Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139 by Daniela Ceccarelli, Daniela Ceccarelli, Geneviève Garriss, Seon Y. Choi, Seon Y. Choi, Nur A. Hasan, Nur A. Hasan, Ramunas Stepanauskas, Mihai Pop, Anwar Huq, Anwar Huq, Rita R. Colwell, Rita R. Colwell, Rita R. Colwell, Rita R. Colwell

“…Plasmids were revealed by employing single-cell genomics and their genome content suggests self-mobilization and, for pSDH-2, a toxin-antitoxin (TA) system for plasmid stabilization was identified. …”
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Single-Cell RNA Sequencing With Combined Use of Bulk RNA Sequencing to Reveal Cell Heterogeneity and Molecular Changes at Acute Stage of Ischemic Stroke in Mouse Cortex Penumbra Ar... by Kang Guo, Jianing Luo, Dayun Feng, Lin Wu, Xin Wang, Li Xia, Kai Tao, Xun Wu, Wenxing Cui, Yixuan He, Bing Wang, Zhenwei Zhao, Zhiguo Zhang

“…In addition to classical gene markers, single-cell genomics demonstrates unique information on subclusters of several cell types and metabolism changes in an ischemic stroke. …”
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Whole-blood ribonucleic acid sequencing analysis in methemoglobinemia: a case report by Chikai Mitsuhara, Yuki Togami, Tomoya Hirose, Shunichiro Nakao, Hiroshi Ito, Hisatake Matsumoto, Hiroshi Ogura, Daisuke Okuzaki, Jun Oda

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Decoding Genetics of Congenital Heart Disease Using Patient-Derived Induced Pluripotent Stem Cells (iPSCs) by Hui Lin, Hui Lin, Hui Lin, Kim L. McBride, Kim L. McBride, Kim L. McBride, Kim L. McBride, Vidu Garg, Vidu Garg, Vidu Garg, Vidu Garg, Ming-Tao Zhao, Ming-Tao Zhao, Ming-Tao Zhao

“…In this review, we discuss the recent progress in genetics of CHD deciphered by large-scale genome sequencing and explore how genome-edited patient iPSCs are poised to decode the genetic etiologies of CHD by coupling with single-cell genomics and organoid technologies.…”
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RBPJ Deficiency Sensitizes Pancreatic Acinar Cells to KRAS-Mediated Pancreatic Intraepithelial Neoplasia InitiationSummary by Leiling Pan, Medhanie A. Mulaw, Johann Gout, Min Guo, Hina Zarrin, Peggy Schwarz, Bernd Baumann, Thomas Seufferlein, Martin Wagner, Franz Oswald

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Single Circulating-Tumor-Cell-Targeted Sequencing to Identify Somatic Variants in Liquid Biopsies in Non-Small-Cell Lung Cancer Patients by Mouadh Barbirou, Amanda Miller, Yariswamy Manjunath, Arturo B. Ramirez, Nolan G. Ericson, Kevin F. Staveley-O’Carroll, Jonathan B. Mitchem, Wesley C. Warren, Aadel A. Chaudhuri, Yi Huang, Guangfu Li, Peter J. Tonellato, Jussuf T. Kaifi

“…Single CTC-targeted NGS detects heterogeneous and shared mutational signatures within and between NSCLC patients. CTC single-cell genomics have potential for integration in NSCLC precision oncology.…”
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CD8 T cell-mediated depletion of HBV surface-antigen-expressing, bilineal-differentiated liver carcinoma cells generates highly aggressive escape variants by Na Qiu, Akshaya Srikanth, Medhanie Mulaw, Umesh Tharehalli, Shanthiya Selvachandran, Martin Wagner, Thomas Seufferlein, Katja Stifter, André Lechel, Reinhold Schirmbeck

