Related papers: BAUM: A DNA Assembler by Adaptive Unique Mapping a…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
Spurred by widening gap between data processing speed and data communication speed in Von-Neumann computing architectures, some bioinformatic applications have harnessed the computational power of Processing-in-Memory (PIM) platforms.…
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Detection of extremely rare variant alleles, such as tumour DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
The advent of next-generation sequencing (NGS) technologies enables researchers to sequence complex microbial communities directly from environment. Since assembly typically produces only genome fragments, also known as contigs, instead of…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
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…
While model serving has unlocked unprecedented capabilities, the high cost of serving large-scale models continues to be a significant barrier to widespread accessibility and rapid innovation. Compiler optimizations have long driven…
We tackle the problem of sequential brick assembly with LEGO bricks to create combinatorial 3D structures. This problem is challenging since this brick assembly task encompasses the characteristics of combinatorial optimization problems. In…
This paper investigates a large unitarily invariant system (LUIS) involving a unitarily invariant sensing matrix, an arbitrarily fixed signal distribution, and forward error control (FEC) coding. A universal Gram-Schmidt orthogonalization…
Motivation: RNA-seq has made feasible the analysis of a whole set of expressed mRNAs. Mapping-based assembly of RNA-seq reads sometimes is infeasible due to lack of high-quality references. However, de novo assembly is very challenging due…
The aim of this work is to propose a meta-algorithm for automatic classification in the presence of discrete binary classes. Classifier learning in the presence of overlapping class distributions is a challenging problem in machine…
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…