4.5 Article

Promoting validation and cross-phylogenetic integration in model organism research

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Instruments & Instrumentation

A wide-field micro-computed tomography detector: micron resolution at half-centimetre scale

Maksim A. Yakovlev et al.

Summary: This article presents a unique detector system that can achieve both wide field of view and high resolution for three-dimensional imaging of complex samples. The system has sub-micron pixel resolution and is capable of imaging micron-scale structures. It offers a means to study tissue and cellular morphology changes in larger samples.

JOURNAL OF SYNCHROTRON RADIATION (2022)

Editorial Material Cell Biology

The power of Drosophila in modeling human disease mechanisms

Esther M. Verheyen

Summary: This article introduces the launch of the Drosophila as a Disease Model subject collection and highlights the importance of Drosophila research in human disease modeling and translational medicine.

DISEASE MODELS & MECHANISMS (2022)

Article Genetics & Heredity

ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research

J. Michael Harnish et al.

Summary: Next-generation sequencing is an important diagnostic tool for rare disease gene discovery. Collaboration between scientists, clinicians, and patients is crucial for resolving medical mysteries and understanding human gene function. Interaction between scientists and research funders can accelerate the translation of discoveries into therapeutic research.

HUMAN MUTATION (2022)

Review Genetics & Heredity

Advancing human disease research with fish evolutionary mutant models

Emily A. Beck et al.

Summary: EMMs provide unique avenues to study gene-by-environment interactions and mutations in noncoding regions, improving our understanding of complex diseases. Fish, as the most diverse group of vertebrates, exhibit specialized phenotypes that could be pathogenic in humans but are adaptive in their specialized habitats.

TRENDS IN GENETICS (2022)

Article Genetics & Heredity

Harmonizing model organism data in the Alliance of Genome Resources

Paul W. Sternberg

Summary: The Alliance of Genome Resources is a collaborative effort of 7 knowledgebase projects aimed at providing better service, a harmonized view of data, and a sustainable infrastructure. It offers comparative views of gene function, gene expression, and human disease relevance. The information is presented on uniform gene pages for easy summarization.

GENETICS (2022)

Article Genetics & Heredity

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Damir Baranasic et al.

Summary: Zebrafish, an important model organism for studying embryonic development and human diseases, lacks a systematic functional annotation program. The international DANIO-CODE consortium addressed this issue by creating a central repository to store and process zebrafish developmental functional genomic data. They improved existing annotations and identified over 140,000 cis-regulatory elements throughout development. They also compared regulatory elements and epigenomic landscapes between zebrafish and mouse, predicting functional relationships between them. This study extends the utility of zebrafish developmental genomics to mammals.

NATURE GENETICS (2022)

Editorial Material Genetics & Heredity

Decoding the zebrafish genome

Nathan D. Lawson

NATURE GENETICS (2022)

Article Biology

An expanded toolkit for Drosophila gene tagging using synthesized homology donor constructs for CRISPR-mediated homologous recombination

Oguz Kanca et al.

Summary: In this study, a new set of constructs was developed to replace the coding region of genes lacking suitable introns, generating knock-out/knock-in alleles that express GAL4 similarly to the targeted gene. Custom vector backbones were also developed to improve and facilitate transgenesis in fruit flies. These upgrades significantly enhance the ability to target nearly every fly gene.
Article Biotechnology & Applied Microbiology

Drug discovery and chemical probing in Drosophila

Cassandra Millet-Boureima et al.

Summary: Drosophila, with its excellent genetic conservation and small size, is an attractive model for drug testing and studying disease models. The effective drug-testing pipeline described in this study enables the identification of novel molecular insights and the development of prototype drugs at a fraction of the time and cost.

GENOME (2021)

Article Developmental Biology

Proximity-dependent labeling methods for proteomic profiling in living cells: An update

Justin A. Bosch et al.

