24 papers · ranked by Valyu relevance
James M. Heather, Benjamin Chain
Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA…
Henrik Stranneheim, Joakim Lundeberg
In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid technological advances have enormously expanded sequencing…
Jose Antonio Garrido-Cardenas, Federico Garcia-Maroto, Jose Antonio Alvarez-Bermejo, Francisco Manzano-Agugliaro + 1 more
'Jose Antonio Alvarez-Bermejo' 'Francisco Manzano-Agugliaro' 'María Jesús Lobo-Castañón'] The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been…
Olaitan Akintunde, Trichina Tucker, Valerie J. Carabetta
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to elucidate the exact composition and sequence of DNA molecules. Discoveries and the…
Peter B. Gahan, Heidi Schwarzenbach, Philippe Anker, Stefan Holdenrieder + 1 more
'Stefan Holdenrieder' 'Abel Bronkhorst'] We discuss the early history of the structure of DNA and its involvement in gene structure as well as its mobility in and between cells and between tissues in the form of circulating cell-free DNA (cfDNA). This is followed by a view of the present status of the studies on cfDNA…
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma + 2 more
'Jian Ma' 'Huimin Zhao' 'Olgica Milenković'] Abstract—We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random access DNA storage…
O.G. Akintunde, Trichina Tucker, Valerie J. Carabetta
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to elucidate the exact composition and sequence of DNA molecules. Discoveries and the…
Sara Goodwin, James Gurtowski, Scott Ethe-Sayers, Panchajanya Deshpande + 2 more
Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we…
Erman Ayday, Emiliano De Cristofaro, Jean‐Pierre Hubaux, Gene Tsudik
In recent years, Whole Genome Sequencing (WGS) evolved from a futuristic-sounding research project to an increasingly affordable technology for determining complete genome sequences of complex organisms, including humans. This prompts a wide range of revolutionary applications, as WGS promises to improve modern…
John M. Urban, Jacob Bliss, Charles E. Lawrence, Susan A. Gerbi
Oxford Nanopore Technologies’ nanopore sequencing device, the MinION, holds the promise of sequencing ultra-long DNA fragments >100kb. An obstacle to realizing this promise is delivering ultra-long DNA molecules to the nanopores. We present our progress in developing cost-effective ways to overcome this obstacle and…
Richard Marin, Carlos Baldo
In this study, we explore how quantum pathfinding algorithm called Gaussian Amplitude Amplification (GAA) can be used to solve the DNA sequencing problem. To do this, sequencing by hybridization was assumed wherein short fragments of the nucleic acids called oligonucleotides of length l were gathered and were then…
Steven Y. Ko, Lauren M. Sassoubre, Jarosław Żola
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA sequencing outside of laboratory, leading to faster and more accessible DNA-based…
Yaniv Erlich
Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. This goal of the sequencing revolution has been successfully completed. Looking forward, the next goal of the revolution can be ushered in by the advent of sequencing sensors miniaturized sequencing devices…
Md Vasimuddin, Sanchit Misra, Srinivas Aluru
Rapid advances in next-generation sequencing technologies are improving the throughput and cost of sequencing at a rate significantly faster than the Moore’s law. This necessitates equivalent rate of acceleration of NGS secondary analysis that assembles reads into full genomes and identifies variants between genomes.…
Peter Vegh, Sophie Donovan, Susan Rosser, Giovanni Stracquadanio + 1 more
Biofoundries are automated high-throughput facilities specialising in the design, construction and testing of engineered/synthetic DNA constructs (plasmids), often from genetic parts. A critical step of this process is assessing the fidelity of the assembled DNA construct to the desired design. Current methods utilised…
Can Firtina
My very first questions in life were met with my parents' patient and loving answers, which sparked a curiosity leading to many more—some of which shaped this thesis. With every question that followed, I have been fortunate to have a life partner who shares in my wonder and journey with her love and patience. This…
Authors not listed
Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…
Xiaoshu Ma, Yusha Wang, Ruikai Jia, Hua Ye
The Single Molecule Real Time (SMRT) system developed by Pacific Biosciences applies the principle of synthesis while sequencing and uses the SMRT chip as the sequencing carrier. The high starting amount and good integrity of DNA required by PacBio library construction has always been a headache. Generally, the total…
Yipeng Yin, Reed Arneson, Yinan Yuan, Shiyue Fang
The longest oligos that can be chemically synthesized using known methods are typically considered to be 200-mers. Here, we report direct synthesis of an 800-mer green fluorescent protein (GFP) gene and a 1,728-mer Φ29 DNA polymerase gene on an automated synthesizer. Key innovations that enabled the breakthrough…
Authors not listed
The COVID-19 pandemic underscored the global need for rapid, sensitive, and multiplexed diagnostic assays for viral detection. RT-qPCR remains the standard for SARS-CoV-2 RNA detection, while antigen-based protein assays provide faster, though less sensitive, alternatives. Here, we present a novel diagnostic platform…
Xiaoting Xue, Helena Persson, Lei Ye
Accurate and rapid detection of nucleic acid sequences is of utmost importance in various fields, including disease monitoring, clinical treatment, gene analysis and drug discovery. In this study, we developed a "turn-on" fluorescence biosensor that enables simple and highly efficient detection of nucleic acid…
Authors not listed
Synthetic cells emulate fundamental biological behaviors, such as growth, metabolism, and evolution, under non-equilibrium conditions, but have lacked genotype-driven selection, which is essential for Darwinian evolution. Here, we introduce short DNA sequences as genotypes into fuel-dependent, peptide-RNA-based…
HANIYEH ABDOLLAHZADEH, Tonya Peeples, Mohammad Shahcheraghi
DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This…
Jürgen Behr, Timm Michel, Maya Giridhar, Santra Santhosh + 11 more
Large- to ultra-large-scale synthesis of nucleic acids is becoming an increasingly important tool for understanding and manipulating biological systems, as well as for developing new technologies based on engineered biological materials, including DNA-based nanofabrication, aptamers and writing digital data at the…