Related papers: PhaBOX: A web server for identifying and character…
Multibillion-clone landscape phage display libraries were prepared by the fusion of the phage major coat protein pVIII with foreign random peptides. Phage particles and their proteins specific for cancer and bacterial cells were selected…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
The current catalyst discovery and development pipeline for energy-intensive applications like methane conversion remains bottlenecked by expensive trial-and-error experimentation, irreproducible chemical intuition, and a lack of frameworks…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Modern data analytics requires a huge amount of computing power and processes a massive amount of data. At the same time, the underlying computing platform is becoming much more heterogeneous on both hardware and software. Even though…
Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no consistent framework to integrate and run these tools across projects. Currently,…
One primary goal of human microbiome studies is to predict host traits based on human microbiota. However, microbial community sequencing data present significant challenges to the development of statistical methods. In particular, the…
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the…
Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…
Ensembles are popular methods for solving practical supervised learning problems. They reduce the risk of having underperforming models in production-grade software. Although critical, methods for learning heterogeneous regression ensembles…
Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. For communities of up to medium diversity,…
In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view…
Phonocardiography has recently gained popularity in low-cost and remote monitoring, including passive fetal heart monitoring. Development for methods which analyse phonocardiographical data try to capitalize on this opportunity, and in…
We present a new method for detecting and identifying bacteria by measuring impedance fluctuations (impedance noise) caused by ion release by the bacteria during phage infestation. This new method significantly increases the measured signal…
Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation…
Extremal Graph Theory heavily relies on exploring bounds and inequalities between graph invariants, a task complicated by the rapid combinatorial explosion of graphs. Various tools have been developed to assist researchers in navigating…
Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large metagenomic…
Metagenomics has led to significant advancements in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…