Summary: Proteome composition of organelles and subcellular regions can be analyzed using proximity labeling-based methods coupled with mass spectrometry (MS) to understand cellular organization and protein interactome networks. These methods utilize enzymes that generate reactive radicals to covalently tag neighboring proteins, allowing for systematic analysis of spatially restricted proteomes. By fusing enzymes to specific proteins or signal peptides targeting to particular subcellular regions, spatial expression can be achieved for studying protein-protein interactions or identifying components in discrete subcellular compartments.

WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY (2021)

Review Developmental Biology

The zebrafish issue: 25 years on

Mary C. Mullins et al.

Summary: In the 1990s, labs in Germany and the US conducted the largest genetic mutagenesis screen using zebrafish; the 25th anniversary of the zebrafish issue prompted five researchers to reflect on its significance and impact.

DEVELOPMENT (2021)

Article Developmental Biology

Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster

M. Alessandra Vigano et al.

Summary: Protein interactions play a crucial role in cellular development and function, and the development of specific protein binders has created a new toolbox for direct protein manipulation. Single short tags have been shown to efficiently bind and manipulate proteins of interest in living cells, opening up new possibilities for studying dynamic cellular processes.

DEVELOPMENT (2021)

Article Developmental Biology

Postembryonic screen for mutations affecting spine development in zebra fish

Ryan S. Gray et al.

Summary: The spine provides structural support, protects the spinal cord, and allows muscle movements. Adolescent idiopathic scoliosis (AIS) is a common spine disorder in humans with unknown genetic basis. Genetic screening in zebrafish has shed light on spine development and homeostasis mechanisms.

DEVELOPMENTAL BIOLOGY (2021)

Editorial Material History & Philosophy Of Science

Medical toolkit organisms and Covid-19

Ulrich E. Stegmann

Summary: The Covid-19 pandemic has heightened interest in animals with superior antiviral defenses, and their role in biomedical research is distinct from that of disease models.

HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES (2021)

Article Multidisciplinary Sciences

Neuronal ROS-induced glial lipid droplet formation is altered by loss of Alzheimer's disease-associated genes

Matthew J. Moulton et al.

Summary: The study reveals that the increasing genetic risk factors for Alzheimer's disease have unclear contributions to the disease mechanism, but the neuron-to-glia lipid transfer pathway induced by ROS plays a key role in protecting against neurotoxicity.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Editorial Material Biology

What have we learned?

Peter Rodgers et al.

Article Genetics & Heredity

Model organisms contribute to diagnosis and discovery in the undiagnosed diseases network: current state and a future vision

Dustin Baldridge et al.

Summary: With the decrease in sequencing costs, there has been a rapid increase in genetic and genomic data, raising the challenge of determining which variants cause phenotypes and diseases. Platforms using model organisms have enabled the discovery of new gene-disease relationships and the identification of variant pathogenicity, leading to suggestions for new therapies.

ORPHANET JOURNAL OF RARE DISEASES (2021)

Review Chemistry, Medicinal

Use of Zebrafish in Drug Discovery Toxicology

Steven Cassar et al.

CHEMICAL RESEARCH IN TOXICOLOGY (2020)

Article Biochemistry & Molecular Biology

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

Kent A. Shefchek et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Physiology

Probing Pedomorphy and Prolonged Lifespan in Naked Mole-Rats and Dwarf Mice

Rochelle Buffenstein et al.

PHYSIOLOGY (2020)

Review Endocrinology & Metabolism

High Fidelity of Mouse Models Mimicking Human Genetic Skeletal Disorders

Robert Brommage et al.

FRONTIERS IN ENDOCRINOLOGY (2020)

Article Multidisciplinary Sciences

An expanded library of orthogonal split inteins enables modular multi-peptide assemblies

Filipe Pinto et al.

NATURE COMMUNICATIONS (2020)

Review Biochemical Research Methods

Caenorhabditis elegans as a model system for human diseases

Maria Markaki et al.

