Related papers: PASS: De novo assembler for short peptide sequence…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for…
Event cameras are bio-inspired sensors that capture intensity changes asynchronously with distinct advantages, such as high temporal resolution. Existing methods for event-based object/action recognition predominantly sample and convert…
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…
Multidimensional NMR spectroscopy is one of the basic tools for determining the structure of biomolecules. Unfortunately, the resolution of the spectra is often limited by inter-nuclear couplings. This limitation cannot be overcome by…
High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times…
Image Super-Resolution (SR) aims to reconstruct high-resolution images from low-resolution counterparts, but the computational complexity of deep learning-based methods often hinders practical deployment. CAMixer is the pioneering work to…
Peptide sequencing-the process of identifying amino acid sequences from mass spectrometry data-is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about…
Probabilistic amplitude shaping (PAS) combines an outer shaping layer with an inner, systematic forward error correction (FEC) layer to close the shaping gap. Proposed for PAS, constant composition distribution matching (CCDM) produces…
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…
We present a new use of Answer Set Programming (ASP) to discover the molecular structure of chemical samples based on the relative abundance of elements and structural fragments, as measured in mass spectrometry. To constrain the…
Recently, many software tools have been developed to perform quantification in LC-MS analyses. However, most of them are specific to either a quantification strategy (e.g. label-free or isotopic labelling) or a mass-spectrometry system…
The recent development of deep learning methods provides a new approach to optimize the belief propagation (BP) decoding of linear codes. However, the limitation of existing works is that the scale of neural networks increases rapidly with…
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences…
We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages…
Intrinsically Disordered Proteins (IDPs) perform a broad range of biological functions. Their relevance has motivated intense research activity seeking to characterize their sequence/structure/function relationships. However, the…
Pairwise-constrained clustering incorporates side information through must-link (ML) and cannot-link (CL) relations between samples. While these constraints can improve cluster quality, they complicate optimization at scale and limit…