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Molecular surface representations have been advertised as a great tool to study protein structure and functions, including protein-ligand binding affinity modeling. However, the conventional surface-area-based methods fail to deliver a…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Motivation: Protein function prediction is a challenging task and an open problem in computational biology. The Critical Assessment of protein Function Annotation (CAFA) is a triennial, community-driven initiative that provides an…
Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of…
Tabular data is a fundamental form of data structure. The evolution of table analysis tools reflects humanity's continuous progress in data acquisition, management, and processing. The dynamic changes in table columns arise from…
Isotachophoresis (ITP) is a versatile electrophoretic technique which can be used for sample preconcentration, separation, purification, mixing, and control and acceleration of chemical reactions. Although the basic technique is nearly a…
Table Question Answering (TQA) is an important but under-explored task. Most of the existing QA datasets are in unstructured text format and only few of them use tables as the context. To the best of our knowledge, none of TQA datasets…
This paper describes a machine learning and data science pipeline for structured information extraction from documents, implemented as a suite of open-source tools and extensions to existing tools. It centers around a methodology for…
The grand challenge of protein engineering is the development of computational models that can characterize and generate protein sequences for any arbitrary function. However, progress today is limited by lack of 1) benchmarks with which to…
Table question answering (TQA) focuses on answering questions based on tabular data. Developing TQA systems targets effective interaction with tabular data for tasks such as cell retrieval and data analysis. While recent work has leveraged…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Tensor PCA is a stylized statistical inference problem introduced by Montanari and Richard to study the computational difficulty of estimating an unknown parameter from higher-order moment tensors. Unlike its matrix counterpart, Tensor PCA…
Tabular data, widely used in various applications such as industrial control systems, finance, and supply chain, often contains complex interrelationships among its attributes. Data disentanglement seeks to transform such data into latent…
Crosslinking Mass Spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats,…
Data augmentation is widely utilized as an effective technique to enhance the generalization performance of deep models. However, data augmentation may inevitably introduce distribution shifts and noises, which significantly constrain the…
Due to the highly complex chemical structure of biomolecules, the extensive understanding of the electronic information for proteomics can be challenging. Here, we constructed a charge transfer database at residue level derived from…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for…
A large proportion of organic molecules relevant to medicine and biotechnology contain one or more ionizable groups, which means that fundamental physical and chemical properties (e.g. the charge of the molecule) depend on the pH of the…