Opening the genetic toolbox of niche model organisms with high throughput techniques: Novel proteins in regeneration as a case study

Orbitrap Mass Spectrometry

(2013) Roman A. Zubarev et al.   ANALYTICAL CHEMISTRY

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly

(2013) Warren R Francis et al.   BMC GENOMICS

De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration

(2013) Cheng-Han Wu et al.   BMC GENOMICS

A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens

(2013) Ilgar Abdullayev et al.   EXPERIMENTAL CELL RESEARCH

Stable Isotope Labeling in Zebrafish Allowsin VivoMonitoring of Cardiac Morphogenesis

(2013) Anne Konzer et al.   MOLECULAR & CELLULAR PROTEOMICS

Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish

(2013) Fanwei Meng et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

High-throughput sequencing for biology and medicine

(2013) W. W. Soon et al.   Molecular Systems Biology

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

TALEN-Based Gene Disruption in the Dengue Vector Aedes aegypti

(2013) Azadeh Aryan et al.   PLoS One

Comparative Transcriptional Profiling of the Axolotl Limb Identifies a Tripartite Regeneration-Specific Gene Program

(2013) Dunja Knapp et al.   PLoS One

Transcriptome Analysis of Newt Lens Regeneration Reveals Distinct Gradients in Gene Expression Patterns

(2013) Konstantinos Sousounis et al.   PLoS One

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Reconstitution of the Myocardium in Regenerating Newt Hearts is Preceded by Transient Deposition of Extracellular Matrix Components

(2013) Tanja Piatkowski et al.   STEM CELLS AND DEVELOPMENT

SILAC Proteomics of Planarians Identifies Ncoa5 as a Conserved Component of Pluripotent Stem Cells

(2013) Alexander Böser et al.   Cell Reports

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema

(2013) Ron Stewart et al.   PLoS Computational Biology

Integrative “Omics”-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses

(2013) Bork A. Berghoff et al.   PLoS Genetics

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

(2013) Pedro G Ferreira et al.   GENOME BIOLOGY

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

(2013) Christopher I Keeling et al.   GENOME BIOLOGY

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

(2013) Mario Looso et al.   GENOME BIOLOGY

Quantitative mass spectrometry in proteomics

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

(2012) Mark P Peterson et al.   BMC GENOMICS

Generation of albinoXenopus tropicalisusing zinc-finger nucleases

(2012) Keisuke Nakajima et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Spiked-in Pulsed in Vivo Labeling Identifies a New Member of the CCN Family in Regenerating Newt Hearts

(2012) Mario Looso et al.   JOURNAL OF PROTEOME RESEARCH

Conus consors Snail Venom Proteomics Proposes Functions, Pathways, and Novel Families Involved in Its Venomic System

(2012) Adrijana Leonardi et al.   JOURNAL OF PROTEOME RESEARCH

Quantification of theN-glycosylated Secretome by Super-SILAC During Breast Cancer Progression and in Human Blood Samples

(2012) Paul J. Boersema et al.   MOLECULAR & CELLULAR PROTEOMICS

Super-SILAC Allows Classification of Diffuse Large B-cell Lymphoma Subtypes by Their Protein Expression Profiles

(2012) Sally J. Deeb 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

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs)

(2012) Y. Lei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Survey of the camel urinary proteome by shotgun proteomics using a multiple database search strategy

(2012) Abdulqader A. Alhaider et al.   PROTEOMICS

Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins

(2012) Jacek R. Wiśniewski et al.   Proteomics Clinical Applications

Proteomics: Bases for protein complexity understanding

(2012) Domenico Rotilio et al.   THROMBOSIS RESEARCH

Recapitulation of developmental cardiogenesis governs the morphological and functional regeneration of adult newt hearts following injury

(2011) Nevin Witman et al.   DEVELOPMENTAL BIOLOGY

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

(2011) C. Adamidi et al.   GENOME RESEARCH

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

(2010) Thilo Borchardt et al.   BMC GENOMICS

De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

(2010) Xiao-Wei Wang et al.   BMC GENOMICS

Advanced Identification of Proteins in Uncharacterized Proteomes by Pulsedin VivoStable Isotope Labeling-based Mass Spectrometry

(2010) Mario Looso et al.   MOLECULAR & CELLULAR PROTEOMICS

The SILAC Fly Allows for Accurate Protein Quantificationin Vivo

(2010) Matthias D. Sury et al.   MOLECULAR & CELLULAR PROTEOMICS

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation

(2010) Chris Jopling et al.   NATURE

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic analysis of blastema formation in regenerating axolotl limbs

(2009) Nandini Rao et al.   BMC BIOLOGY

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

(2009) Eli Meyer et al.   BMC GENOMICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and Supports a Paraphyletic Basal Acoelomorpha

(2009) J. Paps et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transposon-mediated genome manipulation in vertebrates

(2009) Zoltán Ivics et al.   NATURE METHODS

SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function

(2008) Marcus Krüger et al.   CELL

ChIPping away at gene regulation

(2008) Charles E Massie et al.   EMBO REPORTS

Protein identification pipeline for the homology-driven proteomics

(2008) Magno Junqueira et al.   Journal of Proteomics

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Parallel confocal detection of single molecules in real time

(2008) Paul M. Lundquist et al.   OPTICS LETTERS

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris et al.   SCIENCE

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS