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Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a…
Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed…
A major public health issue is the growing resistance of bacteria to antibiotics. An important part of the needed response is the discovery and development of new antimicrobial strategies. These require the screening of potential new drugs,…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Research increasingly relies on computational methods to analyze experimental data and predict molecular properties. Current approaches often require researchers to use a variety of tools for statistical analysis and machine learning,…
Accurate estimates of microbial species abundances are needed to advance our understanding of the role that microbiomes play in human and environmental health. However, artificially constructed microbiomes demonstrate that intuitive…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…
Antimicrobial resistance is becoming a major threat to public health throughout the world. Researchers are attempting to contrast it by developing both new antibiotics and patient-specific treatments. In the second case, whole-genome…
The human body consists of microbiomes associated with the development and prevention of several diseases. These microbial organisms form several complex interactions that are informative to the scientific community for explaining disease…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
In the effort to aid cytologic diagnostics by establishing automatic single cell screening using high throughput digital holographic microscopy for clinical studies thousands of images and millions of cells are captured. The bottleneck lies…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…