Ignas Bunikis

Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation

ten Berk de Boer, Esmee; Ameur, Adam; Bunikis, Ignas; Ek, Marlene et al.

Part of Scientific Reports, 2024

• DOI for Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation
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A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern

Höglund, Jacob; Dias, Guilherme; Olsen, Remi-André; Soares, André et al.

Part of Genome Biology and Evolution, 2024

• DOI for A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern
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Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring

Pettersson, Mats; Quintela, Maria; Besnier, Francois; Deng, Qiaoling et al.

Part of Genome Biology and Evolution, 2024

• DOI for Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring
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Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes

Jayaprasad, Suvratha; Peona, Valentina; Ellerstrand, Simon J.; Rossini, Roberto et al.

Part of Molecular Ecology, 2024

• DOI for Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes
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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Lysenkova, Mariya; Arvidsson, Gustav; Bunikis, Ignas; Lundmark, Anders et al.

Part of Life Science Alliance, 2024

• DOI for A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
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Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation

ten Berk de Boer, Esmee; Ameur, Adam; Bunikis, Ignas; Ek, Marlene et al.

Part of Scientific Reports, 2024

• DOI for Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation
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A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern

Höglund, Jacob; Dias, Guilherme; Olsen, Remi-André; Soares, André et al.

Part of Genome Biology and Evolution, 2024

• DOI for A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern
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Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring

Pettersson, Mats; Quintela, Maria; Besnier, Francois; Deng, Qiaoling et al.

Part of Genome Biology and Evolution, 2024

• DOI for Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring
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Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes

Jayaprasad, Suvratha; Peona, Valentina; Ellerstrand, Simon J.; Rossini, Roberto et al.

Part of Molecular Ecology, 2024

• DOI for Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes
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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Lysenkova, Mariya; Arvidsson, Gustav; Bunikis, Ignas; Lundmark, Anders et al.

Part of Life Science Alliance, 2024

• DOI for A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
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Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum

Gutierrez-Valencia, Juanita; Zervakis, Panagiotis-Ioannis; Postel, Zoe; Fracassetti, Marco et al.

Part of Molecular biology and evolution, 2024

• DOI for Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum
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Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins

Unneberg, Per; Larsson, Mårten; Olsson, Anna; Wallerman, Ola et al.

Part of Nature Communications, 2024

• DOI for Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins
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Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards

Feiner, Nathalie; Yang, Weizhao; Bunikis, Ignas; While, Geoffrey M. et al.

Part of Science Advances, 2024

• DOI for Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards
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Long-read whole-genome analysis of human single cells

Hård, Joanna; Mold, Jeff E; Eisfeldt, Jesper; Tellgren-Roth, Christian et al.

Part of Nature Communications, 2023

• DOI for Long-read whole-genome analysis of human single cells
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Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

Lysenkova Wiklander, Mariya; Övernäs, Elin; Lagensjö, Johanna; Raine, Amanda et al.

Part of BMC Research Notes, 2023

• DOI for Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH
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Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas

Weishaupt, Holger; Čančer, Matko; Rosén, Gabriela; Holmberg, Karl O. et al.

Part of Neuro-Oncology, p. 97-107, 2023

• DOI for Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas
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The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes

Westerdahl, Helena; Mellinger, Samantha; Sigeman, Hanna; Kutschera, Verena E. et al.

Part of Molecular Ecology Resources, p. 2379-2395, 2022

• DOI for The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Gutierrez-Valencia, Juanita; Fracassetti, Marco; Berdan, Emma L.; Bunikis, Ignas et al.

Part of Current Biology, p. 4360-4371000000, 2022

• DOI for Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level
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The Carniolan Honeybee from Slovenia-A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies

Moskric, Ajda; Marinc, Andraz; Ferk, Polonca; Leskosek, Brane et al.

Part of Insects, 2022

• DOI for The Carniolan Honeybee from Slovenia-A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies
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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component

Christmas, Matthew; Jones, Julia; Olsson, Anna; Wallerman, Ola et al.

Part of Molecular Ecology, p. 1111-1127, 2022

• DOI for A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component
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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

Peona, Valentina; Blom, Mozes P. K.; Xu, Luohao; Burri, Reto et al.

