Department: Comparative Biomedical Sciences

Campus: Camden

Denis is a Reader in Comparative genomics. His research interests focus primarily on evolutionary genomics and animal genetics. He is currently working on ruminant genome evolution and chromosome evolution of avian species, UK sheep genetics, and interactive visualization tools and algorithms dedicated to whole-genome studies.

After graduating from the Novosibirsk State University, Dr. Larkin obtained Ph.D. degree in Genetics from the Institute of Cytology and Genetics, Novosibirsk. Then he spent nine years at the University of Illinois at Urbana-Champaign where his research was focused on studying chromosomal evolution and selection in mammals and other species using state-of-the-art methods of molecular genomics and bioinformatics. Earlier in his career he constructed high-resolution cattle radiation hybrid and physical maps which were used as backbones for the assembly of the cattle and pig genome sequences.

Dr. Larkin developed Evolution Highway an interactive tool to visualise comparative chromosome maps as well as SyntenyTracker, an algorithm to build homologous synteny blocks from the whole-genome maps or sequence alignments. He performed the analysis of milk production traits in the North American Holstein-Friesian population, and the genetic structure of Welsh sheep breeds.

After his move to the UK in 2010 Dr. Larkin spent three years as a lecturer in animal genetics at Aberystwyth University. Dr. Larkin joined the Royal Veterinary College in 2013. In 2012 Denis Larkin was awarded a BBSRC New Investigator award to support his research on comparative assembly of vertebrate genomes and later he received a BBSRC responsive mode grant to improve genome assemblies and study chromosome evolution in birds.

Dr. Larkin’s current efforts are directed towards analysis of various aspects of genome evolution using sequenced animal, worm and insect genomes and a study of signatures of artificial selection in the UK sheep. The main activities of his group include the analysis of chromosomal and other aspects of the blind mole rat evolution (in collaboration with Prof. Nevo’s group at the University of Haifa), ruminant genome evolution (contribution to the G10K community, collaboration with Prof. Lewin, UCD and BGI), reconstruction of ancestral mammalian karyotypes (with Prof. Lewin, UCD, Dr. Ma, UIUC), avian genomics (with Prof. Griffin, University of Kent), genomic selection in sheep (with Innovis, Roslin Institute, Aberystwyth University) and the UK sheep population structure (collaboration with Dr. Slavov from Aberystwyth University and Meat Promotion Wales (HCC). His laboratory develops algorithms and tools for the whole-genome analysis (e.g., Kim et al., 2013) and collaborates closely with several groups from China. For example, one of his ongoing projects running in close collaboration with BGI focuses on comparative genome analysis of sequenced ruminant genomes.

Tools and resources we built:

Evolution Highway (old version)

Evolution Highway (avian data)

Evolution Highway (insect data)

Evolution Highway (blind mole rat)

Evolutioh Highway (tibetan antelope)

Evolution Highway (mammalian ancestors)

SyntenyTracker

RACA (collaboration with Jian Ma, Jaebum Kim, Harris Lewin)

Evolution Factory

Local mirror of the UCSC genome browser (10K ruminant data) (currently under the RVC firewall).

Most of Dr Larkin's publications are available from his ResearchGate profile: https://www.researchgate.net/profile/Denis_Larkin

A complete, up-to-date list of publications is also available from Google Scholar: https://scholar.google.co.uk/citations?user=hVpcNAkAAAAJ&hl=en (H=25).


42. Kim J, Farré M, Auvil L, Capitanu B, Larkin DM*, Ma J* & Lewin HA*. 2017. Reconstruction and evolutionary history of eutherian chromosomes. Proc Natl Acad Sci U S A. Jun 19. pii: 201702012. doi: 10.1073/pnas.1702012114.  [Epub ahead of print]. *corresponding authors. IF=9.4 [link]

41. Damas J., O'Connor R., Farré M., Lenis V.P., Martell H.J., Mandawala A., Fowler K., Joseph S., Swain M.T., Griffin D.K. & Larkin D.M. 2016. Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research. [Epub ahead of print]. IF=11.35 [link]

40. Capilla L., Sánchez-Guillén R.A., Farré M., Paytuví-Gallart A., Malinverni R., Ventura J., Larkin D.M. & Ruiz-Herrera A. 2016. Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia. Genome Biology and Evolution [Epub ahead of print]. IF=4.23 [link]

40. Farré M., Narayan J., Slavov G.T., Damas J., Auvil L., Li C., Jarvis E.D., Burt D.W., Griffin D.K. & Larkin D.M. 2016. Novel insights into chromosome evolution in birds, archosaurs, and reptiles. Genome Biology and Evolution 8(8):2442-51. IF=4.23 [link]

39. Adams H.A., Sonstegard T.S., VanRaden P.M., Null D.J., Van Tassell C.P., Larkin D.M. & Lewin H.A. 2016. Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle. Journal of Dairy Science  99(8):6693-701. IF=2.57 [link]

38. Beynon S., Slavov G.T., Farre M., Sunduimijid B., Waddams K., Davies B., Haresign W., Kijas J., MacLeod I.M., Newbold C.J., Davies L. & Larkin D.M. 2015. Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genetics. 16(1):65. IF=2.36. [link].

