14 papers · ranked by Valyu relevance
Mst. Fahmida Sultana Naznin, Swarup Sidhartho Mondol, Adnan Ibney Faruq, Ahmed Mahir Sultan Rumi + 2 more
The fast-growing amount of data needs reliable and long-lasting storage solutions. DNA has emerged as a promising medium due to its high information density and long-term stability. However, DNA storage is a complex process where each stage introduces noise and errors, including synthesis errors, storage decay, and…
Timothy Atkinson, Thomas D. Barrett, Scott Cameron, Bora Guloglu + 5 more
Exploring the vast and largely uncharted territory of amino acid sequences is crucial for understanding complex protein functions and the engineering of novel therapeutic proteins. Whilst generative machine learning has advanced protein sequence modelling, no existing approach is proficient for both unconditional and…
Nicola Mulberry, Tanja Stadler
A combination of recent advancements in molecular recording devices and sequencing technologies has made it possible to generate lineage tracing data on the order of thousands of cells. Dynamic lineage recorders are able to generate random, heritable mutations which accumulate continuously on the timescale of…
Sophie Seidel, Antoine Zwaans, Samuel Regalado, Junhong Choi + 2 more
CRISPR-based lineage tracing offers a promising avenue to decipher single cell lineage trees, especially in organisms that are challenging for microscopy. A recent advancement in this domain is lineage tracing based on sequential genome editing, which not only records genetic edits but also the order in which they…
D. Lin, Y. F. Ji, J. A. A. McArt, J. Li
While global medical research is poised to benefit from the rapid advance of artificial intelligence (AI) technologies, veterinary medicine research often faces significant limitations due to data scarcity and availability issues. To address this issue, we proposed a generative modeling framework, SynLS, for generating…
Yue Liu, Marc W. Howard
Sequential neural activity has been observed in many parts of the brain and has been proposed as a neural mechanism for memory. The natural world expresses temporal relationships at a wide range of scales. Because we cannot know the relevant scales a priori it is desirable that memory, and thus the generated sequences…
Callum Burnard, Alban Mancheron, William Ritchie
A publicly available human genome serves as both a valuable resource for researchers and a potential risk to the individual who provided the genome. Many actors with selfish intentions could exploit it to extract information about the donor’s health or that of their relatives. Recent efforts have employed artificial…
Sophie Seidel, Antoine Zwaans, Samuel Regalado, Junhong Choi + 2 more
CRISPR-based lineage tracing offers a promising avenue to decipher single cell lineage trees, especially in organisms that are challenging for microscopy. A recent advancement in this domain is lineage tracing based on sequential genome editing, which not only records genetic edits but also the order in which they…
Machiko Ohbayashi
The production of action sequences is a fundamental aspect of human motor skills. To examine whether primary motor cortex (M1) is involved in maintenance of sequential movements, we trained two monkeys (Cebus apella) to perform two sequential reaching tasks. In one task, sequential movements were instructed by visual…
Fritz Lekschas, Brant Peterson, Daniel Haehn, Eric Ma + 2 more
We present PEAX, a novel feature-based technique for interactive visual pattern search in sequential data, like time series or data mapped to a genome sequence. Visually searching for patterns by similarity is often challenging because of the large search space, the visual complexity of patterns, and the user’s…
Youhan Lee, Jaehoon Kim
With the fact that protein functionality is tied to its structure and shape, a protein design paradigm of generating proteins tailored to specific shape contexts has been utilized for various biological applications. Recently, researchers have shown that top-down strategies are possible with the aid of deep learning…
Ariya Shajii, Ibrahim Numanagić, Alexander T. Leighton, Haley Greenyer + 2 more
Exponentially-growing next-generation sequencing data requires high-performance tools and algorithms. Nevertheless, the implementation of high-performance computational genomics software is inaccessible to many scientists because it requires extensive knowledge of low-level software optimization techniques, forcing…
Anthony J. Greenberg
Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory-efficient…
Rohan Patel, Kenneth Pham, Harshini Chandrashekar, Jennifer E. Phillips-Cremins
Sequential Oligopaints DNA FISH is an imaging technique that measures higher-order genome folding at single-allele resolution via multiplexed, probe-based tracing. Currently there is a paucity of algorithms to identify 3D genome features in sequential Oligopaints data. Here, we present FISHnet, a graph theory method…