22 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…
Tobias Andermann, Maria Fernanda Torres Jiménez, Pável Matos-Maraví, Romina Batista + 7 more
'Romina Batista' 'José L. Blanco-Pastor' 'A. Lovisa S. Gustafsson' 'Logan Kistler' 'Isabel M. Liberal' 'Bengt Oxelman' 'Christine D. Bacon' 'Alexandre Antonelli'] High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating…
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…
Claudia Knief
Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the…
Georgios A Pavlopoulos, Anastasis Oulas, Ernesto Iacucci, Alejandro Sifrim + 4 more
'Alejandro Sifrim' 'Yves Moreau' 'Reinhard Schneider' 'Jan Aerts' 'Ioannis Iliopoulos'] Elucidating the content of a DNA sequence is critical to deeper understand and decode the genetic information for any biological system. As next generation sequencing (NGS) techniques have become cheaper and more advanced in…
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…
Eva C Berglund, Anna Kiialainen, Ann-Christine Syvänen
Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying…
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…
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.…
Wenxiong Zhou, Li Kang, Shuo Qiao, Haifeng Duan + 19 more
High-throughput sequencing technologies generate a vast number of DNA sequence reads simultaneously, which are subsequently analyzed using the information contained within these fragmented reads. The assessment of sequencing technology relies on information efficiency, which measures the amount of information entropy…
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…
Wout Bittremieux, Varun Ananth, William E. Fondrie, Carlo Melendez + 5 more
Protein tandem mass spectrometry data is most often interpreted by matching observed mass spectra to a protein database derived from the reference genome of the sample being analyzed. In many application domains, however, a relevant protein database is unavailable or incomplete, and in such settings de novo sequencing…
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…
Authors not listed
Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing proteins, metaproteomics offers insights on community phenotypes and the roles…
Xiaoyin Chen, Yu-Chi Sun, George M Church, Je Hyuk Lee + 1 more
Cellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out cellular barcodes tradeoff spatial resolution with throughput. Bulk sequencing achieves high throughput but sacrifices spatial resolution, whereas…
Christos Argyropoulos
component based applications using Object Orientation, PDL, Alien, FFI, Inline and OpenMP Authors: ['Christos Argyropoulos'] Component-Based Software Engineering (CBSE) is a methodology that assembles pre-existing, reusable software components into new applications, which is particularly relevant for fast moving…
Xin Yin, Zhao Song, Karin S. Dorman, Aditya Ramamoorthy
—THIS PAPER IS ELIGIBLE FOR THE STUDENT PAPER AWARD. In this work we present a flexible, probabilistic and reference-free method of error correction for high throughput DNA sequencing data. The key is to exploit the hig h coverage of sequencing data and model short sequence output s as independent realizations of a…
Alexander J. Petri, Mai Thi-Huyen Nguyen, Anjali Rajwar, Erik Benson + 1 more
Synthetic combinatorial DNA libraries are widely used to produce protein variants, optimize binders, and for high throughput studies of protein - DNA interactions. The libraries can be made by researchers or vendors and high-throughput sequencing is used for both quality control and to study the outcome of selection…
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…
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…
David A. Morrison
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the requirements for a solution. The goal of alignment is often stated to be to…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…