Douglas Scofield

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations

David, Gabriel; Bertolotti, Alicia; Layer, Ryan; Scofield, Douglas et al.

Ingår i Genome Biology and Evolution, 2024

• DOI för Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations
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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

Arnqvist, Göran; Westerberg, Ivar; Galbraith, James; Sayadi, Ahmed et al.

Ingår i G3, 2024

• DOI för A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
• Ladda ner fulltext (pdf) av A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles

Kaufmann, Philipp; Wiberg, R. Axel W.; Papachristos, Konstantinos; Scofield, Douglas et al.

Ingår i Molecular biology and evolution, 2023

• DOI för Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles
• Ladda ner fulltext (pdf) av Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles

QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)

Gil-Munoz, Francisco; Bernhardsson, Carolina; Ranade, Sonali Sachin; Scofield, Douglas et al.

Ingår i Tree Genetics & Genomes, 2023

• DOI för QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)
• Ladda ner fulltext (pdf) av QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)

Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei

Chen, Hwei-yen; Krieg, Therese; Mautz, Brian; Jolly, Cecile et al.

Ingår i Evolution Letters, s. 478-489, 2023

• DOI för Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei
• Ladda ner fulltext (pdf) av Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations

David, Gabriel; Bertolotti, Alicia; Layer, Ryan; Scofield, Douglas et al.

Ingår i Genome Biology and Evolution, 2024

• DOI för Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations
• Ladda ner fulltext (pdf) av Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations

A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

Arnqvist, Göran; Westerberg, Ivar; Galbraith, James; Sayadi, Ahmed et al.

Ingår i G3, 2024

• DOI för A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
• Ladda ner fulltext (pdf) av A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles

Kaufmann, Philipp; Wiberg, R. Axel W.; Papachristos, Konstantinos; Scofield, Douglas et al.

Ingår i Molecular biology and evolution, 2023

• DOI för Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles
• Ladda ner fulltext (pdf) av Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles

QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)

Gil-Munoz, Francisco; Bernhardsson, Carolina; Ranade, Sonali Sachin; Scofield, Douglas et al.

Ingår i Tree Genetics & Genomes, 2023

• DOI för QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)
• Ladda ner fulltext (pdf) av QTL mapping of the narrow-branch "Pendula" phenotype in Norway spruce (Picea abies L. Karst.)

Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei

Chen, Hwei-yen; Krieg, Therese; Mautz, Brian; Jolly, Cecile et al.

Ingår i Evolution Letters, s. 478-489, 2023

• DOI för Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei
• Ladda ner fulltext (pdf) av Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei

Selection on Accessible Chromatin Regions in Capsella grandiflora

Horvath, Robert; Josephs, Emily B.; Pesquet, Edouard; Stinchcombe, John R. et al.

Ingår i Molecular biology and evolution, s. 5563-5575, 2021

• DOI för Selection on Accessible Chromatin Regions in Capsella grandiflora
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Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens

Schlebusch, Carina; Sjödin, Per; Breton, Gwenna; Günther, Torsten et al.

Ingår i Molecular biology and evolution, s. 2944-2954, 2020

• DOI för Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens
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An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

Bernhardsson, Carolina; Vidalis, Amaryllis; Wang, Xi; Scofield, Douglas et al.

Ingår i G3, s. 1623-1632, 2019

• DOI för An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce

Baison, John; Vidalis, Amaryllis; Zhou, Linghua; Chen, Zhi-Qiang et al.

Ingår i The Plant Journal, s. 83-100, 2019

• DOI för Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce

Summer comes to the Southern Ocean: How phytoplankton shape bacterioplankton communities far into the deep dark sea

Richert, Inga; Yager, Patricia L.; Dinasquet, Julie; Logares, Ramiro et al.

Ingår i Ecosphere, 2019

• DOI för Summer comes to the Southern Ocean: How phytoplankton shape bacterioplankton communities far into the deep dark sea

A major locus controls local adaptation and adaptive life history variation in a perennial plant

Wang, Jing; Ding, Jihua; Tan, Biyue; Robinson, Kathryn M. et al.

Ingår i Genome Biology, 2018

• DOI för A major locus controls local adaptation and adaptive life history variation in a perennial plant

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Lin, Yao-Cheng; Wang, Jing; Delhomme, Nicolas; Schiffthaler, Bastian et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, 2018

• DOI för Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing

Onuţ-Brännström, Ioana; Benjamin, Mitchell; Scofield, Douglas G.; Starri, Heiðmarsson et al.