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The Nereid on the rise: Platynereis as a model system by B. Duygu Özpolat, Nadine Randel, Elizabeth A. Williams, Luis Alberto Bezares-Calderón, Gabriele Andreatta, Guillaume Balavoine, Paola Y. Bertucci, David E. K. Ferrier, Maria Cristina Gambi, Eve Gazave, Mette Handberg-Thorsager, Jörg Hardege, Cameron Hird, Yu-Wen Hsieh, Jerome Hui, Kevin Nzumbi Mutemi, Stephan Q. Schneider, Oleg Simakov, Hernando M. Vergara, Michel Vervoort, Gáspár Jékely, Kristin Tessmar-Raible, Florian Raible, Detlev Arendt

“…Platynereis is used as a model for genetics, regeneration, reproduction biology, development, evolution, chronobiology, neurobiology, ecology, ecotoxicology, and most recently also for connectomics and single-cell genomics. Research on the Nereid started with studies on eye development and spiralian embryogenesis in the nineteenth and early twentieth centuries. …”
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TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration by Michael Karl Melzer, Silvia Schirge, Johann Gout, Frank Arnold, Dharini Srinivasan, Ingo Burtscher, Chantal Allgöwer, Medhanie Mulaw, Friedemann Zengerling, Cagatay Günes, Heiko Lickert, Vincent M. Christoffels, Stefan Liebau, Martin Wagner, Thomas Seufferlein, Christian Bolenz, Anne M. Moon, Lukas Perkhofer, Alexander Kleger

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Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments by Jordan T. Bird, Eric D. Tague, Laura Zinke, Jenna M. Schmidt, Andrew D. Steen, Brandi Reese, Ian P. G. Marshall, Gordon Webster, Andrew Weightman, Hector F. Castro, Shawn R. Campagna, Karen G. Lloyd

“…We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured Atribacteria, Aminicenantes, Actinobacteria group OPB41, Aerophobetes, Chloroflexi, Deltaproteobacteria, Desulfatiglans, Bathyarchaeota, and Euryarchaeota marine group II lineages. …”
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A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers by Martin-Gayo, Enrique, Cole, Michael B., Ouyang, Zhengyu, Cronin, Jacqueline, Lichterfeld, Mathias, Walker, Bruce D., Yosef, Nir, Yu, Xu G., Kolb, Kellie Elizabeth, Kazer, Samuel Weisgurt, Ordovas-Montanes, Jose Manuel, Shalek, Alexander K

“…Keywords: HIV-1; dendritic cell; single-cell; RNA-seq; single-cell genomics; elite controller; adjuvant; reproducibility; differential expression…”
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Tissue specific imprinting on innate lymphoid cells during homeostasis and disease process revealed by integrative inference of single-cell transcriptomics by Peng Song, Peng Song, Ke Cao, Yonghuan Mao, Yonghuan Mao, Shichao Ai, Feng Sun, Qiongyuan Hu, Song Liu, Meng Wang, Xiaofeng Lu, Wenxian Guan, Xiaofei Shen, Xiaofei Shen

“…IntroductionInnate lymphoid cells (ILCs) are key components of the immune system, yet the similarity and distinction of the properties across tissues under homeostasis, inflammation and tumor process remain elusive.MethodsHere we performed integrative inference of ILCs to reveal their transcriptional profiles and heterogeneity from single-cell genomics. We collected a large number of ILCs from human six different tissues which can represent unique immune niches (circulation, lymphoid tissue, normal and inflamed mucosa, tumor microenvironment), to systematically address the transcriptional imprinting.ResultsILCs are profoundly imprinted by their organ of residence, and tissue-specific distinctions are apparent under pathological conditions. …”
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Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil by L. V. Alteio, F. Schulz, R. Seshadri, N. Varghese, W. Rodriguez-Reillo, E. Ryan, D. Goudeau, S. A. Eichorst, R. R. Malmstrom, R. M. Bowers, L. A. Katz, J. L. Blanchard, T. Woyke

