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1. Full Text Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations
by Igoshin, Alexander V and Yurchenko, Andrey A and Belonogova, Nadezhda M and Petrovsky, Dmitry V and Aitnazarov, Ruslan B and Soloshenko, Vladimir A and Yudin, Nikolay S and Larkin, Denis M
BMC Genetics, ISSN 1471-2156, 03/2019, Volume 20, Issue Suppl 1, pp. 26 - 14
Background: Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding.... 
GWAS | Cattle | Body temperature | Selection | Cold climate | DCMS | MSANTD4 | Adaptation | GRIA4 | LOCALIZATION | MODEL | HEREFORD CATTLE | GLUTAMATE RECEPTORS | DISEASE | GENETICS & HEREDITY | NMDA | PROTEINS | EXPRESSION | HISTORY | Genome-wide association studies | Usage | Genetic aspects | Single nucleotide polymorphisms | Research | Haplotypes | Temperature | Candidates | Climate | Laboratories | Genomics | Climatic conditions | Thermoregulation | Genomes | Single-nucleotide polymorphism | Temperature effects | Population | Genetics | Tumor necrosis factor-TNF | Deoxyribonucleic acid--DNA | Phenotypes | Breeding | Metabolism | Gene expression | Stress | Studies | Heat | Cold shock | Livestock | Polymorphism
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2. Full Text A Near Chromosome Assembly of the Dromedary Camel Genome
by Ruvinskiy, D and Larkin, DM and Farre, M
FRONTIERS IN GENETICS, ISSN 1664-8021, 02/2019, Volume 10, p. 32
The dromedary camel is an economically and socially important species of livestock in many parts of the world, being used for transport and the production of... 
camelids | genome | ANNOTATION | chromosome | CATTLE | GENETICS & HEREDITY | assembly | dromedary camel | INSIGHTS | Economic aspects | Genomes | Genetic aspects | Camels | Research | Chromosomes
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3. Full Text Construction of red fox chromosomal fragments from the short-read genome assembly
by Rando, Halie M and Farré, Marta and Robson, Michael P and Won, Naomi B and Johnson, Jennifer L and Buch, Ronak and Bastounes, Estelle R and Xiang, Xueyan and Feng, Shaohong and Liu, Shiping and Xiong, Zijun and Kim, Jaebum and Zhang, Guojie and Trut, Lyudmila N and Larkin, Denis M and Kukekova, Anna V
Genes, ISSN 2073-4425, 06/2018, Volume 9, Issue 6, p. 308
The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X... 
Chromosome assembly | Carnivora | Comparative genomics | Canidae | 10K Genomes Project | Evolutionary breakpoints | Genome assembly | Chromosome evolution | Vulpes vulpes | chromosome assembly | BANDING PATTERNS | SILVER FOX | chromosome evolution | comparative genomics | genome assembly | EVOLUTION | SEQUENCE | CAT | GENETICS & HEREDITY | evolutionary breakpoints | KARYOTYPE | DOG | MAP | MAMMALS | Foxes | Next-generation sequencing | Animal behavior | Computer applications | Synteny | Science | Meiosis | Gene mapping | Chromosomes
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4. Full Text Time lapse: A glimpse into prehistoric genomics
by Griffin, Darren K and Larkin, Denis M and O'Connor, Rebecca E
European Journal of Medical Genetics, ISSN 1769-7212, 03/2019
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5. Reconstruction and evolutionary history of eutherian chromosomes
by Jaebum Kim and Marta Farré and Loretta Auvil and Boris Capitanu and Denis M Larkin and Jian Ma and Harris A Lewin
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 07/2017, Volume 114, Issue 27, p. E5379
Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in... 
