13 papers · ranked by Valyu relevance
Jingcheng Zhang, Lei Chen, Jinlin Sun, Shumin Li + 5 more
DNA has emerged as a compelling archival storage medium, offering unprecedented information density and millennia-scale durability. Despite its promise, DNA-based data storage faces critical challenges due to error-prone processes during DNA synthesis, storage, and sequencing. In this study, we introduce Gungnir, a…
Kevin D. Volkel, Paul W. Hook, Albert Keung, Winston Timp + 1 more
As nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-time signal analysis, and the ability to read both DNA and RNA. We need flexible and…
Dennis Yeung, Francesco Negro, Ivan Vujaklija
Neural interfacing via decomposition of high-density surface electromyography (HD-sEMG) should be robust to signal non-stationarities incurred by changes in joint pose and contraction intensity. We present an adaptive real-time motor unit (MU) decoding algorithm and test it on HD-sEMG collected from the extensor carpi…
Seungbin Park, Megan Lipton, Maria C. Dadarlat
Two-photon imaging has been a critical tool for dissecting brain circuits and understanding brain function. However, relating slow two-photon calcium imaging data to fast behaviors has been challenging due to relatively low imaging sampling rates, thus limiting potential applications to neural prostheses. Here, we show…
Alejandro Santos-Mayo, Faith Gilbert, Laura Ahumada, Caitlin Traiser + 4 more
Neuroscience research has increasingly used decoding techniques, in which multivariate statistical methods identify patterns in neural data that allow the classification of experimental conditions or participant groups. Typically, the features used for decoding are spatial in nature, including voxel patterns and…
Alexandra Sneddon, Nikolay Shirokikh, Eduardo Eyras
Algorithms developed for basecalling Nanopore signals have primarily focused on DNA to date and utilise the raw signal as the only input. However, it is known that messenger RNA (mRNA), which dominates Nanopore direct RNA (dRNA) sequencing libraries, contains specific nucleotide patterns that are implicitly encoded in…
Mingkang Li, Ruixue Wang, Guihua Wan, Yuqi Yang + 1 more
Calcium imaging has gained extensive application in neural decoding tasks because of its high precision in observing cortical neural activity. Nevertheless, the immense data volume and complexity of automated signal extraction algorithms in calcium imaging result in significant delays in extracting neuronal calcium…
Delaney M. Selb, Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew + 1 more
A fundamental question in neuroscience is how sensory signals are decoded from noisy cortical activity. We address this question in the olfactory system, decoding the route by which odorants arrive into the nasal cavity: through the nostrils (orthonasal), or through the back of the throat (retronasal). We recently…
Zheng Zhang, Timothy G. Constandinou
Translational efforts on spike-signal-based implantable brain-machine interfaces (BMIs) are increasingly aiming to minimise bandwidth while maintaining decoding performance. Developing these BMIs requires advances in neuroscience and electronic technology, as well as using low-complexity spike detection algorithms and…
Jia Lu, Ryan Tsoi, Nan Luo, Yuanchi Ha + 8 more
Dynamical systems often generate distinct outputs according to different initial conditions, and one can infer the corresponding input configuration given an output. This property captures the essence of information encoding and decoding. Here, we demonstrate the use of self-organized patterns, combined with machine…
Andreas L. Gimpel, Alex Remschak, Wendelin J. Stark, Reinhard Heckel + 1 more
A wide range of codecs with vastly different error-correction approaches have been proposed and implemented for DNA data storage to date. However, while many codecs claim to provide superior performance, no studies have systematically benchmarked codec implementations to establish the current state-of-the-art in DNA…
Patrick Kunzmann
Alignment searches are fast heuristic methods to identify similar regions between two sequences. This group of algorithms is ubiquitously used in a myriad of software to find homologous sequences or to map sequence reads to genomes. Often the first step in alignment searches is k-mer decomposition: listing all…
Roland Wittler
To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σ^k^ k-mers and the interval [0, σ^k^ −1], where σ is the alphabet size. In many…