“…To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. …”
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Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR by Maria-Cecilia Chiriac, Paul-Adrian Bulzu, Adrian-Stefan Andrei, Yusuke Okazaki, Shin-ichi Nakano, Markus Haber, Vinicius Silva Kavagutti, Paul Layoun, Rohit Ghai, Michaela M. Salcher

“…Abstract Background The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). …”
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Glioblastoma cell fate is differentially regulated by the microenvironments of the tumor bulk and infiltrative margin by Claudia Garcia-Diaz, Anni Pöysti, Elisabetta Mereu, Melanie P. Clements, Lucy J. Brooks, Felipe Galvez-Cancino, Simon P. Castillo, Wenhao Tang, Gordon Beattie, Lilas Courtot, Sara Ruiz, Federico Roncaroli, Yinyin Yuan, Samuel Marguerat, Sergio A. Quezada, Holger Heyn, Simona Parrinello

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Carboxypeptidase E is a prognostic biomarker co-expressed with osteoblastic genes in osteosarcoma by Dafu Chen, Ben Wan, Yuning Cheng, Yuwen Luo, Xueshan Bai, Jianxun Guo, Guangping Li, Tao Jin, Jingjun Nie, Weifeng Liu, Renxian Wang

“…Additionally, we explored the specific expression of CPE in OS tissues by reanalyzing single-cell genomics. Interestingly, CPE was found to be co-expressed with osteoblast lineage cell clusters that expressed RUNX2, SP7, SPP1, and IBSP marker genes in OS. …”
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Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3 by Fang Ye, Shuang Zhang, Yuting Fu, Lei Yang, Guodong Zhang, Yijun Wu, Jun Pan, Haide Chen, Xinru Wang, Lifeng Ma, Haofu Niu, Mengmeng Jiang, Tingyue Zhang, Danmei Jia, Jingjing Wang, Yongcheng Wang, Xiaoping Han, Guoji Guo

“…Abstract Single cell chromatin accessibility profiling and transcriptome sequencing are the most widely used technologies for single-cell genomics. Here, we present Microwell-seq3, a high-throughput and facile platform for high-sensitivity single-nucleus chromatin accessibility or full-length transcriptome profiling. …”
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BCL11B Drives Human Mammary Stem Cell Self-Renewal In Vitro by Inhibiting Basal Differentiation by Daniel H. Miller, Dexter X. Jin, Ethan S. Sokol, Janel R. Cabrera, Daphne A. Superville, Rebecca A. Gorelov, Charlotte Kuperwasser, Piyush B. Gupta

“…Keywords: human mammary gland biology, mammary epithelial stem cells, BCL11B, epigenetics, single-cell genomics, epithelial differentiation, three-dimensional cell culture…”
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Continental scientific drilling and microbiology: (extremely) low biomass in bedrock of central Sweden by G. Westmeijer, C. Escudero, C. Escudero, C. Bergin, S. Turner, M. Ståhle, M. Mehrshad, P. Leroy, M. Buck, P. López-Hernández, P. López-Hernández, J. Kallmeyer, R. Amils, S. Bertilsson, M. Dopson

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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq by Tirosh, I., Izar, B., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., Fallahi-Sichani, M., Dutton-Regester, K., Lin, J.-R., Cohen, O., Shah, P., Lu, D., Villani, A.-C., Andreev, A. Y., Van Allen, E. M., Bertagnolli, M., Sorger, P. K., Sullivan, R. J., Flaherty, K. T., Frederick, D. T., Jane-Valbuena, J., Rozenblatt-Rosen, O., Prakadan, Sanjay, Wadsworth, Marc Havens, Genshaft, Alex S., Hughes, Travis K., Ziegler, Carly, Kazer, Samuel Weisgurt, Gaillard de Saint Germain, Alethe, Kolb, Kellie Elizabeth, Johannessen, Cory M., Yoon, Clifford H., Shalek, Alexander K, Regev, Aviv, Garraway, Levi A.

“…Overall, we begin to unravel the cellular ecosystem of tumors and how single-cell genomics offers insights with implications for both targeted and immune therapies.…”
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