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Designing regulatory DNA elements with precise cell-type-specific activity is broadly relevant for cell engineering and gene therapy. Deep generative models can generate functional gene-regulatory elements, but existing methods struggle to…
This paper presents a novel beacon light coding protocol, which enables fast and accurate identification of the beacons in an image. The protocol is provably robust to a predefined set of detection and decoding errors, and does not require…
Biological systems possess remarkable capabilities for self-recognition and morphological regeneration, often relying solely on local interactions. Inspired by these decentralized processes, we present a novel system of physical 3D…
Visual localization algorithms have achieved significant improvements in performance thanks to recent advances in camera technology and vision-based techniques. However, there remains one critical caveat: all current approaches that are…
Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the…
Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…
Understanding cell identity and function through single-cell level sequencing data remains a key challenge in computational biology. We present a novel framework that leverages gene-specific textual annotations from the NCBI Gene database…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Autoencoding has achieved great empirical success as a framework for learning generative models for natural images. Autoencoders often use generic deep networks as the encoder or decoder, which are difficult to interpret, and the learned…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
In the context of the Internet of Bio-Nano Things (IoBNT), nano-devices are envisioned to perform complex tasks collaboratively, i.e., by communicating with each other. One candidate for the implementation of such devices are engineered…
We propose a new sequencing protocol that combines recent advances in combinatorial pooling design and second-generation sequencing technology to efficiently approach de novo selective genome sequencing. We show that combinatorial pooling…
This paper presents advancements in automated early-stage prediction of the success of reprogramming human induced pluripotent stem cells (iPSCs) as a potential source for regenerative cell therapies.The minuscule success rate of…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…
Metacells are disjoint and homogeneous groups of single-cell profiles, representing discrete and highly granular cell states. Existing metacell algorithms tend to use only one modality to infer metacells, even though single-cell multi-omics…
In this paper, we discuss codes for distributed storage systems with hierarchical repair properties. Specifically, we devote attention to the repair problem of the rack-aware storage model with locality, aiming to enhance the system's…
The recent advances in single-cell technologies have enabled us to profile genomic features at unprecedented resolution and datasets from multiple domains are available, including datasets that profile different types of genomic features…
This paper proposes a framework for designing robust precoders for a multi-input single-output (MISO) system that performs integrated sensing and communication (ISAC) across multiple cells and users. We use Cramer-Rao-Bound (CRB) to measure…
Large-scale MIMO systems can yield a substantial improvement in spectral efficiency for future communication systems. Due to the finer spatial resolution achieved by a huge number of antennas at the base stations, these systems have shown…