Amin Allalou

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

Gudmundsson, Sanna; Wilbe, Maria; Gorniok, Beata Filipek; Molin, Anna-Maja et al.

Part of Scientific Reports, 2019

• DOI for TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
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Passive in-vehicle driver breath alcohol detection using advanced sensor signal acquisition and fusion

Ljungblad, Jonas; Hök, Bertil; Allalou, Amin; Pettersson, Håkan

Part of Traffic Injury Prevention, 2017

• DOI for Passive in-vehicle driver breath alcohol detection using advanced sensor signal acquisition and fusion
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Decoding gene expression in 2D and 3D

Bombrun, Maxime; Ranefall, Petter; Lindblad, Joakim; Allalou, Amin et al.

Part of Image Analysis, p. 257-268, 2017

• DOI for Decoding gene expression in 2D and 3D
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Automated deep-phenotyping of the vertebrate brain

Allalou, Amin; Wu, Yuelong; Ghannad-Rezaie, Mostafa; Eimon, Peter M. et al.

Part of eLIFE, 2017

• DOI for Automated deep-phenotyping of the vertebrate brain

High-throughput hyperdimensional vertebrate phenotyping

Pardo-Martin, Carlos; Allalou, Amin; Medina, Jaime; Eimon, Peter M. et al.

Part of Nature Communications, p. 1467, 2013

• DOI for High-throughput hyperdimensional vertebrate phenotyping

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

Chang, Tsung-Yao; Pardo-Martin, Carlos; Allalou, Amin; Wählby, Carolina et al.

Part of Lab on a Chip, p. 711-716, 2012

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

Methods for 2D and 3D Quantitative Microscopy of Biological Samples

Allalou, Amin

2011

• Download full text (pdf) of Methods for 2D and 3D Quantitative Microscopy of Biological Samples

High-throughput cellular-resolution in vivo vertebrate screening

Pardo-Martin, Carlos; Chang, Tsung-Yao; Allalou, Amin; Wählby, Carolina et al.

Part of Proc. 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2011

Increasing the dynamic range of in situ PLA

Clausson, Carl-Magnus; Allalou, Amin; Weibrecht, Irene; Mahmoudi, Salah et al.

Part of Nature Methods, p. 892-893, 2011

• DOI for Increasing the dynamic range of in situ PLA

Signal Detection in 3D by Stable Wave Signal Verification

Allalou, Amin; Wählby, Carolina

Part of Proceedings of SSBA 2009, 2009

BlobFinder, a tool for fluorescence microscopy image cytometry

Allalou, Amin; Wählby, Carolina

Part of Computer Methods and Programs in Biomedicine, p. 58-65, 2009

• DOI for BlobFinder, a tool for fluorescence microscopy image cytometry
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A detailed analysis of 3D subcellular signal localization

Pinidiyaarachchi, Amalka; Zieba, Agata; Allalou, Amin; Pardali, Katerina et al.

Part of Cytometry Part A, p. 319-328, 2009

• DOI for A detailed analysis of 3D subcellular signal localization

Image Based Measurements of Single Cell mtDNA Mutation Load

Allalou, Amin; van de Rijke, Frans M.; Jahangir Tafrechi, Roos; Raap, Anton K. et al.

Part of Image Analysis, Proceedings, p. 631-640, 2007

• DOI for Image Based Measurements of Single Cell mtDNA Mutation Load

Image based measurements of single cell mtDNA mutation load MTD 2007

Allalou, Amin; van de Rijke, Frans; Jahangir Tafrechi, Roos; Raap, Anton et al.

Part of Medicinteknikdagarna 2007, 2007

Segmentation of Cytoplasms of Cultured Cells

Allalou, Amin; Wählby, Carolina; van de Rijke, Frans; Jahangir Tafrechi, Roos et al.

Part of In Proceedings SSBA 2007, Symposium on image analysis, Linköping, 2007

Genome-wide interaction study with body mass index identifies CYP7A1 and GIPR as genetic modulators of metabolic dysfunction-associated steatotic liver disease

Jamialahmadi, Oveis; Mujica, Endrina; Morris, Lowri; Mancina, Rosellina Margherita et al.

