2022

Zhang, Yiyuan, Cordina-Duverger, Emilie, Komarzynski, Sandra, Attari, Amal M., Huang, Qi, Aristizabal, Guillen, Faraut, Brice, Léger, Damien, Adam, René, Guénel, Pascal, Brettschneider, Julia, Finkenstädt, Bärbel and Lévi, Francis (2022) Digital circadian and sleep health in individual hospital shift workers : a cross sectional telemonitoring study. eBioMedicine, 81 . 104121. doi:10.1016/j.ebiom.2022.104121

2021

Unosson, Måns, Brancaccio, Marco, Hastings, Michael H., Johansen, Adam M. and Finkenstädt, Bärbel (2021) A spatio-temporal model to reveal oscillator phenotypes in molecular clocks : parameter estimation elucidates circadian gene transcription dynamics in single-cells. PLoS Computational Biology, 17 (12). e1009698. doi:10.1371/journal.pcbi.1009698

Dulong, S., Huang, Qi, Innominato, P. F., Karaboue, A., Bouchahda, M., Pruvost, A., Théodoro, F., Agrofoglio, L. A., Adam, R., Finkenstädt, Bärbel and Lévi, Francis A. (2021) Circadian and chemotherapy-related changes in urinary modified nucleosides excretion in patients with metastatic colorectal cancer. Scientific Reports, 11 (1). 24015. doi:10.1038/s41598-021-03247-2

Hadj-Amar, Beniamino, Finkenstädt, Bärbel, Fiecas, Mark and Huckstepp, Robert T. R. (2021) Identifying the recurrence of sleep apnea using a harmonic hidden Markov model. The Annals of Applied Statistics, 15 (3). pp. 1171-1193. doi:10.1214/21-AOAS1455

McNamara, Anne V, Awais, Raheela, Momiji, Hiroshi, Dunham, Lee, Featherstone, Karen, Harper, Claire V, Adamson, Antony A, Semprini, Sabrina, Jones, Nicholas A, Spiller, David G, Mullins, John J, Finkenstädt, Bärbel, Rand, David A., White, Michael R. H. and Davis, Julian R. E. (2021) Transcription factor Pit-1 affects transcriptional timing in the dual-promoter human prolactin gene. Endocrinology, 162 (4). bqaa249. doi:10.1210/endocr/bqaa249

Cavallaro, Massimo, Walsh, Mark David, Jones, Matt, Teahan, James, Tiberi, Simone, Finkenstädt, Bärbel and Hebenstreit, Daniel (2021) Data for 3'-5' crosstalk contributes to transcriptional bursting. [Dataset]

Cavallaro, Massimo, Walsh, Mark D., Jones, Matt, Teahan, James, Tiberi, Simone, Finkenstädt, Bärbel and Hebenstreit, Daniel (2021) 3’-5’ crosstalk contributes to transcriptional bursting. Genome Biology, 22 . 56. doi:10.1186/s13059-020-02227-5

2020

Touloupou, Panayiota, Finkenstädt, Bärbel, Besser, Thomas E., French, Nigel P. and Spencer, Simon E. F. (2020) Bayesian inference for multi-strain epidemics with application to Escherichia coli O157 : H7 in feedlot cattle. The Annals of Applied Statistics, 14 (4). pp. 1925-1944. doi:10.1214/20-AOAS1366

Lévi, Francis A., Komarzynski, Sandra, Huang, Qi, Young, Teresa, Ang, Yeng, Fuller, Claire, Bolborea, Matei, Brettschneider, Julia, Fursse, Joanna, Finkenstädt, Bärbel, White, David Pollard and Innominato, Pasquale F. (2020) Tele-monitoring of cancer patients’ rhythms during daily life identifies actionable determinants of circadian and sleep disruption. Cancers, 12 (7). 1938. doi:10.3390/cancers12071938

Hadj-Amar, Beniamino, Finkenstädt, Bärbel, Fiecas, Mark, Lévi, Francis A. and Huckstepp, Robert T. R. (2020) Bayesian model search for nonstationary periodic time series. Journal of the American Statistical Association, 115 (531). pp. 1320-1335. doi:10.1080/01621459.2019.1623043

Touloupou, Panayiota, Finkenstädt, Bärbel and Spencer, Simon E. F. (2020) Scalable Bayesian inference for coupled hidden Markov and semi-Markov models. Journal of Computational and Graphical Statistics, 29 (2). 238-249 . doi:10.1080/10618600.2019.1654880

2019

Komarzynski, Sandra, Bolborea, Matei, Huang, Qi, Finkenstädt, Bärbel and Lévi, Francis A. (2019) Predictability of individual circadian phase during daily routine for medical applications of circadian clocks. JCI Insight, 4 (18). e130423. doi:10.1172/jci.insight.130423

Touloupou, Panayiota, Finkenstädt, Bärbel and Spencer, Simon E. F. (2019) Data for Scalable Bayesian inference for coupled hidden Markov and semi-Markov models. [Dataset]

