Development and Application of High-Throughput Single Cell Lipid Profiling: A Study of SNCA-A53T Human Dopamine Neurons by Stuart G. Snowden, Hugo J.R. Fernandes, Josh Kent, Stefanie Foskolou, Peri Tate, Sarah F. Field, Emmanouil Metzakopian, Albert Koulman

“…Summary: Advances in single cell genomics and transcriptomics have shown that at tissue level there is complex cellular heterogeneity. …”
Get full text

CD90 is not constitutively expressed in functional innate lymphoid cells by Jan-Hendrik Schroeder, Gordon Beattie, Gordon Beattie, Jonathan W. Lo, Jonathan W. Lo, Tomasz Zabinski, Nick Powell, Joana F. Neves, Richard G. Jenner, Graham M. Lord, Graham M. Lord

Get full text

Omics for deciphering oral microecology by Yongwang Lin, Xiaoyue Liang, Zhengyi Li, Tao Gong, Biao Ren, Yuqing Li, Xian Peng

“…New long-read platforms improve genome assembly from complex samples. Single-cell genomics provides insights into uncultured taxa. …”
Get full text

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes by Jia-Ren Lin, Benjamin Izar, Shu Wang, Clarence Yapp, Shaolin Mei, Parin M Shah, Sandro Santagata, Peter K Sorger

“…The simplicity and adaptability of t-CyCIF makes it an effective method for pre-clinical and clinical research and a natural complement to single-cell genomics.…”
Get full text

Shank3 related muscular hypotonia is accompanied by increased intracellular calcium concentrations and ion channel dysregulation in striated muscle tissue by Berra Yildiz, Berra Yildiz, Lisa Schiedt, Lisa Schiedt, Medhanie Mulaw, Jürgen Bockmann, Sarah Jesse, Anne-Kathrin Lutz, Tobias M. Boeckers, Tobias M. Boeckers

Get full text

Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms by Erik A. Burlingame, Jennifer Eng, Guillaume Thibault, Koei Chin, Joe W. Gray, Young Hwan Chang

“…Many of the methods used in MTI analysis are crossovers from other domains like flow cytometry and single-cell genomics, do not scale well, and might be statistically unfit for atlas-level MTI data, constituting a crucial bottleneck in the search for the next generation of clinically relevant biomarkers. …”
Get full text

Tailoring Cardiac Synthetic Transcriptional Modulation Towards Precision Medicine by Eric Schoger, Eric Schoger, Eric Schoger, Sara Lelek, Sara Lelek, Daniela Panáková, Daniela Panáková, Laura Cecilia Zelarayán, Laura Cecilia Zelarayán, Laura Cecilia Zelarayán

“…Thanks to a fast-developing field of single cell genomics, we are facing an unprecedented leap in information available pertaining organ biology offering a comprehensive overview. …”
Get full text

Up‐regulated LRRN2 expression as a marker for graft quality in living donor liver transplantation by Takahiro Tomiyama, Takuya Yamamoto, Shokichi Takahama, Takeo Toshima, Shinji Itoh, Noboru Harada, Mototsugu Shimokawa, Daisuke Okuzaki, Masaki Mori, Tomoharu Yoshizumi

Get full text

Single Cell Mass Cytometry of Non-Small Cell Lung Cancer Cells Reveals Complexity of In Vivo and Three-Dimensional Models over the Petri-Dish by Róbert Alföldi, József Á. Balog, Nóra Faragó, Miklós Halmai, Edit Kotogány, Patrícia Neuperger, Lajos I. Nagy, Liliána Z. Fehér, Gábor J. Szebeni, László G. Puskás

“…Single cell genomics and proteomics with the combination of innovative three-dimensional (3D) cell culture techniques can open new avenues toward the understanding of intra-tumor heterogeneity. …”
Get full text

Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi by Bing Wu, Muzammil Hussain, Weiwei Zhang, Marc Stadler, Xingzhong Liu, Meichun Xiang

