Publications

Tissue morphogenesis relies on repeated use of dynamic behaviors at the levels of intracellular structures, individual cells, and cell groups. Rapidly accumulating live imaging datasets make it increasingly important to formalize and automate the task of mapping recurrent dynamic behaviors (motifs), as it is done in speech recognition and other data mining applications. Here, we present a “template-based search” approach for accurate mapping of sub- to multi-cellular morphogenetic motifs using a time series data mining framework. We formulated the task of motif mapping as a subsequence matching problem and solved it using dynamic time warping, while relying on high throughput graph-theoretic algorithms for efficient exploration of the search space. This formulation allows our algorithm to accurately identify the complete duration of each instance and automatically label different stages throughout its progress, such as cell cycle phases during cell division. To illustrate our approach, we mapped cell intercalations during germband extension in the early Drosophila embryo. Our framework enabled statistical analysis of intercalary cell behaviors in wild-type and mutant embryos, comparison of temporal dynamics in contracting and growing junctions in different genotypes, and the identification of a novel mode of iterative cell intercalation. Our formulation of tissue morphogenesis using time series opens new avenues for systematic decomposition of tissue morphogenesis.

The large-scale clustering of matter is impacted by baryonic physics, particularly AGN feedback. Modelling or mitigating this impact will be essential for making full use of upcoming measurements of cosmic shear and other large-scale structure probes. We study baryonic effects on the matter bispectrum, using measurements from a selection of state-of-the-art hydrodynamical simulations: IllustrisTNG, Illustris, EAGLE, and BAHAMAS. We identify a low-redshift enhancement of the bispectrum, peaking at k∼3hMpc−1, that is present in several simulations, and discuss how it can be associated to the evolving nature of AGN feedback at late times. This enhancement does not appear in the matter power spectrum, and therefore represents a new source of degeneracy breaking between two- and three-point statistics. In addition, we provide physical interpretations for other aspects of these measurements, and make initial comparisons to predictions from perturbation theory, empirical fitting formulas, and the response function formalism. We publicly release our measurements (including estimates of their uncertainty due to sample variance) and bispectrum measurement code as resources for the community.

Tissue morphogenesis relies on repeated use of dynamic behaviors at the levels of intracellular structures, individual cells, and cell groups. Rapidly accumulating live imaging datasets make it increasingly important to formalize and automate the task of mapping recurrent dynamic behaviors (motifs), as it is done in speech recognition and other data mining applications. Here, we present a “template-based search” approach for accurate mapping of sub- to multi-cellular morphogenetic motifs using a time series data mining framework. We formulated the task of motif mapping as a subsequence matching problem and solved it using dynamic time warping, while relying on high throughput graph-theoretic algorithms for efficient exploration of the search space. This formulation allows our algorithm to accurately identify the complete duration of each instance and automatically label different stages throughout its progress, such as cell cycle phases during cell division. To illustrate our approach, we mapped cell intercalations during germband extension in the early Drosophila embryo. Our framework enabled statistical analysis of intercalary cell behaviors in wild-type and mutant embryos, comparison of temporal dynamics in contracting and growing junctions in different genotypes, and the identification of a novel mode of iterative cell intercalation. Our formulation of tissue morphogenesis using time series opens new avenues for systematic decomposition of tissue morphogenesis.

Convolutional neural networks (CNNs) have become a standard for analysis of biological sequences. Tuning of network architectures is essential for CNN’s performance, yet it requires substantial knowledge of machine learning and commitment of time and effort. This process thus imposes a major barrier to broad and effective application of modern deep learning in genomics. Here, we present AMBER, a fully automated framework to efficiently design and apply CNNs for genomic sequences. AMBER designs optimal models for user-specified biological questions through the state-of-the-art Neural Architecture Search (NAS). We applied AMBER to the task of modelling genomic regulatory features and demonstrated that the predictions of the AMBER-designed model are significantly more accurate than the equivalent baseline non-NAS models and match or even exceed published expert-designed models. Interpretation of AMBER architecture search revealed its design principles of utilizing the full space of computational operations for accurately modelling genomic sequences. Furthermore, we illustrated the use of AMBER to accurately discover functional genomic variants in allele-specific binding and disease heritability enrichment. AMBER provides an efficient automated method for designing accurate deep learning models in genomics.