CURRENT OPINION IN BIOTECHNOLOGY (2020)

Review Medicine, General & Internal

State-of-the-Art Technology of Model Organisms for Current Human Medicine

Masamitsu Konno et al.

DIAGNOSTICS (2020)

Article Multidisciplinary Sciences

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Jill E. Moore et al.

NATURE (2020)

Review Cell Biology

A most formidable arsenal: genetic technologies for building a better mouse

James F. Clark et al.

GENES & DEVELOPMENT (2020)

Review Multidisciplinary Sciences

Animal models for COVID-19

Cesar Munoz-Fontela et al.

NATURE (2020)

Review Biology

From whole-mount to single-cell spatial assessment of gene expression in 3D

Lisa N. Waylen et al.

COMMUNICATIONS BIOLOGY (2020)

Review Neurosciences

The Drosophila Split Gal4 System for Neural Circuit Mapping

Haojiang Luan et al.

FRONTIERS IN NEURAL CIRCUITS (2020)

Review Biotechnology & Applied Microbiology

The genome editing revolution: review

Ahmad M. Khalil

JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY (2020)

Review Biochemistry & Molecular Biology

New models for human disease from the International Mouse Phenotyping Consortium

Pilar Cacheiro et al.

MAMMALIAN GENOME (2019)

Article Biochemistry & Molecular Biology

The fruit fly at the interface of diagnosis and pathogenic mechanisms of rare and common human diseases

Hugo J. Bellen et al.

HUMAN MOLECULAR GENETICS (2019)

Article Biochemistry & Molecular Biology

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

Elizabeth K. Ruzzo et al.

Article Cell Biology

A novel rabbit model of Duchenne muscular dystrophy generated by CRISPR/Cas9

Tingting Sui et al.

DISEASE MODELS & MECHANISMS (2018)

Review Cell Biology

Genetically engineered pigs as models for human disease

Carolin Perleberg et al.

DISEASE MODELS & MECHANISMS (2018)

Article Medicine, Research & Experimental

The US Federal Tox21 Program: A Strategic and Operational Plan for Continued Leadership

Russell S. Thomas et al.

ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION (2018)

Article Biology

A gene-specific T2A-GAL4 library for Drosophila

Pei-Tseng Lee et al.

Article Multidisciplinary Sciences

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment

Misty R. Riddle et al.

NATURE (2018)

Review Developmental Biology

Fishing forward and reverse: Advances in zebrafish phenomics

Ricardo Fuentes et al.

MECHANISMS OF DEVELOPMENT (2018)

Article Medicine, General & Internal

Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease

K. Splinter et al.

NEW ENGLAND JOURNAL OF MEDICINE (2018)

Review Toxicology

The C-elegans model in toxicity testing

Piper Reid Hunt

JOURNAL OF APPLIED TOXICOLOGY (2017)

Article Biochemical Research Methods

cGAL, a temperature-robust GAL4-UAS system for Caenorhabditis elegans

Han Wang et al.

NATURE METHODS (2017)

Article Veterinary Sciences

Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN

Yvonne M. Bradford et al.

ILAR JOURNAL (2017)

Article Multidisciplinary Sciences

Whole-brain serial-section electron microscopy in larval zebrafish

David Grant Colburn Hildebrand et al.

NATURE (2017)

Article Genetics & Heredity

Guidelines for morpholino use in zebrafish

Didier Y. R. Stainier et al.

PLOS GENETICS (2017)

Article Biochemistry & Molecular Biology

Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling

Jaeho Paek et al.

Article Multidisciplinary Sciences

Forward-genetics analysis of sleep in randomly mutagenized mice

Hiromasa Funato et al.

NATURE (2016)

Article Multidisciplinary Sciences

Comment: The FAIR Guiding Principles for scientific data management and stewardship

Mark D. Wilkinson et al.