“…Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. …”
Get full text

Mobile genes in the human microbiome are structured from global to individual scales by Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Wortman, J. R., Birren, B. W., Blainey, P. C., Singh, A. K., Gevers, D., Brito, Ilana Lauren, Smillie, Chris S, Alm, Eric J, Xavier, Ramnik Joseph

“…Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. …”
Get full text
Get full text
Get full text

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI by Joshua J. Hamilton, Sarahi L. Garcia, Brittany S. Brown, Ben O. Oyserman, Francisco Moya-Flores, Stefan Bertilsson, Rex R. Malmstrom, Katrina T. Forest, Katherine D. McMahon

“…ABSTRACT An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. …”
Get full text

Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis by Jelle van Creij, Ben Auxier, Jianyong An, Raúl Y. Wijfjes, Claudia Bergin, Anna Rosling, Ton Bisseling, Zhiyong Pan, Erik Limpens

Get full text

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale by Mengqi Sun, Yuanchao Zhan, David Marsan, David Páez-Espino, Lanlan Cai, Feng Chen

“…Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment. …”
Get full text

Stimulation of interferon-β responses by aberrant SARS-CoV-2 small viral RNAs acting as retinoic acid-inducible gene-I agonists by Yasuha Arai, Itaru Yamanaka, Toru Okamoto, Ayana Isobe, Naomi Nakai, Naoko Kamimura, Tatsuya Suzuki, Tomo Daidoji, Takao Ono, Takaaki Nakaya, Kazuhiko Matsumoto, Daisuke Okuzaki, Yohei Watanabe

Get full text

Clean room microbiome complexity impacts planetary protection bioburden by Ryan Hendrickson, Camilla Urbaniak, Jeremiah J. Minich, Heidi S. Aronson, Cameron Martino, Ramunas Stepanauskas, Rob Knight, Kasthuri Venkateswaran

“…The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter. …”
Get full text

Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients by Sander Tuit, Camilla Salvagno, Theodore S. Kapellos, Cheei-Sing Hau, Lea Seep, Marie Oestreich, Kathrin Klee, Karin E. de Visser, Thomas Ulas, Joachim L. Schultze

Get full text

Status of the Archaeal and Bacterial Census: an Update by Patrick D. Schloss, Rene A. Girard, Thomas Martin, Joshua Edwards, J. Cameron Thrash

“…Continued use of traditional approaches and new technologies such as single-cell genomics and short-read assembly are likely to improve our ability to sample rare OTUs if it is possible to overcome this sampling bias. …”
Get full text

Live Single-Cell Metabolomics With Matrix-Free Laser/Desorption Ionization Mass Spectrometry to Address Microalgal Physiology by Tim U. H. Baumeister, Marine Vallet, Filip Kaftan, Aleš Svatoš, Georg Pohnert, Georg Pohnert

“…While microscopy and single cell genomics can address the taxonomic inventory, the cellular metabolome has yet to be thoroughly explored to determine the physiological status of microalgae. …”
Get full text

Functional interactions between neurofibromatosis tumor suppressors underlie Schwann cell tumor de-differentiation and treatment resistance by Harish N. Vasudevan, Emily Payne, Cyrille L. Delley, S. John Liu, Kanish Mirchia, Matthew J. Sale, Sydney Lastella, Maria Sacconi Nunez, Calixto-Hope G. Lucas, Charlotte D. Eaton, Tim Casey-Clyde, Stephen T. Magill, William C. Chen, Steve E. Braunstein, Arie Perry, Line Jacques, Alyssa T. Reddy, Melike Pekmezci, Adam R. Abate, Frank McCormick, David R. Raleigh

“…Here we integrate bulk and single-cell genomics, biochemistry, and pharmacology across human samples, cell lines, and mouse allografts to identify cellular de-differentiation mechanisms driving malignant transformation and treatment resistance. …”
Get full text