Publications

Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia

Garza, Raquel; Sharma, Yogita; Atacho, Diahann A.M.; Thiruvalluvan, Arun et al.

Part of Cell Reports, 2023.

DOI for Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia

Wildlife endogenous retroviruses: colonization, consequences, and cooption

Jern, Patric; Greenwood, Alex D.

Part of Trends in Genetics, 2023.

DOI for Wildlife endogenous retroviruses: colonization, consequences, and cooption

Expansion of a retrovirus lineage in the koala genome

Lillie, Mette; Hill, Jason; Pettersson, Mats; Jern, Patric

Part of Proceedings of the National Academy of Sciences of the United States of America, 2022.

DOI for Expansion of a retrovirus lineage in the koala genome Download full text (pdf) of Expansion of a retrovirus lineage in the koala genome

Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut

Edvardsen, Rolf Brudvik; Wallerman, Ola; Furmanek, Tomasz; Kleppe, Lene et al.

Part of PLOS Genetics, 2022.

DOI for Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut Download full text (pdf) of Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut

Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

Hill, Jason; Lillie, Mette; Pettersson, Mats; Rubin, Carl-Johan et al.

Part of Nature Communications, 2022.

DOI for Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches Download full text (pdf) of Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies

Nguyen, Diem; Peona, Valentina; Unneberg, Per; Suh, Alexander et al.

Part of Fungal Genetics Reports, 2022.

DOI for Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies Download full text (pdf) of Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies

Activation of endogenous retroviruses during brain development causes an inflammatory response

Jönsson, Marie E.; Garza, Raquel; Sharma, Yogita; Petri, Rebecca et al.

Part of EMBO Journal, 2021.

DOI for Activation of endogenous retroviruses during brain development causes an inflammatory response Download full text (pdf) of Activation of endogenous retroviruses during brain development causes an inflammatory response

Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring

Chen, Junfeng; Bi, Huijuan; Pettersson, Mats; Sato, Daiki et al.

Part of Communications Biology, 2021.

DOI for Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring Download full text (pdf) of Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

Peona, Valentina; Palacios-Gimenez, Octavio M.; Blommaert, Julie; Liu, Jing et al.

Part of Philosophical Transactions of the Royal Society of London. Biological Sciences, 2021.

DOI for The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities Download full text (pdf) of The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

ZBED6 binding motifs correlate with endogenous retroviruses and Syncytin genes

Pettersson, Mats E.; Jern, Patric

Part of Virus Evolution, 2021.

DOI for ZBED6 binding motifs correlate with endogenous retroviruses and Syncytin genes Download full text (pdf) of ZBED6 binding motifs correlate with endogenous retroviruses and Syncytin genes

Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

Li, Jingyi; Davis, Brian W.; Jern, Patric; Dorshorst, Ben J. et al.

Part of Mobile DNA, 2019.

DOI for Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken Download full text (pdf) of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups

Pettersson, Mats E.; Jern, Patric

Part of Genes, 2019.

DOI for Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups Download full text (pdf) of Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups

Bridging gaps in transposable element research with single-molecule and single-cell technologies

Kutter, C; Jern, Patric; Suh, Alexander

Part of Mobile DNA, 2018.

DOI for Bridging gaps in transposable element research with single-molecule and single-cell technologies Download full text (pdf) of Bridging gaps in transposable element research with single-molecule and single-cell technologies

Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations

Rivas-Carrillo, Salvador Daniel; Pettersson, Mats; Rubin, Carl-Johan; Jern, Patric

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 11012-11017, 2018.

DOI for Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations Download full text (pdf) of Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations

TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells

Brattås, Per Ludvik; Jönsson, Marie E.; Fasching, Liana; Nelander Wahlestedt, Jenny et al.

Part of Cell reports, p. 1-11, 2017.

DOI for TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells Download full text (pdf) of TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells

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

cgmisc: Enhanced Genome-wide Association Analyses and Visualisation

Kierczak, Marcin; Jablonska, Jagoda; Forsberg, S. K.; Bianchi, Matteo et al.

Part of Bioinformatics, p. 3830-3831, 2015.

DOI for cgmisc: Enhanced Genome-wide Association Analyses and Visualisation Download full text (pdf) of cgmisc: Enhanced Genome-wide Association Analyses and Visualisation

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

Hayward, Alexander; Cornwallis, Charlie K.; Jern, Patric

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 464-469, 2015.

DOI for Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)

Delhomme, N.; Sundström, Görel; Zamani, Neda; Lantz, Henrik et al.

Part of PLOS ONE, 2015.

DOI for Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies) Download full text (pdf) of Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

Fasching, L.; Kapopoulou, A.; Sachdeva, R.; Petri, R. et al.

Part of Cell reports, p. 20-28, 2015.

DOI for TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells Download full text (pdf) of TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

Broad-scale phylogenomics provides insights into retrovirus–host evolution

Hayward, Alexander; Grabherr, Manfred; Jern, Patric

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 20146-20151, 2013.

DOI for Broad-scale phylogenomics provides insights into retrovirus–host evolution

Unsupervised genome-wide recognition of local relationship patterns

Zamani, Neda; Russell, Pamela; Lantz, Henrik; Hoeppner, Marc et al.

