12 papers · ranked by Valyu relevance
Lior Galanti, Dennis Shasha, Kristin C. Gunsalus
Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation depends on the ability to classify sequences based on correct decoding of these combinatorial barcodes. The probability of…
Ruzbeh Mosadeghi, Daniel Foyt, Louis Sharp, Catherine Taylor + 7 more
High-throughput pooled screening has advanced functional genomics, but most existing methods rely on endpoint sequencing and are blind to dynamic, time-resolved phenotypes. We developed RainBar (Rainbow Barcodes), an optical barcoding system that supports pooled live-cell imaging with single-cell resolution. RainBar…
Lior Galanti, Dennis Shasha, Kristin C. Gunsalus
Output from high throughput sequencing instruments often exceeds what is necessary to assay a single sample. To better utilize this capacity, multiple samples are independently tagged with a unique “barcode” sequence and are then pooled, or “multiplexed”, and sequenced together. Classifying, or “demultiplexing”, the…
Axel Andersson, Ferran Diego, Fred A. Hamprecht, Carolina Wählby
In Situ Transcriptomics (IST) is a set of image-based transcriptomics approaches that enables localisation of gene expression directly in tissue samples. IST techniques produce multiplexed image series in which fluorescent spots are either present or absent across imaging rounds and colour channels. A spot’s presence…
Jenkin Tsui, Naila Adam, Woongcheol Choi, Luna Y. Liu + 10 more
Imaging-based spatial transcriptomics technologies have opened new avenues for studying cellular organization and gene expression within intact tissues. However, the accuracy of downstream analyses depends critically on the decoding step that reconstructs barcodes from fluorescence patterns and maps them to gene…
John A. Hawkins, Stephen K. Jones, Ilya J. Finkelstein, William H. Press
Many large-scale high-throughput experiments use DNA barcodes—short DNA sequences prepended to DNA libraries—for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or…
Enes Senel, Nikolaus Rajewsky, Nikos Karaiskos
Advancing technologies that quantify gene expression in space are transforming contemporary biology research. A class of spatial transcriptomics methods uses barcoded bead arrays that are optically decoded via microscopy and are later matched to sequenced data from the respective libraries. To obtain a detailed…
Jenkin Tsui, Naila Adam, Woongcheol Choi, Luna Liu + 10 more
Imaging based spatial transcriptomics technologies such as MERFISH have opened new avenues for studying cellular organization and gene expression within intact tissues. However, the accuracy of downstream analyses depends critically on the decoding step that reconstructs barcodes from fluorescence patterns and maps…
Jonathan A. White, Chuqi Lu, Lincoln Ombelets, Long Cai
Difficulty in resolving spatially overlapping barcodes is a major bottleneck for imaging-based spatial genomics methods. Here, we present an approach for untangling overlapping barcodes by using strong encoding and global optimization to reduce spurious solutions resulting from recombinations of barcodes. We…
Riko Corwin Uphoff, Steffen Schüler, Ivo Grosse, Matthias Müller-Hannemann
DNA barcodes, which are short DNA strings, are regularly used as tags in pooled sequencing experiments to enable the identification of reads originating from the same sample. A crucial task in the subsequent analysis of pooled sequences is barcode calling, where one must identify the corresponding barcode for each…
William H. Press
Predefined sets of short DNA sequences are commonly used as barcodes to identify individual biomolecules in pooled populations. Such use requires either sufficiently small DNA error rates, or else an error-correction methodology. Most existing DNA error-correcting codes (ECCs) correct only one or two errors per barcode…
Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer + 11 more
Tissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays to date have lacked global transcriptome information, throughput or single-cell resolution.…