Related papers: NanoFrame: A web-based DNA wireframe design tool f…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
An algorithm is developed for structure identification of amorphous carbonaceous nanomaterials with a joint x-ray and neutron diffraction data analysis, using the data on the chemical composition of the sample from other diagnostics. The…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
The ultimate goal of drug design is to find novel compounds with desirable pharmacological properties. Designing molecules retaining particular scaffolds as the core structures of the molecules is one of the efficient ways to obtain…
Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this…
The design of DNN accelerators includes two key parts: HW resource configuration and mapping strategy. Intensive research has been conducted to optimize each of them independently. Unfortunately, optimizing for both together is extremely…
Tomographic imaging reveals internal structures of 3D objects and is crucial for medical diagnoses. Visualizing the morphology and appearance of non-planar sparse anatomical structures that extend over multiple 2D slices in tomographic…
This paper introduces WireBend-kit, a desktop wirebending machine and computational design tool for creating 3D wireframe structures. Combined, they allow users to rapidly and inexpensively create custom 3D wireframe structures from…
The increasing amount of information and the absence of an effective tool for assisting users with minimal technical knowledge lead us to use associative thinking paradigm for implementation of a software solution - Panorama. In this study,…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Neural networks based on soft and biological matter constitute an interesting potential alternative to traditional implementations based on electric circuits. DNA is a particularly promising system in this context due its natural ability to…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Recently, DNA data storage systems have attracted many researchers worldwide. Motivated by the success stories of such systems, in this work we propose a software called BacSoft to clone the data in a bacterial plasmid by using the concept…
Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the…
We present a framework, DISORF, to enable online 3D reconstruction and visualization of scenes captured by resource-constrained mobile robots and edge devices. To address the limited computing capabilities of edge devices and potentially…
Neuroevolution has greatly promoted Deep Neural Network (DNN) architecture design and its applications, while there is a lack of methods available across different DNN types concerning both their scale and performance. In this study, we…
The role of graphene nanowindows in the nanohydroxyapatite bone scaffold preparation is important for the preparation of mechanically robust scaffolds and implementation in bone recovery. Here, we report a graphene-nanohydroxyapatite…