20 papers · ranked by Valyu relevance
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…
Yusha Wang, Xiaoshu Ma, Lei Yang, Hua Ye + 1 more
The development of Sanger sequencing and next-generation sequencing methods within the past few years have assisted investigators profile the diversity and relative abundances of heterogenous species in vector preparations. Especially Recombinant adeno-associated viruses (rAAVs), genome editing, and mRNA related…
Haicheng Li, Junhua Niu, Yalan Sheng, Yifan Liu + 1 more
DNA modifications, such as N^6^-methyladenine (6mA), play important roles in various processes in eukaryotes. Single molecule, real-time (SMRT) sequencing enables the direct detection of DNA modifications without requiring special sample preparation. However, most SMRT-based studies of 6mA rely on ensemble-level…
Arjun S. Nanda, Ke Wu, Iryna Irkliyenko, Brian Woo + 10 more
'Megan S. Ostrowski' 'Andrew S. Clugston' 'Leanne C. Sayles' 'Lingru Xu' 'Ansuman T. Satpathy' 'Hao G. Nguyen' 'E. Alejandro Sweet-Cordero' 'Hani Goodarzi' 'Sivakanthan Kasinathan' 'Vijay Ramani'] Concurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of…
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…
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…
Shiqiang Luo, Xingyuan Chen, Dingyuan Zeng, Ning Tang + 5 more
'Qingyan Zhong' 'Aiping Mao' 'Ruofan Xu' 'Tizhen Yan'] To compare single-molecule real-time technology (SMRT) and conventional genetic diagnostic technology of rare types of thalassemia mutations, and to analyze the molecular characteristics and phenotypes of rare thalassemia gene variants, we used 434 cases with…
Arjun S Nanda, Ke Wu, Sivakanthan Kasinathan, Megan S Ostrowski + 5 more
We present SMRT-Tag: a multiplexable, PCR-free approach for constructing low-input, single-molecule Pacific Biosciences (PacBio) sequencing libraries through Tn5 transposition. As proof-of-concept, we apply SMRT-Tag to resolve human genetic and epigenetic variation in gold-standard human reference samples. SMRT-Tag…
Dylan H Westfall, Wenjie Deng, Alec Pankow, Hugh Murrell + 6 more
Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing, which can require extensive optimizations to overcome. We present complete…
Nikolett Szakállas, Barbara K. Barták, Gábor Valcz, Zsófia B. Nagy + 2 more
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads…
Wentao Yang, Xue Qing Wang, Aaron M Wenger, Fan Wei + 3 more
A major challenge in epigenetics is uncovering the dynamic distribution of nucleosomes and other DNA-binding proteins, which plays a crucial role in regulating cellular functions. Established approaches such as ATAC-seq, ChIP-seq, and CUT&RUN provide valuable insights but are limited by the ensemble nature of their…
Iraad F. Bronner, Emma Dawson, Naomi Park, Olaf Piepenburg + 1 more
'Michael A. Quail'] The Darwin Tree of Life (DToL) project aims to generate high-quality reference genomes for all eukaryotic organisms in Britain and Ireland. At the time of writing, PacBio HiFi reads are generated for all samples using the Sequel IIe systems by the Wellcome Sanger Institute’s Scientific Operations…
Javier Martínez del Río, Luis Menéndez-Arias, Amnon Hizi
Retroviruses, like other RNA viruses, mutate at very high rates and exist as genetically heterogeneous populations. The error-prone activity of viral reverse transcriptase (RT) is largely responsible for the observed variability, most notably in HIV-1. In addition, RTs are widely used in biotechnology to detect RNAs…
Aeverie E. R. Heuchan, Ruban Rex Peter Durairaj, Alys N. Aston, Emma L. Randall + 6 more
Expanded repeat disorders remain without a disease modifying treatment. Some of the most important modifiers of disease severity include inherited repeat size, their somatic mosaicism, and whether they contain interruptions. Targeted sequencing approaches are becoming the gold standard on how these parameters are…
Mohammed Alser, Joël Lindegger, Can Fırtına, Nour Almadhoun + 4 more
'Haiyu Mao' 'Gagandeep Singh' 'Juan Gómez-Luna' 'Onur Mutlu'] We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently exist major…
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…
Sanket Doshi, Mihir Gohel, Manish K. Gupta
—In the current world due to the huge demand for storage, DNA-based storage solution sounds quite promising because of their longevity, low power consumption, and high capacity. However in real life storing data in the form of DNA is quite expensive, and challenging. Therefore researchers and developers develop such…
Quanjiang Ji, Hongyuan Zhang, Yifei Zhang, Wei-Xiao Wang + 4 more
New therapeutic strategies for rapid and effective treatment of tuberculosis are highly desirable, and their development can be drastically accelerated by facile genetic manipulation methods in Mycobacterium tuberculosis. CRISPR base editors allow for rapid, robust, and programmed single base substitutions and gene…
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…
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…