Part of Molecular Ecology Resources, p. 263-286, 2021

• DOI for Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise
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Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics

Christmas, Matthew; Jones, Julia C.; Olsson, Anna; Wallerman, Ola et al.

Part of Molecular biology and evolution, p. 3126-3143, 2021

• DOI for Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics
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Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration

Sigeman, Hanna; Strandh, Maria; Proux-Wera, Estelle; Kutschera, Verena E. et al.

Part of Molecular biology and evolution, p. 5275-5291, 2021

• DOI for Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration
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Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2+

Berggrund, Malin; Gustavsson, Inger M.; Aarnio, Riina; Lindberg, Julia Hedlund et al.

Part of Virology Journal, 2020

• DOI for Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2+
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Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

Höijer, Ida; Johansson, Josefin; Gudmundsson, Sanna; Chin, Chen-Shan et al.

Part of Genome Biology, 2020

• DOI for Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
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Discovery and population genomics of structural variation in a songbird genus

Weissensteiner, Matthias H.; Bunikis, Ignas; Catalan, Ana; Francoijs, Kees-Jan et al.

Part of Nature Communications, 2020

• DOI for Discovery and population genomics of structural variation in a songbird genus
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Chromosomal inversions associated with environmental adaptation in honeybees

Christmas, Matthew J; Wallberg, Andreas; Bunikis, Ignas; Olsson, Anna et al.

Part of Molecular Ecology, p. 1358-1374, 2019

• DOI for Chromosomal inversions associated with environmental adaptation in honeybees

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

Wallberg, Andreas; Bunikis, Ignas; Vinnere, Olga; Mosbech, Mai-Britt et al.

Part of BMC Genomics, 2019

• DOI for A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
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A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection

Pettersson, Mats; Rochus, Christina Marie; Han, Fan; Chen, Junfeng et al.

Part of Genome Research, p. 1919-1928, 2019

• DOI for A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
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Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon

Martijn, Joran; Lind, Anders E.; Schön, Max E.; Spiertz, Ian et al.

Part of Environmental Microbiology, p. 2485-2498, 2019

• DOI for Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon
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Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

Andrade, Pedro; Pinho, Catarina; Perez i de lanuza, Guillem; Afonso, Sandra et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 5633-5642, 2019

• DOI for Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

Ameur, Adam; Che, Huiwen; Martin, Marcel; Bunikis, Ignas et al.

Part of Genes, 2018

• DOI for De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data
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Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

Weissensteiner, Matthias H.; Pang, Andy W. C.; Bunikis, Ignas; Höijer, Ida et al.

Part of Genome Research, p. 697-708, 2017

• DOI for Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping

Olsen, Remi-Andre; Bunikis, Ignas; Tiukova, Ievgeniia; Holmberg, Kicki et al.

Part of GigaScience, 2015

• DOI for De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping
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CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects

Ameur, Adam; Bunikis, Ignas; Enroth, Stefan; Gyllensten, Ulf

Part of Database, 2014

• DOI for CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing

Ameur, Adam; Meiring, Tracy L.; Bunikis, Ignas; Häggqvist, Susana et al.

Part of Scientific Reports, p. 4398, 2014

• DOI for Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
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Targeted RNA Sequencing Assay Efficiently Identifies Cryptic KMT2A (MLL)-Fusions in Acute Leukemia Patients

Sevov, Marie; Bunikis, Ignas; Häggqvist, Susana; Höglund, Martin et al.

Part of Blood, 2014

Transcriptome of the Alternative Ethanol Production Strain Dekkera bruxellensis CBS 11270 in Sugar Limited, Low Oxygen Cultivation

Tiukova, Ievgeniia A.; Petterson, Mats E.; Tellgren-Roth, Christian; Bunikis, Ignas et al.

Part of PLOS ONE, 2013

• DOI for Transcriptome of the Alternative Ethanol Production Strain Dekkera bruxellensis CBS 11270 in Sugar Limited, Low Oxygen Cultivation
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Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors

Edlund, Karolina; Larsson, Ola; Ameur, Adam; Bunikis, Ignas et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 9551-9556, 2012

• DOI for Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors