Applications & Publications

Technical Notes (1)
Publications (54)

Publications

High-content screening (HCS) workflows for FAIR image data management with OMERO

Massei et al.
May 09, 2025
Sci Rep 15, 16236 (2025). https://doi.org/10.1038/s41598-025-00720-0

View Abstract

RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS

Dharmadhikari et al.
February 17, 2025
Nat Commun. 2025; 16: 1703. Published online 2025 Feb 17. doi 10.1038/s41467-025-56876-w

View Abstract

Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning

Mazzaferro et al.
February 13, 2025
Sci Rep. 2025; 15: 5408. Published online 2025 Feb 13. doi: 10.1038/s41598-025-89823-2

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m6A-mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly

Nishizaki et al.
January 30, 2025
https://doi.org/10.1002/aur.3314

View Abstract

Aurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context

Gries et al.
November 08, 2024
Neoplasia. 2025 Jan; 59: 101078. Published online 2024 Nov 8. doi: 10.1016/j.neo.2024.101078

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Gene expansions contributing to human brain evolution

Soto et al.
September 26, 2024
Version 1. bioRxiv. Preprint. 2024 Sep 26. doi: 10.1101/2024.09.26.615256

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An explainable map of human gastruloid morphospace reveals gastrulation failure modes and predicts teratogens

Rufo et al.
September 23, 2024
Version 1. bioRxiv. Preprint. 2024 Sep 23. doi: 10.1101/2024.09.20.614192

View Abstract

Zebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development

Uribe-Salazar et al.
September 11, 2024
Version 2. bioRxiv. Preprint. 2024 Sep 11 [revised 2024 Sep 27]. doi: 10.1101/2024.09.11.612570

View Abstract

Identification of Environmental Compounds That May Trigger Early Female Puberty by Activating Human GnRHR and KISS1R

Yang et al.
September 10, 2024
Endocrinology. 2024 Oct; 165(10): bqae103. Published online 2024 Sep 10. doi: 10.1210/endocr/bqae103

View Abstract

The zebrafish embryo as a model for chemically-induced steatosis: A case study with three pesticides

Heusinkveld et al.
August 14, 2024
Toxicology,Volume 508,2024,153927,ISSN 0300-483X,https://doi.org/10.1016/j.tox.2024.153927.(https://www.sciencedirect.com/science/article/pii/S0300483X24002087)

An atypical form of 60S ribosomal subunit in Diamond-Blackfan anemia linked to RPL17 variants

Fellmann at al.
August 01, 2024
JCI Insight. 2024 Sep 10; 9(17): e172475. Published online 2024 Aug 1. doi: 10.1172/jci.insight.172475

View Abstract

Pathogenic variants in TMEM184B cause a neurodevelopmental syndrome via alteration of metabolic signaling

Chapman et al.
July 01, 2024
Version 1. medRxiv. Preprint. 2024 Jul 1. doi: 10.1101/2024.06.27.24309417

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GC/HRMS Analysis of E-Liquids Complements In Vivo Modeling Methods and can Help to Predict Toxicity

Walker-Frankin et al.
June 05, 2024
ACS Omega. 2024 Jun 18; 9(24): 26641–26650. Published online 2024 Jun 5. doi: 10.1021/acsomega.4c03416

View Abstract

ZebraReg-a novel platform for discovering regulators of cardiac regeneration using zebrafish

Apolínová et al.
May 10, 2024
Front Cell Dev Biol. 2024; 12: 1384423. Published online 2024 May 10. doi: 10.3389/fcell.2024.1384423

View Abstract

Burn pit-related smoke causes developmental and behavioral toxicity in zebrafish: Influence of material type and emissions chemistry

Smoot et al.
April 14, 2024
Heliyon. 2024 Apr 30; 10(8): e29675. Published online 2024 Apr 14. doi: 10.1016/j.heliyon.2024.e29675

View Abstract

Adaptive Optics in an Oblique Plane Microscope

McFadden et al.
March 22, 2024
Version 1. bioRxiv. Preprint. 2024 Mar 22. doi: 10.1101/2024.03.21.586191Published in: Biomed Opt Express. 2024 Aug 1; 15(8): 4498–4512.