Momiji, Hiroshi, Hassall, Kirsty, Featherstone, Karen, McNamara, Anne, Patist, Amanda, Spiller, David G., Christian, Helen, White, Michael R. H., Davis, Julian R. E., Finkenstädt, Bärbel and Rand, D. A. (David A.) (2019) Disentangling juxtacrine from paracrine signalling in dynamic tissue. PLoS Computational Biology, 15 (6). e1007030. doi:10.1371/journal.pcbi.1007030

Calderazzo, Silvia, Brancaccio, Marco and Finkenstädt, Bärbel (2019) Filtering and inference for stochastic oscillators with distributed delays. Bioinformatics, 35 (8). pp. 1380-1387. doi:10.1093/bioinformatics/bty782

2018

Tiberi, Simone, Walsh, Mark David, Cavallaro, Massimo, Hebenstreit, Daniel and Finkenstädt, Bärbel (2018) Bayesian inference on stochastic gene transcription from flow cytometry data. Bioinformatics, 34 (17). i647-i655. doi:10.1093/bioinformatics/bty568

Komarzynski, Sandra, Huang, Qi, Innominato, Pasquale F., Maurice, Monique, Arbaud, Alexandre, Beau, Jacques, Bouchahda, Mohamed, Ulusakarya, Ayhan, Beaumatin, Nicolas, Breda, Gabrièle, Finkenstädt, Bärbel and Lévi, Francis A. (2018) Relevance of a mobile internet platform for capturing inter- and intrasubject variabilities in circadian coordination during daily routine : pilot study. Journal of Medical Internet Research, 20 (6). e204. doi:10.2196/jmir.9779

Huang, Qi, Cohen, Dwayne, Komarzynski, Sandra, Li, Xiao-Mei, Innominato, Pasquale F., Lévi, Francis A. and Finkenstädt, Bärbel (2018) Hidden Markov models for monitoring circadian rhythmicity in telemetric activity data. Journal of The Royal Society Interface, 15 (139). doi:10.1098/rsif-2017-0885

2017

Dunham, Lee S. S., Momiji, Hiroshi, Harper, Claire V., Downton, Polly J., Hey, Kirsty L., McNamara, Anne, Featherstone, Karen, Spiller, David G., Rand, David A., Finkenstädt, Bärbel, White, Michael R. H. and Davis, Julian R.E. (2017) Asymmetry between activation and deactivation during a transcriptional pulse. Cell Systems, 5 (6). 646-653.E5. doi:10.1016/j.cels.2017.10.013

Minas, Giorgos, Jenkins, Dafyd J., Rand, D. A. (David A.) and Finkenstädt, Bärbel (2017) Inferring transcriptional logic from multiple dynamic experiments. Bioinformatics, 33 (21). pp. 3437-3444. doi:10.1093/bioinformatics/btx407

Minas, Giorgos, Momiji, Hiroshi, Jenkins, Dafyd J., Costa, Maria J. (Maria João), Rand, David A. and Finkenstädt, Bärbel (2017) ReTrOS : a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data. BMC Bioinformatics, 18 (316). doi:doi: 10.1186/s12859-017-1695-8

2016

(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

Featherstone, Katie, Hey, Kirsty L., Momiji, Hiroshi, McNamara, A. V., Patist, A. L., Woodburn, J., Spiller , D. G., Christian, H. C., McNeilly, A. S., Mullins, J. J. , Finkenstädt, Bärbel, Rand, D. A. (David A.), White, M. R. H. and David, J. R. E. (2016) Spatially coordinated dynamic gene transcription in living pituitary tissue. eLife, 5 . e08494. doi:10.7554/eLife.08494

2015

Hey, Kirsty L., Momiji, Hiroshi, Featherstone, Karen, Davis, Julian R.E., White, Michael R.H., Rand, D. A. (David A.) and Finkenstädt, Bärbel (2015) A stochastic transcriptional switch model for single cell imaging data. Biostatistics, 16 (4). pp. 655-669. doi:10.1093/biostatistics/kxv010

2014

Sidaway-Lee, Kate, Costa, Maria J. (Maria João), Rand, D. A. (David A.), Finkenstädt, Bärbel and Penfield, Steven (2014) Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response. Genome Biology, Volume 15 (Number 3). Article number R45. doi:10.1186/gb-2014-15-3-r45

2013

Woodcock, Dan J., Vance, Keith W., Komorowski, Michal, Koentges, Georgy, Finkenstädt, Bärbel and Rand, D. A. (David A.) (2013) A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number. Bioinformatics, Volume 29 (Number 12). pp. 1519-1525. doi:10.1093/bioinformatics/btt201