Breakpoints | Apes | Nucleotide sequence | Chimpanzees | Synteny | Fragments | Homology | Genomes | Mammals | Chromosome rearrangements | Fragmentation | Conserved sequence | Placenta | Etiology | Rodents | Evolution | Assemblies | Chromosomes | Speciation
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6. Full Text Analyses of pig genomes provide insight into porcine demography and evolution
by Groenen, Martien A.M and Archibald, Alan L and Uenishi, Hirohide and Tuggle, Christopher K and Takeuchi, Yasuhiro and Rothschild, Max F and Rogel-Gaillard, Claire and Park, Chankyu and Milan, Denis and Megens, Hendrik-Jan and Li, Shengting and Larkin, Denis M and Kim, Heebal and Frantz, Laurent A.F and Caccamo, Mario and Ahn, Hyeonju and Aken, Bronwen L and Anselmo, Anna and Anthon, Christian and Auvil, Loretta and Badaoui, Bouabid and Beattie, Craig W and Bendixen, Christian and Berman, Daniel and Blecha, Frank and Blomberg, Jonas and Bolund, Lars and Bosse, Mirte and Botti, Sara and Bujie, Zhan and Bystrom, Megan and Capitanu, Boris and Carvalho-Silva, Denise and Chardon, Patrick and Chen, Celine and Cheng, Ryan and Choi, Sang-Haeng and Chow, William and Clark, Richard C and Clee, Christopher and Crooijmans, Richard P.M.A and Dawson, Harry D and Dehais, Patrice and De Sapio, Fioravante and Dibbits, Bert and Drou, Nizar and Du, Zhi-Qiang and Eversole, Kellye and Fadista, Joao and Fairley, Susan and Faraut, Thomas and Faulkner, Geoffrey J and Fowler, Katie E and Fredholm, Merete and Fritz, Eric and Gilbert, James G.R and Giuffra, Elisabetta and Gorodkin, Jan and Griffin, Darren K and Harrow, Jennifer L and Hayward, Alexander and Howe, Kerstin and Hu, Zhi-Liang and Humphray, Sean J and Hunt, Toby and Hornshoøj, Henrik and Jeon, Jin-Tae and Jern, Patric and Jones, Matthew and Jurka, Jerzy and Kanamori, Hiroyuki and Kapetanovic, Ronan and Kim, Jaebum and Kim, Jae-Hwan and Kim, Kyu-Won and Kim, Tae-Hun and Larson, Greger and Lee, Kyooyeol and Lee, Kyung-Tai and Leggett, Richard and Lewin, Harris A and Li, Yingrui and Liu, Wansheng and Loveland, Jane E and Lu, Yao and Lunney, Joan K and Ma, Jian and Madsen, Ole and Mann, Katherine and Matthews, Lucy and McLaren, Stuart and Morozumi, Takeya and Murtaugh, Michael P and Narayan, Jitendra and Nguyen, Dinh Truong and Ni, Peixiang and Oh, Song-Jung and Onteru, Suneel and Panitz, Frank and Park, Eung-Woo and ... and Medicinska fakulteten and Science for Life Laboratory, SciLifeLab and Fysiologi and Medicinska och farmaceutiska vetenskapsområdet and Institutionen för medicinsk biokemi och mikrobiologi and Klinisk virologi and Uppsala universitet and Institutionen för medicinska vetenskaper and Klinisk mikrobiologi och infektionsmedicin and Institutionen för neurovetenskap
Nature, ISSN 0028-0836, 11/2012, Volume 491, Issue 7424, pp. 393 - 398
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes... 
COMPLEX | GENE | VARIANTS | MULTIDISCIPLINARY SCIENCES | SEQUENCE | RECEPTOR | TASTE | LOCUS | SUS-SCROFA | Sus scrofa - genetics | Animals | Demography | Genome - genetics | Molecular Sequence Data | Models, Animal | Phylogeny | Sus scrofa - classification | Population Dynamics | Chromosome mapping | Genetic aspects | Genomes | Research | Identification and classification | Wild boar | Hogs | Genetics | Evolution | Genes | Genomics | Life Sciences | Animal biology | Biological Sciences | Biology with specialization in Evolutionary Functional Genomics | Lantbruksvetenskaper | Animal and Dairy Science | Agricultural Sciences | Biologi med inriktning mot evolutionär funktionsgenomik | Genetik | Naturvetenskap | Biologiska vetenskaper | Husdjursvetenskap | Biology with specialization in Evolutionary Genetics | Evolutionsbiologi | Biologi med inriktning mot evolutionär genetik | Natural Sciences | Evolutionary Biology
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7. Full Text Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation
by Joseph, S and O'Connor, RE and Al Mutery, AF and Watson, M and Larkin, DM and Griffin, DK
DIVERSITY-BASEL, ISSN 1424-2818, 12/2018, Volume 10, Issue 4, p. 113
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus... 
