A5051116977- Circadian rhythm and melatonin
- Light effects on plants
- Ovarian function and disorders
- Reproductive tract infections research
- Nutrition, Genetics, and Disease
- Nutritional Studies and Diet
- Neuroendocrine regulation and behavior
- Machine Learning in Healthcare
- Artificial Intelligence in Healthcare
- Bioinformatics and Genomic Networks
- Urinary Tract Infections Management
- Gene expression and cancer classification
- Imbalanced Data Classification Techniques
- Evolutionary Psychology and Human Behavior
- Adolescent Sexual and Reproductive Health
- Data Analysis with R
- Mobile Health and mHealth Applications
- Pregnancy and preeclampsia studies
- demographic modeling and climate adaptation
- Pelvic floor disorders treatments
- Reproductive System and Pregnancy
- Demographic Trends and Gender Preferences
- Gut microbiota and health
- Time Series Analysis and Forecasting
- Food Industry and Aquatic Biology
Stanford University
2018-2024
École Polytechnique Fédérale de Lausanne
2012-2023
University of Amsterdam
2021
Stanford Medicine
2018-2019
Biological rhythms play a fundamental role in the physiology and behavior of most living organisms. Rhythmic circadian expression clock-controlled genes is orchestrated by molecular clock that relies on interconnected negative feedback loops transcription regulators. Here we show exerts its function also through regulation mRNA translation. Namely, influences temporal translation subset mRNAs involved ribosome biogenesis controlling initiation factors as well clock-dependent rhythmic...
Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization cell physiology in mammals. To understand transcriptional and epigenetic basis rhythms mouse liver genome-wide, we generated DNA occupancy profiles by RNA polymerase II (Pol II) as well histone modifications H3K4me3 H3K36me3. We used these data to quantify relationships phases amplitudes between different marks. found that rhythmic Pol recruitment at promoters rather than...
For most women of reproductive age, assessing menstrual health and fertility typically involves regular visits to a gynecologist or another clinician. While these evaluations provide critical information on an individual's status, they rely memory-based self-reports, the results are rarely, if ever, assessed at population level. In recent years, mobile apps for tracking have become very popular, allowing us evaluate reliability frequency millions self-observations, thereby providing...
Significance Rhythms in gene expression propelled by the circadian clock and environmental signals are ubiquitous across cells tissues. In particular, mouse tissues, thousands of transcripts show oscillations with a period 24 hours. Keys question how such rhythms propagate eventually exert functions, but also these generated. Here, we developed mathematical model based on total RNA-seq to classify genes according respective contributions transcriptional posttranscriptional regulation toward...
Abstract The vaginal ecosystem is closely tied to human health and reproductive outcomes, yet its dynamics in the wake of childbirth remain poorly characterized. Here, we profile microbiota cytokine milieu participants sampled longitudinally throughout pregnancy for at least one year postpartum. We show that delivery, regardless mode, associated with a pro-inflammatory response loss Lactobacillus dominance. By contrast, neither progression gestation nor approach labor strongly altered...
Diverse and non-Lactobacillus-dominated vaginal microbial communities are associated with adverse health outcomes such as preterm birth the acquisition of sexually transmitted infections. Despite importance recognizing understanding key risk-associated features these communities, their heterogeneous structure properties remain ill-defined. Clustering approaches commonly used to characterize but they lack sensitivity robustness in resolving substructures revealing transitions between...
Predicting pregnancy has been a fundamental problem in women's health for more than 50 years. Previous datasets have collected via carefully curated medical studies, but the recent growth of tracking mobile apps offers potential reaching much broader population. However, feasibility predicting from data is unclear. Here we develop four models - logistic regression model, and 3 LSTM to predict woman's probability becoming pregnant using app, Clue by BioWink GmbH. Evaluating our on dataset 79...
U2OS cells harbor a circadian clock but express only few rhythmic genes in constant conditions. We identified 3040 binding sites of the regulators BMAL1, CLOCK and CRY1 genome. Most even promoters do not correlate with detectable transcript levels. Luciferase fusions reveal that supports robust low amplitude transcription rhythms representative promoters. However, these potentially clock-controlled is masked by non-circadian overwrites weaker contribution Our data suggest an intrinsically...
Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering cell division cycle. We have used this system and H3K4me3, Pol II III profiling to characterize adaptations transcription. Our results broadly define a class of genes close H3K4me3 peaks, whose occupancy is high stable, another class, distant from strongly increases hepatectomy. regulation thus entails both highly expressed housekeeping expression can adapt increased demand.
