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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 native breeds of sheep and cattle. 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), UK sheep population structure (collaboration Aberystwyth University and Meat Promotion Wales (HCC) and detection of signatures of selection in native Russian sheep and cattle breeds. 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:

 (old version)

(avian data)

(insect data)

(blind mole rat)

(tibetan antelope)

(mammalian ancestors)

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

(currently under the RVC firewall).

Most of Dr Larkin's publications are available from his ResearchGate profile: 

A complete, up-to-date list of publications is also available from Google Scholar:  (H=42).

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60. Buggiotti L., Yudin N.S. & Larkin D.M. 2022. Copy number variants in two northernmost cattle breeds from Russia involve actin genes. Genes. 13(9):1595. IF=4.14. []

59. Ruvinsky D.E., Igoshin A., Ilina A. & Larkin D.M. 2022. Resequencing the Yaroslavl cattle genomes reveals signatures of selection and a rare haplotype on BTA28 likely to be related to breed phenotypes. Animal Genetics. June 16; DOI:10.1111/age.13230. IF=2.88. []

58. Buggiotti L, Yurchenko A.A., Yudin N.S., Vander Jagt C.J., Vorobieva N.V., Kusliy M.A., Vasiliev S.K., Rodionov A.N., Boronetskaya O.I., Zinovieva N.A., Graphodatsky A.S., Daetwyler H.D. & Larkin D.M. 2021. Demographic history, adaptation, and NRAP convergent evolution at amino acid residue 100 in the world northernmost cattle from Siberia. Mol Biol Evol. Mar 30; DOI: 10.1093/molbev/msab078. IF=11.06. [].

57. Sweet-Jones J., Yurchenko A.A., Yudin N.S., Swain M. & Larkin D.M. 2020. Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits. Animal Genetics. DOI:10.1111/age.13015. IF= 1.8.  []

56. Farré M., Kim J., Proskuraykova A.A., Zhang Y., Kulemzina A.I., Li Q., Zhou Y., Xiong Y., Johnson J.L., Perelman P., JohnsonW.E., Warren W., Kukekova A.V., Zhang G., O’Brien S.J., Ryder O.A., Graphodatsky A.S., Ma J., Lewin H.A. & Larkin D.M. 2019. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Research [published in advance February 13] DOI: 10.1101/gr.239863.118. IF=9.43. []

55. Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takác P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. 2019. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biol. 20(1):187. IF=13.21. [].

54. Yurchenko A.A., Deniskova T.E., Yudin N.S., Dotsev A.V., Khamiruev T.N., Selionova M.I.,Egorov S.V., Reyer H., Wimmers K., Brem G., Zinovieva N.A & Larkin D.M. 2019. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 20 (S1): 294. IF=3.73. .

53. Torgasheva A.A., Malinovskaya L.P., Zadesenets K.S., Karamysheva T.V., Kisilova E.A., Pristyazhnyuk I.E., Shnaider E.P., Volodkina V., Galkina S.A., Larkin D.M.*, Rubtsov N.B. & Borodin P.M.* 2019. Germline-restricted chromosome (GRC) is widespread among songbirds. PNAS. [published in advance April 29] doi: 10.1073/pnas.1817373116 *corresponding authors. IF=9.5. .

52. Igoshin A.V., Yurchenko A.A., Belonogova N.M., Petrovsky D.V., Aitnazarov R.B., Soloshenko V.A., Yudin N.S. & Larkin D.M. 2019. 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. BMC Genetics 20 (S1). IF= 2.5. .

51. Farré M., Kim J., Proskuraykova A.A., Zhang Y., Kulemzina A.I., Li Q., Zhou Y., Xiong Y., Johnson J.L., Perelman P., Johnson W.E., Warren W., Kukekova A.V., Zhang G.,O’Brien S.J., Ryder O.A., Graphodatsky A.S., Ma J., Lewin H.A. & Larkin D.M. 2019. Coevolution of chromosome changes and gene regulation in ruminants. Genome Research doi:10.1101/gr.239863.118. IF=10.1. .

50. Farré M.*, Li Q., Zhou Y., Damas J., Chemnick L.J., Kim J., Ryder O.A., Ma J., Zhang G., Larkin D.M.* & Lewin H.A.*. 2019. A Near-Chromosome-Scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari Desert. GigaScience giy162, https://doi.org/10.1093/gigascience/giy162. IF=7.27. .

49. O’Connor R., Farré M., Joseph S., Damas J., Kiazim L., Jennings R., Bennett S., Slack E., Allanson E., Larkin D.M.* & Griffin D.K.* 2018. Full chromosomal-level genome assembly of highly rearranged avian genomes provides novel insight into the mechanisms of chromosomal change. Genome Biology 19:171 *equal authors. IF=13.21. .

48. Damas J., Kim J., Farré M., Griffin D.K. & Larkin D.M. 2018. Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro and microchromosomes. Genome Biology 19:155. IF=13.21. .

47. Yurchenko A., Daetwyler H.D., Yudin N., Schnabel R.D., Vander Jagt C.J., Soloshenko V., Lhasaranov B., Popov R., Taylor J.F. & Larkin D.M. 2018. Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental acclimation and adaptation. Scientific Reports 8:12984. IF= 4.12. .

46. O'Connor R., Romanov M., Barrett P., Farré M., Damas J., Ferguson-Smith M., Valenzuela N., Larkin D.M.* & Griffn D.K.* 2018. Dinosaur genomes: tracing chromosome evolution suggests close resemblance to modern birds. Nature Communications 9: 1883. *equal authors. IF=12.12. .

45. Drpic D., Almeida A., Aguiar P., Renda F., Damas J., Lewin H.A., Larkin D.M., Khodjakov A. & Maiato H. 2018. Chromosome segregation is biased by kinetochore architecture. Current Biology 28, 1-13.e1-e5. IF=8.85. .

44. Lenis V.P. Swain M. & Larkin D.M. 2018. G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequences.GigaScience. doi.org/10.1093/gigascience/giy017. IF=7.46. . 

43. Yurchenko A., Yudin N., Aitnazarov R., Plyusnina A., Brukhin V., Soloshenko V., Lhazaranov B., Popov R., Plymeshov K. & Larkin D.M. 2017. Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds. Heredity. doi: 10.1038/s41437-017-0024-3 (cover paper). IF=3.80. . Readers' Choice: The best of Heredity 2018.

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=9.40. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. .

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. 

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

Grants:

ESEB outreach activity grant .

Evolution Factory: an interactive game to teach school kids the principles of chromosome evolution: (currently requires a 27" screen and Java).  

Recent press releases, webinars, popular papers:

(Illumina On-Demand Webinar)

New research from the RVC explores the genetic adaptions and evolution of livestock and wild animals in response to extreme climates?

Scientists discover songbirds have an unusual chromosome

(Genomeweb)

 (Laboratory News)

(Laboratory News)