falcons | SEQUENCES | chromosomes | AVIAN GENOME | FALCONIFORMES | PEREGRINE | avian | genome | karyotype | EVOLUTION | ECOLOGY | AVES | BIRDS | INSIGHTS
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8. Full Text G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences
by Lenis, Vasileios Panagiotis E and Swain, Martin and Larkin, Denis M
GigaScience, ISSN 2047-217X, 05/2018, Volume 7, Issue 5
Background: Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence... 
highly conserved elements (HCE) | ELEMENTS | PROJECT | ALIGNMENT | RECONSTRUCTION | MULTIDISCIPLINARY SCIENCES | genome evolution | sequencing anchoring | ANCESTRAL GENOMES | sequence mapping | whole-genome alignment | VERTEBRATE
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9. Full Text Comparative genomics reveals insights into avian genome evolution and adaptation
by Correction Zhang, Guojie and Li, Cai and Li, Qiye and Li, Bo and Larkin, Denis M and Lee, Chul and Storz, Jay F and Antunes, Agostinho and Greenwold, Matthew J and Meredith, Robert W and Ödeen, Anders and Cui, Jie and Zhou, Qi and Xu, Luohao and Pan, Hailin and Wang, Zongji and Jin, Lijun and Zhang, Pei and Hu, Haofu and Yang, Wei and Hu, Jiang and Xiao, Jin and Yang, Zhikai and Liu, Yang and Xie, Qiaolin and Yu, Hao and Lian, Jinmin and Wen, Ping and Zhang, Fang and Li, Hui and Zeng, Yongli and Xiong, Zijun and Liu, Shiping and Zhou, Long and Huang, Zhiyong and An, Na and Wang, Jie and Zheng, Qiumei and Xiong, Yingqi and Wang, Guangbiao and Wang, Bo and Wang, Jingjing and Fan, Yu and Da Fonseca, Rute R and Alfaro-Núñez, Alonzo and Schubert, Mikkel and Orlando, Ludovic and Mourier, Tobias and Howard, Jason T and Ganapathy, Ganeshkumar and Pfenning, Andreas and Whitney, Osceola and Rivas, Miriam V and Hara, Erina and Smith, Julia and Farré, Marta and Narayan, Jitendra and Slavov, Gancho and Romanov, Michael N and Borges, Rui and Machado, João Paulo and Khan, Imran and Springer, Mark S and Gatesy, John and Hoffmann, Federico G and Opazo, Juan C and Håstad, Olle and Sawyer, Roger H and Kim, Heebal and Kim, Kyu-Won and Kim, Hyeon Jeong and Cho, Seoae and Li, Ning and Huang, Yinhua and Bruford, Michael W and Zhan, Xiangjiang and Dixon, Andrew and Bertelsen, Mads F and Derryberry, Elizabeth and Warren, Wesley and Wilson, Richard K and Li, Shengbin and Ray, David A and Green, Richard E and O'Brien, Stephen J and Griffin, Darren and Johnson, Warren E and Haussler, David and Ryder, Oliver A and Willerslev, Eske and Graves, Gary R and Alström, Per and Fjeldså, Jon and Mindell, David P and Edwards, Scott V and Braun, Edward L and Rahbek, Carsten and Burt, David W and Houde, Peter and Zhang, Yong and ... and Avian Genome Consortium and Teknisk-naturvetenskapliga vetenskapsområdet and Biologiska sektionen and Uppsala universitet and Zooekologi and Institutionen för ekologi och genetik
Science, ISSN 0036-8075, 12/2014, Volume 346, Issue 6215, pp. 1311 - 1320
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full... 
