Application progress of single-cell sequencing technology in breast cancer research by LIU Qiang, FANG Yi, WANG Jing

“…The single-cell sequencing technology emerged in recent years has been greatly improved in terms of sensitivity, accuracy and efficiency, enabling us to analyze single-cell genome information in complex mixed cells, which has shown great performance in studying tumor heterogeneity. …”
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A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. by Seth D Axen, Onur Erbilgin, Cheryl A Kerfeld

“…In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. …”
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Going deeper: metagenome of a hadopelagic microbial community. by Emiley A Eloe, Douglas W Fadrosh, Mark Novotny, Lisa Zeigler Allen, Maria Kim, Mary-Jane Lombardo, Joyclyn Yee-Greenbaum, Shibu Yooseph, Eric E Allen, Roger Lasken, Shannon J Williamson, Douglas H Bartlett

“…As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. …”
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Discovery of microenvironment drivers of cell states, plasticity and drug response by Navia, Andrew Warren

“…The recent emergence of single-cell genomic technologies like single-cell RNA sequencing (scRNA-seq) now enable us to characterize systematically and comprehensively the roles of intrinsic versus extrinsic responses in driving disease sequalae. …”
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Regulation and heterogeneity of human mucosal-associated invariant T (MAIT) cells in blood and liver by Garner, LC

“…In this thesis, I have used bulk and single-cell genomic technologies to investigate the regulation and heterogeneity of human blood and liver MAIT cells, and to explore the transcriptional response of blood MAIT cells to TCR and cytokine stimulation. …”

Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts by Byron J. Smith, Byron J. Smith, Xiangpeng Li, Zhou Jason Shi, Zhou Jason Shi, Adam Abate, Adam Abate, Katherine S. Pollard, Katherine S. Pollard, Katherine S. Pollard

“…We further validate our strain inferences using single-cell genomic sequencing from a human stool sample. …”
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Single-Cell RNA-Sequencing Reveals Epithelial Cell Signature of Multiple Subtypes in Chemically Induced Acute Lung Injury by Chao Cao, Obulkasim Memete, Yiru Shao, Lin Zhang, Fuli Liu, Yu Dun, Daikun He, Jian Zhou, Jie Shen

“…This progenitor cell type may develop into alveolar cells, indicating its stem cell differentiation potential. We present a single-cell genome-scale transcription map that can help uncover disease-associated cytologic signatures for understanding biological changes and regeneration of lung tissues during CALI.…”
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Methods for the genetic manipulation of marine bacteria by Zahraa Zeaiter, Francesca Mapelli, Elena Crotti, Sara Borin

“…Keywords: Conjugation, Electroporation, Genetic manipulation, Genome engineering, Marine bacteria, Metagenomic library, Natural competence, Next-generation DNA sequencing, Single-cell genome analysis, Suicide vectors, Transformation…”
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Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase by Malvina Vogler, Malvina Vogler, Ram Karan, Dominik Renn, Alexandra Vancea, Marie-Theres Vielberg, Stefan W. Grötzinger, Priya DasSarma, Shiladitya DasSarma, Jörg Eppinger, Michael Groll, Magnus Rueping

“…In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. …”
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Androgen receptor expression on circulating tumor cells in metastatic breast cancer. by Takeo Fujii, James M Reuben, Lei Huo, Jose Rodrigo Espinosa Fernandez, Yun Gong, Rachel Krupa, Mahipal V Suraneni, Ryon P Graf, Jerry Lee, Stephanie Greene, Angel Rodriguez, Lyndsey Dugan, Jessica Louw, Bora Lim, Carlos H Barcenas, Angela N Marx, Debu Tripathy, Yipeng Wang, Mark Landers, Ryan Dittamore, Naoto T Ueno

“…Of these 10 patients, 3 also had ER expression in CK+ CTCs. Single cell genomic analysis of 78 CTCs from 1 of these 3 patients identified three distinct copy number patterns. …”
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Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors by Xiaoyan Ma, Daphne Ezer, Boris Adryan, Tim J. Stevens

“…Results Using published canonical Hi-C data and single-cell genome structures, we assess the spatial proximity of a genome-wide array of potential TF-TF co-localizations in human and mouse cell lines. …”
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Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea by Christos A. Christakis, Tamar Barkay, Eric S. Boyd

“…Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. …”
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SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes [version 2; peer review: 2 approved] by Vincent Hervé, Nachida Tadrent, Franck Dedeine

“…Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. …”
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Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer by Pascale Kündig, Charlotte Giesen, Hartland Jackson, Bernd Bodenmiller, Bärbel Papassotirolopus, Sandra Nicole Freiberger, Catharine Aquino, Lennart Opitz, Zsuzsanna Varga

“…Clonal evolution in accumulated single cell genomic alterations is a further possible explanation in carcinogenesis. …”
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Genetic and molecular basis of myeloid neoplasms at single cell resolution by Rodriguez Meira, A

“…To do so, it is essential to characterize clonal diversity in MPN at the genetic and molecular level. Single cell genomic techniques are ideally placed to resolve such heterogeneity. …”

Genetic Characterization of Cancer of Unknown Primary Using Liquid Biopsy Approaches by Noemi Laprovitera, Noemi Laprovitera, Irene Salamon, Irene Salamon, Francesco Gelsomino, Francesco Gelsomino, Elisa Porcellini, Mattia Riefolo, Mattia Riefolo, Marianna Garonzi, Paola Tononi, Sabrina Valente, Silvia Sabbioni, Francesca Fontana, Nicolò Manaresi, Antonia D’Errico, Antonia D’Errico, Maria A. Pantaleo, Maria A. Pantaleo, Andrea Ardizzoni, Andrea Ardizzoni, Manuela Ferracin

“…CTCs were isolated with CELLSEARCH® and DEPArrayTM NxT and Parsortix systems, immunophenotypically characterized and used for single-cell genomic characterization with Ampli1TM kits. …”
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