Costa, Maria J. (Maria João), Finkenstädt, Bärbel, Gould, Peter D., Foreman, Julia, Halliday, Karen J., Hall, Anthony, Roche, Véronique, Lévi, Francis A. and Rand, D. A. (David A.) (2013) Inference on periodicity of circadian time series. Biostatistics, Volume 14 (Number 4). pp. 792-806. doi:10.1093/biostatistics/kxt020

Jenkins, Dafyd J., Finkenstädt, Bärbel and Rand, D. A. (David A.) (2013) A temporal switch model for estimating transcriptional activity in gene expression. Bioinformatics, Volume 29 (Number 9). pp. 1158-1165. doi:10.1093/bioinformatics/btt111

Gould, Peter D., Ugarte, Nicolas, Domijan, Mirela, Costa, Maria J. (Maria João), Foreman, Julia, MacGregor, Dana, Rose, Ken, Griffiths, Jayne, Millar, A. J. (Andrew J.), Finkenstädt, Bärbel, Penfield, Steven, Rand, D. A. (David A.), Halliday, Karen J. and Hall, Anthony J. W. (2013) Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. Molecular Systems Biology, Volume 9 . Article no. 650. doi:10.1038/msb.2013.7

Finkenstädt, Bärbel, Woodcock, Dan J., Komorowski, Michal, Harper, Claire V., Davis, Julian R. E., White, Mike R. H. and Rand, D. A. (David A.) (2013) Quantifying intrinsic and extrinsic noise in gene transcription using the linear noise approximation : an application to single cell data. Annals of Applied Statistics, Volume 7 ( Number 4). pp. 1960-1982.

2012

(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

Pinto, A. A., Ferreira, M., Finkenstädt, Bärbel, Oliveira, B. and Yannacopoulos, A. N. (2012) On the convergence to Walrasian prices in random matching Edgeworthian economies. Central European Journal of Operations Research, Volume 20 (Number 3). pp. 485-495. doi:10.1007/s10100-011-0208-5

Rittman, Martyn, Hoffmann, Søren V., Gilroy, Emma, Hicks, Matthew R., Finkenstädt, Bärbel and Rodger, Alison (2012) Probing the structure of long DNA molecules in solution using synchrotron radiation linear dichroism. Physical Chemistry Chemical Physics, Vol.14 (No.1). pp. 353-366. doi:10.1039/c1cp22371b

2011

Harper, Claire V., Finkenstädt, Bärbel, Woodcock, Dan J., Friedrichsen, Sönke, Semprini, Sabrina, Ashall, Louise, Spiller, David G., Mullins, John J., Rand, D. A. (David A.), Davis, Julian R. E. and White, Michael R. H. (2011) Dynamic analysis of stochastic transcription cycles. PLos Biology, Vol.9 (No.4). doi:10.1371/journal.pbio.1000607

Ferreira, M., Finkenstädt, Bärbel, Oliveira, B. M. P. M., Pinto, Alberto A. and Yannacopoulos, A. N. (2011) Bargaining skills in an Edgeworthian economy. In: Peixoto, Mauricio Matos and Pinto, Alberto A. and Rand, David A., (eds.) Dynamics, Games and Science I : DYNA 2008, in Honor of Maurício Peixoto and David Rand, University of Minho, Braga, Portugal, September 8-12, 2008. Springer Proceedings in Mathematics, Volume 1 (Number 2011). Springer, pp. 339-352. ISBN 9783642114557

2010

Komorowski, Michal, Finkenstädt, Bärbel and Rand, D. A. (David A.) (2010) Using a single fluorescent reporter gene to infer half-life of extrinsic noise and other parameters of gene expression. Biophysical Journal, Vol.98 (No.12). pp. 2759-2769. doi:10.1016/j.bpj.2010.03.032

2009

Komorowski, Michal, Finkenstädt, Bärbel, Harper, Claire V. and Rand, D. A. (David A.) (2009) Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinformatics, Vol.10 (No.343). doi:10.1186/1471-2105-10-343

2008

Finkenstädt, Bärbel, Heron, Elizabeth A., Komorowski, Michal, Edwards, Kieron, Tang, Sanyi, Harper, Claire V., Davis, Julian R. E., White, Michael R. H., Millar, A. J. (Andrew J.) and Rand, D. A. (David A.) (2008) Reconstruction of transcriptional dynamics from gene reporter data using differential equations. Bioinformatics, Vol.24 (No.24). pp. 2901-2907. doi:10.1093/bioinformatics/btn562

2007

Heron, Elizabeth A., Finkenstädt, Bärbel and Rand, D. A. (David A.) (2007) Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study. Bioinformatics, Vol.23 (No.19). pp. 2596-2603. doi:10.1093/bioinformatics/btm367

2006

Lekone, Phenyo E. and Finkenstädt, Bärbel (2006) Statistical inference in a stochastic epidemic SEIR model with control intervention : Ebola as a case study. Biometrics, Volume 62 (Number 4). pp. 1170-1177. doi:10.1111/j.1541-0420.2006.00609.x