Nima Rafati

Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene

Mao, Xiaomeng; Rafati, Nima; Tellgren-Roth, Christian; Ingvarsson, PÀr K. et al.

Part of Genome Biology, 2026

• DOI for Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene
• Download full text (pdf) of Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene

Genomic and neurobiological bases of variation in fighting strategies in gamecocks

Shimmura, Tsuyoshi; Kurachi, Takuma; Matsuda, Yuki; Rafati, Nima et al.

Part of Molecular biology and evolution, 2026

• DOI for Genomic and neurobiological bases of variation in fighting strategies in gamecocks
• Download full text (pdf) of Genomic and neurobiological bases of variation in fighting strategies in gamecocks

Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease

Barba-Reyes, Juan M.; Harder, Lisbeth; Salas, Sergio Marco; Jaisa-aad, Methasit et al.

Part of Acta Neuropathologica, 2025

• DOI for Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease
• Download full text (pdf) of Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease

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.

Part of Nature Methods, 2025

• DOI for Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
• Download full text (pdf) of 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.

Part of Cellular Oncology, p. 209-227, 2024

• DOI for Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour
• Download full text (pdf) of Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour

Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene

Mao, Xiaomeng; Rafati, Nima; Tellgren-Roth, Christian; Ingvarsson, PÀr K. et al.

Part of Genome Biology, 2026

• DOI for Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene
• Download full text (pdf) of Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene

Genomic and neurobiological bases of variation in fighting strategies in gamecocks

Shimmura, Tsuyoshi; Kurachi, Takuma; Matsuda, Yuki; Rafati, Nima et al.

Part of Molecular biology and evolution, 2026

• DOI for Genomic and neurobiological bases of variation in fighting strategies in gamecocks
• Download full text (pdf) of Genomic and neurobiological bases of variation in fighting strategies in gamecocks

Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease

Barba-Reyes, Juan M.; Harder, Lisbeth; Salas, Sergio Marco; Jaisa-aad, Methasit et al.

Part of Acta Neuropathologica, 2025

• DOI for Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease
• Download full text (pdf) of Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease

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.

Part of Nature Methods, 2025

• DOI for Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
• Download full text (pdf) of 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.

Part of Cellular Oncology, p. 209-227, 2024

• DOI for Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour
• Download full text (pdf) of 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.

Part of Genetics, 2023

• DOI for Copy number variations and their effect on the plasma proteome
• Download full text (pdf) of 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.

Part of Nature Communications, 2022

• DOI for Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability
• Download full text (pdf) of 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.

Part of Molecular biology and evolution, 2022

• DOI for The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations
• Download full text (pdf) of The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations

Genomic dynamics of brown trout populations released to a novel environment

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

Part of Ecology and Evolution, 2022

• DOI for Genomic dynamics of brown trout populations released to a novel environment
• Download full text (pdf) of Genomic dynamics of brown trout populations released to a novel environment

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.

Part of Oncogenesis, 2022

• DOI for MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma
• Download full text (pdf) of MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma

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.

Part of Journal of Clinical Endocrinology and Metabolism, p. 3265-3282, 2021

• DOI for Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8
• Download full text (pdf) of Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8

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

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

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 24359-24368, 2020

• DOI for Reconstruction of the birth of a male sex chromosome present in Atlantic herring
• Download full text (pdf) of Reconstruction of the birth of a male sex chromosome present in Atlantic herring

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.

Part of Genome Biology and Evolution, p. 1918-1928, 2020

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

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.

Part of BMC Genomics, 2020

• DOI for Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs
• Download full text (pdf) of Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

DNA demethylation regulates gene expression in IgE-activated mouse mast cells.

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

Part of Allergy. European Journal of Allergy and Clinical Immunology, p. 1776-1780, 2020

• DOI for DNA demethylation regulates gene expression in IgE-activated mouse mast cells.
• Download full text (pdf) of DNA demethylation regulates gene expression in IgE-activated mouse mast cells.

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.

Part of Scientific Reports, 2019

• DOI for Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
• Download full text (pdf) of Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

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.

Part of BMC Genomics, 2018

• DOI for Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
• Download full text (pdf) of Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

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.

Part of Molecular Ecology, p. 1457-1478, 2018

• DOI for 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.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 7380-7385, 2018

• DOI for 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.

Part of eLIFE, 2017

• DOI for Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
• Download full text (pdf) of Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

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.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2017

• DOI for 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.

Part of G3, p. 2213-2223, 2016

• DOI for Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
• Download full text (pdf) of Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

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.

Part of eLIFE, 2016

• DOI for The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
• Download full text (pdf) of The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

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.

Part of Endocrinology, p. 737-751, 2016

• DOI for 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.

Part of Scientific Reports, 2015

• DOI for Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene
• Download full text (pdf) of Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene

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.

Part of Science, p. 1074-1079, 2014

• DOI for 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.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19345-19350, 2012

• DOI for 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

• Download full text (pdf) of Exploring genetic diversity in natural and domestic populations through next generation sequencing

Dynamic evolution of a sex-linked region

Mao, Xiaomeng; Rafati, Nima; Tellgren-Roth, Christian; Ingvarsson, Pär et al.