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A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
The evolution of synchrotrons towards higher brilliance beams has increased the possible sample-to-detector propagation distances for which the source confusion circle does not lead to geometrical blurring. This makes it possible to push…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Petrographic analysis based on microfacies identification in thin sections is widely used in sedimentary environment interpretation and paleoecological reconstruction. Fossil recognition from microfacies is an essential procedure for…
Information retrieval involves selecting artifacts from a corpus that are most relevant to a given search query. The flavor of retrieval typically used in classical applications can be termed as homogeneous and relaxed, where queries and…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…
Obtaining a relevant dataset is central to conducting empirical studies in software engineering. However, in the context of mining software repositories, the lack of appropriate tooling for large scale mining tasks hinders the creation of…
Machine Learning models are used in a wide variety of domains. However, machine learning methods often require a large amount of data in order to be successful. This is especially troublesome in domains where collecting real-world data is…
The rapidly expanding corpus of medical research literature presents major challenges in the understanding of previous work, the extraction of maximum information from collected data, and the identification of promising research directions.…
Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as the whole mouse brain stained with heavy elements, and,…
Deep learning (DL) techniques have shown unprecedented success when applied to images, waveforms, and text. Generally, when the sample size ($N$) is much bigger than the number of features ($d$), DL often outperforms other machine learning…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
To build the connectomics map of the brain, we developed a new algorithm that can automatically refine the Membrane Detection Probability Maps (MDPM) generated to perform automatic segmentation of electron microscopy (EM) images. To achieve…
The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for for such…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
Continual Learning seeks to develop a model capable of incrementally assimilating new information while retaining prior knowledge. However, current research predominantly addresses a straightforward learning context, wherein all data…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Efficient querying and retrieval of healthcare data is posing a critical challenge today with numerous connected devices continuously generating petabytes of images, text, and internet of things (IoT) sensor data. One approach to…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…