Flow Cytometry Publications - D. rerio (zebrafish)

Adaptive Optics in an Oblique Plane Microscope

McFadden et al.
March 22, 2024
bioRxiv 2024.03.21.586191; doi:

Automated in vivo drug screen in zebrafish identifies synapse-stabilising drugs with relevance to spinal muscular atrophy

Oprisoreanu et al.
April 26, 2021
Dis Model Mech (2021) 14 (4): dmm047761.

Assessment of Autism Zebrafish Mutant Models Using a High-Throughput Larval Phenotyping Platform

Colón-Rodríguez A, et al.
November 23, 2020
Front. Cell Dev. Biol. 8:586296.; doi: 10.3389/fcell.2020.586296

Morphometric analysis of developing zebrafish embryos allow predicting teratogenicity modes of action in higher vertebrates

Jarque et al.
August 19, 2020
Reproductive Toxicology 96 (2020) 337-348;

The identification of dual protective agents against cisplatin-induced oto-and nephrotoxicity using the zebrafish model

Wertman JN, Melong N, Stoyek MR, et al.
July 28, 2020
[published online ahead of print, 2020 Jul 28]. Elife. 2020;9:e56235. doi:10.7554/eLife.56235

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/ Cas9-based approach

von der Heyde et al.
July 16, 2020
Sci Rep 10, 11831 (2020).

TCF12 haploinsufficiency causes autosomal dominant Kallmann syndrome and reveals network-level interactions between causal loci

Davis et al.
July 03, 2020
Human Molecular Genetics, , ddaa120,

Integrative discovery of treatments for high-risk neuroblastoma

Almstedt et al.
January 03, 2020
Nat Commun. 2020 Jan 3;11(1):71. doi: 10.1038/s41467-019-13817-8.

The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension

Morikawa et al.
November 12, 2019
Science Signaling 12 Nov 2019: Vol. 12, Issue 607, eaay4430 DOI: 10.1126/scisignal.aay4430

Comparison of Zebrafish Larvae and hiPSC Cardiomyocytes for Predicting Drug-Induced Cardiotoxicity in Humans

Sylvia Dyballa et al.
October 01, 2019
Toxicological Sciences, Volume 171, Issue 2, October 2019, Pages 283–295,

TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish

Gudmundsson et al.
September 01, 2019
Sci Rep. 2019; 9: 10730. Published online 2019 Jul 24. doi: 10.1038/s41598-019-46632-8

Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis

Bandaru et al.
June 11, 2019
bioRxiv 502674; doi:

Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features

Ansar et al.
May 09, 2019

An automated screening method for detecting compounds with goitrogenic activity using transgenic zebrafish embryos’

Jarque et al.
August 29, 2018
PLOS ONE | August 29, 2018

An automated high-resolution in vivo screen in zebrafish to identify chemical regulators of myelination

Early et al.
July 06, 2018
DOI: 10.7554/eLife.35136 DOI: 10.7554/eLife.35136

Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging

Guo et al.
April 26, 2017; Received 9 Nov 2016; revised 31 Jan 2017; accepted 31 Jan 2017; published 26 Apr 2017

A truncating mutation in CEP55 is the likely cause of MARCH, a novel syndrome affecting neuronal mitosis.

Frosk et al.
March 06, 2017
J Med Genet. 2017 Mar 6. pii: jmedgenet-2016-104296. doi: 10.1136/jmedgenet-2016-104296. [Epub ahead of print]

SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome

Shaw et al.
January 09, 2017
Nature Genetics (2017) doi:10.1038/ng.3743

De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder

Kury et al.
January 03, 2017

ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates

David T White, Arife Unal Eroglu, Guohua Wang, Liyun Zhang, Sumitra Sengupta, Ding Ding, Surendra K Rajpurohit, Steven L Walker, Hongkai Ji, Jiang Qian & Jeff S Mumm
November 10, 2016
Nature Protocols 11, 2432–2453 (2016) doi:10.1038/nprot.2016.142

Developing systems for high-throughput screening of infectious diseases using zebrafish

Veneman, Wouter Jurjen
December 05, 2015
Department of Animal Sciences and Health, Institute of Biology, Faculty of Science, Leiden University

Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.

