Unravelling single cell genomics : micro and nanotools / by Bontoux, Nathalie, Dauphinot, Luce, Potier, Marie-Claude, Royal Society of Chemistry (Great Britain)

Revealing the vectors of cellular identity with single-cell genomics by Wagner, Allon, Regev, Aviv, Yosef, Nir

“…Single-cell genomics has now made it possible to create a comprehensive atlas of human cells. …”
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Scaling single-cell genomics from phenomenology to mechanism by Tanay, Amos, Regev, Aviv

“…Initial single-cell genomic studies provided a remarkably rich phenomenology of heterogeneous cellular states, but transforming observational studies into models of dynamics and causal mechanisms in tissues poses fresh challenges and requires stronger integration of theoretical, computational and experimental frameworks.…”
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Resolving medulloblastoma cellular architecture by single-cell genomics by Hovestadt, Volker, Smith, Kyle S., Bihannic, Laure, Filbin, Mariella G., Shaw, McKenzie L., Baumgartner, Alicia, DeWitt, John C., Groves, Andrew, Mayr, Lisa, Weisman, Hannah R., Richman, Alyssa R., Shore, Marni E., Goumnerova, Liliana, Rosencrance, Celeste, Carter, Robert A., Phoenix, Timothy N., Hadley, Jennifer L., Tong, Yiai, Houston, Jim, Ashmun, Richard A., DeCuypere, Michael, Sharma, Tanvi, Flasch, Diane, Silkov, Antonina, Ligon, Keith L., Pomeroy, Scott L., Rivera, Miguel N., Rozenblatt-Rosen, Orit, Rusert, Jessica M., Wechsler-Reya, Robert J., Li, Xiao-Nan, Peyrl, Andreas, Gojo, Johannes, Kirchhofer, Dominik, Lötsch, Daniela, Czech, Thomas, Dorfer, Christian, Haberler, Christine, Geyeregger, Rene, Halfmann, Angela, Gawad, Charles, Easton, John, Pfister, Stefan M., Gajjar, Amar, Regev, Aviv, Orr, Brent A., Slavc, Irene, Robinson, Giles W., Bernstein, Bradley E., Suvà, Mario L., Northcott, Paul A.

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The future is now: single-cell genomics of bacteria and archaea by Blainey, Paul C.

“…Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. …”
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Single-cell genomics for dissection of complex malaria infections. by Nair, S, Nkhoma, S, Serre, D, Zimmerman, P, Gorena, K, Daniel, B, Nosten, F, Anderson, T, Cheeseman, I

“…We demonstrate that our single-cell genomics approach can be used to generate parasite genome sequences directly from patient blood in order to unravel the complexity of P. vivax and P. falciparum infections. …”

Application of single-cell genomics in cancer: promise and challenges. by Wills, Q, Mead, A

“…Recent advances in single-cell genomics are opening up unprecedented opportunities to transform cancer genomics. …”

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics by Pachiadaki, Maria G., Brown, Julia M., Brown, Joseph, Bezuidt, Oliver, Berube, Paul M., Biller, Steven, Poulton, Nicole J., Burkart, Michael D., La Clair, James J., Chisholm, Sallie (Penny), Stepanauskas, Ramunas

“…Randomized, scaled-up single-cell genomics of marine microorganisms reveals a high degree of uniqueness between individual cells, implying limited clonality within populations, and establishes that a large fraction of global genetic diversity can be recovered from a single sample, suggesting effective global dispersal of prokaryoplankton.…”
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Single-cell genomic variation induced by mutational processes in cancer by Boyden, Edward

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Insights into Alzheimer’s disease from single-cell genomic approaches by Murdock, Mitchell H, Tsai, Li-Huei

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Laser Microdissection of the Alveolar Duct Enables Single-Cell Genomic Analysis by Bennett, Robert D., Ysasi, Alexandra B., Belle, Janeil M., Wagner, Willi L., Konerding, Moritz A., Pyne, Saumyadipta, Mentzer, Steven J., Blainey, Paul C

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Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics by Regev, Aviv

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Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus by Kashtan, Nadav, Roggen, Sara E., Rodrigue, Sebastien, Thompson, Jessica Weidemier, Biller, Steven, Coe, Allison, Ding, Huiming, Marttinen, Pekka, Malmstrom, Rex R., Stocker, Roman, Stepanauskas, Ramunas, Chisholm, Sallie (Penny), Follows, Michael J, Roggensack, Sara

“…In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. …”
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Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics by Hughes, Travis K., Wadsworth, Marc Havens, Shalek, Alex

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Single cell genomics data analyses reveal novel biological insights by Hu, X

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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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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Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments by Berube, Paul M., Biller, Steven, Hackl, Thomas, Hogle, Shane L., Satinsky, Brandon Meyer, Becker, Jamie William, Braakman, Rogier, Collins, Sara B., Kelly, Libusha, Berta-Thompson, Jessie, Coe, Allison, Bergauer, Kristin, Bouman, Heather A., Browning, Thomas J., De Corte, Daniele, Hassler, Christel, Hulata, Yotam, Jacquot, Jeremy E., Maas, Elizabeth W., Reinthaler, Thomas, Sintes, Eva, Yokokawa, Taichi, Lindell, Debbie, Stepanauskas, Ramunas, Chisholm, Sallie W

“…Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. …”
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Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

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