23 papers · ranked by Valyu relevance
Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Mark Helm + 2 more
Oxford Nanopore Technologies’ (ONT) sequencing platform offers an excellent opportunity to perform real-time analysis during sequencing. This feature allows for early insights into experimental data and accelerates a potential decision-making process for further analysis, which can be particularly relevant in the…
Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Anne M Busch + 5 more
In standard sequencing experiments, practical steps and data analysis are usually performed independently, with the latter initiated by bioinformatics experts once after sequencing is complete. Nowadays, new technologies such as Oxford Nanopore Technologies (ONT) offer a unique opportunity to start downstream analysis…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 10 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Maria Tsakiroglou, Anthony Evans, Munir Pirmohamed
Diagnostics require precision and predictive ability to be clinically useful. Integration of multi-omic with clinical data is crucial to our understanding of disease pathogenesis and diagnosis. However, interpretation of overwhelming amounts of information at the individual level requires sophisticated computational…
Dharmesh D. Bhuva, Joseph Cursons, Melissa J. Davis
Transcriptomic signatures are useful in defining the molecular phenotypes of cells, tissues, and patient samples. Their most successful and widespread clinical application is the stratification of breast cancer patients into molecular (PAM50) subtypes. In most cases, gene expression signatures are developed using…
Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J Gallagher + 7 more
'Iain J Gallagher' 'Andrew A. Pitsillides' 'Claude‐Henry Volmar' 'William E Kraus' 'James D. Johnson' 'Stuart M. Phillips' 'Claes Wahlestedt' 'James A. Timmons'] Title: Abstract Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug…
Daria Meyer, Winfried Göttsch, Jannes Spannenberg, Patrick Bohn + 7 more
Nucleic acid sequencing is the process of identifying the sequence of DNA or RNA, with DNA used for genomes and RNA for transcriptomes. Deciphering this information has the potential to greatly advance our understanding of genomic features and cellular functions. In comparison to other available sequencing methods…
Gal Avital, Tamar Hashimshony, Itai Yanai
New methods employ RNA-seq to study single cells within complex tissues by in situ sequencing or mRNA capture from single photoactivated cells.
Dongshan Ya, Yingmei Zhang, Qi Cui, Yanlin Jiang + 6 more
'Ning Tian' 'Wenjing Xiang' 'Xiaohui Lin' 'Qinghua Li' 'Rujia Liao'] Spatial transcriptome technology acquires gene expression profiles while retaining spatial location information, it displays the gene expression properties of cells in situ. Through the investigation of cell heterogeneity, microenvironment, function…
Ye Wang, Michael Mashock, Zhuang Tong, Xiaofeng Mu + 6 more
'Xin Zhou' 'Hong Zhang' 'Gexin Zhao' 'Bin Liu' 'Xinmin Li'] RNA sequencing (RNAseq) is one of the most commonly used techniques in life sciences, and has been widely used in cancer research, drug development, and cancer diagnosis and prognosis. Driven by various biological and technical questions, the techniques of…
Valentine Svensson, Roser Vento‐Tormo, Sarah A. Teichmann
The ability to measure the transcriptomes of single cells has only been feasible for a few years, and is becoming an extremely popular assay. While many types of analysis and questions can be answered using single cell RNA-sequencing, a central focus is the ability to survey the diversity of cell types within a sample.…
Ákos Vértes, Albert B. Arul, Péter Avar, Andrew R. Korte + 12 more
'Lida Parvin' 'Ziad J. Sahab' 'Deborah I. Bunin' 'Merrill Knapp' 'Denise Nishita' 'A.J. Poggio' 'Mark-Oliver Stehr' 'Carolyn Talcott' 'Brian M. Davis' 'Christine A. Morton' 'Christopher J. Sevinsky' 'Maria I. Zavodszky'] Akos Vertes 1 , Albert-Baskar Arul 1 , Peter Avar 1 , Andrew R. Korte 1 , Lida Parvin 1 , Ziad J.…
Minh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott, Huihui Zhang + 2 more
The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This opens immense potential to shorten the sample-to-results time and is likely to lead to enormous benefits in rapid diagnosis of bacterial infection and identification of drug resistance. However, there are very few…
Suneth Samarasinghe, Ira Deveson, Hasindu Gamaarachchi
Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is running, reducing the turnaround time of the results. We introduce realfreq, a framework for obtaining real-time base modification frequencies while a nanopore sequencer is in…
Botond Sipos, Greg Slodkowicz, Tim Massingham, Nick Goldman
In line with the importance of RNA-seq, the bioinformatics community has produced numerous data analysis tools incorporating methods to correct sample-specific biases. However, few advanced simulation tools exist to enable benchmarking of competing correction methods. We introduce the first framework to reproduce the…
A. Hutton, Jesse G. Meyer
Trajectory inference is used to order single-cell omics data along a path that reflects a continuous transition between cells. This approach is useful for studying processes like cell differentiation, where a stem cell matures into a specialized cell type, or investigating state changes in pathological conditions. In…
Yuanhua Huang, Guido Sanguinetti
Isoform quantification is an important goal of RNA-seq experiments, yet it remains problematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental designs, such as time series or dosage response experiments. Time series RNA-seq…
Katherine E. Prater, Kevin Lin
Acknowledgements: KEP would like to sincerely thank Drs. Ali Shojaie (UW Biostatistics) and Wei Sun (Fred Hutch Department of Biostatistics) for their helpful input and support on bioinformatics and single-cell analysis pipeline development. The authors would also like to thank Drs. Suman Jayadev, Jonathan R.…
Zahra AghahosseinaliShirazi, P. Rangel, Camila P. E. de Souza
via the EM Algorithm Authors: ['Zahra AghahosseinaliShirazi' 'P. Rangel' 'Camila P. E. de Souza'] Biological cells can be distinguished by their phenotype or at the molecular level, based on their genome, epigenome, and transcriptome. This paper focuses on the transcriptome, which encompasses all the RNA transcripts in…
Sanghyuk Ko
Different types of diagnostics methods were introduced to the public due to the recent global pandemic. From the real-time reverse transcript polymerase chain reaction (RT-qPCR) to antigen lateral flow assay (LFA), these tests allow relatively accurate and rapid diagnosis of the infection with SARS-CoV-2 virus. Because…
Authors not listed
The foundational Henri-Michaelis-Menten equation, derived from measurements of initial reaction rates, describes enzyme kinetics using the Michaelis-Menten constant (KM) and maximum velocity (Vmax). While traditional methods focus on initial rates, progress curve analysis, which monitors the entire reaction process…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…