Ingår i Scientific Reports, 2018

• DOI för Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing
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Tracking the NGS revolution: managing life science research on shared high-performance computing clusters

Dahlö, Martin; Scofield, Douglas; Schaal, Wesley; Spjuth, Ola

Ingår i GigaScience, 2018

• DOI för Tracking the NGS revolution: managing life science research on shared high-performance computing clusters
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Bacteria colonising Penstemon digitalis show volatile and tissue-specific responses to a natural concentration range of the floral volatile linalool

Burdon, Rosalie C. F.; Junker, Robert R.; Scofield, Douglas; Parachnowitsch, Amy L.

Ingår i Chemoecology, s. 11-19, 2018

• DOI för Bacteria colonising Penstemon digitalis show volatile and tissue-specific responses to a natural concentration range of the floral volatile linalool

RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase

Wang, Mi; Uebbing, Severin; Pawitan, Yudi; Scofield, Douglas G.

Ingår i Molecular Ecology Resources, s. 1247-1262, 2018

• DOI för RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase

Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

Steige, Kim A.; Laenen, Benjamin; Reimegård, Johan; Scofield, Douglas G. et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 1087-1092, 2017

• DOI för Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes

Cossu, Rosa Maria; Casola, Claudio; Giacomello, Stefania; Vidalis, Amaryllis et al.

Ingår i Genome Biology and Evolution, s. 3449-3462, 2017

• DOI för LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes

Haploid selection within a single ejaculate increases offspring fitness

Alavioon, Ghazal; Hotzy, Cosima; Nakhro, Khriezhanuo; Rudolf, Sandra et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 8053-8058, 2017

• DOI för Haploid selection within a single ejaculate increases offspring fitness

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Par K.

Ingår i Molecular biology and evolution, s. 1754-1767, 2016

• DOI för Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens
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Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

Eiler, Alexander; Mondav, Rhiannon; Sinclair, Lucas; Fernandez-Vidal, Leyden et al.

Ingår i The ISME Journal, s. 1902-1914, 2016

• DOI för Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Urbina, Hector; Scofield, Douglas G.; Cafaro, Matias; Rosling, Anna

Ingår i Mycoscience, s. 217-227, 2016

• DOI för DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Par K.

Ingår i Genetics, s. 1185-1200, 2016

• DOI för Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species
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The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution

Zuccolo, Andrea; Scofield, Douglas G.; De Paoli, Emanuele; Morgante, Michele

Ingår i Gene, s. 89-99, 2015

• DOI för The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution

Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella

Steige, Kim A.; Reimegård, Johan; Koenig, Daniel; Scofield, Douglas G. et al.

Ingår i Molecular biology and evolution, s. 2501-2514, 2015

• DOI för Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella
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Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Nee)

Sork, Victoria L.; Smouse, Peter E.; Grivet, Delphine; Scofield, Douglas G.

Ingår i Evolutionary Ecology, s. 927-945, 2015

• DOI för Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Nee)

A definitive demonstration of fitness effects due to somatic mutation in a plant

Scofield, Douglas G.

Ingår i Heredity, s. 361-362, 2014

• DOI för A definitive demonstration of fitness effects due to somatic mutation in a plant

What seeds tell us about birds: A multi-year analysis of acorn woodpecker foraging movements

Thompson, Pamela G.; Scofield, Douglas; Sork, Victoria

Ingår i Movement Ecology, s. 12, 2014

• DOI för What seeds tell us about birds: A multi-year analysis of acorn woodpecker foraging movements
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Coefficients of Conservatism Values and the Floristic Quality Index for the vascular plants of south Florida

Mortellaro, Steve; Barry, Mike; Gann, George; Zahina, John et al.

Ingår i Southeastern naturalist (Steuben, Me.), s. 1-62, 2012

• DOI för Coefficients of Conservatism Values and the Floristic Quality Index for the vascular plants of south Florida

Use of Alpha, Beta, and Gamma Diversity Measures to Characterize Seed Dispersal by Animals

Scofield, Douglas; Smouse, Peter E.; Karubian, Jordan; Sork, Victoria L.

Ingår i American Naturalist, s. 719-732, 2012

• DOI för Use of Alpha, Beta, and Gamma Diversity Measures to Characterize Seed Dispersal by Animals

Using Seedling and Pericarp Tissues to Determine Maternal Parentage of Dispersed Valley Oak Recruits

Smouse, Peter E.; Sork, Victoria L.; Scofield, Douglas G.; Grivet, Delphine

Ingår i Journal of Heredity, s. 250-259, 2012

• DOI för Using Seedling and Pericarp Tissues to Determine Maternal Parentage of Dispersed Valley Oak Recruits

Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata N,e) in two California oak savanna-woodlands

Scofield, Douglas G.; Alfaro, Victor Ryan; Sork, Victoria L.; Grivet, Delphine et al.