Topic modeling is a popular method used to describe biological count data. With topic models, the user must specify number of topics $K$. Since there no definitive way choose $K$ and since true value might not exist, we develop method, which call alignment, study relationships across models with different In addition, present three diagnostics based on alignment. These techniques can show how many are consistently if only transiently present, or splits into more when increases. This strategy...
Abstract The mechanisms of human birth seasonality have been debated for over 150 years 1 . In particular, the question whether sexual activity or fertility variations drive has remained open and challenging to test without large-scale data on 2,3 Analyzing from half-a-million users worldwide collected female health tracking app Clue combined with records, we inferred that is primarily driven by seasonal fertility, yet increased around holidays explains minor peaks in curve. Our came...
DATA REPORT article Front. Nutr., 04 July 2018Sec. Nutrition Methodology Volume 5 - 2018 | https://doi.org/10.3389/fnut.2018.00057
Abstract Diverse and non- Lactobacillus -dominated vaginal microbial communities are associated with adverse health outcomes such as preterm birth the acquisition of sexually transmitted infections. Despite importance recognizing understanding key risk-associated features these communities, their heterogeneous structure properties remain ill-defined. Clustering approaches commonly used to characterize but they lack sensitivity robustness in resolving substructures revealing transitions...
Abstract For most women of reproductive age, assessing menstrual health and fertility typically involves regular visits to a gynecologist or another clinician. While these evaluations provide critical information on an individual’s status, they rely memory-based self-reports, the results are rarely, if ever, assessed at population level. In recent years, mobile apps for tracking have become very popular, allowing us evaluate reliability frequency millions self-observations, thereby providing...
Nutrition is a key contributor to health. Recently, several studies have identified associations between factors such as microbiota composition and health-related responses dietary intake, raising the potential of personalized nutritional recommendations. To further our understanding nutrition, detailed individual data must be collected from participants in their day-to-day lives. However, this challenging conventional that require clinical measurements site visits. So-called digital or...
Globally, millions of women track their menstrual cycle and fertility via smartphone-based health apps, generating multivariate time series with frequent missing data. To leverage this type data for studies or the effect on symptoms diseases, it is critical to have methods identifying reproductive events, such as ovulation, pregnancy losses births. Here, we present a hierarchical approach relying hidden semi-Markov models that adapts changes in tracking behavior, explicitly captures...
Topic modeling is a popular method used to describe biological count data. With topic models, the user must specify number of topics $K$. Since there no definitive way choose $K$ and since true value might not exist, we develop techniques study relationships across models with different This can show how many are consistently present if only transiently present, or splits in two when increases. strategy gives more insight into process generating data than choosing single would. We design...
Abstract The vaginal ecosystem is closely tied to human health and reproductive outcomes. However, its dynamics in the wake of childbirth remain poorly characterized. Here, we profiled microbiota cytokine milieu subjects sampled throughout pregnancy (two cohorts; n = 196 pregnancies) and, a subset, for one year postpartum (one cohort; 72 pregnancies). Delivery was associated with pro-inflammatory response depletion dominant taxa – typically, Lactobacillus species. By contrast, neither...
Abstract Globally, millions of women track their menstrual cycle and fertility via smartphone-based health apps, generating multivariate time series with frequent missing data. To leverage data from self-tracking tools in epidemiological studies on or the cycle’s effects diseases symptoms, it is critical to have methods for identifying reproductive events, e . g ovulation, pregnancy losses births. We present two coupled hidden semi-Markov models that adapt changes tracking behavior,...
Predicting pregnancy has been a fundamental problem in women's health for more than 50 years. Previous datasets have collected via carefully curated medical studies, but the recent growth of tracking mobile apps offers potential reaching much broader population. However, feasibility predicting from data is unclear. Here we develop four models -- logistic regression model, and 3 LSTM to predict woman's probability becoming pregnant using app, Clue by BioWink GmbH. Evaluating our on dataset 79...
Keywords: circadian clock ; transcription post-transcription mRNA half-life mathematical modelling dynamical regulation of gene expression These Ecole polytechnique federale de Lausanne EPFL, n° 5911 (2013)Programme doctoral Approches moleculaires du vivantFaculte des sciences la vieInstitut interfacultaire Bioingenierie (SV)Unite Prof. NaefJury: J. Lingner (president), D. Gatfield, C. Green, Vanicek Public defense: 2013-11-1 Reference doi:10.5075/epfl-thesis-5911Print copy in library...
Nutrition is a key contributor to health. Recently, several studies have identified associations between factors such as microbiota composition and health-related responses dietary intake, raising the potential of personalized nutritional recommendations. To further our understanding nutrition, detailed individual data must be collected from participants in their day-to-day lives. However, this challenging conventional that require clinical measurements site visits. So-called digital or...