2017

Vrljicak, Pavle, Lucas, Emma S., Lansdowne, Lauren, Lucciola, Raffaella, Muter, Joanne, Dyer, Nigel P., Brosens, Jan J. and Ott, Sascha (2017) Analysis of chromatin accessibility in decidualizing human endometrial stromal cells. FASEB Journal . doi:10.1096/fj.201701098R (In Press)

Brighton, Paul (Paul J.), Maruyama, Yojiro, Fishwick, Katherine, Vrljicak, Pavle, Tewary, Shreeya, Fujihara, Risa, Muter, Joanne, Lucas, Emma S., Yamada, Taihei, Woods, Laura, Lucciola, Raffaella, Lee, Yie Hou, Takeda, Satoru, Ott, Sascha, Hemberger, Myriam, Quenby, Siobhan and Brosens, Jan J. (2017) Clearance of senescent decidual cells by uterine natural killer cells in cycling human endometrium. eLife (6). e31274. doi:10.1101/172593 (In Press)

Polanski, Krzysztof , Gao, Bo, Mason, Sam (Sam A.), Brown, Paul E., Ott, Sascha, Denby, Katherine J. and Wild, David L. (2017) Bringing numerous methods for expression and promoter analysis to a public cloud computing service. Bioinformatics . doi:10.1093/bioinformatics/btx692 (In Press)

Brignall, Ruth, Cauchy, Pierre, Bevington, Sarah L., Gorman, Bethany, Pisco, Angela O., Bagnall, James, Boddington, Christopher, Rowe, William, England, Hazel, Rich, Kevin, Schmidt, Lorraine, Dyer, Nigel P., Travis, Mark A., Ott, Sascha, Jackson, Dean A., Cockerill, Peter N. and Paszek, Pawel (2017) Integration of kinase and calcium signaling at the level of chromatin underlies inducible gene activation in T cells. The Journal of Immunology, 199 (8). pp. 2652-2667. ji1602033. doi:10.4049/jimmunol.1602033

Donia, Marco, Kjeldsen, Julie Westerlin, Andersen, Rikke, Westergaard, Marie Christine Wulff, Bianchi, Valentina, Legut, Mateusz, Attaf, Meriem, Szomolay, Barbara, Ott, Sascha, Dolton, Garry, Lyngaa, Rikke, Hadrup, Sine Reker, Sewell, Andrew K. and Svane, Inge Marie (2017) PD-1 + polyfunctional T cells dominate the periphery after tumor-infiltrating lymphocyte therapy for cancer. Clinical Cancer Research . doi:10.1158/1078-0432.CCR-16-1692 (In Press)

2016

Lucas, Emma S., Dyer, Nigel P., Fishwick, Katherine, Ott, Sascha and Brosens, Jan J. (2016) Success after failure : the role of endometrial stem cells in recurrent miscarriage. Reproduction . REP-16. doi:10.1530/REP-16-0306 (In Press)

(2016) Time-series transcriptomics reveals that AGAMOUS-LIKE22 affects primary metabolism and developmental processes in drought-stressed Arabidopsis. The Plant Cell, 28 (2). pp. 345-366. doi:10.1105/tpc.15.00910

Bevington, S. L., Cauchy, P., Piper, Jason, Bertrand, E., Lalli, N, Jarvis, R. C., Gilding, L. N., Ott, Sascha, Bonifer, C. and Cockerill, P. N. (2016) Inducible chromatin priming is associated with the establishment of immunological memory in T cells. The EMBO Journal, 35 (5). pp. 515-535. doi:doi:10.15252/embj.201592534

Real, Francisco X., Ward, Douglas G., Baxter, Laura, Gordon, Naheema S., Ott, Sascha, Savage, Richard S., Beggs, Andrew D., James, Jonathan D., Lickiss, Jennifer, Green, Shaun, Wallis, Yvonne, Wei, Wenbin, James, Nicholas D., Zeegers, Maurice P., Cheng, K. K., Mathews, Glenn M., Patel, Prashant, Griffiths, Michael and Bryan, Richard T. (2016) Multiplex PCR and next generation sequencing for the non-invasive detection of bladder cancer. PLoS One, 11 (2). pp. 1-11. e0149756. doi:10.1371/journal.pone.0149756

Lucas, Emma S., Dyer, Nigel P., Murakami, Keisuke, Hou Lee, Yie, Chan, Yi-Wah, Grimaldi, Giulia, Muter, Joanne, Brighton, Paul (Paul J.), Moore, Jonathan D., Patel, Gnyaneshwari, Chan, Jerry K.Y., Takeda, Satoru, Lam, Eric W-F., Quenby, Siobhan, Ott, Sascha and Brosens, Jan J. (2016) Loss of endometrial plasticity in recurrent pregnancy loss. Stem Cells, 34 (2). pp. 346-356. doi:10.1002/stem.2222

Dyer, Nigel, Young, Lawrence S. and Ott, Sascha (2016) Artifacts in the data of Hu et al. Nature Genetics, 48 (1). pp. 2-3. doi:10.1038/ng.3392

