Printing Microbial Dark Matter: Using Single Cell Dispensing and Genomics to Investigate the Patescibacteria/Candidate Phyla Radiation by Sandra Wiegand, Hang T. Dam, Julian Riba, John Vollmers, Anne-Kristin Kaster, Anne-Kristin Kaster

“…In the recent past, cultivation-independent methods like single-cell genomics (SCG) enabled the discovery of many previously unknown microorganisms, among them the Patescibacteria/Candidate Phyla Radiation (CPR). …”
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scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics by Franziska Hildebrandt, Mubasher Mohammed, Alexis Dziedziech, Alexis Dziedziech, Amol K. Bhandage, Anna-Maria Divne, Fredrik Barrenäs, Antonio Barragan, Johan Henriksson, Johan Ankarklev, Johan Ankarklev

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Decontamination of MDA reagents for single cell whole genome amplification. by Tanja Woyke, Alexander Sczyrba, Janey Lee, Christian Rinke, Damon Tighe, Scott Clingenpeel, Rex Malmstrom, Ramunas Stepanauskas, Jan-Fang Cheng

“…Single cell genomics is a powerful and increasingly popular tool for studying the genetic make-up of uncultured microbes. …”
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The evolving definition of plant cell type by Sahand Amini, Jeffrey J. Doyle, Jeffrey J. Doyle, Marc Libault, Marc Libault

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An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells by Henning Onsbring, Alexander K. Tice, Brandon T. Barton, Matthew W. Brown, Thijs J. G. Ettema

“…Unfortunately, single-cell genomics for protists is often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. …”
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Transcriptional differences between coronavirus disease 2019 and bacterial sepsis by Hiroshi Ito, Masakazu Ishikawa, Hisatake Matsumoto, Fuminori Sugihara, Daisuke Okuzaki, Haruhiko Hirata, Hiroshi Ogura

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Mutated clones driving leukemic transformation are already detectable at the single-cell level in CD34-positive cells in the chronic phase of primary myelofibrosis by Sandra Parenti, Sebastiano Rontauroli, Chiara Carretta, Selene Mallia, Elena Genovese, Chiara Chiereghin, Clelia Peano, Lara Tavernari, Elisa Bianchi, Sebastian Fantini, Stefano Sartini, Oriana Romano, Silvio Bicciato, Enrico Tagliafico, Matteo Della Porta, Rossella Manfredini

“…Single-cell genomics allowed the reconstruction of clonal hierarchy and demonstrated that TET2 was the first mutated gene while FLT3 was the last one. …”
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scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics by Qian Li

“…Abstract Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference and accurate prediction of cellular dynamics with minimal influence from batch effects. …”
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Decision level integration of unimodal and multimodal single cell data with scTriangulate by Guangyuan Li, Baobao Song, Harinder Singh, V. B. Surya Prasath, H. Leighton Grimes, Nathan Salomonis

“…Single-cell genomics has expanded to measure diverse molecular modalities within the same cell. …”
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GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers by Anuja Sathe, Carlos Ayala, Xiangqi Bai, Susan M. Grimes, Byrne Lee, Cindy Kin, Andrew Shelton, George Poultsides, Hanlee P. Ji

“…Our experimental strategy combining single-cell genomics with preclinical models can successfully identify mechanisms of action of novel immunotherapy agents. …”
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Alveolar macrophage transcriptomic profiling in COPD shows major lipid metabolism changes by Wataru Fujii, Theodore S. Kapellos, Kevin Baßler, Kristian Händler, Lisa Holsten, Rainer Knoll, Stefanie Warnat-Herresthal, Marie Oestreich, Emily R. Hinkley, Jan Hasenauer, Carmen Pizarro, Christoph Thiele, Anna C. Aschenbrenner, Thomas Ulas, Dirk Skowasch, Joachim L. Schultze

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Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges by Ute Hentschel, Sheila Marie Pimentel-Elardo, Sebastian Proksch, Lubomir Grozdanov

“…Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge <em>Aplysina aerophoba</em>,<em> </em>which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a <em>Chloroflexi</em> sponge symbiont. …”
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Integration of single-cell multi-omics data by regression analysis on unpaired observations by Qiuyue Yuan, Zhana Duren

“…Thus, huge amounts of single-cell genomics data of unpaired observations on different cells are generated. …”
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Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism by Alan D. W. Dobson, Fergal O’Gara, David P. H. Lejon, John P. Morrissey, Stephen A. Jackson, Jonathan Kennedy, Burkhardt Flemer

“…The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.…”
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Multi-CUT&Tag to simultaneously profile multiple chromatin factors by Sneha Gopalan, Thomas G. Fazzio

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Elastic dosage compensation by X-chromosome upregulation by Antonio Lentini, Huaitao Cheng, J. C. Noble, Natali Papanicolaou, Christos Coucoravas, Nathanael Andrews, Qiaolin Deng, Martin Enge, Björn Reinius

“…Using allelic single-cell genomics, the authors characterize the dynamics of X-chromosome upregulation and inactivation along mouse embryonic and stem cell development, calling to question keys aspects of the established model of mammalian dosage compensation.…”
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scSTEM: clustering pseudotime ordered single-cell data by Qi Song, Jingtao Wang, Ziv Bar-Joseph

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Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs by Eric D. Becraft, Eric D. Becraft, Jeremy A. Dodsworth, Jeremy A. Dodsworth, Senthil K. Murugapiran, Senthil K. Murugapiran, Scott C. Thomas, J. Ingemar Ohlsson, Ramunas Stepanauskas, Brian P. Hedlund, Brian P. Hedlund, Wesley D. Swingley

“…In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. …”
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Single-cell RNA-seq analysis identifies distinct myeloid cells in a case with encephalitis temporally associated with COVID-19 vaccination by Masakazu Ishikawa, Masakazu Ishikawa, Yuki Shimada, Tatsuhiko Ozono, Hisatake Matsumoto, Hisatake Matsumoto, Hiroshi Ogura, Keigo Kihara, Hideki Mochizuki, Tatsusada Okuno, Shuhei Sakakibara, Makoto Kinoshita, Daisuke Okuzaki, Daisuke Okuzaki, Daisuke Okuzaki, Daisuke Okuzaki

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Collection of cells for single-cell RNA sequencing using high-resolution fluorescence microscopy by Hendrika A. Segeren, Kiki C. Andree, Lisa Oomens, Bart Westendorp

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