UK, 2007 - 2009
BSc in Mathematics, University of Salzburg, Austria, 2007
PhD in Genetics, University of Salzburg, Austria, 2005
MSc in Genetics, University of Salzburg, Austria, 2000
- Cavallaro, Massimo, Walsh, Mark D., Jones, Matt, Teahan, James, Tiberi, Simone, Finkenstädt, Bärbel, Hebenstreit, Daniel, 2021. 3'-5? crosstalk contributes to transcriptional bursting. Genome Biology, 22
- Davies, Philip, Jones, Matt, Liu, Juntai, Hebenstreit, Daniel, 2021. Anti-bias training for (sc)RNA-seq : experimental and computational approaches to improve precision. Briefings in Bioinformatics
- Westgate, Connar S. J., Botfield, Hannah F., Alimajstorovic, Zerin, Yiangou, Andreas, Walsh, Mark D., Smith, Gabrielle, Singhal, Rishi, Mitchell, James L., Grech, Olivia, Markey, Keira A., Hebenstreit, Daniel, Tennant, Daniel A., Tomlinson, Jeremy W., Mollan, Susan P., Ludwig, Christian, Akerman, Ildem, Lavery, Gareth G., Sinclair, Alexandra J., 2021. Systemic and adipocyte transcriptional and metabolic dysregulation in idiopathic intracranial hypertension. JCI Insight, 6 (10)
- Gassner, Franz, Zaborsky, Nadja, Buchumenski, Ilana, Levanon, Erez, Gatterbauer, Matthias, Schubert, Maria, Rauscher, Stefanie, Hebenstreit, Daniel, Nadeu, Ferran, Campo, Elias, Egle, Alexander, Greil, Richard, Geisberger, Roland, 2021. RNA editing contributes to epitranscriptome diversity in chronic lymphocytic leukemia. Leukemia, 35, pp. 1053-1063
- Zhang, Jie, Cavallaro, Massimo, Hebenstreit, Daniel, 2021. Timing polymerase pausing with TV-PRO-seq : dissecting the interplay of pausing duration and location, and gene expression. Cell Reports Methods
- Privitera, Lucia, Morè, Lorenzo, Cooper, Daniel D., Richardson, Philippa, Tsogka, Marianthi, Hebenstreit, Daniel, Arthur, J. Simon C., Frenguelli, Bruno G., 2020. Experience recruits MSK1 to expand the dynamic range of synapses and enhance cognition. The Journal of neuroscience : the official journal of the Society for Neuroscience
- Singh, A. K., Zhang, Jie, Hebenstreit, Daniel, Brogna, Saverio, 2020. Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells. microPublication Biology
- Dryer, Nigel P., Shahrazaie, Vahid, Hebenstreit, Daniel, 2019. LiBiNorm : an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics. PeerJ, 7
- Singh, Anand K., Choudhury, Subhendu Roy, De, Sandip, Zhang, Jie, Kissane, Stephen, Dwivedi, Vibha, Ramanathan, Preethi, Petric, Marija, Orsini, Luisa, Hebenstreit, Daniel, Brogna, Saverio, 2019. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. eLife, 8
- Zaborsky, Nadja, Gassner, Franz, Höpner, Jan, Schubert, Maria, Hebenstreit, Daniel, Stark, Richard Jan, Asslaber, Daniela, Steiner, Markus, Geisberger, Roland, Greil, Richard, Egle , Alexander, 2019. Exome sequencing of the TCL1 mouse model for CLL reveals genetic heterogeneity and dynamics during disease development. Leukemia, 33 (4), pp. 957-968
- Hebenstreit, Daniel, 2018. Tuning a musical instrument with vibrato system : a mathematical framework to study mechanics and acoustics and to calculate optimal tuning strategies. The Journal of the Acoustical Society of America, 143 (6)
- 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., 2018. Nicotinamide nucleotide transhydrogenase as a novel treatment target in adrenocortical carcinoma. Endocrinology, 159 (8), pp. 2836-2849
- Tiberi, Simone, Walsh, Mark David, Cavallaro, Massimo, Hebenstreit, Daniel, Finkenstädt, Bärbel, 2018. Bayesian inference on stochastic gene transcription from ?ow cytometry data. Bioinformatics, 34 (17), pp. i647-i655
- Gassner, Franz, Schubert, Maria, Rebhandl, Stefan, Spandl, Karina, Zaborsky, Nadja, Catakovic, Kemal, Blaimer, Stephanie, Hebenstreit, Daniel, Griel, Richard, Geisberger, Roland, 2017. Imprecision and DNA break repair biased towards incompatible end joining in leukemia. Molecular Cancer Research, 16 (3), pp. 428-438
- 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, 2017. AKR1C3-mediated adipose androgen generation drives lipotoxicity in women with polycystic ovary syndrome. The Journal of Clinical Endocrinology & Metabolism, 102 (9), pp. 3327-3339
- Archer, Nathan, Walsh, Mark, Shahrezaie, Vahid, Hebenstreit, Daniel, 2016. Modeling enzyme processivity reveals that RNA-Seq libraries are biased in characteristic and correctable ways. Cell Systems, 3 (5), pp. 467-479
- Xie, Xin, Stubbington, Michael J. T., Nissen, Jesper K., Andersen, Kristian G., Hebenstreit, Daniel, Teichmann, Sarah A., Betz, Alexander G., 2015. The regulatory T Cell lineage factor Foxp3 regulates gene expression through several distinct mechanisms mostly independent of direct DNA binding. PLoS Genetics, 11 (6)
- 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., 2014. Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis. Cell Reports, 7 (4), pp. 1130-1142