2015

Piper, Jason, Assi, Salam A., Cauchy, Pierre, Ladroue, Christophe, Cockerill, Peter N., Bonifer, Constanze and Ott, Sascha (2015) Wellington-bootstrap : differential DNase-seq footprinting identifies cell-type determining transcription factors. BMC Genomics, 16 (1). pp. 1-8. doi:10.1186/s12864-015-2081-4

(2015) Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with pseudomonas syringae pv tomato DC3000. The Plant Cell, 27 (11). pp. 3038-3064. doi:10.1105/tpc.15.00471

Vance, Keith W., Woodcock, Dan J., Reid, John E., Bretschneider, Till, Ott, Sascha and Koentges, Georgy (2015) Conserved cis-regulatory modules control robustness in Msx1 expression at single-cell resolution. Genome Biology and Evolution, 7 (9). pp. 2762-2778. doi:10.1093/gbe/evv179

Cauchy, Pierre, James, Sally R., Zacarias-Cabeza, Joaquin, Ptasinska, Anetta, Imperato, Maria Rosaria, Assi, Salam A., Piper, Jason, Canestraro, Martina, Hoogenkamp, Maarten, Raghavan, Manoj, Loke, Justin, Akiki, Susanna, Clokie, Samuel J. H., Richards, Stephen J., Westhead, David R., Griffiths, Michael J., Ott, Sascha, Bonifer, Constanze and Cockerill, Peter N. (2015) Chronic FLT3-ITD signaling in acute myeloid leukemia is connected to a specific chromatin signature. Cell reports, 12 (5). pp. 821-836. doi:10.1016/j.celrep.2015.06.069

2014

Ptasinska, Anetta, Assi, Salam A., Martinez-Soria, Natalia, Imperato, Maria Rosaria, Piper, Jason, Cauchy, Pierre, Pickin, Anna, James, Sally R., Hoogenkamp, Maarten, Williamson, Dan, Wu, Mengchu, Tenen, Daniel G., Ott, Sascha, Westhead, David R., Cockerill, Peter N., Heidenreich, Olaf and Bonifer, Constanze (2014) Identification of a dynamic core transcriptional network in t(8;21) AML that regulates Differentiation block and self-renewal. Cell Reports, 8 (6). pp. 1974-1988. 24. doi:10.1016/j.celrep.2014.08.024

Papanayotou, Costis, Benhaddou, Ataaillah, Camus, Anne, Perea-Gomez, Aitana, Jouneau, Alice, Mezger, Valérie, Langa, Francina, Ott, Sascha, Sabéran-Djoneidi, Délara and Collignon, Jérôme (2014) A novel Nodal enhancer dependent on pluripotency factors and Smad2/3 signaling conditions a regulatory switch during epiblast maturation. PLoS Biology, Volume 12 (Number 6). Article number e1001890. doi:10.1371/journal.pbio.1001890

Polanski, Krzysztof , Rhodes, Johanna, Hills, Claire E., Zhang, Peijun, Jenkins, Dafyd J., Kiddle, Steven J., Jironkin, Aleksey, Beynon, Jim, Buchanan-Wollaston, Vicky, Ott, Sascha and Denby, Katherine J. (2014) Wigwams : identifying gene modules co-regulated across multiple biological conditions. Bioinformatics, Volume 30 (Number 7). pp. 962-970. doi:10.1093/bioinformatics/btt728

Ott, Sascha and Hebenstreit, Daniel (2014) Supply and demand : apply market forces to peer review. Nature, Volume 506 (Number 7488). p. 295. doi:10.1038/506295b

Gould, Phillip S., Dyer, Nigel P., Croft, Wayne D., Ott, Sascha and Easton, A. J. (Andrew J.) (2014) Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination-reinitiation mechanism. RNA, 20 . pp. 373-381. doi:10.1261/rna.041574.113

2013

Piper, Jason, Elze, Markus C., Cauchy, Pierre, Cockerill, Peter N., Bonifer, Constanze and Ott, Sascha (2013) Wellington : a novel method for the accurate identification of digital genomic footprints from DNase-seq data. Nucleic Acids Research, Volume 41 (Number 21). Article number e201. doi:10.1093/nar/gkt850

Bechtold, Ulrike, Albihlal, Waleed S., Lawson, Tracy, Fryer, Michael J., Sparrow, Penelope A. C., Richard, François, Persad, Ramona, Bowden, Laura, Hickman, Richard D. G., Martin, Cathie, Beynon, Jim, Buchanan-Wollaston, Vicky, Baker, N. R., Morison, James I. L., Schoffl, Friedrich, Ott, Sascha and Mullineaux, Philip M. (2013) Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b overexpression enhances water productivity, resistance to drought, and infection. Journal of Experimental Botany, Volume 64 (Number 11). pp. 3467-3481. doi:10.1093/jxb/ert185