37. Koepfli K.P., Paten B., the Genome 10K Community of Scientists & O’Brien S.J. 2015. The genome 10K project: a way forward further. Annual Review of Animal Biosciences. 3:57-111. [link].

36. Romanov M.N., Farré M., Lightgow P.E., Fowler K.E., Skinner B.M., O'Connor R., Vignal A., Faraut T., Backström N., Jarvis E.D., Matsuda Y., Nishida C., Zhang G., Houde P, Ellegren H., Burt D.W. & Larkin D.M.*, Darren K. Griffin*. 2014. Reconstruction of the avian genome organization and evolution from a chromosomal perspective suggests that chicken (Gallus gallus) most closely resembles the dinosaur avian ancestor. BMC Genomics. 15:1060. *corresponding authors. IF=4.04. [link].

35. Zhang G., Li C., Li Q., Li B., Larkin D.M*., et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 346:1311-1320. *co-leader of the chromosome evolution group. IF=31.48. [link].

34. Heaton M.P., Leymaster K.A., Kalbfleisch T.S., Kijas J.W., Clarke S.M., McEwan J., Maddox J.F., Basnayake V., Petrik D.T., Simpson B., Smith T.P., Chitko-McKown C.G., International Sheep Genomics Consortium. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS One. 16;9:e94851. IF=3.23. [link].

33. International Glossina Genome Initiative. 2014. Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science. 344: 380-386. IF=31.48. [link].

32. Fang X.*, Nevo E.*, Han L.*, Levanon E.Y.*, Zhao J.*, Avivi A.*, Larkin D.M.*, Jiang X.*, Feranchuk S., Zhu Y., Fishman A., Feng Y., Sher N., Xiong Z., Hankeln T., Huang Z., Gorbunova V., Zhang L., Zhao W., Wildman D.E., Xiong Y., Gudkov A., Zheng Q., Rechavi G., Liu S., Bazak L., Chen J., Knisbacher B.A., Lu Y., Shams I., Gajda K., Farré M., Kim J., Lewin H.A., Ma J., Band M., Bicker A., Kranz A., Mattheus T., Schmidt H., Seluanov A., Azpurua J., McGowen M.R., Jacob E.B., Peng S., Zhu X., Liao X., Li S., Krogh A., Zhou X., Brodsky L. & Wang J. 2014. Genome-wide analysis uncovers evolution of the blind mole rat, Spalax: adaptive complexes to stressful life underground. Nature Communications 5 (3966). *equal authors. IF=10.74. [link].

31. Trifonov V.A., Dementyeva P.V., Larkin D.M., O’Brien P.C.M., Perelman P.L., Yang F., Ferguson-Smith M.A. & Graphodatsky A.S. 2013. Transcription of protein-coding genes on B chromosomes of the Siberian roe deer (Capreolus pygargus) BMC Biol., 11:90. IF=7.98. [link].

30. MacLeod I.M., Larkin D.M., Lewin H.A., Hayes B.J. & Goddard M.E. 2013 Reconstructing demographic history from haplotype homozygosity in whole genome sequence data: an example from Bovinae. Mol Biol Evol. 9:2209-2223. IF=14.31. [link].

29. Ge R.-L., Cai Q, Shen Y.-Y., Asan, Ma L., Zhang Y., Yi X., Chen Y., Yang L., Huang Y., He R., Hui Y., Hao M., Li Y., Wang B., Ou X., Xu J., Zhang Y., Wu K., Geng C., Zhou W.-P., Zhou T.-C., Irwin D.M., Yang Y., Ying L., Bao H., Kim J., Larkin D.M., Ma J., Lewin H.A., Xing J., Auvil L., Capitanu B., Zhang X., Zhang G., Murphy, R.W., Wang J., Zhang Y.-P. & Wang J. 2013. The de novo genome sequence of the Tibetan antelope and identification of genetic adaptation to high altitude.  Nature Communications. 4:1858. IF=10.74. [link].

28. Kim J.*, Larkin D.M.* , Cai Q., Asan, Zhang Y., Ge R., Auvil L., Capitanu B., Zhang G., Lewin H.A. & Ma J. 2013. RACA: Reference-Assisted Chromosome Assembly 2013. The Proceedings of the National Academy of Sciences of the USA 110: 1785-1790. *equal authors. IF=9.81. [link].

