Related papers: Site-specific recombinatorics: in situ cellular ba…
Site-specific recombination on supercoiled circular DNA yields a variety of knotted or catenated products. We develop a model of this process, and give extensive experimental evidence that the assumptions of our model are reasonable. We…
The barcode of a persistence module serves as a complete combinatorial invariant of its isomorphism class. Barcodes are typically extracted by performing changes of basis on a persistence module until the constituent matrices have a special…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory…
Node failures are inevitable in distributed storage systems (DSS). To enable efficient repair when faced with such failures, two main techniques are known: Regenerating codes, i.e., codes that minimize the total repair bandwidth; and codes…
Batched network coding (BNC) is a low-complexity solution to network transmission in multi-hop packet networks with packet loss. BNC encodes the source data into batches of packets. As a network coding scheme, the intermediate nodes perform…
Erasure coding techniques are used to increase the reliability of distributed storage systems while minimizing storage overhead. Also of interest is minimization of the bandwidth required to repair the system following a node failure. In a…
The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…
The present work provides a new approach to evolve ligand structures which represent possible drug to be docked to the active site of the target protein. The structure is represented as a tree where each non-empty node represents a…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Single-cell RNA sequencing (scRNA-seq) technologies have enabled the profiling of gene expression for a collection of cells across time during a dynamic biological process. Given that each time point provides only a static snapshot,…
Cellular Electron CryoTomography (CECT) is a 3D imaging technique that captures information about the structure and spatial organization of macromolecular complexes within single cells, in near-native state and at sub-molecular resolution.…
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…
Agent-based simulation platforms play a key role in enabling fast-to-run evolution experiments that can be precisely controlled and observed in detail. Availability of high-resolution snapshots of lineage ancestries from digital…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
Cell formation is a critical step in the design of cellular manufacturing systems. Recently, it was tackled using a cut-based-graph-partitioning model. This model meets real-life production systems requirements as it uses the actual amount…
Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…
When delineating lesions from medical images, a human expert can always keep in mind the anatomical structure behind the voxels. However, although high-quality (though not perfect) anatomical information can be retrieved from computed…