Single-Cell Omics
Dear Prof CERASALE MORTEO,
Our
Special Issue on Single-Cell 'Omics, guest-edited by Sarah Teichmann of the Sanger Institute and Sten Linnarsson of the Karolinska Institutet, is now launched.
Advances in single-cell approaches are now enabling us to study differences between cell types and subpopulations, at the level of the genome, transcriptome and epigenome. Single-cell technologies are being used to study diverse areas of biology and disease, such as development, microbial population composition, and cancer evolution.
We highlight these advances with cutting-edge research, review and comment articles. Look out for more special issue papers coming soon.
Table Of Contents
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Single-Cell Omics
Guest Editors: Sarah Teichmann and Sten Linnarsson
Advances in single-cell approaches are now enabling us to study differences between cell types and subpopulations, at the level of the genome, transcriptome and epigenome. Single-cell technologies are being used to study diverse areas of biology and disease, such as development, microbial population composition, and cancer evolution.
Genome Biology highlights the emergence of this field with a special issue focused on single-cell methods and their applications.
METHOD
High-throughput single-cell technologies have great potential to discover new cell types; however, it remains challenging to detect rare cell types that are distinct from a large population. We present a novel...
Lan Jiang, Huidong Chen, Luca Pinello and Guo-Cheng Yuan
Genome Biology 2016 17:144
Published on: 1 July 2016
OPEN LETTER
Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories t...
Raúl Catena, Alaz Özcan, Andrea Jacobs, Stephane Chevrier and Bernd Bodenmiller
Genome Biology 2016 17:142
Published on: 29 June 2016
RESEARCH
Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accel...
Bjorn Bakker, Aaron Taudt, Mirjam E. Belderbos, David Porubsky, Diana C. J. Spierings, Tristan V. de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S. J. M. de Bont, Anke van den Berg, Victor Guryev, Peter M. Lansdorp, Maria Colomé-Tatché and Floris Foijer
Genome Biology 2016 17:115
Published on: 31 May 2016
RESEARCH
Alzheimer’s disease (AD) is a neurodegenerative disease of the brain and the most common form of dementia in the elderly. Aneuploidy, a state in which cells have an abnormal number of chromosomes, has been pro...
Hilda van den Bos, Diana C. J. Spierings, Aaron Taudt, Bjorn Bakker, David Porubský, Ester Falconer, Carolina Novoa, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Victor Guryev, Wilfred F. A. den Dunnen, Floris Foijer, Maria Colomé-Tatché, Hendrikus W. G. M. Boddeke and Peter M. Lansdorp
Genome Biology 2016 17:116
Published on: 31 May 2016
The
Erratum to this article has been published in
Genome Biology 2016
17:143
RESEARCH HIGHLIGHT
Computational methods have been developed to reconstruct evolutionary lineages from tumors using single-cell genomic data. The resulting tumor trees have important applications in cancer research and clinical ...
Alexander Davis and Nicholas E. Navin
Genome Biology 2016 17:113
Published on: 26 May 2016
METHOD
Current approaches to single-cell transcriptomic analysis are computationally intensive and require assay-specific modeling, which limits their scope and generality. We propose a novel method that compares and...
Vasilis Ntranos, Govinda M. Kamath, Jesse M. Zhang, Lior Pachter and David N. Tse
Genome Biology 2016 17:112
Published on: 26 May 2016
METHOD
Single cell experiments provide an unprecedented opportunity to reconstruct a sequence of changes in a biological process from individual “snapshots” of cells. However, nonlinear gene expression changes, genes...
Joshua D. Welch, Alexander J. Hartemink and Jan F. Prins
Genome Biology 2016 17:106
Published on: 23 May 2016
RESEARCH
Differentiation of lymphocytes is frequently accompanied by cell cycle changes, interplay that is of central importance for immunity but is still incompletely understood. Here, we interrogate and quantitativel...
Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew N. J. McKenzie, Ruddy Montandon, Oliver Billker…
Genome Biology 2016 17:103
Published on: 12 May 2016
The
Erratum to this article has been published in
Genome Biology 2016
17:133
EDITORIAL
Sten Linnarsson and Sarah A. Teichmann
Genome Biology 2016 17:97
Published on: 10 May 2016
RESEARCH
Co-expression networks have been a useful tool for functional genomics, providing important clues about the cellular and biochemical mechanisms that are active in normal and disease processes. However, co-expr...
Megan Crow, Anirban Paul, Sara Ballouz, Z. Josh Huang and Jesse Gillis
Genome Biology 2016 17:101
Published on: 6 May 2016
METHOD
Understanding the mutational heterogeneity within tumors is a keystone for the development of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to identify the evolutionary hist...
