22 papers · ranked by Valyu relevance
Yating Pan, Wenjian Cao, Ying Mu, Qiangyuan Zhu
Single-cell RNA sequencing (scRNA-seq) technology provides a powerful tool for understanding complex biosystems at the single-cell and single-molecule level. The past decade has been a golden period for the development of single-cell sequencing, with scRNA-seq undergoing a tremendous leap in sensitivity and throughput.…
Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld + 4 more
Large-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states^1^. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencing techniques lack…
Matthias Eder, Nicholas Stroustrup
RNA-sequencing provides high-dimensional, quantitative measurements of the states of cells, tissues, organs, and whole organisms. Plate-based RNA-seq protocols allow for a wider range of experimental designs than droplet sequencing methods, but are less scalable due to the practical challenges of plate-based liquid…
Joseph W. Foley, Chunfang Zhu, Philippe Jolivet, Shirley X. Zhu + 3 more
'Peipei Lu' 'Michael J. Meaney' 'Robert B. West'] RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here, we…
Xiliang Wang, Yao He, Qiming Zhang, Xianwen Ren + 1 more
Single-cell RNA sequencing (scRNA-seq) is generally used for profiling transcriptome of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of…
Matthias Eder, Nicholas Stroustrup
RNA-sequencing provides high-dimensional, quantitative measurements of the states of cells, tissues, organs, and whole organisms. Plate-based RNA-seq protocols allow for a wider range of experimental designs than droplet sequencing methods, but are less scalable due to the practical challenges of plate-based liquid…
Michael Hagemann-Jensen, Christoph Ziegenhain, Rickard Sandberg
Current single-cell RNA sequencing (scRNA-seq) methods with high cellular throughputs sacrifice full-transcript coverage and often sensitivity. Here we describe Smart-seq3xpress, which miniaturizes and streamlines the Smart-seq3 protocol to substantially reduce reagent use and increase cellular throughput.…
Joseph W. Foley, Chunfang Zhu, Philippe Jolivet, Shirley X. Zhu + 3 more
RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed, paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here we present a new method, Smart-3SEQ, that accurately…
Christoph Ziegenhain, Swati Parekh, Beate Vieth, Martha Smets + 3 more
Single-cell mRNA sequencing (scRNA-seq) allows to profile heterogeneous cell populations, offering exciting possibilities to tackle a variety of biological and medical questions. A range of methods has been recently developed, making it necessary to systematically compare their sensitivity, accuracy, precision and…
Dejian Zhao, Deyou Zheng
Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, a NGS library preparation method called SMART, or Switching Mechanism At the 5’ end of the RNA Transcript, is introduced to prepare ChIP-seq (chromatin immunoprecipitation and deep sequencing) libraries from small…
Dejian Zhao, Deyou Zheng
Background Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcript, is introduced to prepare ChIP-seq (chromatin immunoprecipitation and deep sequencing)…
Oriya Vardi, Inbal Shamir, Elisheva Javasky, Alon Goren + 2 more
'Itamar Simon' 'Obul Reddy Bandapalli'] Avoiding biases in next generation sequencing (NGS) library preparation is crucial for obtaining reliable sequencing data. Recently, a new library preparation method has been introduced which has eliminated the need for the ligation step. This method, termed SMART (switching…
Trevor Gokey, David L. Mobley
Molecular mechanics force fields require a chemical perception model to assign parameters to molecules. A recent advancement in force fields is the use of the SMARTS substructure query language as the perception model. Although it is straightforward to write SMARTS patterns to define new force field parameters, it is…
Authors not listed
Steric molecular descriptors designed for machine learning (ML) applications are critical for connecting structure-function relationships to mechanistic insight. However, many of these descriptors are not suitable for application to com-plex systems, such as catalyst reactive site pockets. In this context, we recently…
Rob Chew, Michael J. Wenger, Caroline Kery, Jason Nance + 3 more
'Keith Richards' 'Emily Hadley' 'Peter Baumgartner'] SMART is an open source web application designed to help data scientists and research teams efficiently build labeled training data sets for supervised machine learning tasks. SMART provides users with an intuitive interface for creating labeled data sets, supports…
Matthew Brendel, Chang Su, Zilong Bai, Hao Zhang + 2 more
'Fei Wang'] Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states and phenotypes, and has helped elucidate biological processes, such…
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…
Michael Statt, Kristopher Brown, Santosh Suram, Linda Hung + 3 more
In this work, we present DBgen, a Python library that provides a framework for defining extract-transform-load (ETL) pipelines to create and populate SQL databases. DBgen is most useful when the underlying data has complex relationships, requires multi-step analysis, is large-scale, and the type of data being collected…
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…
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…
Lerong Li, Momiao Xiong
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an attractive option to characterize the global changes in transcription. RNA-seq is…
Khalid Raza, Sabahuddin Ahmad
Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. This novel approach is a newbie and has critical advantages over the traditional Capillary Electrophoresis (CE) based Sanger Sequencing. The advancement of NGS has led to numerous…