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A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
High-quality, usable, and effective software is essential for supporting astronomers in the discovery-focused tasks of data analysis and visualisation. As the volume, and perhaps more crucially, the velocity of astronomical data grows, the…
Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
The human brain is the most complex object of study we encounter today. Mapping the neuronal-level connections between the more than 80 billion neurons in the brain is a hopeless task for science. By the recent advancement of magnetic…
Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct…
Visually comparing brain networks, or connectomes, is an essential task in the field of neuroscience. Especially relevant to the field of clinical neuroscience, group studies that examine differences between populations or changes over time…
The human brain is a complex network comprised of functionally and anatomically interconnected brain regions. A growing number of studies have suggested that empirical estimates of brain networks may be useful for discovery of biomarkers of…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
Human papillomavirus (HPV) infection is the most common sexually transmitted infection in the world. Persistent oncogenic Human papillomavirus infection has been a leading threat to global health and can lead to serious complications such…
The BIOSCAN project, led by the International Barcode of Life Consortium, seeks to study changes in biodiversity on a global scale. One component of the project is focused on studying the species interaction and dynamics of all insects. In…
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,…
Causality and causal inference have emerged as core research areas at the interface of modern statistics and domains including biomedical sciences, social sciences, computer science, and beyond. The field's inherently interdisciplinary…
The speed and the versatility of today's computers open up new opportunities to simulate complex biological systems. Here we review a computational approach recently proposed by us to model large tumor cell populations and spheroids, and we…
Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology. Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.…
Gender is an important demographic attribute of people. This paper provides a survey of human gender recognition in computer vision. A review of approaches exploiting information from face and whole body (either from a still image or gait…
Functional MRI (fMRI) and diffusion MRI (dMRI) are non-invasive imaging modalities that allow in-vivo analysis of a patient's brain network (known as a connectome). Use of these technologies has enabled faster and better diagnoses and…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
What can humans compute in their heads? We are thinking of a variety of Crypto Protocols, games like Sudoku, Crossword Puzzles, Speed Chess, and so on. The intent of this paper is to apply the ideas and methods of theoretical computer…