Professor David Adelson

• Biography/ Background

  1978 A.B (Biology, Cum Laude) University of California at San Diego, Revelle College.

  1985 Ph.D. (Biomedical Science) John A. Burns School of Medicine, University of Hawaii at Manoa

  1986 - 88 Postoctoral training, Dept of Zoology, Duke University.

  1988 - 2001 Research Scientist - CSIRO. 

  2001 - 2007 Associate Professor of Animal Genomics, Dept of Animal Science, Texas A&M University.

  2007 - present Professor and Chair of Bioinformatics and Computational Genetics, School of Molecular and Biomedical Science.

  2012 - present Zhendong Professor of Molecular Chinese Medicine and Director, Zhendong Australia - China Centre for Molecular Traditional Chinese Medicine.

• Research Interests

  Research interests are 1. genome evolution and architecture of mammals and 2. Elucidation of genetic networks that respond to Traditional Chinese Medicine.  Biological mechanisms underlying genome evolution are believed to originate with retrotransposon insertions that can ultimately lead to segmental (gene) duplications/deletions, incorporation of retrotransposons into protein coding genes (exaptation) or gene duplication via retro-gene formation.  The resulting "churning" of both non-protein coding regions and protein domains are believed to be two of the major forces that drive speciation and adaptation.  My current primary research aim is to understand the magnitude and rate of change associated with retrotransposon insertion. 

  This is an important research problem both in terms of our understanding of evolutionary mechanisms and processes but also because these processes frequently give rise to mutations or structural variation affecting gene regulation and function.  These alterations can result in disease or alter economically important agricultural traits.  We have identified horizontal transfer of retrotransposons as a much more common event than previously realised and are pursuing the implications of this finding with respect to genome evolution in higher organisms.

  Current research projects in genome evolution include characterizing the evolutionary dynamics of retrotransposons in species across the tree of life, assessing the degree of horizontal gene transfer in vertebrates and identifying rates of somatic retrotransposon insertion.

  Current projects in the Zhendong Australia - China Centre for the Molecular Basis of Traditional Chinese Medicine include identifying the alterations to gene expresson networks induced by the Yanshu Injection, also referred to as the Compound Kushen Injection (CKI). The Yanshu injection is an aqueous extract of Kushen (Sophora flavescens) and Baituling (name used for three similar species: Heterosmilax japonica Kunth, Heterosmilax yunanensis Gagne or Hetersmilax chinensis Wang) roots that contains a complex mixture of alkaloids, flavonoids and saponins, some of which have been demonstrated to kill cancer cells or boost the immune response. Yanshu injection is used as an adjunct to Western chemotherapy in the treatment of gastric and liver cancer in China.  The exact formulation of the Yanshu injection varies from batch to batch and existing specifications only indicate the minimum concentration of alkaloids required to pass quality control. This variation in bioactive content is a function of environmental effects such as different growth locales, precipitation, temperature that interact with the genotype of the plants to cause the production of varying levels of bioactives. The existing project plan for the Yanshu injection work is aimed at describing and quantifying the gene expression changes in immortalised cancer cell cultures as they undergo cell death induced by Yanshu. Whilst the primary objective of this work is to identify the multiplicity of pathways targeted by Yanshu in order to identify a likely molecular mechanism for its effect, this is only one aspect of this work. The other significant aspect of the work is to demonstrate a quantitative molecular fingerprint based on gene expression changes that can be used to assay the effect of different batches of Yanshu injection. The molecular fingerprint will serve as an enabling technology for agricultural research to improve yields and production methods of Kushen and Baituling.

• Publications

  
  Since 2009

  1. Salih H, Adelson DL (2009) QTL Global Meta-Analysis. BMC Genomics 10(1):184.

  2. Bovine Genome Sequencing Consortium (2009) The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution Science 324(5926):522-8

  3. Adelson DL, Rayson JM, Edgar RC (2009) Characterization and Distribution of Retrotransposons and Simple Sequence Repeats In The Bovine Genome. Proc Natl Acad Sci 106(31), pp.12855-60.

