News
Congratulations Dr Ziyu Zhao! Congratulations to Ziyu Zhao on successfully defending his PhD.
15 February 2024
Our research in the news. Pepper Huang's recent Chaos paper — a minimal model of peripheral clocks — was highlighted in the Washington Post and other venues.
7 September 2023
Welcome Dr Sneha Kachhara! Dr Sneha Kachhara is joining the group as a postdoctoral fellow. She is interested in complex systems, nonlinear dynamics, networks, and time-series analysis, with applications ranging from cardiac dynamics to variable stars. We are terrifically excited to have her on the team.
31 July 2022
Patent awarded. The group celebrates the award of its first patent. Biomarkers of endogenous biological time (US 11,328,790) provides a method for inferring human circadian phase from blood gene expression profiles.
18 May 2022
Congratulations Dr Ness-Cohn! Congratulations to Elan Ness-Cohn on successfully defending his PhD and starting a new chapter as an Entrepreneurial Fellow of the Chicago Biomedical Consortium.
1 February 2022
Two new circadian biology papers by Elan Ness-Cohn. Elan's TimeCycle method was accepted for publication in Bioinformatics. It is a novel technique for the detection of cycling genes, combining time-delay embedding, nonlinear dimension reduction, persistence homology, and a biologically informed null model. In a separate paper in Science, Elan describes a secondary analysis of circadian transcriptomic data from skin fibroblasts of mice lacking the core clock gene Bmal1.
15 July 2021
We're hiring. We are searching for a data scientist and one to two postdocs to join the team. See join us for details.
4 January 2021
The lab joins the Department of Molecular Biosciences. Effective 1 January 2021, Rosemary is tenured faculty in the Department of Molecular Biosciences in the Weinberg College of Arts and Sciences. The lab is moving to Pancoe, closer to our colleagues and collaborators on the Evanston campus.
1 January 2021
NIH R01 grant awarded. It is well known that with age come changes to one's sleep and circadian rhythms, and evidence suggests that these changes are related to neurodegeneration. The lab has received an NIH R01 grant, "Reconstructing the temporal landscape of gene regulation in aging", to investigate the role of circadian gene regulation in these processes and to develop new mathematical models that can be used to predict Alzheimer's disease risk.
1 October 2020
TimeTrial published in the Journal of Biological Rhythms. While algorithms for detecting cycling transcripts have advanced, there has remained little guidance quantifying the effect of experimental design and analysis choices on cycling detection accuracy. TimeTrial is a user-friendly benchmarking framework for exactly that.
10 July 2020
Congratulations Dr Sahil Shah! Sahil Shah is awarded his PhD in Engineering Sciences and Applied Mathematics after successfully defending his thesis, "Statistical methods for the network-based analysis of genomic data".
25 June 2019
GeneSurrounder published in BMC Bioinformatics. A key challenge in identifying disease-associated genes is analyzing transcriptomic data in the context of the regulatory networks that control cellular processes, so as to capture multi-gene interactions and yield mechanistically interpretable results. GeneSurrounder identifies precise gene targets while incorporating systems-level information.
6 May 2019
Congratulations Dr Phan Nguyen! Phan receives his PhD after successfully defending his thesis, "Methods for inferring gene regulatory networks from time series expression data".
18 December 2018
TimeSignature featured on the BreakThroughs podcast. Simple blood test reveals the body's internal clock.
11 September 2018
Congratulations Dr Gary Wilk! Gary is the first graduate student in the lab to receive his PhD, after successfully defending his thesis, "microRNA regulation of genes with genetic variation and their systems-level consequences in cancer".
18 June 2018
The lab joins the Quantitative Biology Research Center. See the news article and the center website.
24 May 2018