27. Groenen M.A.M, Archibald A.L., Uenishi H., Tuggle C.K., Takeuchi Y., Rothschild M.F., Park C., Li S., Milan D., Megens H.-J., Larkin D.M*., et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature. 49:393-398. *leader of the chromosome evolution group. IF=42.35. [link].

26. Qiu Q., Zhang G., Ma T., Qian W., Wang J., Ye Z., Cao C., Hu Q., Kim J., Larkin D.M., Auvil L., Capitanu B., Ma J., Lewin H.A., Qian X., Lang Y., Zhou R., Wang L., Wang K., Xia J., Liao S., Pan S., Lu X., Hou H., Wang Y., Zang X., Yin Y., Ma H., Zhang J., Wang Z., Zhang Y., Yonezawa T., Hasegawa M., Zhong Y., Liu W., Zhang Y., Huang Z., Zhang S., Long R., Lenstra J.-A., Cooper D.N., Wu Y., Shi P., Wang J. & Liu J. 2012. The yak genome and its adaptation to life at high-altitude. Nature Genetics. 44: 946-949. IF=29.65. [link].

25. Larkin D.M., Daetwyler H., Hernandez A.G., Wright C.L., Hetrick L.A., Boucek L., Bachman S.L., Band M.R., Akraiko T.V., Cohen-Zinder M., Thimmapuram J., Macleod I.M., Harkins T.T., McCague J., Goddard M.E., Hayes B.J. & Lewin H.A. 2012. Resequencing of champions: detection of haplotypes under selection in dairy cattle. The Proceedings of the National Academy of Sciences of the USA. 109: 7693-7698. IF=9.81. [link].

24. Swain M.T.*, Larkin D.M.*, Caffrey C.R., Davies S.J., Loukas A, Skelly  P.J. & Hoffmann K.F. 2011. Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery, Trends in Parasitology 27(12):555-564. (cover paper). *equal authors. IF=6.22. [link].

23. Larkin D.M. 2011. Status of the cattle genome map. Cytogenetics and Genome Research. 134:1-8 (invited review). IF=1.91. [link].

22. Cohen-Zinder M., Donthu R., Larkin D.M., Kumar C.G., Rodriguez-Zas S.L., Andropolis K.E., Oliveira R. & Lewin H.A. 2011. A multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits. Physiol Genomics. 43:1185-97. IF=2.81. [link].

21. Donthu R., Larkin D.M., Heaton M. & Lewin H.A. 2010. In silico discovery, mapping, and genotyping of 1,039 cattle SNPs on a panel of eighteen breeds. Animal Genetics. 41:421-423. IF=2.21. [link].

20. Donthu R., Lewin H.A. & Larkin D.M. 2009. SyntenyTracker: a tool for defining homologous synteny blocks using radiation hybrid maps and whole genome sequence. BMC Research Notes. 2: 148. [link].

19. Lewin H.A, Larkin D.M., Pontius J. & O’Brien S.J. 2009. Every genome sequence needs a good map. Genome Research. 19:770-777. IF=13.85. [link].

18. Piontkivska H., Yang M.Q., Larkin D.M., Lewin H.A., Reecy J. & Elnitski L. 2009. Orthology-mapping of bidirectional promoters enables 5' UTR prediction and identifies species-specific genes. BMC Genomics. 10: 189. IF=4.04. [link].

17. Bovine genome sequencing and analysis consortium. 2009. The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science, 324: 522-528. IF=31.48. [link].

16. Larkin D.M., Pape G., Donthu R., Auvil L., Welge M. & Lewin H.A. 2009. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Research. 19: 770-777. IF=13.85. [link].

15. Rogatcheva M.B., Chen K., Larkin D.M., Meyers S.N., Marron B.M., He W., Schook L.B. & Beever J.E. 2008. Piggy-BACing the human genome I: constructing a porcine BAC physical map through comparative genomics. Animal Biotechnology. 19: 28-42. IF=0.64. [link].

14. Snelling W.M., Chiu R., Schein J.E., Hobbs M., Abbey C.A., Adelson D.L., Aerts J., Bennett G.L., Bosdet I.E., Boussaha M., Brauning R., Caetano A.R., Costa M.M., Crawford A.M., Dalrymple B.P., Eggen A., Everts-van der Wind A., Floriot S., Gautier M., Gill C.A., Green R.D., Holt R., Jann O., Jones S.J., Kappes S.M., Keele J.W., de Jong P.J., Larkin D.M., Lewin H.A., McEwan J.C., McKay S., Marra M.A., Mathewson C.A., Matukumalli L.K., Moore S.S., Murdoch B., Nicholas F.W., Osoegawa K., Roy A., Salih H., Schibler L., Schnabel R.D., Silveri L., Skow L.C., Smith T.P., Sonstegard T.S., Taylor J.F., Tellam R., Van Tassell C.P., Williams J.L., Womack J.E., Wye N.H., Yang G., Zhao S. & International Bovine BAC Mapping Consortium. 2007. A physical map of the bovine genome. Genome Biology. 8: R165. IF=10.47. [link].