  4. Satterfield C, Song G, Kochan K, Riggs P, Simmons R, Elsik C, Adelson DL, Bazer FW, Zhou H, and Spencer TE (2009) Discovery of candidate genes in the endometrium regulating ovine blastocyst growth and conceptus elongation. Physiol. Genomics 39(2):85-99.

  5. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear T, Adelson DL, Penedo MCT , Bellone RR, Bailey E, Mauceli E, Garber M, MacLeod JN, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Blöcker H, Chowdhary BP, Coleman SJ, Della Valle G, Distl O, Edgar RC, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Leeb T, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raison J, Raudsepp T, Rocchi M, Røed KH, Ryder O, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JS, Zody MC, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Lander ES, and Lindblad-Toh K (2009) Genome sequence, comparative analysis and population genetics of the domestic horse. Science 326(5954):865-7.

  6. Rios JJ, Fleming JG, Bryant UK, Carter CN, Huber JC, Long MT, Spencer TE, Adelson DL (2010) OAS1 and RNASEL Polymorphisms Are Associated With Susceptibility To West Nile Encephalitis In Horses. PLoS ONE 5(5): e10537. doi:10.1371/journal.pone.0010537.

  7. Adelson DL, Rayson JM, Edgar RC (2010) Characterization and Distribution of Retrotransposons and Simple Sequence Repeats In The Equine Genome. Animal Genetics 41 (Suppl. 2):91-99. doi:10.1111/j.1365-2052.2010.02115.x

  8. Childers, C, Reese, J, Jaideep, S, Vile, D, Dickens, C, Childs, K, Salih, H, Bennett, A, Hagen D, Adelson, D, Elsik, C. (2010) Bovine Genome Database: Integrated Tools for Genome Annotation and Discovery. Nucleic Acids Research 39(1): 830-834.

  9. Appels, R, Adelson, DL, Moolhuijzen, P, Webster, R, Barrero, R, and Bellgard, M (2011) Genome studies at the PAG 2011 conference Funct Integr Genomics, 11:1-11.

  10. Ling, KH, Brautigan, PJ, Hahn, CH, Daish, T, Rayner, JR, Cheah, PS, Raison, JM, Piltz, S, Mann, JR, Mattiske, DM, Thomas, PQ, Adelson, DL and Scott, HS (2011) Deep sequencing analysis of the developing mouse brain reveals a novel microRNA BMC Genomics, 12:176.

  11. Vidale P, Piras FM, Nergadze FG, Bertoni L, Verini-Supplizi A, Adelson D, Guerin G and Giulotto E (2011) Chromosomal Assignment of Six Genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) in Four Species of the Genus Equus. Animal Biotechnology, 22: 119-123.

  12. Qu Z, Adelson DL (2012) Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes. PLoS ONE 7(8): e42638. doi:10.1371/journal.pone.0042638

  13. Qu Z, Adelson DL (2012) Evolutionary conservation and functional roles of ncRNA. Front. Gene., doi: 10.3389/fgene.2012.00205

  14. Walsh, A, Kortschak, RD, Gardner, MG, Bertozzi, T and Adelson DL (2012), Widespread horizontal transfer of Retrotransposons, Proc Natl Acad Sci published ahead of print December 31, 2012,doi:10.1073/pnas.1205856110.

  15. Qu Z, Adelson DL (2012) Identification And Comparative Analysis Of ncRNAs In Human, Mouse And Zebrafish Indicate A Conserved Role In Regulation Of Genes Expressed In Brain. PLoS ONE 7(12): e52275. doi:10.1371/journal.pone.0052275

  16. Fruzangohar M, Ebrahimie E, Ogunniyi AD, Mahdi LK, Paton JC, Adelson DL (2013) Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PLoS ONE 8(3):e58759. doi: 10.1371/journal.pone.0058759.

  17. Ivancevic, AM, Walsh AM, Kortschak RD, Adelson DL (2013) Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution. BioEssays 35(12):1071-82. doi: 10.1002/bies.201300072.

  18. Roberts, ND, Kortschak, RD, Parker, WT, Schreiber, AW, Branford, S, Scott, HS, Glonek, G, Adelson, DL (2013) A Comparative Analysis of Algorithms for Somatic SNV Detection in Cancer. Bioinformatics doi: 10.1093/bioinformatics/btt375.