Katharina Jahn, Jack Kuipers and Niko Beerenwinkel
Genome Biology 2016 17:86
Published on: 5 May 2016
METHOD
Single-cell transcriptome and single-cell methylome technologies have become powerful tools to study RNA and DNA methylation profiles of single cells at a genome-wide scale. A major challenge has been to under...
Youjin Hu, Kevin Huang, Qin An, Guizhen Du, Ganlu Hu, Jinfeng Xue, Xianmin Zhu, Cun-Yu Wang, Zhigang Xue and Guoping Fan
Genome Biology 2016 17:88
Published on: 5 May 2016
RESEARCH
Recent advances in single-cell techniques have provided the opportunity to finely dissect cellular heterogeneity within populations previously defined by “bulk” assays and to uncover rare cell types. In human ...
Bethan Psaila, Nikolaos Barkas, Deena Iskander, Anindita Roy, Stacie Anderson, Neil Ashley, Valentina S. Caputo, Jens Lichtenberg, Sandra Loaiza, David M. Bodine, Anastasios Karadimitris, Adam J. Mead and Irene Roberts
Genome Biology 2016 17:83
Published on: 3 May 2016
RESEARCH
Intratumoral heterogeneity hampers the success of marker-based anticancer treatment because the targeted therapy may eliminate a specific subpopulation of tumor cells while leaving others unharmed. Accordingly...
Kyu-Tae Kim, Hye Won Lee, Hae-Ock Lee, Hye Jin Song, Da Eun Jeong, Sang Shin, Hyunho Kim, Yoojin Shin, Do-Hyun Nam, Byong Chang Jeong, David G. Kirsch, Kyeung Min Joo and Woong-Yang Park
Genome Biology 2016 17:80
Published on: 29 April 2016
METHOD
Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs,...
Tamar Hashimshony, Naftalie Senderovich, Gal Avital, Agnes Klochendler, Yaron de Leeuw, Leon Anavy, Dave Gennert, Shuqiang Li, Kenneth J. Livak, Orit Rozenblatt-Rosen, Yuval Dor, Aviv Regev and Itai Yanai
Genome Biology 2016 17:77
Published on: 28 April 2016
RESEARCH
The planarian Schmidtea mediterranea is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal has hindered the study of lineage progression and h...
Alyssa M. Molinaro and Bret J. Pearson
Genome Biology 2016 17:87
Published on: 27 April 2016
METHOD
Normalization of single-cell RNA sequencing data is necessary to eliminate cell-specific biases prior to downstream analyses. However, this is not straightforward for noisy single-cell data where many counts a...
Aaron T. L. Lun, Karsten Bach and John C. Marioni
Genome Biology 2016 17:75
Published on: 27 April 2016
OPINION
Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that...
Stephen J. Clark, Heather J. Lee, Sébastien A. Smallwood, Gavin Kelsey and Wolf Reik
Genome Biology 2016 17:72
Published on: 18 April 2016
METHOD
Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods dev...
Edith M. Ross and Florian Markowetz
Genome Biology 2016 17:69
Published on: 15 April 2016
METHOD
Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarc...
Catalina A. Vallejos, Sylvia Richardson and John C. Marioni
Genome Biology 2016 17:70
Published on: 15 April 2016
REVIEW
Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequenc...
Lu Wen and Fuchou Tang
Genome Biology 2016 17:71
Published on: 15 April 2016
RESEARCH HIGHLIGHT
Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples....
Qing Ma and Howard Y. Chang
Genome Biology 2016 17:68
Published on: 14 April 2016
RESEARCH
Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and disease. LncRNAs exhibit cell type- and tissue-specific expres...
Siyuan John Liu, Tomasz J. Nowakowski, Alex A. Pollen, Jan H. Lui, Max A. Horlbeck, Frank J. Attenello, Daniel He, Jonathan S. Weissman, Arnold R. Kriegstein, Aaron A. Diaz and Daniel A. Lim
Genome Biology 2016 17:67
Published on: 14 April 2016
REVIEW
Genome-wide sequencing technologies enable investigations of the structural properties of the genome in various spatial dimensions. Here, we review computational techniques developed to model the three-dimensi...
Monika Sekelja, Jonas Paulsen and Philippe Collas
Genome Biology 2016 17:54
Published on: 7 April 2016
REVIEW
Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come com...
Rhonda Bacher and Christina Kendziorski
Genome Biology 2016 17:63
Published on: 7 April 2016
OPINION
Single-cell transcriptomics has been employed in a growing number of animal studies, but the technique has yet to be widely used in plants. Nonetheless, early studies indicate that single-cell RNA-seq protocol...
Idan Efroni and Kenneth D. Birnbaum
Genome Biology 2016 17:65
Published on: 5 April 2016
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