13. Chae S.H., Kim J.W., Choi J.M., Larkin D.M., Everts-van der Wind A., Park S.H., Yeo J.S. & Choi I. 2007.  Chromosomal localization of korean cattle (Hanwoo) BAC clones via BAC end sequence analysis. Asian-Australian Journal of Animal Sciences. 20: 316-327. IF=0.56. [link].

12. Larkin D.M., Prokhorovich M.A., Astakhova N.M. & Zhdanova N.S. 2006. Comparative mapping of mink chromosome 8p: in situ hybridization of seven cattle BAC clones. Animal Genetics. 37: 429-430. IF=2.21. [link].

11. Larkin, D.M., Astakhova N.M., Prokhorovich M.A., Lewin H.A. & Zhdanova N.S. 2006. Comparative mapping of cattle chromosome 19: cytogenetic localization of 19 BAC clones. Cytogenetic and Genome Research. 112: 235-240. IF=1.91. [link].

10. Hong J.M., Chae S.H., Oriero N., Larkin D.M., Choi C.B., Lee J.Y., Lewin H.A., Bae J.H., Choi I. & Yeo J.S. 2005. Identification and chromosomal localization of repeat sequences through BAC end sequence analysis in Korean cattle. Journal of Genetics. 84: 329-335. IF=1.01. [link].

9. Everts-van der Wind A.*, Larkin D.M.*, Green C.A., Elliott J.S., Olmstead C.A., Chiu R., Schein J.E., Marra M.A., Womack J.E. & Lewin H.A. 2005. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. The Proceedings of the National Academy of Sciences of the USA. 102: 18526-18531. *equal authors. IF=9.81. [link].

8. Meyers S.N., Rogatcheva M.B., Larkin D.M., Yerle M., Milan D., Hawken R.J., Schook L.B. & Beever J.E. 2005. Piggy-BACing the human genome: II. A high-resolution, physically-anchored, comparative map of the porcine autosomes. Genomics. 86: 739-752. IF=2.79. [link].

7. Murphy W.J.*, Larkin D.M.*, Everts-van der Wind A.*, Bourque G., Tesler G., Auvil L., Beever J.E., Chowdhary B.P., Galibert F., Gatzke L., Hitte C., Meyers S.N., Milan D., Ostrander E.A., Pape G., Parker H.G., Raudsepp T., Rogatcheva M.B., Schook L.B., Skow L.C., Welge M., Womack J.E., O'Brien S.J., Pevzner P.A. & Lewin H.A. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 309: 613-617. *equal authors. IF=31.48. [link].

6. Cohen-Zinder M., Seroussi E., Larkin D.M., Loor J.J., Everts-van der Wind A., Lee J.H., Drackley J.K., Band M.R., Hernandez A.G., Shani M., Lewin H.A., Weller J.I. & Ron M. 2005. Identification of a missense mutation in the bovine ABCG2 gene with major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. Genome Research. 15: 936-944. IF=13.85. [link].

5. Everts-van der Wind A., Kata S., Band M.R., Rebeiz M., Larkin D.M., Everts R.E., Green C.A., Liu L., Natarajan S., Goldammer T., Lee J.H., McKay S., Womack J.E. & Lewin H.A. 2004. A 1,463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Research. 14: 1424-1437. IF=13.85. [link].

4. Lui L., Gong G., Natarajan S., Larkin D.M., Everts-van der Wind A., Rebeiz M. & Beever J.E. 2004. Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics. 20: 148-54. IF=4.62. [link].

3. Larkin D.M., Everts-van der Wind A., Rebeiz M., Schweitzer P.A., Bachman S., Green C., Wright C.L., Campos E.J., Benson L.D., Edwards J., Liu L., Osoegawa K., Womack J.E., de Jong P.E. & Lewin H.A. 2003. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Research. 13: 1966-1972 (cover paper). IF=13.85. [link].

2. Larkin D.M., Serov O.L, Borodin P.M., Zhdanova N.S. & Searle J.B. 2000. Comparative mapping in mammals: shrew genome map. Acta Theriologica. 45: 131-141. IF=1.16. [link].

1. Larkin D.M., Serov O.L. & Zhdanova N.S. 2000. Mapping of 5 HSA17 genes to chromosome h of common shrew (Sorex araneus).  Acta Theriologica. 45: 143-146. IF=1.16. [link].

Genetics and Inheritance, 1st year BVetMed; Introduction to Evolution, Gateway course.

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