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RNA molecules follow a succession of enzyme-mediated processing steps from transcription until maturation. The participating enzymes, for example the spliceosome for mRNAs and Drosha and Dicer for microRNAs, are also produced in the cell…
Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric…
A crystallographic cell is a representation of a lattice, but each lattice can be represented just as well by any of an infinite number of such unit cells. Searching for matches to an experimentally determined crystallographic unit cell in…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
Emergent processes in complex systems such as cellular automata can perform computations of increasing complexity, and could possibly lead to artificial evolution. Such a feat would require scaling up current simulation sizes to allow for…
The challenge of clustering short text data lies in balancing informativeness with interpretability. Traditional evaluation metrics often overlook this trade-off. Inspired by linguistic principles of communicative efficiency, this paper…
Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather…
Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…
Biosensor data has the potential ability to improve disease control and detection. However, the analysis of these data under free-living conditions is not feasible with current statistical techniques. To address this challenge, we introduce…
We present a systematic coarse-graining (CG) strategy for many particle molecular systems based on cluster expansion techniques. We construct a hierarchy of coarse-grained Hamiltonians with interaction potentials consisting of two, three…
This article presents a scalable implementation of nonlinear Gramian-based control synthesis for control-affine systems, including a minimum energy control construction. These synthesis advances are achieved by addressing key computational…
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…
The vast majority of biological sequences encode unknown functions and bear little resemblance to experimentally characterized proteins, limiting both our understanding of biology and our ability to harness functional potential for the…
The mechanical properties of biological tissues are strongly correlated to the specific distribution of their collagen fibers. Monitoring the dynamic reorganization of the collagen network during mechanical stretching is however a technical…
Cancer is a complex genetic disease involving uncontrolled cell growth and proliferation, and necessitates effective targeting of dysregulated cellular pathways underlying cancer progression. Multiple genetic and epigenetic alterations…
Many fundamental cellular processes involve small numbers of molecules. When numbers are small, fluctuations dominate, and stochastic models, which account for these fluctuations, are required. In this chapter, we describe minimal…
The behaviour of a system of ion channels formed across the cell membrane is presented. The infinite number of channels with an infinite coupling is introduced first as a reference point for the detailed derivation of the…
Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
This paper presents our experience specifying and verifying the correctness of ZooKeeper, a complex and evolving distributed coordination system. We use TLA+ to model fine-grained behaviors of ZooKeeper and use the TLC model checker to…