20 papers · ranked by Valyu relevance
Dragomirka Jovic, Xue Liang, Hua Zeng, Lin Lin + 2 more
'Yonglun Luo'] Title: Abstract Single-cell RNA sequencing (scRNA-seq) technology has become the state-of-the-art approach for unravelling the heterogeneity and complexity of RNA transcripts within individual cells, as well as revealing the composition of different cell types and functions within highly organized…
Wen-min Zhou, Yan-yan Yan, Qiao-ru Guo, Hong Ji + 7 more
'Tian-tian Xu' 'Bolat Makabel' 'Christian Pilarsky' 'Gen He' 'Xi-yong Yu' 'Jian-ye Zhang'] The inherent heterogeneity of individual cells in cell populations plays significant roles in disease development and progression, which is critical for disease diagnosis and treatment. Substantial evidences show that the…
Nafiseh Erfanian, A. Ali Heydari, Pablo Iañez, Afshin Derakhshani + 5 more
Traditional bulk sequencing methods are limited to measuring the average signal in a group of cells, potentially masking heterogeneity, and rare populations. The single-cell resolution, however, enhances our understanding of complex biological systems and diseases, such as cancer, the immune system, and chronic…
Amy L Bowes, Maxime Tarabichi, Nischalan Pillay, Peter Van Loo
Intratumour heterogeneity (ITH) and tumour evolution are well-documented phenomena in human cancers. While the advent of next-generation sequencing technologies has facilitated the large-scale capture of genomic data, the field of single-cell genomics is nascent but rapidly advancing and generating many new insights…
Binle Tian, Qi Li
As one of the most lethal cancers, primary liver cancer (PLC) has high tumor heterogeneity, including the heterogeneity between cancer cells. Traditional methods which have been used to identify tumor heterogeneity for a long time are based on large mixed cell samples, and the research results usually show average…
Siyuan Chen, Weibo Jiang, Yanhui Du, Manshi Yang + 3 more
'Huan Li' 'Mengying Cui'] Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and…
Koen Theunis, Sebastiaan Vanuytven, Florian Rambow, Daniel Brown + 9 more
Single-cell multi-omics methods are enabling the study of cell state diversity, which is largely determined by the interplay of the genome, epigenome, and transcriptome. Here, we describe Gtag&T-seq, a genome-and-transcriptome sequencing (G&T-seq) protocol of the same single cells that omits whole-genome amplification…
Susan M. Grimes, Heon Seok Kim, Sharmili Roy, Anuja Sathe + 7 more
In this proof-of-concept study, we developed a single cell method that identifies somatic alterations found in coding regions of mRNAs and integrates these mutation genotypes with their matching cell transcriptomes. We used nanopore adaptive sampling on single cell cDNA libraries, generated long read sequences from…
Vuong Tran, Efthymia Papalexi, Sarah Schroeder, Grace Kim + 13 more
Single cell RNA sequencing (scRNA-seq) has become a core tool for researchers to understand biology. As scRNA-seq has become more ubiquitous, many applications demand higher scalability and sensitivity. Split-pool combinatorial barcoding makes it possible to scale projects to hundreds of samples and millions of cells…
Shuang Ge, Shuqing Sun, Huan Xu, Qiang Cheng + 1 more
Advances and Challenges from a Data Science Perspective Authors: ['Shuang Ge' 'Shuqing Sun' 'Huan Xu' 'Qiang Cheng' 'Zhixiang Ren'] The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial…
P. Marafini, DG. Smith, AR. Lamstaes, RE. Contreras + 22 more
Existing tools for single cell genomics require complex physical frameworks for the indexing of cellular nucleic acids, including proprietary instrumentation, droplet emulsions, and laborious combinatorial indexing schemes. The complexity and cost of these tools significantly constrains the use of single cell…
VE Kennedy, R Roy, CAC Peretz, A Koh + 3 more
Recently, single-cell DNA sequencing (scDNA-seq) and multi-modal profiling with the addition of cell-surface antibodies (scDAb-seq) have provided key insights into cancer heterogeneity. Scaling these technologies across large patient cohorts, however, is cost and time prohibitive. Multiplexing, in which cells from…
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…
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…
José Camacho, Michael Armstrong, Luz García, Caridad Díaz + 1 more
'Carolina Gómez‐Llorente'] Over the past few years, technological advances have allowed for measurement of omics data at the cell level, creating a new type of data generally referred to as single-cell (sc) omics. On the other hand, the so-called spatial omics are a family of techniques that generate biological…
Jafar Isbarov, Elmir Mahammadov
analysis Authors: ['Jafar Isbarov' 'Elmir Mahammadov'] Single-cell analysis is an increasingly relevant approach in "omics" studies. In the last decade, it has been applied to various fields, including cancer biology, neuroscience, and, especially, developmental biology. This rise in popularity has been accompanied…
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.…
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…
Xiaoting Xue, Helena Persson, Lei Ye
Accurate and rapid detection of nucleic acid sequences is of utmost importance in various fields, including disease monitoring, clinical treatment, gene analysis and drug discovery. In this study, we developed a "turn-on" fluorescence biosensor that enables simple and highly efficient detection of nucleic acid…
Amal Homer, Andrea Knoll, Uschi Gruber, Oliver Seitz
Fluorogenic hybridization probes allow the detection and localization of specific mRNA molecules in living cells without the need for genetic engineering. However, with the fluorescence properties of currently available oligonucleotide probes, detection in live cells is difficult when the mRNA target is expressed at…