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Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
Learning with Noisy Labels (LNL) has attracted significant attention from the research community. Many recent LNL methods rely on the assumption that clean samples tend to have "small loss". However, this assumption always fails to…
Patient education materials for solid-organ transplantation vary substantially across U.S. centers, yet no systematic method exists to quantify this heterogeneity at scale. We introduce a framework that grounds the same patient questions in…
Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Several real-world and abstract structures and systems are characterized by marked hierarchy to the point of being expressed as trees. Because the study of these entities often involves sampling (or discovering) the tree nodes in a specific…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
For the task of semantic segmentation, high-resolution (pixel-level) ground truth is very expensive to collect, especially for high resolution images such as gigapixel pathology images. On the other hand, collecting low resolution labels…
The ability to automatically estimate the quality and coverage of the samples produced by a generative model is a vital requirement for driving algorithm research. We present an evaluation metric that can separately and reliably measure…
Motivation. Cancer heterogeneity is observed at multiple biological levels. To improve our understanding of these differences and their relevance in medicine, approaches to link organ- and tissue-level information from diagnostic images and…
Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can…
Gene covariation networks are commonly used to study biological processes. The inference of gene covariation networks from observational data can be challenging, especially considering the large number of players involved and the small…
There is a growing interest in cell-type-specific analysis from bulk samples with a mixture of different cell types. A critical first step in such analyses is the accurate estimation of cell-type proportions in a bulk sample. Although many…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the…
For the vast majority of genome wide association studies (GWAS) published so far, statistical analysis was performed by testing markers individually. In this article we present some elementary statistical considerations which clearly show…
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…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…