Aaron J. Mackey
Assistant Professor of Public Health Science and
  Biochemistry & Molecular Genetics
Ph.D., University of Virginia
Statistical and Computational Genomics

Laboratory
Home Page

 

We are interested in the development and employment of advanced computational and statistical techniques to more fully exploit the richness of genomic data, and to better understand the genetic and etiologic basis of human disease processes. More specifically, our research focuses on various approaches to integrate genome-scale information across multiple domains, both experimental and conceptual. As such, we participate in a wide range of projects related to the genetics of complex human disease (e.g. type 1 diabetes, stroke), molecular mechanisms of pathobiology (e.g. regulation of T cell development, epigenetics of atherosclerosis), and the etiology of sensitivity/resistance of tumors to various cancer therapies. Spanning most of our projects is a relentless motivation to move beyond mere identification of individual, participatory "units" involved in biological process, to a more holistic, systems-level understanding of molecular mechanisms of disease action.

This work demands a nuanced knowledge of ever-changing genomic technologies, active familiarity with the ever-growing plethora of associated bioinformatic tools, and an ability to manage the complexity associated with integrating information across each domain. As such, we have developed the means to both craft and deploy our analyses via reproducible, high-throughput scientific workflows, whose outputs are automatically generated statistical graphs, charts, tables, presentations and reports. As a practitioner of open-source, open-science and open-notebook philosophies, we regularly post our ongoing analyses and snippets of computational protocols to our lab website, where we (and the world) can discuss our findings and ideas, prior to publication or presentation.


Selected References

Roller DG, Axelrod M, Capaldo BJ, Jensen K, Mackey A, Weber MJ, Gioeli D. (2012) "Synthetic lethal screening with small-molecule inhibitors provides a pathway to rational combination therapies for melanoma." Mol Cancer Ther. 11(11):2505-15. doi: 10.1158/1535-7163.MCT-12-0461.Epub 2012 Sep 7. [PubMed]

Huang K, Mellor KE, Paul SN, Lawson MJ, Mackey AJ, Timko MP. (2012) "Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides." BMC Genomics. Aug 13:402. doi: 10.1186/1471-2164-13-402. [PubMed]

Marie CS, Verkerke HP, Paul SN, Mackey AJ, Petri WA Jr. (2012) "Leptin protects host cells from Entamoeba histolytica cytotoxicity by a STAT3-dependent mechanism." Infect Immun. 80:1934-43. doi: 10.1128/IAI.06140-11. Epub 2012 Feb13. [PubMed]

Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, Casillas S, HanY, Magwire MM, Cridland JM, Richardson MF, Anholt RR, Barrón M, Bess C,Blankenburg KP, Carbone MA, Castellano D, Chaboub L, Duncan L, Harris Z, JavaidM, Jayaseelan JC, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P,Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DM, Nazareth L, Newsham I,Perales L, Pu LL, Qu C, Rŕmia M, Reid JG, Rollmann SM, Rozas J, Saada N,Turlapati L, Worley KC, Wu YQ, Yamamoto A, Zhu Y, Bergman CM, Thornton KR,Mittelman D, Gibbs RA. (2012) "The Drosophila melanogaster Genetic Reference Panel." Nature. Feb 482(7384):173-8. doi: 10.1038/nature10811. [PubMed]

Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, CanbäckB, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, KilaruS, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, MackeyAJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, RehmeyerCJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R,Vision TJ, Zeng Q, Zolan ME, Pukkila PJ. (2010) "Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)." Proc Natl Acad Sci U S A. Jun 107(26):11889-94. doi:10.1073/pnas.1003391107. Epub 2010 Jun 14. [PubMed]

Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D; nGASPConsortium, Stein LD. (2008) "nGASP--the nematode genome annotation assessment project." BMC Bioinformatics. Dec 9:549. doi: 10.1186/1471-2105-9-549. [PubMed]

Tribolium Genome Sequencing Consortium, Richards S, Gibbs RA, Weinstock GM, BrownSJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M,Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R,Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, BuhayCJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C,Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, HawesA, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM,Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J,Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS,Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L,Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P,Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V,Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B,Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM,Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P,Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM,Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, LutzR, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB,Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H,Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA,Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW,Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R,Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z,Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M,Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G,Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, VerleyenP, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Foręt S,Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y,Miller SC, Grossmann D, Bucher G. (2008) "The genome of the model beetle and pest Tribolium castaneum." Nature. Apr 452(7190):949-55. doi: 10.1038/nature06784. Epub 2008 Mar 23. [PubMed]

Liu Q, Mackey AJ, Roos DS, Pereira FC. (2008) "Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction." Bioinformatics. Mar 24:597-605. doi: 10.1093/bioinformatics/btn004.Epub 2008 Jan 10. [PubMed]

Chen F, Mackey AJ, Vermunt JK, Roos DS. (2007) "Assessing performance of orthology detection strategies applied to eukaryotic genomes." PLoS One. Apr 2:e383. [PubMed]

Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM. (2007) "Creating a honey bee consensus gene set." Genome Biol. 8:R13. [PubMed]

Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD,Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO,Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC,Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O,Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G,Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z,Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R,Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A,Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S,Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevičre AM, Goel M,Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J,Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, GibbonsIR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, TongprasitW, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, CalestaniC, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD,Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM,Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M,Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, GalindoBE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M,Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G,Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C,Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, RizzoF, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G,Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L,Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A,Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G,Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. (2006) "The genome of the sea urchin Strongylocentrotus purpuratus." Science. Nov 314(5801):941-52. [PubMed]