SCIENTIFIC DATA (2016)

Article Biochemistry & Molecular Biology

Using Ambystoma mexicanum (Mexican axolotl) embryos, chemical genetics, and microarray analysis to identify signaling pathways associated with tissue regeneration

Larissa V. Ponomareva et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY (2015)

Article Genetics & Heredity

The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

Anthony A. Philippakis et al.

HUMAN MUTATION (2015)

Article Biochemistry & Molecular Biology

A Drosophila Genetic Resource of Mutants to Study Mechanisms Underlying Human Genetic Diseases

Shinya Yamamoto et al.

Article Multidisciplinary Sciences

The zebrafish reference genome sequence and its relationship to the human genome

Kerstin Howe et al.

NATURE (2013)

Review Genetics & Heredity

Genotype to phenotype: lessons from model organisms for human genetics

Ben Lehner

NATURE REVIEWS GENETICS (2013)

Editorial Material Developmental Biology

The zebrafish issue of Development

Christiane Nuesslein-Volhard

DEVELOPMENT (2012)

Article Multidisciplinary Sciences

An integrated encyclopedia of DNA elements in the human genome

Ian Dunham et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

Fluorescent fusion protein knockout mediated by anti-GFP nanobody

Emmanuel Caussinus et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

Article Multidisciplinary Sciences

Functional Assessment of Human Coding Mutations Affecting Skin Pigmentation Using Zebrafish

Zurab R. Tsetskhladze et al.

PLOS ONE (2012)

Review Cell Biology

Whole-animal imaging, gene function, and the Zebrafish Phenome Project

Keith C. Cheng et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2011)

Article Multidisciplinary Sciences

OrthoList: A Compendium of C. elegans Genes with Human Orthologs

Daniel D. Shaye et al.

PLOS ONE (2011)

Article Biochemistry & Molecular Biology

Cell Signaling by Receptor Tyrosine Kinases

Mark A. Lemmon et al.

Article Multidisciplinary Sciences

Systematic discovery of nonobvious human disease models through orthologous phenotypes

Kriston L. McGary et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

Unlocking the secrets of the genome

Susan E. Celniker et al.

NATURE (2009)

Editorial Material Multidisciplinary Sciences

Repurposing with a Difference

Mark S. Boguski et al.

SCIENCE (2009)

Article Multidisciplinary Sciences

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Erez Lieberman-Aiden et al.

SCIENCE (2009)

Article Biochemistry & Molecular Biology

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

Nicole L. Washington et al.

PLOS BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Gene discovery and annotation using LCM-454 transcriptome sequencing

Scott J. Emrich et al.

GENOME RESEARCH (2007)

Article Multidisciplinary Sciences

SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans

RL Lamason et al.

SCIENCE (2005)

Article Biochemistry & Molecular Biology

STAT5 contributes to interferon resistance of melanoma cells

C Wellbrock et al.

CURRENT BIOLOGY (2005)

Review Genetics & Heredity

The art and design of genetic screens: Mouse

BT Kile et al.

NATURE REVIEWS GENETICS (2005)

Article Genetics & Heredity

Chemical mutagenesis of the mouse genome:: an overview

JL Guénet

GENETICA (2004)

Article Multidisciplinary Sciences

Identification of 315 genes essential for early zebrafish development

A Amsterdam et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Multidisciplinary Sciences

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

T Shiraki et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Microbiology

Zebrafish-Mycobacterium marinum model for mycobacterial pathogenesis

MG Prouty et al.

FEMS MICROBIOLOGY LETTERS (2003)

Review Genetics & Heredity

The art and design of genetic screens:: Caenorhabditis elegans

EM Jorgensen et al.

NATURE REVIEWS GENETICS (2002)

Review Genetics & Heredity

The art and design of genetic screens: Drosophila melanogaster

D St Johnston

NATURE REVIEWS GENETICS (2002)

Letter Genetics & Heredity

Effective targeted gene 'knockdown' in zebrafish

A Nasevicius et al.

NATURE GENETICS (2000)