Part of Clinical and Molecular Hepatology, p. 1252-1268, 2025

• DOI for Genome-wide interaction study with body mass index identifies CYP7A1 and GIPR as genetic modulators of metabolic dysfunction-associated steatotic liver disease
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Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting

Al-Radi, Omayma; Ingelshed, Katrine; Eichhorn, Lisa; Josefsson, Heidi et al.

Part of Cell Death and Disease, 2025

• DOI for Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting
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Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes

Arnold, Hannah; Panara, Virginia; Allalou, Amin; Koltowska, Katarzyna

Part of STAR Protocols, 2025

• DOI for Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes
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Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.

Mazzaferro, Eugenia; Mujica, Endrina; Zhang, Hanqing; Emmanouilidou, Anastasia et al.

Part of Scientific Reports, p. 5408, 2025

• DOI for Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.
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Aurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context

Gries, Alexandre; Kumar, Karthiga Santhana; Kuttler, Fabien; Özalp, Özgün et al.

Part of Neoplasia, 2025

• DOI for Aurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context
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Genome-wide interaction study with body mass index identifies CYP7A1 and GIPR as genetic modulators of metabolic dysfunction-associated steatotic liver disease

Jamialahmadi, Oveis; Mujica, Endrina; Morris, Lowri; Mancina, Rosellina Margherita et al.

Part of Clinical and Molecular Hepatology, p. 1252-1268, 2025

• DOI for Genome-wide interaction study with body mass index identifies CYP7A1 and GIPR as genetic modulators of metabolic dysfunction-associated steatotic liver disease
• Download full text (pdf) of Genome-wide interaction study with body mass index identifies CYP7A1 and GIPR as genetic modulators of metabolic dysfunction-associated steatotic liver disease

Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting

Al-Radi, Omayma; Ingelshed, Katrine; Eichhorn, Lisa; Josefsson, Heidi et al.

Part of Cell Death and Disease, 2025

• DOI for Pharmacological activation of p53 induces dose-dependent changes in endothelial cell fate during angiogenic sprouting
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Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes

Arnold, Hannah; Panara, Virginia; Allalou, Amin; Koltowska, Katarzyna

Part of STAR Protocols, 2025

• DOI for Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes
• Download full text (pdf) of Protocol to computationally average confocal images of zebrafish lymphatic vessels to identify phenotypes

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

Mazzaferro, Eugenia; Mujica, Endrina; Zhang, Hanqing; Emmanouilidou, Anastasia et al.

Part of Scientific Reports, p. 5408, 2025

• DOI for Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.
• Download full text (pdf) of Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.

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

Gries, Alexandre; Kumar, Karthiga Santhana; Kuttler, Fabien; Özalp, Özgün et al.

Part of Neoplasia, 2025

• DOI for Aurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context
• Download full text (pdf) of Aurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context

Multiple cis-regulatory elements control prox1a expression in distinct lymphatic vascular beds

Panara, Virginia; Yu, Hujun; Peng, Di; Staxäng, Karin et al.

Part of Development, 2024

• DOI for Multiple cis-regulatory elements control prox1a expression in distinct lymphatic vascular beds

mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners

Arnold, Hannah; Panara, Virginia; Hussmann, Melina; Gorniok, Beata Filipek et al.

Part of Cell Reports, 2022

• DOI for mafba and mafbb differentially regulate lymphatic endothelial cell migration in topographically distinct manners
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Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development

Habicher, Judith; Varshney, Gaurav K.; Waldmann, Laura; Snitting, Daniel et al.

Part of PLOS Genetics, 2022

• DOI for Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development
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The Role of Gdf5 in the Development of the Zebrafish Fin Endoskeleton

Waldmann, Laura; Leyhr, Jake; Zhang, Hanqing; Allalou, Amin et al.

Part of Developmental Dynamics, p. 1535-1549, 2022

• DOI for The Role of Gdf5 in the Development of the Zebrafish Fin Endoskeleton
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A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint

Leyhr, Jake; Waldmann, Laura; Filipek-Górniok, Beata; Zhang, Hanqing et al.

