Hidden diversity in honey bee gut symbionts detected by single-cell genomics. by Philipp Engel, Ramunas Stepanauskas, Nancy A Moran

“…Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. …”
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Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics by Helen E. Dukes, Kara A. Tinker, Elizabeth A. Ottesen

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Robust temporal map of human in vitro myelopoiesis using single-cell genomics by Clara Alsinet, Maria Nascimento Primo, Valentina Lorenzi, Erica Bello, Iva Kelava, Carla P. Jones, Roser Vilarrasa-Blasi, Carmen Sancho-Serra, Andrew J. Knights, Jong-Eun Park, Beata S. Wyspianska, Gosia Trynka, David F. Tough, Andrew Bassett, Daniel J. Gaffney, Damiana Alvarez-Errico, Roser Vento-Tormo

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Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity by Gaublomme, Jellert T., Yosef, Nir, Lee, Youjin, Gertner, Rona S., Yang, Li V., Wu, Chuan, Pandolfi, Pier Paolo, Mak, Tak, Satija, Rahul, Kuchroo, Vijay K., Park, Hongkun, Regev, Aviv, Shalek, Alexander K

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Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface by Landry, Zachary C., Vergin, Kevin, Mannenbach, Christopher, Block, Stephen, Yang, Qiao, Carlson, Craig, Giovannoni, Stephen, Blainey, Paul C

“…Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. …”
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Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics by Koji Arikawa, Keigo Ide, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Taruho Endoh, Ayumi Matsuhashi, Haruko Takeyama, Masahito Hosokawa

Subjects: “…Single-cell genomics…”
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Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing by Muammar eMansor, Trinity L Hamilton, Matthew S Fantle, Jennifer eMacalady

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CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential by Youtao Lu, Jaehee Lee, Jifen Li, Srinivasa Rao Allu, Jinhui Wang, HyunBum Kim, Kevin L. Bullaughey, Stephen A. Fisher, C. Erik Nordgren, Jean G. Rosario, Stewart A. Anderson, Alexandra V. Ulyanova, Steven Brem, H. Isaac Chen, John A. Wolf, M. Sean Grady, Sergei A. Vinogradov, Junhyong Kim, James Eberwine

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Topological Data Analysis in Time Series: Temporal Filtration and Application to Single-Cell Genomics by Baihan Lin

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A unified model of human hemoglobin switching through single-cell genome editing by Yong Shen, Jeffrey M. Verboon, Yuannyu Zhang, Nan Liu, Yoon Jung Kim, Samantha Marglous, Satish K. Nandakumar, Richard A. Voit, Claudia Fiorini, Ayesha Ejaz, Anindita Basak, Stuart H. Orkin, Jian Xu, Vijay G. Sankaran

“…Here, the authors develop a single-cell genome editing functional assay to model how effects of mutation-harbouring functional elements contribute to HbF expression.…”
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CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics by Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A. Morris

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Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics by Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z. Yeung, William M. Mauck, Peter Smibert, Rahul Satija

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Single-Cell Genomics: Enabling the Functional Elucidation of Infectious Diseases in Multi-Cell Genomes by Shweta Sahni, Partha Chattopadhyay, Kriti Khare, Rajesh Pandey

Subjects: “…Single Cell Genomics (SCG)…”
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Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae by Max E. Schön, Vasily V. Zlatogursky, Rohan P. Singh, Camille Poirier, Susanne Wilken, Varsha Mathur, Jürgen F. H. Strassert, Jarone Pinhassi, Alexandra Z. Worden, Patrick J. Keeling, Thijs J. G. Ettema, Jeremy G. Wideman, Fabien Burki

“…This study used single-cell genomics and phylogenomics to infer the evolutionary origin of the plastid-lacking phylum Picozoa, a group of marine microbial heterotrophic eukaryotes, showing that they belong to the Archaeplastida and changing our understanding of plastid evolution.…”
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Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types by Benjamin E. Mead, Jose Ordovas-Montanes, Alexandra P. Braun, Lauren E. Levy, Prerna Bhargava, Matthew J. Szucs, Dustin A. Ammendolia, Melanie A. MacMullan, Xiaolei Yin, Travis K. Hughes, Marc H. Wadsworth, Rushdy Ahmad, Seth Rakoff-Nahoum, Steven A. Carr, Robert Langer, James J. Collins, Alex K. Shalek, Jeffrey M. Karp

“…Abstract Background Single-cell genomic methods now provide unprecedented resolution for characterizing the component cell types and states of tissues such as the epithelial subsets of the gastrointestinal tract. …”
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Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics by Kiyomi Morita, Feng Wang, Katharina Jahn, Tianyuan Hu, Tomoyuki Tanaka, Yuya Sasaki, Jack Kuipers, Sanam Loghavi, Sa A. Wang, Yuanqing Yan, Ken Furudate, Jairo Matthews, Latasha Little, Curtis Gumbs, Jianhua Zhang, Xingzhi Song, Erika Thompson, Keyur P. Patel, Carlos E. Bueso-Ramos, Courtney D. DiNardo, Farhad Ravandi, Elias Jabbour, Michael Andreeff, Jorge Cortes, Kapil Bhalla, Guillermo Garcia-Manero, Hagop Kantarjian, Marina Konopleva, Daisuke Nakada, Nicholas Navin, Niko Beerenwinkel, P. Andrew Futreal, Koichi Takahashi

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Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans by Kristína Záhonová, Gordon Lax, Savar D. Sinha, Guy Leonard, Thomas A. Richards, Julius Lukeš, Jeremy G. Wideman

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Trajectory inference from single-cell genomics data with a process time model. by Meichen Fang, Gennady Gorin, Lior Pachter

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Strain-level profiling of viable microbial community by selective single-cell genome sequencing by Masahito Hosokawa, Taruho Endoh, Kazuma Kamata, Koji Arikawa, Yohei Nishikawa, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Haruko Takeyama

“…Here, we present a method for viable bacteria-targeted single-cell genome sequencing, called PMA-SAG-gel, to obtain comprehensive whole-genome sequences of surviving uncultured bacteria from microbial communities. …”
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Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types by Szucs, Matthew J, Ammendolia, Dustin A, MacMullan, Melanie A, Rakoff-Nahoum, Seth, Mead, Benjamin Elliott, Ordovas-Montanes, Jose Manuel, Braun, Alexandra Provost, Levy, Lauren, Saluja, Prerna Bhargava, Yin, Xiaolei, Hughes, Travis K., Wadsworth, Marc Havens, Ahmad, Rushdy, Carr, Steven A, Langer, Robert S, Collins, James J., Shalek, Alexander K, Karp, Jeffrey Michael

“…Background Single-cell genomic methods now provide unprecedented resolution for characterizing the component cell types and states of tissues such as the epithelial subsets of the gastrointestinal tract. …”
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