Hickman, Richard J., Hill, C., Penfold, Christopher A., Breeze, Emily, Bowden, Laura, Moore, Jonathan D., Zhang, Peijun, Jackson, Alison C., Cooke, Emma J., Bewicke-Copley, Findlay, Mead, A., Beynon, Jim, Wild, David L., Denby, Katherine J., Ott, Sascha and Buchanan-Wollaston, Vicky (2013) A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. The Plant Journal, Volume 75 (Number 1). pp. 26-39. doi:10.1111/tpj.12194

Brown, Paul E., Baxter, Laura, Hickman, Richard J., Beynon, Jim, Moore, Jonathan D. and Ott, Sascha (2013) MEME-LaB : motif analysis in clusters. Bioinformatics . doi:10.1093/bioinformatics/btt248

Laranjeiro, R., Tamai, T. K., Peyric, E., Krusche, Peter, Ott, Sascha and Whitmore, D. (2013) Cyclin-dependent kinase inhibitor p20 controls circadian cell-cycle timing. Proceedings of the National Academy of Sciences of the United States of America, Volume 110 (Number 17). pp. 6835-6840. doi:10.1073/pnas.1217912110

2012

Baxter, Laura, Jironkin, Aleksey, Hickman, R. D. G., Moore, Jonathan D., Barrington, Christopher, Krusche, Peter, Dyer, Nigel, Buchanan-Wollaston, Vicky, Tiskin, Alexander, Beynon, Jim, Denby, Katherine J. and Ott, Sascha (2012) Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. The Plant Cell, Vol.24 (No.10). pp. 3949-3965. doi:10.1105/tpc.112.103010

(2012) Arabidopsis defense against Botrytis cinerea : chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. The Plant Cell, Vol.24 (No.9). pp. 3530-3557. doi:10.1105/tpc.112.102046

2011

Downey, Mike J., Jeziorska, Danuta M., Ott, Sascha, Tamai, T. Katherine, Koentges, Georgy, Vance, Keith W. and Bretschneider, Till (2011) Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution. PLoS ONE, Vol.6 (No.12). e27886. doi:10.1371/journal.pone.0027886

(2011) High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell, The, Vol.23 (No.3). pp. 873-894. doi:10.1105/tpc.111.083345

Granier, Céline, Gurchenkov, Vasily, Perea-Gomez, Aitana, Camus, Anne, Ott, Sascha, Papanayotou, Costis, Iranzo, Julian, Moreau, Anne, Reid, John, Koentges, Georgy, Sabéran-Djoneidi, Délara and Collignon, Jérôme (2011) Nodal cis-regulatory elements reveal epiblast and primitive endoderm heterogeneity in the peri-implantation mouse embryo. Developmental Biology, Vol.349 (No.2). pp. 350-362. doi:10.1016/j.ydbio.2010.10.036

2010

Picot, Emma, Krusche, Peter, Tiskin, Alexander, Carré, Isabelle A. and Ott, Sascha (2010) Evolutionary analysis of regulatory sequences (EARS) in plants. Plant Journal, Vol.64 (No.1). pp. 165-176. doi:10.1111/j.1365-313X.2010.04314.x

Koohy, Hashem, Dyer, Nigel, Reid, John E., Koentges, Georgy and Ott, Sascha (2010) An alignment-free model for comparison of regulatory sequences. Bioinformatics, Vol.26 (No.19). pp. 2391-2397. doi:10.1093/bioinformatics/btq453

Vance, Keith W., Shaw, Heather M., Rodriguez, Mercedes, Ott, Sascha and Goding, Colin R. (2010) The retinoblastoma protein modulates Tbx2 functional specificity. Molecular Biology of the Cell, Vol.21 (No.15). pp. 2770-2779. doi:10.1091/mbc.E09-12-1029

Sánchez-Romero, María Antonia, Busby, S. (Stephen), Dyer, Nigel, Ott, Sascha, Millard, Andrew D. and Grainger, David C. (2010) Dynamic distribution of SeqA protein across the chromosome of Escherichia coli K-12. mBio, Vol.1 (No.1). Article number e00012-10. doi:10.1128/mBio.00012-10

Reid, J. E. (John E.), Evans, Kenneth J., Dyer, Nigel, Wernisch, Lorenz and Ott, Sascha (2010) Variable structure motifs for transcription factor binding sites. BMC Genomics, Vol.11 (Article 30). doi:10.1186/1471-2164-11-30

2009

Spensley, Mark, Kim, Jae-Yean, Picot, Emma, Reid, John, Ott, Sascha, Helliwell, Chris and Carré, Isabelle A. (2009) Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL. Plant Cell, Vol.21 (No.9). pp. 2606-2623. doi:10.1105/tpc.109.069898

Reid, J. E. (John E.), Ott, Sascha and Wernisch, Lorenz (2009) Transcriptional programs : modelling higher order structure in transcriptional control. BMC Bioinformatics, Vol.10 . Article no. 218. doi:10.1186/1471-2105-10-218