View Abstract

Adaptive Optics in an Oblique Plane Microscope

McFadden et al.
March 22, 2024
bioRxiv 2024.03.21.586191; doi: https://doi.org/10.1101/2024.03.21.586191

Single-Cell Analysis of Rohon-Beard Neurons Implicates Fgf Signaling in Axon Maintenance and Cell Survival

Tuttle et al.
February 29, 2024
J Neurosci. 2024 Apr 17; 44(16): e1600232024. Prepublished online 2024 Feb 29. doi: 10.1523/JNEUROSCI.1600-23.2024

View Abstract

A retroviral link to vertebrate myelination through retrotransposon-RNA-mediated control of myelin gene expression

Ghosh et al.
February 15, 2024
Cell, Volume 187, Issue 4p814-830.e23,February 15, 2024

View Abstract

Macrophage mediated mesoscale brain mechanical homeostasis mechanically imaged via optical tweezers and Brillouin microscopy in vivo

So et al.
December 27, 2023
Version 2. bioRxiv. Preprint. 2023 Dec 27 [revised 2024 Mar 6]. doi: 10.1101/2023.12.27.573380

View Abstract

Biallelic loss-of-function variants in CACHD1 cause a novel neurodevelopmental syndrome with facial dysmorphism and multisystem congenital abnormalities

Scala et al.
December 27, 2023
Genet Med. Author manuscript; available in PMC 2025 Apr 1.Published in final edited form as: Genet Med. 2024 Apr; 26(4): 101057. Published online 2023 Dec 27. doi: 10.1016/j.gim.2023.101057

View Abstract

Analysis of vascular disruption in zebrafish embryos as an endpoint to predict developmental toxicity

Nöth et al.
December 21, 2023
Reproductive Toxicology, Open access, Published: 21 December 2023, Volume 98, pages 537–549, (2024)

View Abstract

Abrogation of MAP4K4 protein function causes congenital anomalies in humans and zebrafish

Patterson et al.
April 26, 2023
Sci Adv. 2023 Apr; 9(17): eade0631. Published online 2023 Apr 26. doi: 10.1126/sciadv.ade0631Correction in: Sci Adv. 2023 Nov 24; 9(47): eadl5515.

View Abstract

A mechanistic understanding of the effects of polyethylene terephthalate nanoplastics in the zebrafish (Danio rerio) embryo

Bashirova et al.
February 02, 2023
Sci Rep. 2023; 13: 1891. Published online 2023 Feb 2. doi: 10.1038/s41598-023-28712-y

View Abstract

Gold nanoparticle-enhanced X-ray microtomography of the rodent reveals region-specific cerebrospinal fluid circulation in the brain

Pan et al.
January 27, 2023
Nat Commun. 2023; 14: 453. Published online 2023 Jan 27. doi: 10.1038/s41467-023-36083-1

View Abstract

Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

Mattis et al.
January 12, 2023
Diabetologia. 2023; 66(4): 674–694. Published online 2023 Jan 12. doi: 10.1007/s00125-022-05856-6

View Abstract

Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy

Grange et al.
November 04, 2022
Nat Commun. 2022; 13: 6664. Published online 2022 Nov 4. doi: 10.1038/s41467-022-34349-8

View Abstract

c-Kit Receptor Maintains Sensory Axon Innervation of the Skin through Src Family Kinases

Tuttle et al.
September 07, 2022
J Neurosci. 2022 Sep 7; 42(36): 6835–6847. doi: 10.1523/JNEUROSCI.0618-22.2022

View Abstract

Grouping of chemicals into mode of action classes by automated effect pattern analysis using the zebrafish embryo toxicity test

Teixidó et al.
March 07, 2022
Reproductive Toxicology, Open Access, Volume 96, pages 1353–1369, Published: 07 March 2022

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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. https://doi.org/10.1242/dmm.047761

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; https://doi.org/10.1016/j.reprotox.2020.08.004

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). https://doi.org/10.1038/s41598-020-68567-1

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, https://doi.org/10.1093/hmg/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, https://doi.org/10.1093/toxsci/kfz165

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: https://doi.org/10.1101/502674

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

Ansar et al.
May 09, 2019
https://doi.org/10.1016/j.ajhg.2019.04.002

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

Jarque et al.
August 29, 2018
PLOS ONE | https://doi.org/10.1371/journal.pone.0203087 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
https://doi.org/10.1364/BOE.8.002611; 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
http://dx.doi.org/10.1016/j.ajhg.2017.01.003

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.

View Abstract

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

View Abstract

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
JOVE

View Abstract

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

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.

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.