Related papers: Sequencing proteins with transverse ionic transpor…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the…
This work exploits the zeptoliter sensing volume of electrolyte-filled nanopores to determine, simultaneously and in real time, the approximate shape, volume, charge, rotational diffusion coefficient, and dipole moment of individual…
High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pairs, impairing generative model performance. We leverage…
The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared to computational or experimental methods. However, existing…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
This paper studies the sequence reconstruction problem for a channel inspired by protein identification. We introduce a coloring channel, where a sequence is transmitted through a channel that deletes all symbols not belonging to a fixed…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of genes from an organism with no reference genome. With the rapidly increasing throughputs and…
Proteins play a key role in facilitating the infectiousness of the 2019 novel coronavirus. A specific spike protein enables this virus to bind to human cells, and a thorough understanding of its 3-dimensional structure is therefore critical…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Nanopore protein sequencing produces long, noisy ionic current traces in which key molecular phases, such as protein capture and translocation, are embedded. Capture phases mark the successful entry of a protein into the pore and serve as…
Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Recently developed deep learning techniques have significantly improved the accuracy of various speech and image recognition systems. In this paper we adapt some of these techniques for protein secondary structure prediction. We first train…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling…
Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and…
Protein characterization using nanopore-based devices promises to be a breakthrough method in basic research, diagnostics, and analytics. Current research includes the use of machine learning to achieve this task. In this work, a…
Ion channels orchestrate the communication between cells and their environment. These are special proteins capable of changing their shape to allow ions to pass through membranes in response to stimuli like membrane tension. As the letters…