Vancomycin-resistant Enterococcus faecium (VREfm) is an emerging antibiotic-resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonization, in particular following antibiotic treatment, remains largely unknown. We employed amplicon 16S rRNA gene sequencing and metabolomics in a murine model system to try and investigate functional roles of the gut microbiome during VREfm colonization. First-order taxonomic shifts between Bacteroidetes and Tenericutes within the gut microbial community composition were detected both in response to pretreatment using ceftriaxone and to subsequent VREfm challenge. Using neural networking approaches to find cooccurrence profiles of bacteria and metabolites, we detected key metabolome features associated with butyric acid during and after VREfm colonization. These metabolite features were associated with Bacteroides, indicative of a transition toward a preantibiotic naive microbiome. This study shows the impacts of antibiotics on the gut ecosystem and the progression of the microbiome in response to colonization with VREfm. Our results offer insights toward identifying potential nonantibiotic alternatives to eliminate VREfm through metabolic reengineering to preferentially select for Bacteroides.

IL-4 activates macrophages to adopt distinct phenotypes associated with clearance of helminth infections and tissue repair, but the phenotype depends on the cellular lineage of these macrophages. The molecular basis of chromatin remodeling in response to IL-4 stimulation in tissue-resident and monocyte-derived macrophages is not understood. In this study, we find that IL-4 activation of different lineages of peritoneal macrophages in mice is accompanied by lineage-specific chromatin remodeling in regions enriched with binding motifs of the pioneer transcription factor PU.1. PU.1 motif is similarly associated with both tissue-resident and monocyte-derived IL-4-induced accessible regions but has different lineage-specific DNA shape features and predicted cofactors. Mutation studies based on natural genetic variation between C57BL/6 and BALB/c mouse strains indicate that accessibility of these IL-4-induced regions can be regulated through differences in DNA shape without direct disruption of PU.1 motifs. We propose a model whereby DNA shape features of stimulation-dependent genomic elements contribute to differences in the accessible chromatin landscape of alternatively activated macrophages on different genetic backgrounds that may contribute to phenotypic variations in immune responses.

Clustered Regularly Interspace Short Palindromic Repeats (CRISPR)-Cas9 genome editing methods provide the tools necessary to examine phenotypic impacts of targeted perturbations in high-throughput screens. While these technologies have the potential to reveal functional elements with direct therapeutic applications, statistical techniques to analyze noncoding screen data remain limited. We present CRISPR-Decryptr, a computational tool for the analysis of CRISPR noncoding screens. Our method leverages experimental design: accounting for multiple conditions, controls, and replicates to infer the regulatory landscape of noncoding genomic regions. We validate our method on a variety of mutagenesis, CRISPR activation, and CRISPR interference screens, extracting new insights from previously published data.

Amyloid-β peptide (Aβ) accumulation in the brain is a hallmark of Alzheimer’s Disease. An important mechanism of Aβ clearance in the brain is uptake and degradation by microglia. Presenilin 1 (PS1) is the catalytic subunit of γ-secretase, an enzyme complex responsible for the maturation of multiple substrates, such as Aβ. Although PS1 has been extensively studied in neurons, the role of PS1 in microglia is incompletely understood. Here we report that microglia containing phospho-deficient mutant PS1 display a slower kinetic response to micro injury in the brain in vivo and the inability to degrade Aβ oligomers due to a phagolysosome dysfunction. An Alzheimer’s mouse model containing phospho-deficient PS1 show severe Aβ accumulation in microglia as well as the postsynaptic protein PSD95. Our results demonstrate a novel mechanism by which PS1 modulates microglial function and contributes to Alzheimer’s -associated phenotypes.

When testing for a rare disease, prevalence estimates can be highly sensitive to uncertainty in the specificity and sensitivity of the test. Bayesian inference is a natural way to propagate these uncertainties, with hierarchical modeling capturing variation in these parameters across experiments. Another concern is the people in the sample not being representative of the general population. Statistical adjustment cannot without strong assumptions correct for selection bias in an opt-in sample, but multilevel regression and poststratification can at least adjust for known differences between sample and population. We demonstrate these models with code in R and Stan and discuss their application to a controversial recent study of COVID-19 antibodies in a sample of people from the Stanford University area. Wide posterior intervals make it impossible to evaluate the quantitative claims of that study regarding the number of unreported infections. For future studies, the methods described here should facilitate more accurate estimates of disease prevalence from imperfect tests performed on non-representative samples

We introduce a mechanism for light-induced Floquet engineering of the Fermi surface to dynamically tip the balance between competing instabilities in correlated condensed matter systems in the vicinity of a Van Hove singularity. We first calculate how the Fermi surface is deformed by an off-resonant, high-frequency light field and then determine the impact of this deformation on the ordering tendencies using an unbiased functional renormalization group approach. As a testbed, we investigate Floquet engineering in cuprates driven by light. We find that the d-wave superconducting ordering tendency in this system can be strongly enhanced over the Mott insulating one. This gives rise to extended regions of induced d-wave superconductivity in the effective phase diagram in the presence of a light field.