Mala Isrie 1,2 et al.
October 14, 2015
Am J Hum Genet. 2015 Dec 3;97(6):790-800. doi: 10.1016/j.ajhg.2015.10.014.

1Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium;  2Laboratory for Genetics of Cognition, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium

First quantitative high-throughput screen in zebrafish identifies novel pathways for increasing pancreatic ß-cell mass

Wang et al.
July 28, 2015
eLife. 2015; 4: e08261. Published online 2015 Jul 28. doi: 10.7554/eLife.08261

Semi-automated detection of goitrogenic compounds using transgenic zebrafish embryos and the VAST BioImager platform

SETAC Europe 25th Annual Meeting
Sergio Jarque¹, Eva Fetter², Marek Pípal¹, Marie Smutná¹, Ludek Blaha¹, Stefan Scholz².
May 03, 2015

1RECETOX, Masaryk University, Faculty of Science, Kamenice 753/5, 625 00, Brno

2Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318 Leipzig, Germany

Establishment and optimization of a high throughput setup to study Staphylococcus epidermidis and Mycobacterium marinum infection as a model for drug discovery.

Veneman WJ¹, Marín-Juez R², de Sonneville J³, Ordas A4, Jong-Raadsen S², Meijer AH4, Spaink HP5.
June 26, 2014

1Institute of Biology, Leiden University; 2ZF-screens BV. 3Life Science Methods BV. 4Institute of Biology, Leiden University. 5Institute of Biology, Leiden University

Robotic injection of zebrafish embryos for high-throughput screening in disease models

Herman P. Spainka, Chao Cuib, Malgorzata I. Wiwegera, b, Hans J. Jansenb, Wouter J. Venemana, Rubén Marín-Juezb, Jan de Sonnevillec, Anita Ordasa, Vincenzo Torracaa, Wietske van der Enta, William P. Leendersd, Annemarie H. Meijer,a, B. Ewa Snaar-Jagalskaa, Ron P. Dirksb,
August 15, 2013
Volume 62, Issue 3, 15 August 2013, Methods 62: 246–254

a Department of Molecular Cell Biology, Institute of Biology, Leiden University, The Netherlands, b ZF-screens B.V., Leiden, The Netherlands, c Life Science Methods B.V., Leiden, The Netherlands, d Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery

Wouter J Veneman, Oliver W Stockhammer, Leonie de Boer, Sebastian A Zaat, Annemarie H Meijer and Herman P Spaink
April 15, 2013
BMC Genomics 2013, 14:255 doi:10.1186/1471-2164-14-255

High-throughput hyperdimensional vertebrate phenotyping

Carlos Pardo-Martin, Amin Allalou, Jaime Medina, Peter M. Eimon, Carolina Wählby Mehmet Fatih Yanik
February 12, 2013
Nature Communications 4, Article number:1467, doi:10.1038/ncomms2475

Presenting VAST BioImager™: A new modular, expandable platform to automate the orientation of 2-7 day old zebrafish larvae for imaging

The Nordic Countries Zebrafish Meeting on the Zebrafish as a model for Development and Disease
Union Biometrica, Geel, Belgium, Union Biometrica, Holliston, MA, USA Yanik lab, MIT, Boston, MA, USA
November 21, 2012

Development and Validation of an Automated High-Throughput System for Zebrafish In Vivo Screenings

Ainhoa Letamendia¹, Celia Quevedo¹, Izaskun Ibarbia¹, Juan M. Virto¹, Olaia Holgado¹, Maria Diez¹, Juan Carlos Izpisua Belmonte²,³, Carles Callol-Massot¹
May 15, 2012
PLoS ONE 7(5): e36690. doi:10.1371/journal.pone.0036690

1Biobide S.L., San Sebastian, Guipuzcoa, Spain, 2Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America, 3Center of Regenerative Medicine in Barcelona, Barcelona, Spain

Fully automated cellular-resolution vertebrate screening platform with parallel animal processing

Chang TY, Pardo-Martin C, Allalou A, Wählby C, Yanik MF.
February 01, 2012
Lab Chip. 2012 Feb 21;12(4):711-6. doi: 10.1039/c1lc20849g. Epub 2011 Dec 8.