MUTATION-RATE | INTRON SIZE | GENE DUPLICATION | MULTIDISCIPLINARY SCIENCES | CHICKEN | TRANSPOSABLE ELEMENTS | DIVERSITY | VERTEBRATE | BIRDS | FUNCTIONAL DIVERSIFICATION | RAPID EVOLUTION | Adaptation, Physiological | Genes | Genomics | Synteny | Male | Phylogeny | Biodiversity | Genetic Variation | Conserved Sequence | Female | Molecular Sequence Annotation | Selection, Genetic | Reproduction - genetics | Vocalization, Animal | Birds - classification | Flight, Animal | Birds - physiology | Sequence Analysis, DNA | Biological Evolution | Vision, Ocular - genetics | Animals | Diet | Birds - genetics | Genome | Evolution, Molecular | Genetic research | Genetic aspects | Bird populations | Zoological research | Adaptation (Biology) | Research | Evolutionary biology | Birds | Evolutionary | Deletion | Evolution | Genomes | Nucleotides | Erosion | Adaptation | Biological Sciences | Evolutionsbiologi | Naturvetenskap | Natural Sciences | Evolutionary Biology | Biologiska vetenskaper
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10. Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors
by Iona M MacLeod and Denis M Larkin and Harris A Lewin and Ben J Hayes and Mike E Goddard
Molecular Biology and Evolution, ISSN 0737-4038, 09/2013, Volume 30, Issue 9, p. 2209
  Whole-genome sequence is potentially the richest source of genetic data for inferring ancestral demography. However, full sequence also presents significant... 
Estimation bias | Demography | Cattle | Genomes
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11. Full Text Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps
by William J. Murphy and Denis M. Larkin and Annelie Everts-van der Wind and Guillaume Bourque and Glenn Tesler and Loretta Auvil and Jonathan E. Beever and Bhanu P. Chowdhary and Francis Galibert and Lisa Gatzke and Christophe Hitte and Stacey N. Meyers and Denis Milan and Elaine A. Ostrander and Greg Pape and Heidi G. Parker and Terje Raudsepp and Margarita B. Rogatcheva and Lawrence B. Schook and Loren C. Skow and Michael Welge and James E. Womack and Stephen J. O'Brien and Pavel A. Pevzner and Harris A. Lewin
Science, ISSN 0036-8075, 7/2005, Volume 309, Issue 5734, pp. 613 - 617
The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating... 
Telomeres | Human genome | Humans | Genes | Centromeres | Dogs | Primates | Evolution | Reports | Genomes | Chromosomes | RADIATION HYBRID MAP | HUMAN GENOME SEQUENCE | MULTIDISCIPLINARY SCIENCES | RESOLUTION | SEGMENTAL DUPLICATIONS | BREAKPOINT | MOUSE GENOMES | CENTROMERE | REARRANGEMENTS | INVERSION | REGION | Mammals - genetics | Chromosomes, Mammalian - genetics | Horses - genetics | Synteny | Cats - genetics | Swine - genetics | Chromosome Inversion | Neoplasms - genetics | Dogs - genetics | Chromosomal Instability | Chromosome Breakage | Telomere - genetics | Mice - genetics | Chromosomes, Human - genetics | Computational Biology | Chromosome Mapping | Rats - genetics | Cattle - genetics | Animals | Centromere - genetics | Chromosome Aberrations | Genome | Genome, Human | Evolution, Molecular | Case studies | Comparative analysis | Evolutionary biology | Mammals | Human Genome Project | Biological diversity
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12. Full Text Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs
by O'Connor, Rebecca E and Romanov, Michael N and Kiazim, Lucas G and Barrett, Paul M and Farré, Marta and Damas, Joana and Ferguson-Smith, Malcolm and Valenzuela, Nicole and Larkin, Denis M and Griffin, Darren K
Nature Communications, ISSN 2041-1723, 12/2018, Volume 9, Issue 1, pp. 1883 - 9
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic... 
DENSITY | ORIGIN | MULTIDISCIPLINARY SCIENCES | SIZE | PERSPECTIVES | DYNAMICS | BIRDS | REVEALS | INSIGHTS | Animals | Dinosaurs - classification | Dinosaurs - genetics | Chromosomes - genetics | Genomics | Karyotyping | Birds - classification | Phylogeny | Birds - genetics | Genome | Evolution, Molecular | Fossils | Dinosaurs | Chromatin | Divergence | Transcription | Biological evolution | Turtles | Birds | Evolution | Genomes | Chromosomes | Molecular chains
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