25 papers · ranked by Valyu relevance
Lukas Valihrach, Peter Androvic, Mikael Kubista
Single-cell analysis has become an established method to study cell heterogeneity and for rare cell characterization. Despite the high cost and technical constraints, applications are increasing every year in all fields of biology. Following the trend, there is a tremendous development of tools for single-cell…
Slavov, Nikolai
Over the last decade, proteomic analysis of single cells by mass spectrometry transitioned from an uncertain possibility to a set of robust and rapidly advancing technologies supporting the accurate quantification of thousands of proteins. We review the major drivers of this progress, from establishing feasibility to…
Antonio Federico, Angela Serra, My Kieu Ha, Pekka Kohonen + 16 more
'Jang-Sik Choi' 'Irene Liampa' 'Penny Nymark' 'Natasha Sanabria' 'Luca Cattelani' 'Michele Fratello' 'Pia Anneli Sofia Kinaret' 'Karolina Jagiello' 'Tomasz Puzyn' 'Georgia Melagraki' 'Mary Gulumian' 'Antreas Afantitis' 'Haralambos Sarimveis' 'Tae-Hyun Yoon' 'Roland Grafström' 'Dario Greco'] Preprocessing of…
Jesse Q. Zhang, Christian A. Siltanen, Leqian Liu, Kai-Chun Chang + 2 more
Single cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through gene expression alone. Linking sequencing with optical analysis has provided insight into the molecular basis behind cellular function, but current approaches have limited…
Emma King-Smith, Simon Berritt, Louise Bernier, Xinjun Hou + 7 more
High-throughput experimentation (HTE) has the potential to improve our understanding of organic chemistry by systematically interrogating reactivity across diverse chemical spaces. Notable bottlenecks include few publicly available large-scale datasets and the need for facile interpretation of these data's hidden…
Kai Schmid, Hildegard Dohmen, Nadja Ritschel, Carmen Selignow + 5 more
High-throughput sequencing techniques have become established in routine research in the past years, not only because of the decreasing costs per sample but also because of their high-throughput and generation of high-quality data. However, these techniques also have weaknesses. Thus, a next generation sequencing (NGS)…
Jennifer Ma, Gary Tran, Alwin M. D. Wan, Edmond W. K. Young + 3 more
'Eugenia Kumacheva' 'Norman N. Iscove' 'Peter W. Zandstra'] Gene expression analysis of individual cells enables characterization of heterogeneous and rare cell populations, yet widespread implementation of existing single-cell gene analysis techniques has been hindered due to limitations in scale, ease, and cost.…
Justus T. Metternich, Sujit K. Patjoshi, Tanuja Kistwal, Sebastian Kruss
Optical sensors/probes are powerful tools to identify and image (biological) molecules. Because of their optoelectronic properties, nanomaterials are often used as building blocks. Such nanosensors are assembled from an optically sensitive nanomaterial, a (biological) recognition unit, and linker chemistry that…
Jan Winter, Marc Schwering, Oliver Pelz, Benedikt Rauscher + 3 more
Pooled CRISPR/Cas9 screens are a powerful and versatile tool for the systematic investigation of cellular processes in a variety of organisms. Such screens generate large amounts of data that present a new challenge to analyze and interpret. Here, we developed a web application to analyze, document and explore pooled…
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…
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…
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…
Harrison Specht, Nikolai Slavov
Many pressing medical challenges – such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers – have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to transcend these limitations by developing powerful…
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…
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…
Michael Lanzillotti, Jennifer Brodbelt
Broad interest in nucleic acids – both their therapeutic capabilities and understanding the nuances of their structure and resulting function – has increased in recent years. Post-transcriptional modifications in particular have become an important analysis target, as these covalent modifications to the sugars…
Matthew Lewis, Elena Chekmeneva, Stephane Camuzeaux, Caroline Sands + 11 more
Metabolomics utilising liquid chromatography mass spectrometry (LC-MS) offers biomedical researchers a powerful means of assessing and comparing human phenotypes via measurement of the metabolome in biological samples. Platforms for LC-MS-based global profiling quantify hundreds or thousands of small molecule…
Eleen Y. Shum, Janice H. Lai, Sixing Li, Haeun G. Lee + 5 more
Digital PCR (dPCR) was first conceived for single molecule quantitation. However, current dPCR systems often require DNA templates to share partitions due to limited partitioning capacities. Here, we introduce Ultra-dPCR, a next generation dPCR system where DNA counting is performed in a single-molecule regimen through…
Harikrishnan Jayamohan, Valentin Romanov, H. Li, Jiyoung Son + 3 more
'Raheel Samuel' 'John Nelson' 'Bruce K. Gale'] Advances in molecular biology are enabling rapid and efficient analyses for effective intervention in domains like biology research, infectious disease management, food safety and bio-defense. The emergence of microfluidics and nanotechnologies has enabled both new…
Emma Laks, Hans Zahn, Daniel Lai, Andrew McPherson + 41 more
Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing…
Lukas Žemaitis, Rūta Palepšienė, Simonas Juzėnas, Gediminas Alzbutas + 9 more
'Pierre-Yves Burgi' 'Thomas Heinis' 'Jérôme Charmet' 'Silvia Angeloni Suter' 'Martin Jost' 'Renaldas Raišutis' 'Friedrich Simmel' 'Ignas Galminas' 'Isabelle Chemin'] In recent years, Oxford Nanopore Technologies (ONT) has gained substantial attention across various domains of nucleic acid research, owing to its unique…
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu
Quality control (QC) and preprocessing of FASTQ files are necessary steps to provide clean data for downstream analysis. Traditionally, for each operation, such as QC, adapter trimming and quality filtering, a different tool is used. These tools are usually not fast enough since they are mostly developed in high-level…
Kristin G. Beaumont, Wissam Hamou, Nenad Bozinovic, Thomas R. Silvers + 15 more
Genetic and functional complexity of bulk tumor has become evident through rapid advances in sequencing technologies. As a unique integrated approach to characterizing tumor heterogeneity, we demonstrate the multifaceted capabilities of a novel nanofluidic platform to enable single-cell phenotypic and genetic profiling…
Jacob Beal
Flow cytometry is a powerful quantitative assay supporting highthroughput collection of single-cell data with a high dynamic range. For flow cytometry to yield reproducible data with a quantitative relationship to the underlying biology, however, requires that 1) appropriate process controls are collected along with…
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…