A High-Throughput Screen for Tuberculosis Progression

Ralph Carvalho¹,³* Jan de Sonneville,² Oliver W. Stockhammer,³ Nigel D. L. Savage,4 Wouter J. Veneman,³ Tom H. M. Ottenhoff,4 Ron P. Dirks¹ Annemarie H. Meijer,³ and Herman P. Spaink ³
February 16, 2011
PLoS One. 2011; 6(2): e16779.

1ZF-screens B.V., Leiden, The Netherlands, 2Institute of Chemistry, Leiden University, Leiden, The Netherlands, 3Institute of Biology, Leiden University, Leiden, The Netherlands,4Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands

Zebrafish high throughput screening using robotic injection technology

The zebrafish embryo model in toxicology and teratology: Karlsruhe, Germany 2nd-3rd September 2010
Herman Spaink¹, Ron Dirks², Jan de Sonneville¹, Ralph Carvalho², Oliver Stockhammer¹,², Ewa Snaar-Jagalska¹, Annemarie Meijer¹
September 02, 2010

1Leiden University, Leiden The Netherlands; 2ZF-screens B.V. Leiden, The Netherlands

High-throughput in vivo vertebrate screening.

Pardo-Martin C, Chang TY, Koo BK, Gilleland CL, Wasserman SC, Yanik MF.
August 01, 2010
Nat Methods. 2010 Aug;7(8):634-6. doi: 10.1038/nmeth.1481. Epub 2010 Jul 18.

Zebrafish High-Throughput Screening of Innate Immune Responses.

Zebrafish Disease Modeling III, June 21-24, 2010 Dana-Farber Cancer Institute, Boston, MA
Herman Spaink¹, Ron Dirks², Jan de Sonneville¹, Ralph Carvalho², Oliver Stockhammer¹,², Ewa Snaar-Jagalska¹, Annemarie Meijer¹
June 21, 2010

1Leiden University, Leiden The Netherlands; 2ZF-screens B.V. Leiden, The Netherlands

Zebrafish are an excellent model for studying the mechanisms of the innate immune defense against pathogens. A high throughput approach is described for a study of the innate immunity in response to bacterial pathogens. The COPAS flow cytometer provided the data analysis in a quick, unbiased and high throughput manner.

A High-Throughput Assay To Measure Whole Body Metabolic Rate Using Zebrafish Larvae.

2009 Lab Automation, January 25-28, Palm Springs, CA
Khadijah Makky1, Petar Duvnjak1, Kallal Pramanik2, Ramani Ramchandran2, and Alan N. Mayer1
January 25, 2009

Department of Pediatrics, Gastroenterology1 and Developmental Biology Sections2, Medical College of Wisconsin and Children’s Research Institute, Milwaukee, WI 53226

Whole animal acid secretion can be used as readout for energy metabolism, thus enabling high-throughput chemical and genetic screens for regulators of metabolic rate in a vertebrate. The COPAS sorter was critical for automation.

A Whole-Animal Microplate Assay for Metabolic Rate Using Zebrafish

Makky K, Duvnjak P, Pramanik K, Ramchandran R, Mayer AN
November 18, 2008
Journal of Biomolecular Screening, Vol. 13, No. 10, 960-967 (2008)
DOI: 10.1177/1087057108326080

Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA.

To study genetics and drugs that impact metabolic rates, whole-animal acid secretion was used as an indicator for energy metabolism.  Because of rapid kinetics, COPAS was used for large-scale screening of zebrafish.

Multiparametric analysis of neuromast hair cells in intact early larvae using a large particle sorter.

2005 West Coast Zebrafish Meeting, September 9 – 10
Bo Wang, Julia Thompson and Rock Pulak
September 09, 2005

Union Biometrica Inc., 84 October Hill Rd, Holliston, MA 01746 USA

Drug Discovery - Automated Drug Screening Using Zebrafish: COPAS XL Allows for Increased Throughput

September 01, 2002
Genetic Engineering News Volume 22, Number 15, September 1, 2002, pp. 32, 35.