16 papers · ranked by Valyu relevance
Linda C. Meiser, Bichlien H. Nguyen, Yuan-Jyue Chen, Jeff Nivala + 3 more
'Karin Strauss' 'Luis Ceze' 'Robert N. Grass'] Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold…
Francesca Granito, Andreas L. Gimpel, Wendelin J. Stark, Reinhard Heckel + 1 more
DNA represents a promising solution for high-density and long-term data storage. In this study, we explore the scalability and robustness of DNA-of-Things (DoT) technology by embedding digital data encoded in silica-encapsulated DNA in newspaper ink. In honor of the 75th anniversary of the German Basic Law the…
Oluwafemi A. Sarumi, Maximilian Hahn, Dominik Heider
The availability of high throughput sequencing tools coupled with the declining costs in the production of DNA sequences has led to the generation of enormous amounts of omics data curated in several databases such as NCBI and EMBL. Identification of similar DNA sequences from these databases is one of the fundamental…
Zhihan Zhou, Weimin Wu, Harrison Ho, Jiayi Wang + 4 more
'Ramana V Davuluri' 'Zhong Wang' 'Han Liu'] We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA and RNA) is vital yet challenging…
Zhihan Zhou, Weimin Wu, Harrison Ho, Jiayi Wang + 4 more
In this section, we introduce the dataset we used for DNABERT-S training and evaluation. Each training sample of DNABERT-S is a pair of nonoverlapping DNA sequences extracted from the same species. We focus on microbe species since the genetic diversity within this group provides a rich substrate for examining the…
Penghao Wang, Ziniu Mu, Lijun Sun, Shuqing Si + 1 more
DNA is a natural storage medium with the advantages of high storage density and long service life compared with traditional media. DNA storage can meet the current storage requirements for massive data. Owing to the limitations of the DNA storage technology, the data need to be converted into short DNA sequences for…
Alex El-Shaikh, Marius Welzel, Dominik Heider, Bernhard Seeger
Due to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA…
Cecilia Wetzl, Diana Soukarie, Jokin Yeregui Elosua, Ibon Santiago
Memory in Water-Resistant Electrospun Polymer Fibers for Nondestructive Data Retrieval Authors: ['Cecilia Wetzl' 'Diana Soukarie' 'Jokin Yeregui Elosua' 'Ibon Santiago'] DNA is a digital memory storage medium with advantageous properties, including longevity and high information density. Embedding information-bearing…
Pavan Holur, K C Enevoldsen, Shreyas Rajesh, Lajoyce Mboning + 5 more
While our first-generation reference-free DNA embedding (RDE) models provide alignment performance that almost matches the performance of traditional aligners (refined over decades), there is room for considerable improvement. First, our RDE models have been trained using samples that span only around 2% of the human…
Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Arooj Zaib, Andreas Dengel
'Andreas Dengel'] Deoxyribonucleic acid (DNA) serves as fundamental genetic blueprint that governs development, functioning, growth, and reproduction of all living organisms. DNA can be altered through germline and somatic mutations. Germline mutations underlie hereditary conditions, while somatic mutations can be…
Golam Md Mortuza, Jorge Guerrero, Shoshanna Llewellyn, Michael D. Tobiason + 4 more
'Michael D. Tobiason' 'George D. Dickinson' 'William L. Hughes' 'Reza Zadegan' 'Tim Andersen'] Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both increased the capacity and decreased the cost of storing information in de…
Xiaoluo Huang, Junting Cui, Wei Qiang, Jianwen Ye + 4 more
'Xinying Xie' 'Yuanzhen Li' 'Junbiao Dai'] Title: Abstract Deoxyribonucleic acid (DNA) has been suggested as a very promising medium for data storage in recent years. Although numerous studies have advocated for DNA data storage, its practical application remains obscure and there is a lack of a user-oriented platform.…
Osamu Maruyama, Yinuo Li, Hiroki Narita, Hidehiro Toh + 2 more
'Wan Kin Au Yeung' 'Hiroyuki Sasaki'] Background Epigenetic modifications established in mammalian gametes are largely reprogrammed during early development, however, are partly inherited by the embryo to support its development. In this study, we examine CpG island (CGI) sequences to predict whether a mouse blastocyst…
Minsang Yu, Doyeon Lim, Jungwoo Kim, Youngjun Song
DNA can be used to store digital data, and synthetic short-sequence DNA pools are developed to store high quantities of digital data. However, synthetic DNA data cannot be actively processed in DNA pools. An active DNA data editing process is developed using splint ligation in a droplet-controlled fluidics (DCF)…
Doyeon Lim, Taeseok Kang, Wonjin Lee, Zeeshan Haider + 5 more
DNA offers the promise of high-density, long-term storage, yet current systems face limitations due to polymerase chain reaction-based manual workflows that are inherently slow, error prone, and difficult to scale for practical applications. Here, we present an electric field-guided DNA pool elongation system that…
Zakieh Tayyebi, Allison R. Pine, Christina S. Leslie
Standard scATAC sequencing (scATAC-seq) analysis pipelines represent cells as sparse numeric vectors relative to an atlas of peaks or genomic tiles and consequently ignore genomic sequence information at accessible loci. Here we present CellSpace, an efficient and scalable sequence-informed embedding algorithm for…