Related papers: DrosOCB: a high resolution map of conserved non co…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes, inducing de novo gene formation, or altering gene expression. Here, we investigate…
Organismal phenotypes emerge from a complex set of genotypic interactions. While technological advances in sequencing provide a quantitative description of an organism's genotype, characterization of an organism's physical phenotype lags…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…
We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function,…
We present a new non-negative matrix factorization model for $(0,1)$ bounded-support data based on the doubly non-central beta (DNCB) distribution, a generalization of the beta distribution. The expressiveness of the DNCB distribution is…
Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…
Knowledge of molecular subtypes of gliomas can provide valuable information for tailored therapies. This study aimed to investigate the use of deep convolutional neural networks (DCNNs) for noninvasive glioma subtyping with radiological…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Genes carry the instructions for making proteins that are found in a cell as a specific sequence of nucleotides that are found in DNA molecules. But, the regions of these genes that code for proteins may occupy only a small region of the…
Evolution is an extraordinary engine for enzymatic diversity, yet the chemistry it has explored remains a narrow slice of what DNA can encode. Deep generative models can design new proteins that bind ligands, but none have created enzymes…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Understanding protein function is one of the keys to understanding life at the molecular level. It is also important in several scenarios including human disease and drug discovery. In this age of rapid and affordable biological sequencing,…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
High annotation costs are a substantial bottleneck in applying modern deep learning architectures to clinically relevant medical use cases, substantiating the need for novel algorithms to learn from unlabeled data. In this work, we propose…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
With increasingly "big" data available in biomedical research, deriving accurate and reproducible biology knowledge from such big data imposes enormous computational challenges. In this paper, motivated by recently developed stochastic…
Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include UTRs and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast comparison.…