Part of BMC Genomics, p. 347-, 2013.

DOI for Unsupervised genome-wide recognition of local relationship patterns Download full text (pdf) of Unsupervised genome-wide recognition of local relationship patterns

ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions

Hayward, Alexander; Ghazal, Awaisa; Andersson, Göran; Andersson, Leif et al.

Part of PLOS ONE, p. e59940-, 2013.

DOI for ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions Download full text (pdf) of ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions

Analyses of pig genomes provide insight into porcine demography and evolution

Groenen, M. A.; Archibald, A. L.; Uenishi, H.; Tuggle, C. K. et al.

Part of Nature, p. 393-398, 2012.

DOI for Analyses of pig genomes provide insight into porcine demography and evolution

Strong signatures of selection in the domestic pig genome

Rubin, Carl-Johan; Megens, H. -J; Barrio, Alvaro Martinez; Maqbool, K. et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19529-19536, 2012.

DOI for Strong signatures of selection in the domestic pig genome

Studies on the Restriction of Murine Leukemia Viruses by Mouse APOBEC3

Sanchez-Martinez, Silvia; Aloia, Amanda L.; Harvin, Demetria; Mirro, Jane et al.

Part of PLOS ONE, p. e38190-, 2012.

DOI for Studies on the Restriction of Murine Leukemia Viruses by Mouse APOBEC3 Download full text (pdf) of Studies on the Restriction of Murine Leukemia Viruses by Mouse APOBEC3

The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships

Barrio, Alvaro Martinez; Ekerljung, Marie; Jern, Patric; Benachenhou, Farid et al.

Part of PLOS ONE, p. e19832-, 2011.

DOI for The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships

Endogenous non-retroviral RNA virus elements in mammalian genomes.

Horie, Masayuki; Honda, Tomoyuki; Suzuki, Yoshiyuki; Kobayashi, Yuki et al.

Part of Nature, p. 84-87, 2010.

DOI for Endogenous non-retroviral RNA virus elements in mammalian genomes.

Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data

Benachenhou, Farid; Jern, Patric; Oja, Merja; Sperber, Göran et al.

Part of PLos ONE, p. e5179-, 2009.

DOI for Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data Download full text (pdf) of Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data

Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance.

Jern, Patric; Russell, Rebecca A; Pathak, Vinay K; Coffin, John M

Part of PLoS pathogens, p. e1000367-, 2009.

DOI for Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance.

Effects of retroviruses on host genome function.

Jern, Patric; Coffin, John M

Part of Annual Review of Genetics, p. 709-32, 2008.

DOI for Effects of retroviruses on host genome function.

Host-retrovirus arms race: trimming the budget.

Jern, Patric; Coffin, John M

Part of Cell host & microbe, p. 196-7, 2008.

DOI for Host-retrovirus arms race: trimming the budget.

Automated recognition of retroviral sequences in genomic data - RetroTector^©

Sperber, Göran O.; Airola, Tove; Jern, Patric; Blomberg, Jonas

Part of Nucleic Acids Research, p. 4964-4976, 2007.

DOI for Automated recognition of retroviral sequences in genomic data - RetroTector^©

Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses.

Jern, Patric; Stoye, Jonathan P; Coffin, John M

Part of PLoS genetics, p. 2014-22, 2007.

DOI for Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses.

Divergent patterns of recent retroviral integrations in the human and chimpanzee genomes: probable transmissions between other primates and chimpanzees

Jern, Patric; Sperber, Göran; Blomberg, Jonas

Part of Journal of Virology, p. 1367-1375, 2006.

DOI for Divergent patterns of recent retroviral integrations in the human and chimpanzee genomes: probable transmissions between other primates and chimpanzees

Development of broadly targeted human endogenous gammaretroviralpol-based real time PCRs Quantitation of RNA expression in human tissues

Forsman, Anna; Yun, Zhihong; Hu, Lijuan; Uzhameckis, Dmitrijs et al.

Part of Journal of Virological Methods, p. 16-30, 2005.

DOI for Development of broadly targeted human endogenous gammaretroviralpol-based real time PCRs Quantitation of RNA expression in human tissues

Evolutionary Aspects of Human Endogenous Retroviral Sequences (HERVs) and Disease

Blomberg, Jonas; Ushameckis, Dimitrijs; Jern, Patric

Part of Retroviruses and Primate Genome Evolution, 2005.

Sequence variability, gene structure, and expression of full-length human endogenous

Jern, Patric; Sperber, Göran; Ahlsén, Göran; Blomberg, Jonas

Part of J Virol, p. 6325-37, 2005.

Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral

Jern, Patric; Sperber, Göran; Blomberg, Jonas

Part of Retrovirology, p. 50-, 2005.

Definition and variation of human endogenous retrovirus H.

Jern, Patric; Sperber, Göran; Blomberg, Jonas

Part of Virology, p. 93-110, 2004.

Full-length HERV-H elements with env SU open reading frames in the human genome.

Jern, Patric; Lindeskog, Mats; Karlsson, Damita; Blomberg, Jonas

Part of AIDS Res Hum Retroviruses, p. 671-6, 2002.