- Rebhandl, S., Huemer, M., Gassner, F. J., Zaborsky, N., Hebenstreit, Daniel, Catakovic, K., Grössinger, E. M., Greil, R., Geisberger, R., 2014. APOBEC3 signature mutations in chronic lymphocytic leukemia. Leukemia, 28 (9), pp. 1929-1932
- Huemer, Michael, Rebhandl, Stefan, Zaborsky, Nadja, Gassner, Franz, Hainzl, Stefan, Weiss, Lukas, Hebenstreit, Daniel, Greil, Richard, Geisberger, Roland, 2014. AID induces intraclonal diversity and genomic damage in CD86(+) chronic lymphocytic leukemia cells. European Journal of Immunology, 44 (12), pp. 3747-3757
- Hebenstreit, Daniel, 2013. Are gene loops the cause of transcriptional noise?. Trends in Genetics, 29 (6), pp. 333-338
- Hebenstreit, Daniel, Deonarine, Andrew, Babu, M. Madan, Teichmann, Sarah A., 2012. Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells. Current Opinion in Cell Biology, Vol. 24 (No. 3), pp. 350-358
- 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, 2012. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell, Vol. 10 (No. 2), pp. 157-170
- Hebenstreit, Daniel, 2012. Methods, challenges and potentials of single cell RNA-seq. Biology, 1 (3), pp. 658-667
- Hebenstreit, Daniel, Fang, Miaoqing, Gu, Muxin, Charoensawan, Varodom, van Oudenaarden, Alexander, Teichmann, Sarah A., 2011. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Molecular Systems Biology, Vol. 7
- Hebenstreit, Daniel, Teichmann, Sarah A., 2011. Analysis and simulation of gene expression profiles in pure and mixed cell populations. Physical Biology, Vol. 8 (No. 3)
- Hebenstreit, Daniel, Gu, M., Haider, S., Turner, D. J., Lio, P., Teichmann, Sarah A., 2011. EpiChIP : gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Research, Vol. 39 (No. 5), pp. e27-e27
- Maier, E., Hebenstreit, Daniel, Posselt, G., Hammerl, P., Duschl, A., Horejs-Hoeck, J., 2011. Inhibition of Suppressive T Cell Factor 1 (TCF-1) Isoforms in Naive CD4+ T Cells Is Mediated by IL-4/STAT6 Signaling. Journal of Biological Chemistry, Vol. 286 (No. 2), pp. 919-928
- 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., 2008. LEF-1 negatively controls interleukin-4 expression through a proximal promoter regulatory element. Journal of Biological Chemistry, Vol. 283 (No. 33), pp. 22490-22497
- Maier, Elisabeth, Wirnsberger, Gerald, Horejs-Hoeck, Jutta, Duschl, Albert, Hebenstreit, Daniel, 2007. Identification of a distal tandem STAT6 element within the CCL17 locus. Human Immunology, 68 (12), pp. 986-992
- Wirnsberger, Gerald, Hebenstreit, Daniel, Posselt, Gernot, Horejs-Hoeck, Jutta, Duschl, Albert, 2006. IL-4 induces expression of TARC/CCL17 via two STAT6 binding sites. European Journal of Immunology, 36 (7), pp. 1882-1891
- Hebenstreit, Daniel, Wirnsberger, Gerald, Horejs-Hoeck, Jutta, Duschl, Albert, 2006. Signaling mechanisms, interaction partners, and target genes of STAT6. Cytokine & Growth Factor Reviews, 17 (3), pp. 173-188
- Hebenstreit, Daniel, Luft, P., Schmiedlechner, A., Duschl, A., Horejshoeck, J., 2005. SOCS-1 and SOCS-3 inhibit IL-4 and IL-13 induced activation of Eotaxin-3/CCL26 gene expression in HEK293 cells. Molecular Immunology, 42 (3), pp. 295-303
- Hebenstreit, Daniel, Horejs-Hoeck, J., Duschl, A., 2005. JAK/STAT-dependent gene regulation by cytokines. Drug news & perspectives, 18 (4), pp. 243-249
- Hebenstreit, Daniel, Ferreira, F., 2005. Structural changes in calcium-binding allergens : use of circular dichroism to study binding characteristics. Allergy, 60 (9), pp. 1208-1211
- Hebenstreit, Daniel, Luft, P., Schmiedlechner, A., Regl, G., Frischauf, A.-M., Aberger, F., Duschl, A., Horejs-Hoeck, J., 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. The Journal of Immunology, 171 (11), pp. 5901-5907
- Wopfner, N., Willeroider, M., Hebenstreit, Daniel, Ree, R. van, Aalbers, M., Briza, P., Thalhamer, J., Ebner, C., Richter, K., Ferreira, F., 2002. Molecular and immunological characterization of profilin from mugwort pollen. Biological Chemistry, 383 (11), pp. 1779-1789
- Cavallaro, Massimo, Walsh, Mark David, Jones, Matt, Teahan, James, Tiberi, Simone, Finkenstädt, Bärbel, Hebenstreit, Daniel, 2021. Data for 3'-5' crosstalk contributes to transcriptional bursting. Zenodo
- Ott, Sascha, Hebenstreit, Daniel, 2014. Supply and demand : apply market forces to peer review. Nature, Nature Publishing, pp. 295-295
| Title | Funder | Award start | Award end |
|---|---|---|---|
| Defining and exploiting the role of PML protein in innate immune responses to pathogens - MRC Research Grant | MRC | 01 Aug 2017 | 30 Jun 2021 |
| Warwick Integrative Synthetic Biology Centre (WISB) | BBSRC | 14 Nov 2014 | 31 May 2020 |
| Genomic scaling of transcriptional noise | BBSRC | 01 Jan 2014 | 17 Mar 2019 |
| Establishing and optimizing quantitative single cell RNA-sequencing (scRNA-seq) | Royal Society | 31 Dec 2013 | 30 Dec 2014 |