Part of eLIFE, 2022

• DOI for A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
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The broad role of Nkx3.2 in the development of the zebrafish axial skeleton

Waldmann, Laura; Leyhr, Jake; Zhang, Hanqing; Öhman, Caroline et al.

Part of PLOS ONE, 2021

• DOI for The broad role of Nkx3.2 in the development of the zebrafish axial skeleton
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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

von der Heyde, Benedikt; Emmanouilidou, Anastasia; Mazzaferro, Eugenia; Vicenzi, Silvia et al.

Part of Scientific Reports, 2020

• DOI for Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
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zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging

Zhang, Hanqing; Waldmann, Laura; Manuel, Remy; Boije, Henrik et al.

Part of Biomedical Optics Express, p. 4290-4305, 2020

• DOI for zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging
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Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration

del Pozo, Ana; Manuel, Remy; Iglesias Gonzalez, Ana Belen; Koning, Harmen Kornelis et al.

Part of eNeuro, 2020

• DOI for Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration
• Download full text (pdf) of Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration

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

Gudmundsson, Sanna; Wilbe, Maria; Gorniok, Beata Filipek; Molin, Anna-Maja et al.

Part of Scientific Reports, 2019

• DOI for TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
• Download full text (pdf) of TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish

Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects.

Eimon, Peter M; Ghannad-Rezaie, Mostafa; De Rienzo, Gianluca; Allalou, Amin et al.

Part of Nature Communications, 2018

• DOI for Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects.
• Download full text (pdf) of Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects.

Passive in-vehicle driver breath alcohol detection using advanced sensor signal acquisition and fusion

Ljungblad, Jonas; Hök, Bertil; Allalou, Amin; Pettersson, Håkan

Part of Traffic Injury Prevention, 2017

• DOI for Passive in-vehicle driver breath alcohol detection using advanced sensor signal acquisition and fusion
• Download full text (pdf) of Passive in-vehicle driver breath alcohol detection using advanced sensor signal acquisition and fusion

Automated deep-phenotyping of the vertebrate brain

Allalou, Amin; Wu, Yuelong; Ghannad-Rezaie, Mostafa; Eimon, Peter M. et al.

Part of eLIFE, 2017

• DOI for Automated deep-phenotyping of the vertebrate brain

High-throughput hyperdimensional vertebrate phenotyping

Pardo-Martin, Carlos; Allalou, Amin; Medina, Jaime; Eimon, Peter M. et al.

Part of Nature Communications, p. 1467, 2013

• DOI for High-throughput hyperdimensional vertebrate phenotyping

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

Chang, Tsung-Yao; Pardo-Martin, Carlos; Allalou, Amin; Wählby, Carolina et al.

Part of Lab on a Chip, p. 711-716, 2012

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

Increasing the dynamic range of in situ PLA

Clausson, Carl-Magnus; Allalou, Amin; Weibrecht, Irene; Mahmoudi, Salah et al.

Part of Nature Methods, p. 892-893, 2011

• DOI for Increasing the dynamic range of in situ PLA

Robust signal detection in 3D fluorescence microscopy

Allalou, Amin; Pinidiyaarachchi, Amalka; Wählby, Carolina

Part of Cytometry. Part A, p. 86-96, 2010

• DOI for Robust signal detection in 3D fluorescence microscopy

BlobFinder, a tool for fluorescence microscopy image cytometry

Allalou, Amin; Wählby, Carolina

Part of Computer Methods and Programs in Biomedicine, p. 58-65, 2009

• DOI for BlobFinder, a tool for fluorescence microscopy image cytometry
• Download full text (pdf) of BlobFinder, a tool for fluorescence microscopy image cytometry

A detailed analysis of 3D subcellular signal localization

Pinidiyaarachchi, Amalka; Zieba, Agata; Allalou, Amin; Pardali, Katerina et al.

Part of Cytometry Part A, p. 319-328, 2009

• DOI for A detailed analysis of 3D subcellular signal localization

Single-cell A3243G mitochondrial DNA mutation load assays for segregation analysis

Jahangir Tafrechi, Roshan S.; van de Rijke, Frans M.; Allalou, Amin; Larsson, Chatarina et al.

Part of Journal of Histochemistry and Cytochemistry, p. 1159-1166, 2007

• DOI for Single-cell A3243G mitochondrial DNA mutation load assays for segregation analysis

Methods for 2D and 3D Quantitative Microscopy of Biological Samples

Allalou, Amin

2011

• Download full text (pdf) of Methods for 2D and 3D Quantitative Microscopy of Biological Samples

Decoding gene expression in 2D and 3D

Bombrun, Maxime; Ranefall, Petter; Lindblad, Joakim; Allalou, Amin et al.

Part of Image Analysis, p. 257-268, 2017

• DOI for Decoding gene expression in 2D and 3D
• Download full text (pdf) of Decoding gene expression in 2D and 3D

Isotropic 3D imaging of biological specimens at micro and nano scale

Pacureanu, Alexandra; Peyrin, Francoise; Langer, Max; Ishaq, Omer et al.

2012

Making isotropic 3D imaging at microscopic scale accessible to every lab

Pacureanu, Alexandra; Ishaq, Omer; Allalou, Amin; Wählby, Carolina

2012

Cuanto: A Tool for Quantification of Bone Tissue in the Proximityof Implants

Sarve, Hamid; Allalou, Amin; B. Johansson, Carina

Part of Proceedings of SSBA 2011, 2011

Approaches for increasing throughput andinformation content of image-based zebrafishscreens

Allalou, Amin; Curic, Vladimir; Pardo-Martin, Carlos; Yanik, Mehmet Fatih et al.

Part of Proceeding of SSBA 2011, 2011

High-throughput cellular-resolution in vivo vertebrate screening

Pardo-Martin, Carlos; Chang, Tsung-Yao; Allalou, Amin; Wählby, Carolina et al.

Part of Proc. 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 2011

Signal Detection in 3D by Stable Wave Signal Verification

Allalou, Amin; Wählby, Carolina

Part of Proceedings of SSBA 2009, 2009

Image Based Measurements of Single Cell mtDNA Mutation Load

Allalou, Amin; van de Rijke, Frans M.; Jahangir Tafrechi, Roos; Raap, Anton K. et al.

Part of Image Analysis, Proceedings, p. 631-640, 2007

• DOI for Image Based Measurements of Single Cell mtDNA Mutation Load

Image based measurements of single cell mtDNA mutation load MTD 2007

Allalou, Amin; van de Rijke, Frans; Jahangir Tafrechi, Roos; Raap, Anton et al.

Part of Medicinteknikdagarna 2007, 2007

Segmentation of Cytoplasms of Cultured Cells

Allalou, Amin; Wählby, Carolina; van de Rijke, Frans; Jahangir Tafrechi, Roos et al.

Part of In Proceedings SSBA 2007, Symposium on image analysis, Linköping, 2007

The Broad Role of Nkx3.2 in the Development of the Zebrafish Axial Skeleton

Waldmann, Laura; Leyhr, Jake; Zhang, Hanqing; Öhman, Caroline et al.

• DOI for The Broad Role of Nkx3.2 in the Development of the Zebrafish Axial Skeleton

An evolutionarily conserved cis-regulatory element of nkx3.2 drives jaw joint-specific expression in zebrafish

Waldmann, Laura; Leyhr, Jake; Filipek-Gorniok, Beata; Zhang, Hanqing et al.

Distinct cis-regulatory elements drive prox1a expression in specific lymphatic vascular beds

Panara, Virginia; Yu, Oliver; Peng, Di; Skoczylas, Renae et al.

Kita crispants for systematic image-based genetic screens of complex traits in zebrafish larvae

Mazzaferro, Eugenia; Metzendorf, Christoph; Zhang, Hanqing; Mujica, Endrina et al.

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

Mazzaferro, Eugenia; Mujica, Endrina; Zhang, Hanqing; Emmanouilidou, Anastasia et al.

Characterizing candidate genes in GWAS-identified loci that may uncouple excess adiposity from its comorbidities

Mazzaferro, Eugenia; Zhang, Hanqing; Mujica, Endrina; Azizah, Isyatul et al.