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We provide an overview of the emergence of large language models for scientific computing applications. We highlight use cases that involve natural language processing of scientific documents and specialized languages designed to describe…
This paper attempts to connects the evolution of computer languages with the evolution of life, where the later has been dictated by \emph{theory of evolution of species}, and tries to give supportive evidence that the new languages are…
This article is intended as a guide for new graduate students in the field of computational science. With the increasing influx of students from diverse backgrounds joining the ever-popular field, this short guide aims to help students…
The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…
Support vector machines and kernel methods are increasingly popular in genomics and computational biology, due to their good performance in real-world applications and strong modularity that makes them suitable to a wide range of problems,…
Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories:…
In this paper we describe our experience in developing curriculum courses aimed at graduate students in emerging computational fields, including biology and medical science. We focus primarily on computational data analysis and statistical…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
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…
The advent of modern data processing has led to an increasing tendency towards interdisciplinarity, which frequently involves the importation of different technical approaches. Consequently, there is an urgent need for a unified data…
Physics-Informed Machine Learning (PIML) has successfully integrated mechanistic understanding into machine learning, particularly in domains governed by well-known physical laws. This success has motivated efforts to apply PIML to biology,…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small datasets, and provide adaptive suggestions for sequential…
Scientific research frequently involves the use of computational tools and methods. Providing thorough documentation, open-source code, and data -- the creation of reproducible computational research -- helps others understand a…
The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
This thesis details a Python-based software designed to calculate the Jones polynomial, a vital mathematical tool from Knot Theory used for characterizing the topological and geometrical complexity of curves in \( \mathbb{R}^3 \), which is…
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…