  19. Bellone, RR, Holl, H, Setaluri, V, Devi, S, Maddodi, N, Archer, S, Sandmeyer, L, Ludwig, A, Foerster, D, Pruvost, M, Reissmann, M, Bortfeldt, R, Adelson, DL, Lim, SL, Nelson, J, Haase, B, Engensteiner, M, Leeb, T, Forsyth, G, Mienaltowski, MJ, Hofreiter, M, Paijmans, JLA, Gonzalez-Fortes, G, Grahn, B, Brooks, SA (2013) LTR Driven Premature Poly-adenylation in TRPM1 Causes Congenital Stationary Night Blindness and Leopard Complex Spotting in Horse: An Ancient Example of Balancing Selection. PLoS ONE 8(10):e78280. doi: 10.1371/journal.pone.0078280.

  20. Fruzangohar, M, Kroeger, T, Adelson DL. (2013) Improved Part-of-Speech Tagging for Biological Articles using a Novel Suffix Analysis Method. PloS ONE 8(10):e76042. doi: 10.1371/journal.pone.0076042.

  21. Mahdi, LK, Ebrahimie, E, Adelson, DL, Paton, JC, Ogunniyi, AD (2013) A Transcriptional Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumonia. PLoS ONE 8(8):e70862. doi: 10.1371/journal.pone.0070862.

  22. Alanazi, I, Ebrahimie, E, Hoffmann, P, Adelson, DL. (2013) Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis. Apoptosis, (DOI) 10.1007/s10495-013-0887-6

  23. Lim, Sl, Kortschak, RD and Adelson, DL (2014) Discovery of a novel long terminal repeat (LTR2i_SS) in Sus Scrofa. Animal Genetics 45(3):367-372. doi: 10.1111/age.12138. Epub 2014 Mar 12.

  24. Ebrahimi M, Aghagolzadeh P, Shamabadi N, Tahmasebi A, Alsharifi M, Adelson DL, Hemmatzadeh F, Ebrahimie E. (2014) Understanding the underlying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein. PLoS One. 2014 May 8;9(5):e96984. doi: 10.1371/journal.pone.0096984.

  25. Wang D, Qu Z, Adelson DL, Zhu JK, Timmis JN. (2014) Transcription of nuclear organellar DNA in a model plant system. Genome Biol Evol. 2014 May 27;6(6):1327-34. doi: 10.1093/gbe/evu111.

  26. Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SM, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Fuentes-Utrilla P, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristiansen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas JW, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. (2014) The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 Jun 6;344(6188):1168-73. doi: 10.1126/science.1252806.

  27. Gagliardi L, Schreiber AW, Hahn CN, Feng J, Cranston T, Boon H, Hotu C, Oftedal BE, Cutfield R, Adelson DL, Braund WJ, Gordon RD, Rees DA, Grossman AB, Torpy DJ, Scott HS.(2014) ARMC5 mutations are common in familial bilateral macronodular adrenal hyperplasia. J Clin Endocrinol Metab. Vol 99, Issue 9, 1 September 2014, Pages E1784-E1792 (doi: 10.1210/jc.2014-1265)

  28. Buckley RM, Adelson DL (2014) Mammalian genome evolution as a result of epigenetic regulation of transposable elements. Biomolecular Concepts. 5(3):183-194, DOI: 10.1515/bmc-2014-0013

  29. Fruzangohar M, Ebrahimie E, Adelson DL (2014) Application of Global Transcriptome Data in Gene Ontology Classification and Construction of a Gene Ontology Interaction Network. bioRxiv doi: http://dx.doi.org/10.1101/004911

  30. Kortschak RD, Adelson DL (2014) biogo: a simple high-performance bioinformatics toolkit for the Go language. bioRxiv doi: http://dx.doi.org/10.1101/005033

  31. Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear T, Adelson DL, Chowdhary BP, Raudsepp T (2014) Genomic copy number variation in normal equine populations and in horses with XY disorders of sexual development. PLoS Genetics, Volume 10, Issue 10, 1 October 2014, 19p (doi: 10.1371/journal.pgen.1004712).

