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. …”
Get full text
Get full text

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.…”
Get full text
Get full text

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.

Get full text

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. …”
Get full text
Get full text

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. …”

Experimental and bioinformatics considerations in cancer application of single cell genomics by Joanna Hui Juan Tan, Say Li Kong, Joyce A. Tai, Huay Mei Poh, Fei Yao, Yee Yen Sia, Edwin Kok Hao Lim, Angela Maria Takano, Daniel Shao-Weng Tan, Asif Javed, Axel M. Hillmer

Subjects: “…Single cell genomics…”
Get full text

Massively parallel single-cell genomics of microbiomes in rice paddies by Wataru Aoki, Masato Kogawa, Shuhei Matsuda, Keisuke Matsubara, Shintaro Hirata, Yohei Nishikawa, Yohei Nishikawa, Masahito Hosokawa, Masahito Hosokawa, Masahito Hosokawa, Masahito Hosokawa, Haruko Takeyama, Haruko Takeyama, Haruko Takeyama, Haruko Takeyama, Toru Matoh, Mitsuyoshi Ueda

Get full text

Single Cell Genomics Reveals Viruses Consumed by Marine Protists by Julia M. Brown, Jessica M. Labonté, Joseph Brown, Nicholas R. Record, Nicole J. Poulton, Michael E. Sieracki, Ramiro Logares, Ramunas Stepanauskas

Get full text

Sfaira accelerates data and model reuse in single cell genomics by David S. Fischer, Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Lukas Heumos, Sophie Tritschler, Olle Holmberg, Hananeh Aliee, Fabian J. Theis

Subjects: “…Single-cell genomics…”
Get full text

A single-cell genomics pipeline for environmental microbial eukaryotes by Doina Ciobanu, Alicia Clum, Steven Ahrendt, William B. Andreopoulos, Asaf Salamov, Sandy Chan, C. Alisha Quandt, Brian Foster, Jan P. Meier-Kolthoff, Yung Tsu Tang, Patrick Schwientek, Gerald L. Benny, Matthew E. Smith, Diane Bauer, Shweta Deshpande, Kerrie Barry, Alex Copeland, Steven W. Singer, Tanja Woyke, Igor V. Grigoriev, Timothy Y. James, Jan-Fang Cheng

“…We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. …”
Get full text

Artificial polyploidy improves bacterial single cell genome recovery. by Armand E K Dichosa, Michael S Fitzsimons, Chien-Chi Lo, Lea L Weston, Lara G Preteska, Jeremy P Snook, Xiaojing Zhang, Wei Gu, Kim McMurry, Lance D Green, Patrick S Chain, J Chris Detter, Cliff S Han

“…<h4>Background</h4>Single cell genomics (SCG) is a combination of methods whose goal is to decipher the complete genomic sequence from a single cell and has been applied mostly to organisms with smaller genomes, such as bacteria and archaea. …”
Get full text

Sampling time-dependent artifacts in single-cell genomics studies by Ramon Massoni-Badosa, Giovanni Iacono, Catia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodriguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elias Campo, Antonio Julià, José Ignacio Martín-Subero, Holger Heyn

Get full text

Single-cell genomics identifies immune response to neoadjuvant chemoradiotherapy by Uttam K. Sinha, W. Martin Kast, De-Chen Lin

Get full text

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.…”
Get full text

Single-cell genomic variation induced by mutational processes in cancer by Boyden, Edward

Get full text

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

Get full text

CSS: cluster similarity spectrum integration of single-cell genomics data by Zhisong He, Agnieska Brazovskaja, Sebastian Ebert, J. Gray Camp, Barbara Treutlein

Get full text

BarWare: efficient software tools for barcoded single-cell genomics by Elliott Swanson, Julian Reading, Lucas T. Graybuck, Peter J. Skene

“…Abstract Background Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are additional complications in the data deconvolution steps required to assign each cell to their originating samples. …”
Get full text

Laser microdissection of the alveolar duct enables single-cell genomic analysis by Robert eBennett, Alexandra eYsasi, Janeil eBelle, Willi eWagner, Moritz A. Konerding, Paul Clark Blainey, Saumyadipta ePyne, Steven J. Mentzer

Get full text