Ingår i Oecologia, s. 187-196, 2011

• DOI för Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata N,e) in two California oak savanna-woodlands
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When sounds collide: the effect of anthropogenic noise on a breeding assemblage of frogs in Belize, Central America

Kaiser, Kristine; Scofield, Douglas G.; Alloush, Menemsha; Jones, Robin M. et al.

Ingår i Behaviour, s. 215-232, 2011

• DOI för When sounds collide: the effect of anthropogenic noise on a breeding assemblage of frogs in Belize, Central America

Influence of acorn woodpecker social behaviour on transport of coast live oak (Quercus agrifolia) acorns in a southern California oak savanna

Scofield, Douglas G.; Sork, Victoria L.; Smouse, Peter E.

Ingår i Journal of Ecology, s. 561-572, 2010

• DOI för Influence of acorn woodpecker social behaviour on transport of coast live oak (Quercus agrifolia) acorns in a southern California oak savanna

Endogenous Mechanisms for the Origins of Spliceosomal Introns

Catania, Francesco; Gao, Xiang; Scofield, Douglas

Ingår i Journal of Heredity, s. 591-596, 2009

• DOI för Endogenous Mechanisms for the Origins of Spliceosomal Introns

Intron presence-absence polymorphisms in Daphnia

Omilian, Angela; Scofield, Douglas; Lynch, Michael

Ingår i Molecular biology and evolution, s. 2129-2139, 2008

• DOI för Intron presence-absence polymorphisms in Daphnia

Evolutionary Diversification of the Sm Family of RNA-Associated Proteins

Scofield, Douglas; Lynch, Michael

Ingår i Molecular biology and evolution, s. 2255-2267, 2008

• DOI för Evolutionary Diversification of the Sm Family of RNA-Associated Proteins

Position of the final intron in full-length transcripts: Determined by NMD?

Scofield, Douglas; Hong, Xin; Lynch, Michael

Ingår i Molecular biology and evolution, s. 896-899, 2007

• DOI för Position of the final intron in full-length transcripts: Determined by NMD?

Medial pith cells per meter in twigs as a proxy for mitotic growth rate (Phi/m) in the apical meristem

Scofield, Douglas

Ingår i American Journal of Botany, s. 1740-1747, 2006

• DOI för Medial pith cells per meter in twigs as a proxy for mitotic growth rate (Phi/m) in the apical meristem

Intron size, abundance, and distribution within untranslated regions of genes

Hong, Xin; Scofield, Douglas; Lynch, Michael

Ingår i Molecular biology and evolution, s. 2392-2404, 2006

• DOI för Intron size, abundance, and distribution within untranslated regions of genes

Mitosis, stature and evolution of plant mating systems: low-Phi and high-Phi plants

Scofield, Douglas; Schultz, Stewart

Ingår i Proceedings of the Royal Society of London. Biological Sciences, s. 275-282, 2006

• DOI för Mitosis, stature and evolution of plant mating systems: low-Phi and high-Phi plants

The evolution of transcription-initiation sites

Lynch, Michael; Scofield, Douglas; Hong, Xin

Ingår i Molecular biology and evolution, s. 1137-1146, 2005

• DOI för The evolution of transcription-initiation sites

Variant calling using NGS data in European aspen (Populus tremula)

Wang, Jing; Scofield, Douglas G.; Street, Nathaniel R.; Ingvarsson, Pär K.

Ingår i Advances in the Understanding of Biological Sciences using Next Generation Sequencing (NGS) Approaches, Springer, 2015

NMD and the evolution of eukaryotic gene structure

Lynch, Michael; Hong, Xin; Scofield, Douglas G.

Ingår i Nonsense-Mediated mRNA Decay, s. 197-211, Landes Bioscience/Eurekah.com, 2006

Contribution of ecdysone signaling to photoperiodic wing polyphenism in the water strider Gerris buenoi

Gudmunds, Erik; Armisen, David; Mesilaakso, Lauri; Scofield, Douglas et al.

The combination of HiFi and HiC sequencing technologies enables the investigation of structural variants in speciation of Ficedula flycatchers

Chase, Madeline; Scofield, Douglas; Kraft, Fanny-Linn; Segami, Carolina et al.

Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management

Söderquist, Linus; Joffard, Nina; Scofield, Douglas; Milesi, Pascal et al.

Assembly of polymorphic Y chromosomes reveals molecular basis of variation in male body size

Kaufmann, Philipp; Wiberg, R. Axel. W.; Paida, Varvara; Papachristos, Konstantinos et al.