  32. Mahdi LK, Deihimi T, Zamansani F, Fruzangohar M, Adelson DL, Paton JC, Ogunniyi AD, Ebrahimie E. (2014). A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease. BMC Genomics 15:769.

  33. Gecz J, McMichael G, Bainbridge M, Haan E, Corbett M, Gardner A, Thompson S, van Bon B, van Eyk C, Broadbent J, Reynolds C, O'Callaghan M, Nguyen LS, Adelson DL, Russo R, Jhangiani S, Doddapaneni H, Muzny D, Gibbs R, MacLennan A (2015) Whole exome sequencing points to considerable genetic heterogeneity of cerebral palsy. Molecular Psychiatry advance online publication 10 February 2015; doi: 10.1038/mp.2014.189.

  34. Alanazi I, Hoffmann P, Adelson DL (2015) MicroRNAs are part of the regulatory network that controls EGF induced apoptosis, including elements of the JAK/STAT pathway, in A431 cells. PLoS One 0(3): e0120337. doi:10.1371/journal.pone.0120337

  35. Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson, DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Wei C. (2015) Revealing missing isoforms encoded in the human genome by integrating genomics, transcriptomics and proteomics data. Scientific Reports, 5, Article number: 10940, doi:10.1038/srep10940

  36. Lim, SL, Qu Z, Kortschak, RD, Lawrence, DM, Geoghegan J, Hempfling AL, Bergmann M, Goodnow CC, Ormandy CJ, Wong L, Mann J, Scott HS, Jamsai D, Adelson DL, O'Bryan MK. (2015) pi RNA stability is required for adult male germ cell transposon repression and to define the spermatogenic program. PLoS Genetics DOI:10.1371/journal.pgen.1005620.

  37. Ling KH, Brautigan PJ, Moore S, Fraser R, Leong MP, Leong JW, Zainal Abidin S, Lee HC, Cheah PS, Raison JM, Babic M, Lee YK, Daish T, Mattiske DM, Mann JR, Adelson DL, Thomas PQ, Hahn CN, Scott HS.(2016) In depth analysis of the Sox4 gene locus that consists of sense and natural antisense transcripts. Data Brief, 7:282-90. doi: 10.1016/j.dib.2016.01.045.

  38. Ling KH, Brautigan PJ, Moore S, Fraser R, Cheah PS, Raison JM, Babic M, Lee YK, Daish T, Mattiske DM, Mann JR, Adelson DL, Thomas PQ, Hahn CN, Scott HS. (2016) Derivation of an endogenous small RNA from double-stranded Sox4 sense and natural antisense transcripts in the mouse brain. Genomics, 107(2-3):88-99. doi: 10.1016/j.ygeno.2016.01.006.

  39. Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL. (2016) LINEs between species: Evolutionary dynamics of LINE-1 retrotransposons across the eukaryotic tree of life. Genome Biology and Evolution, 14;8(11):3301-3322 (doi: 10.1093/gbe/evw243)

  40. Qu Z, Cui J, Harata-Lee Y, NweAung T, Feng Q, Raison JM, Kortshak RD, Adelson DL. (2016) Identification Of Candidate Anti-Cancer Molecular Mechanisms Of Compound Kushen Injection Using Functional Genomics. Oncotarget DOI: 10.18632/oncotarget.11788.

  41. Wang D, Qu Z, Yang L, Zhang Q, Liu ZH, Do T, Adelson D, Wang Z, Searle I, Zhu JK. (2017) Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. The Plant Journal, DOI:10.1111/tpj.13481

  42. Banjar H, Ranasingha D, Brown F, Adelson D, Kroeger T, Leclercq T, White D, Hughes T, Chaudhri N. (2017) Modelling Predictors of Molecular Response to Frontline Imatinib for Patients with Chronic Myeloid Leukaemia. PLOS ONE 12(1): e0168947. DOI:10.1371/journal.pone.0168947.

  43. Fruzangohar M, Ebrahimie E, Adelson DL (2017) A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data. PLOS ONE 12(2):e0170486. DOI: 10.1371/journal.pone.0170486

  44. Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL (2017) Re-evaluating inheritance in genome evolution: widespread transfer of LINEs between species. bioRxiv DOI: 10.1101/106914.

  45. Buckley RM, Kortschak RD, Raison JM, Adelson DL (2017) Similar evolutionary trajectories for retrotransposon accumulation in mammals. Genome Biology & Evolution doi:10.1093/gbe/evx179.

  46. Kortschak RD, Bleecher Snyder J, Maragkakis M, Adelson DL (2017) bíogo: a simple high-performance bioinformatics toolkit for the Go language. J Open Source Software, DOI: 10.21105/joss.00167.

  47. Kortschak RD, Pedersen BS, Adelson DL (2017) bíogo/hts: high throughput sequence handling for the Go language. J Open Source Software, DOI: 10.21105/joss.00168.

  48. New Aung T, Qu Z, Kortschak RD, Adelson DL (2017) Understanding the Effectiveness of Natural Compound Mixtures in Cancer through their Molecular Mode of Action. Int. J. Med. Sci. 18, 656; doi:10.3390/ijms18030656.

  49. Kortschak RD, Adelson DL (2017) bíogo/ncbi: interfaces to NCBI services for the Go language. J Opens Source Software, http://dx.doi.org/10.21105/joss.00234 .

  50. Yu C, Qu Z, Zhang Y, Zhang X, Lan T, Adelson DL, Wang D, Zhu Y (2017) Seed weight differences between wild and domesticated soybeans are associated with specific changes in gene expression. Plant Cell Reports, (6),1-10, https://doi.org/10.1007/s00299-017-2165-5 .

  51. Hempfling AL, Lim SL, Adelson DL, Evans J, O'Connor AE, Qu Z, Kliesch S, Weidner W, O'Bryan MK, Bergmann M (2017) Cellular expression patterns of HENMT1 and PIWIL1 in human testis: Transposon expression and its regulation by the piRNA pathway. Reproduction, http://dx.doi.org/10.1530/REP-16-0586

  52. Li J, Harata-Lee Y, Denton MD, Feng Q, Rathjen JR, Qu Z, Adelson DL (2017) Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound synthesis. Cell Discovery, (3) 17031, doi:10.1038/celldisc.2017.31.

  53. Buckley RM, Kortschak RD, Adelson DL (2017) Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse. Accepted for publication PLoS Computational Biology.

  54. Zeng L, Pederson SM, Cao D, Qu Z, Hu Z, Adelson DL, Wei C (2017) Genome-wide analysis of repetitive elements associated with gene regulation. in press J. Comp Biol.

  55. Zeng L, Kortschak RD, Raison JM, Bertozzi T, Adelson DL (2018) Superior ab initio Identification, Annotation and Characterisation of TEs and Segmental Duplications from Genome Assemblies. PLoS ONE Vol13:3, e0193588 DOI: 10.1371/journal.pone.0193588.

  56. Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To T-H, Kortschak RD, Raison JM, Qu Z, Chin T-J, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Di Palma F, Alfoldi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poinar H, Reich D (2018) A comprehensive genomic history of extinct and living elephants. Proc. Natl.Acad.Sci https://doi.org/10.1073/pnas.1720554115

  Book Chapters.

  1. Adelson, DL (2012) Bovine Genome Architecture, in Bovine Genomics, Ed. James Womack, Wiley-Blackwell publishers, Pp 123-144.

  2. Adelson, DL, Qu, Z, Raison, JM, Lim, SL (2014) BOVINE GENOMICS, in The Genetics of Cattle, 2nd edition ISBN-13: 978-1780642215 published by CABI, Eds: A. Ruvinsky & D. Garrick, Chapter 7 Bovine Genomics, pp. 130-152.

  3. Adelson,DL, Buckley, RM, Ivancevic, AM, Qu, Z, Zeng, L. (2015) Retrotransposons: Genomic and Trans-Genomic Agents of Change, in Evolutionary Biology - Biodiversification from Genotype to Phenotype, ISBN 978-3-319-19931-3 published by Springer, Ed: P. Pontarotti, Chapter 4, pp. 55-76

   

   

Entry last updated: Thursday, 15 Jun 2023

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