Gregg, Robert W Shabnam, Fathima Shoemaker, Jason E
Published in
Bioinformatics (Oxford, England)
The cGAS pathway is a component of the innate immune system responsible for the detection of pathogenic DNA and upregulation of interferon beta (IFNβ). Experimental evidence shows that IFNβ signaling occurs in highly heterogeneous cells and is stochastic in nature; however, the benefits of these attributes remain unclear. To investigate how stochas...
Beuchel, Carl Kirsten, Holger Ceglarek, Uta Scholz, Markus
Published in
Bioinformatics (Oxford, England)
Many diseases have a metabolic background, which is increasingly investigated due to improved measurement techniques allowing high-throughput assessment of metabolic features in several body fluids. Integrating data from multiple cohorts is of high importance to obtain robust and reproducible results. However, considerable variability across studie...
Jin, Ting Nguyen, Nam D Talos, Flaminia Wang, Daifeng
Published in
Bioinformatics (Oxford, England)
Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. Integrating the increasing amount of population-level genomic data and understanding gene regulatory mechanisms in disease development are still challenging. Machine learning has emerged to solve this, but many m...
Westbrook, Anthony Varki, Elizabeth Thomas, W Kelley
Published in
Bioinformatics (Oxford, England)
Reproducibility is of central importance to the scientific process. The difficulty of consistently replicating and verifying experimental results is magnified in the era of big data, in which bioinformatics analysis often involves complex multi-application pipelines operating on terabytes of data. These processes result in thousands of possible per...
Jain, Dhawal Chu, Chong Alver, Burak Han Lee, Soohyun Lee, Eunjung Alice Park, Peter J
Published in
Bioinformatics (Oxford, England)
Hi-C is a common technique for assessing three-dimensional chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable eleme...
Rodosthenous, Theodoulos Shahrezaei, Vahid Evangelou, Marina
Published in
Bioinformatics (Oxford, England)
Recent developments in technology have enabled researchers to collect multiple OMICS datasets for the same individuals. The conventional approach for understanding the relationships between the collected datasets and the complex trait of interest would be through the analysis of each OMIC dataset separately from the rest, or to test for association...
Lecompte, Lolita Peterlongo, Pierre Lavenier, Dominique Lemaitre, Claire
Published in
Bioinformatics (Oxford, England)
Studies on structural variants (SVs) are expanding rapidly. As a result, and thanks to third generation sequencing technologies, the number of discovered SVs is increasing, especially in the human genome. At the same time, for several applications such as clinical diagnoses, it is important to genotype newly sequenced individuals on well-defined an...
Ke, Yaobin Rao, Jiahua Zhao, Huiying Lu, Yutong Xiao, Nong Yang, Yuedong
Published in
Bioinformatics (Oxford, England)
RNA secondary structure plays a vital role in fundamental cellular processes, and identification of RNA secondary structure is a key step to understand RNA functions. Recently, a few experimental methods were developed to profile genome-wide RNA secondary structure, i.e. the pairing probability of each nucleotide, through high-throughput sequencing...
Uddin, Mostofa Rafid Mahbub, Sazan Rahman, M Saifur Bayzid, Md Shamsuzzoha
Published in
Bioinformatics (Oxford, England)
Protein structures provide basic insight into how they can interact with other proteins, their functions and biological roles in an organism. Experimental methods (e.g. X-ray crystallography and nuclear magnetic resonance spectroscopy) for predicting the secondary structure (SS) of proteins are very expensive and time consuming. Therefore, developi...
Scherr, Tim Streule, Karolin Bartschat, Andreas Böhland, Moritz Stegmaier, Johannes Reischl, Markus Orian-Rousseau, Véronique Mikut, Ralf
Published in
Bioinformatics (Oxford, England)
An automated counting of beads is required for many high-throughput experiments such as studying mimicked bacterial invasion processes. However, state-of-the-art algorithms under- or overestimate the number of beads in low-resolution images. In addition, expert knowledge is needed to adjust parameters. In combination with our image labeling tool, B...
