Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology

(2014) Jan Philipp Junker et al.   CELL

Deep Proteomics of the Xenopus laevis Egg using an mRNA-Derived Reference Database

(2014) Martin Wühr et al.   CURRENT BIOLOGY

High-resolution analysis of gene activity during the Xenopus mid-blastula transition

(2014) Clara Collart et al.   DEVELOPMENT

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development

(2014) Liangliang Sun et al.   Scientific Reports

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

(2013) Sarita S Paranjpe et al.   BMC GENOMICS

Principles of nucleation of H3K27 methylation during embryonic development

(2013) S. J. van Heeringen et al.   GENOME RESEARCH

RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism

(2013) Nirav M. Amin et al.   METHODS

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

(2013) Miler T. Lee et al.   NATURE

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

Single-Cell Metabolomics: Analytical and Biological Perspectives

(2013) R. Zenobi   SCIENCE

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency

(2013) George E. Gentsch et al.   Cell Reports

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

(2012) M. H. Tan et al.   GENOME RESEARCH

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility

(2011) Itai Yanai et al.   DEVELOPMENTAL CELL

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

(2011) J. Munoz et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Xenopus research: metamorphosed by genetics and genomics

(2011) Richard M. Harland et al.   TRENDS IN GENETICS

Functional Comparison of H1 Histones in Xenopus Reveals Isoform-Specific Regulation by Cdk1 and RanGTP

(2010) Benjamin S. Freedman et al.   CURRENT BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Characterization of somatic cell nuclear reprogramming by oocytes in which a linker histone is required for pluripotency gene reactivation

(2010) J. Jullien et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

Protein Dynamics in Individual Human Cells: Experiment and Theory

(2009) Ariel Aharon Cohen et al.   PLoS One

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

(2008) Oliver Keller et al.   BMC BIOINFORMATICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY