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On behalf of the development team, I review the capabilities of the BAGEL program package in this article. BAGEL is a newly-developed full-fledged program package for electronic-structure computation in quantum chemistry, which is released…
For patients suffering from central nervous system tumors, prognosis estimation, treatment decisions, and postoperative assessments are made from the analysis of a set of magnetic resonance (MR) scans. Currently, the lack of open tools for…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
Melanoma is one of the ten most common cancers in the US. Early detection is crucial for survival, but often the cancer is diagnosed in the fatal stage. Deep learning has the potential to improve cancer detection rates, but its…
Effective treatment of cancer requires early diagnosis which involves the patient's awareness of the early signs and symptoms, leading to a consultation with a health provider, who would then promptly refer the patient for confirmation of…
The emergence of data-driven computational materials science offers unprecedented opportunities to explore complex material landscapes, complementing experimental research with the discovery of novel compounds. To enable these developments,…
Scientific workflows facilitate computational, data manipulation, and sometimes visualization steps for scientific data analysis. They are vital for reproducing and validating experiments, usually involving computational steps in scientific…
The diagnosis and segmentation of tumors using any medical diagnostic tool can be challenging due to the varying nature of this pathology. Magnetic Reso- nance Imaging (MRI) is an established diagnostic tool for various diseases and…
It is estimated that approximately 15% of cancers worldwide can be linked to viral infections. The viruses that can cause or increase the risk of cancer include human papillomavirus, hepatitis B and C viruses, Epstein-Barr virus, and human…
The histological assessment of human tissue has emerged as the key challenge for detection and treatment of cancer. A plethora of different data sources ranging from tissue microarray data to gene expression, proteomics or metabolomics data…
Targeted therapies on the basis of genomic aberrations analysis of the tumor have shown promising results in cancer prognosis and treatment. Regardless of tumor type, trials that match patients to targeted therapies for their particular…
The seriation problem seeks to reorder a set of elements given pairwise similarity information, so that elements with higher similarity are closer in the resulting sequence. When a global ordering consistent with the similarity information…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
Automated test case generation tools help businesses to write tests and increase the safety net provided by high regression test coverage when making code changes. Test generation needs to cover as much as possible of the uncovered code…
At present, there is still no officially accepted and extensively verified implementation of computing the gamma difference distribution allowing unequal shape parameters. We explore four computational ways of the gamma difference…
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
Artificial intelligence allows automatic extraction of imaging biomarkers from already-acquired radiologic images. This paradigm of opportunistic imaging adds value to medical imaging without additional imaging costs or patient radiation…