14 papers · ranked by Valyu relevance
Aria Trivedi, Thomas Mathew, Matthew Shulman, Lakshmi Thangam + 4 more
A systematic optimization of throughput and operational stability in Sorting by Interfacial Tension (SIFT) is presented. Reducing droplet size and enabling a broader distribution of droplet trajectories increased the number of droplets processed per sorting element, resulting in about a four fold improvement in…
Joseph de Rutte, Robert Dimatteo, Mark van Zee, Robert Damoiseaux + 1 more
Techniques to analyze and sort single cells based on secreted products have the potential to transform our understanding of cellular biology as well as accelerate the development of next generation cell and antibody therapies. However, secretions are rapidly transported away from cells, such that specialized equipment…
Alessio P. Buccino, Arjun Sridhar, David Feng, Karel Svoboda + 1 more
The scale of in vivo electrophysiology has expanded in recent years, with simultaneous recordings across thousands of electrodes now becoming routine. These advances have enabled a wide range of discoveries, but they also impose substantial computational demands. Spike sorting, the procedure that extracts spikes from…
Zeinab Mohammadi, Daniel Denman, Achim Klug, Tim C. Lei
Sorting neural voltages measured from a multichannel neural probe to extract the single unit activities of neuronal firing, especially in real-time, remains a significant technical challenge, largely due to the large amount of acquired data and the technical difficulties involved in processing and classifying these…
Pierre-Aurélien Gilliot, Thomas E. Gorochowski
The ability to measure the phenotype of millions of different genetic designs using Massively Parallel Reporter Assays (MPRAs) has revolutionised our understanding of genotype-to-phenotype relationships and opened avenues for data-centric approaches to biological design. However, our knowledge of how best to design…
John N. Koberstein, Melissa L. Stewart, Taylor L. Mighell, Chadwick B. Smith + 1 more
The utility of single fluorescent protein biosensors (SFPBs) in biological research is offset by the difficulty in engineering these tools. SFPBs generally consist of three basic components: a circularly permuted fluorescent protein, a ligand-binding domain, and a pair of linkers connecting the two domains. In the…
Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis
Coalescent- and reconciliation-based methods are now widely used to infer species phylogenies from genomic data. They typically use per-gene phylogenies as input, which requires conducting multiple individual tree inferences on a large set of multiple sequence alignments (MSAs). At present, no easy-to-use parallel tool…
Stuart Byma, Akash Dhasade, Adrian Altenhoff, Christophe Dessimoz + 1 more
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find similar pairs in a set of n elements such as protein sequences. Precise…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Seth Stadick
Filtering records using command line tools is a staple of Bioin-formatics. In analysis pipelines and in day-to-day research tools such as awk, grep, and cut are the workhorses of much of our data crunching. To date, there is no command line utility for performing index-free alignment-based filtering of records. Ish is…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Constantin Scholl, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis
Motivated by load balance issues in parallel calculations of the phylogenetic likelihood function, we recently introduced an approximation algorithm for efficiently distributing partitioned alignment data to a given number of CPUs. The goal is to balance the accumulated number of sites per CPU, and, at the same time…
Pierre Carrier, Bill Long, Richard Walsh, Jef Dawson + 4 more
High Performance Computing (HPC) Best Practice offers opportunities to implement lessons learned in areas such as computational chemistry and physics in genomics workflows, specifically Next-Generation Sequencing (NGS) workflows. In this study we will briefly describe how distributed-memory parallelism can be an…
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread…