Nima Rafati

Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

Salas, Sergio Marco; Kuemmerle, Louis B.; Mattsson-Langseth, Christoffer; Tismeyer, Sebastian et al.

Ingår i Nature Methods, 2025

• DOI för Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
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Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour

Zhang, Hanzhao; Konjusha, Dardan; Rafati, Nima; Tararuk, Tatsiana et al.

Ingår i Cellular Oncology, s. 209-227, 2024

• DOI för Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour
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Copy number variations and their effect on the plasma proteome

Schmitz, Daniel; Li, Zhiwei; Lo Faro, Valeria; Rask-Andersen, Mathias et al.

Ingår i Genetics, 2023

• DOI för Copy number variations and their effect on the plasma proteome
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Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability

Kierczak, Marcin; Rafati, Nima; Höglund, Julia; Gourlé, Hadrien et al.

Ingår i Nature Communications, 2022

• DOI för Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability
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The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations

Ament-Velasquez, Sandra Lorena; Gilchrist, Ciaran; Rego, Alexandre; Bendixsen, Devin P. et al.

Ingår i Molecular biology and evolution, 2022

• DOI för The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations
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Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

Salas, Sergio Marco; Kuemmerle, Louis B.; Mattsson-Langseth, Christoffer; Tismeyer, Sebastian et al.

Ingår i Nature Methods, 2025

• DOI för Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
• Ladda ner fulltext (pdf) av Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour

Zhang, Hanzhao; Konjusha, Dardan; Rafati, Nima; Tararuk, Tatsiana et al.

Ingår i Cellular Oncology, s. 209-227, 2024

• DOI för Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour
• Ladda ner fulltext (pdf) av Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour

Copy number variations and their effect on the plasma proteome

Schmitz, Daniel; Li, Zhiwei; Lo Faro, Valeria; Rask-Andersen, Mathias et al.

Ingår i Genetics, 2023

• DOI för Copy number variations and their effect on the plasma proteome
• Ladda ner fulltext (pdf) av Copy number variations and their effect on the plasma proteome

Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability

Kierczak, Marcin; Rafati, Nima; Höglund, Julia; Gourlé, Hadrien et al.

Ingår i Nature Communications, 2022

• DOI för Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability
• Ladda ner fulltext (pdf) av Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability

The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations

Ament-Velasquez, Sandra Lorena; Gilchrist, Ciaran; Rego, Alexandre; Bendixsen, Devin P. et al.

Ingår i Molecular biology and evolution, 2022

• DOI för The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations
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Genomic dynamics of brown trout populations released to a novel environment

Kurland, Sara; Rafati, Nima; Ryman, Nils; Laikre, Linda

Ingår i Ecology and Evolution, 2022

• DOI för Genomic dynamics of brown trout populations released to a novel environment
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MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma

Blixt, Maria; Hellsand, Minas; Konjusha, Dardan; Zhang, Hanzhao et al.

Ingår i Oncogenesis, 2022

• DOI för MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma
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Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8

Paulsson, Johan O.; Rafati, Nima; DiLorenzo, Sebastian; Chen, Yi et al.

Ingår i Journal of Clinical Endocrinology and Metabolism, s. 3265-3282, 2021

• DOI för Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8
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Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness

Sato, Daiki X.; Rafati, Nima; Ring, Henrik; Younis, Shady et al.

Ingår i Genome Biology and Evolution, s. 1918-1928, 2020

• DOI för Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness

Reconstruction of the birth of a male sex chromosome present in Atlantic herring

Rafati, Nima; Chen, Junfeng; Herpin, Amaury; Pettersson, Mats et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 24359-24368, 2020

• DOI för Reconstruction of the birth of a male sex chromosome present in Atlantic herring
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Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

Bianchi, Matteo; Rafati, Nima; Karlsson, Åsa; Murén, Eva et al.

Ingår i BMC Genomics, 2020

• DOI för Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs
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DNA demethylation regulates gene expression in IgE-activated mouse mast cells.

Paivandy, Aida; Grujic, Mirjana; Rafati, Nima; Pejler, Gunnar

Ingår i Allergy. European Journal of Allergy and Clinical Immunology, s. 1776-1780, 2020

• DOI för DNA demethylation regulates gene expression in IgE-activated mouse mast cells.
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Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

Höglund, Julia; Rafati, Nima; Rask-Andersen, Mathias; Enroth, Stefan et al.

Ingår i Scientific Reports, 2019

• DOI för Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
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Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Bornelöv, Susanne; Seroussi, Eyal; Yosefi, Sara; Benjamini, Sharon et al.

Ingår i BMC Genomics, 2018

• DOI för Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
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A genomic map of clinal variation across the European rabbit hybrid zone

Rafati, Nima; Blanco-Aguiar, Jose A.; Rubin, Carl-Johan; Sayyab, Shumaila et al.

Ingår i Molecular Ecology, s. 1457-1478, 2018

• DOI för A genomic map of clinal variation across the European rabbit hybrid zone

Changes in brain architecture are consistent with altered fear processing in domestic rabbits

Brusini, Irene; Carneiro, Miguel; Wang, Chunliang; Rubin, Carl-Johan et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 7380-7385, 2018

• DOI för Changes in brain architecture are consistent with altered fear processing in domestic rabbits

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

Feng, Chungang; Pettersson, Mats; Lamichhaney, Sangeet; Rubin, Carl-Johan et al.

Ingår i eLIFE, 2017

• DOI för Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
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Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

Lamichhaney, Sangeet; Fuentes-Pardo, Angela P.; Rafati, Nima; Ryman, Nils et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, 2017

• DOI för Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

Rafati, Nima; Andersson, Lisa S.; Mikko, Sofia; Feng, Chungang et al.

Ingår i G3, s. 2213-2223, 2016

• DOI för Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Martínez Barrio, Álvaro; Lamichhaney, Sangeet; Fan, Guangyi; Rafati, Nima et al.

Ingår i eLIFE, 2016

• DOI för The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
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Identification of the Long-Sought Leptin in Chicken and Duck: Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function

Seroussi, Eyal; Cinnamon, Yuval; Yosefi, Sara; Genin, Olga et al.

Ingår i Endocrinology, s. 737-751, 2016

• DOI för Identification of the Long-Sought Leptin in Chicken and Duck: Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function

Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene

Saenko, Suzanne V.; Lamichhaney, Sangeet; Barrio, Alvaro Martinez; Rafati, Nima et al.

Ingår i Scientific Reports, 2015

• DOI för Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene
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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Carneiro, Miguel; Rubin, Carl-Johan; Di Palma, Federica; Albert, Frank W. et al.

Ingår i Science, s. 1074-1079, 2014

• DOI för Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

Lamichhaney, Sangeet; Barrio, Alvaro Martinez; Rafati, Nima; Sundström, Görel et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 19345-19350, 2012

• DOI för Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

Exploring genetic diversity in natural and domestic populations through next generation sequencing

Rafati, Nima

2017

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