26 papers · ranked by Valyu relevance
Simon Anders, Paul Theodor Pyl, Wolfgang Huber
A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard work flows, custom scripts are needed. We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many…
Alberto Magi, Matteo Benelli, Alessia Gozzini, Francesca Girolami + 2 more
'Francesca Torricelli' 'Maria Luisa Brandi'] The emergence of next-generation sequencing (NGS) platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial…
Celia Blanco, Sam Verbanic, Burckhard Seelig, Irene A. Chen
In vitro selection using mRNA display is currently a widely used method to isolate functional peptides with desired properties. The analysis of High Throughput Sequencing (HTS) data from in vitro evolution experiments has proven to be a powerful technique but only recently has it been applied to mRNA display…
Marsel Kabilov
High-throughput sequencing is one of a number of omics technologies that generates huge amounts of data in the form of nucleotide sequences. Currently, it is primarily associated with NGS, but, in reality, the era of high-throughput sequencing began in the 90s with the upgrade of the Sanger method, which uses…
Konstantina Athanasopoulou, Michaela A. Boti, Panagiotis G. Adamopoulos, Paraskevi C. Skourou + 2 more
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms…
Meghan L. Bentz, Cristina Clines, Jasmine Padilla, Christopher Horn + 2 more
'Justin Lee' 'Mili Sheth'] PacBio Sequencing is an effective tool for achieving long read lengths to close gaps in whole genome assemblies. Limited information is available for automated, high-throughput library preparation workflows for PacBio sequencing. This paper describes two high throughput methods, one for…
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…
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg + 12 more
'Caitlin Loeffler' 'Jinyang Zhang' 'Agata Muszyńska' 'Jeremy Rotman' 'Laura Tao' 'Brunilda Balliu' 'Elizabeth Tseng' 'Eleazar Eskin' 'Fangqing Zhao' 'Pejman Mohammadi' 'Paweł P. Łabaj' 'Serghei Mangul'] Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA 90095, USA…
Xuejun He, Ningzhi Zhang, Wenye Cao, Yiqiao Xing + 3 more
Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of…
Aljuboori M. Nafea, Yuer Wang, Duanyang Wang, Ahmed M. Salama + 3 more
'Manal A. Aziz' 'Shan Xu' 'Yigang Tong'] Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry…
Darrell O. Ricke, Anna Shcherbina, Adam Michaleas, Philip Fremont-Smith
High throughput DNA sequencing technologies enable improved characterization of forensic DNA samples enabling greater insights into DNA contributor(s). Current DNA forensics techniques rely upon allele sizing of short tandem repeats by capillary electrophoresis. High throughput sequencing enables forensic sample…
Xiaoli Dong, Manuel Kleiner, Christine E. Sharp, Erin Thorson + 3 more
Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an…
Jamie J. Alnasir, Hugh P. Shanahan
Given the wide variability in the quality of NGS data submitted to public repositories, it is essential to identify methods that can perform quality control on these datasets when additional quality control data, such as mean tile data, is missing. This is particularly important because such datasets are routinely…
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.…
Yatish Turakhia, Kevin Jie Zheng, Gill Bejerano, William J. Dally
Genomics is set to transform medicine and our understanding of life in fundamental ways. But the growth in genomics data has been overwhelming - far outpacing Moore's Law. The advent of third generation sequencing technologies is providing new insights into genomic contribution to diseases with complex mutation events…
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…
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…
Torsten Pook, Adnane Nemri, Eric Gerardo Gonzalez Segovia, Henner Simianer + 1 more
High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing technologies when resources are limited. In this work, we are proposing a new…
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…
Liya Popova, Valerie J. Carabetta
The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine.…
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…
Michael Lanzillotti, Jennifer Brodbelt
Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nucleic acids up to 100…
Michael Lanzillotti, Jennifer Brodbelt
Mass spectrometry has proven to be a highly effective tool for characterization of RNA post-transcriptional modifications. For both synthetic RNAs and ones from biological sources, mass spectrometry can interrogate multiple, co-occurring covalent modifications at the nucleotide level simultaneously. To expand the…
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…
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…