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1. Lloyd E, Chhouk, B, Keene AC, and Albertson RC. Diversity in rest-activity patterns among Lake Malawi cichlid fishes suggests novel axis of habitat partitioning. Biorxiv, 2020.07.14.203505, and J. Exp. Biol. in press

2. Warren WC, Boggs TE, Borowsky R, Carlson BM, Ferrfuino E, Gross JF, Hillier L, Hu Z, Keene AC, Kenzior A, Kowalko JE, Tomlinson C, Kremitzki M, Lemieux ME, Graves-Lindsay T, McGaugh SE, Miller JT, Mommersteeg M, Moran RL, Peuss R, Rice E, Riddle MR, Sifuentes-Romero I, Stanhope BA, Tabin CJ, Thakur S, Yoshiyuki Y, and Rohner N.  A chromosome level genome of Astyanax mexicanus surface fish for comparing populations-specific genetic differences contributing to trait evolution. Biorxiv, 2020.07.06.189654, and Nature Comm. In press.

3. Shafer OT and Keene AC.  The functions and regulation of Drosophila sleep. Curr Biol. (2021) 31(1): R38-R49.

4. Collie J, Granela O, Brown EB, and Keene AC. Aggression is induced by resource limitation in the monarch caterpillar. iScience,(2020) 23 (12):101791.

5. Jaggard JB, Lloyd E, Yuiska A, Patch A, Fily Y, Kowalko JE, Appelbaum L, Duboue ER, and Keene AC. Cavefish brain atlases reveal functional and anatomical convergence across independently evolved populations. Science Advances. (2020) 6, 38, eaba3126.

6. Paz A, McDole B, Kowalko JE, Duboue ER, and . Evolution of the acoustic startle response in Mexican cavefish. (2020), 10.1002, jez.b22988.

7. Chin JSR, Loomis CL, Albert LT, Medina-Trenche S, Kowalko J, , and Duboue ER.Analysis of stress responses in larvae reveals heterogeneity among different populations. (2020), 10.1002, jez.b22987.

8. Sifuentes-Romero I, Ferrufino E, Thakur S, Laboissonniere LA, Solomon M, Smith CL, , Trimarchi JM, Kowalko JE.Repeated evolution of eye loss in Mexican cavefish: Evidence of similar developmental mechanisms in independently evolved populations. (2020), 10.1002, jez.b22977.

9. Stahl BA, Jaggard JB, Brown EB, and Keene AC.  Sleep regulates the glial engulfment receptor Draper to promote Wallerian Degeneration.  Current Biology. (2020), 30(6):1092-1101

10.  Pamboro-Laure E, Brown EB and Keene AC.  Dietary fatty acids promote sleep through a taste-independent mechanism.  Genes, Brain, Behavior. (2020) (4):e12629

11. Brown EB, Shah KD, Faville R, Kottler B, and Keene AC. Drosophila insulin-like peptide 2 mediates dietary regulation of sleep intensity. Plos Genetics, 16(3):e1008270.

12. McGaugh SE, Passow CN, Jaggard JB, Stahl BA, and Keene AC.  Unique transcriptional signatures of sleep loss across independently evolved cavefish populations. J. Exp. Zool B, (2020) 334 (7-8):497-510.

13. McGaugh SE, Kowalko JE, Duboue ER, Lewis P, Franz-Odendaal T, Rohner N, and Gross JB, and Keene AC. Dark world rises: The emergence of cavefish as a model for the study of evolution, behavior, and disease. J. Exp. Zool B. (2020) 334 (7-8):397-404.

14. Loomis C, Peuss R, Jaggard JB, Wang Y, McKinney S, Raftopoulos S, Raftopolos A, Whu D, Green M, McGaugh SE, Rohner N, , and Duboue ER. An adult brain atlas reveals broad neuroanatomical changes in independently evolved populations of Mexican cavefish. (2020) 13,88.

15. Chin JSF, Albert LT, Loomis CL, , Duboue ER.Behavioral approaches to studying innate stress in zebrafish. (2019),

16. Stahl BA, Jaggard JB, Chin JSR, Kowalko JE, Keene AC, and Duboue ER. Manipulation of gene function in Mexican cavefish. J. Vis. Exp. (2019), 10.3791/59093.

17. Jaggard JB, Lloyd E, Lopatto A, Duboue ER, and .Automated measurements of sleep and locomotor activity in Mexican cavefish. (2019),

  1. . Stahl BA, Peuss R, McDole B, Kenzior A, Jaggard JB, Gaudenz K, Krishnan K, McGaugh SE, Duboue ER, Keene AC, and Rohner N.  Stable transgenesis in Astyanax mexicanus using the Tol2 transposase system. Dev Dyn. (2019), 10.1002/dvdy.32.

19. Yurgel ME, Kakad P, Zandawala P, Nässel DR, Godenschwege TA, and Keene AC.  Leucokinin neurons are modulated by feeding state and regulate sleep-metabolism interactions. Plos Biol. (2019) 17(2):e2006409

20. Brown EB, Slocumb ME, Szuperak M, Kerbs A, Gibbs AG, Kayser MS, and Keene AC. Starvation resistance is associated with developmentally specified changes in sleep, feeding, and metabolic rate. J Exp Biol. (2019) 10.1242/191049.

21. Zandawala M, Yurgel ME, Texada MJ, Liao S, Rewitz KF, Keene AC, and Nässel DR.  Modulation of Drosophila post-feeding physiology and behavior by the neuropeptide leucokinin. Plos Genet. (2018) 14(11):e1007767.

22. Passow CN, Kono TJY, Stahl BA, Jaggard JB, Keene AC, and McGaugh SE. Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods. Mol Ecol Resources. (2018) doi:10.1111/1755-0998.

23. Stahl BA, Beco E, Davla S, Murakami K, Caicedo Moreno NA, van Meyel DJ, and Keene AC. The taurine transporter Eaat2 functions in ensheathing glia to modulate sleep and metabolic rate. Curr Biol. (2018)  28(22)3700-3708.

24. Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, and McGaugh SE. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Mol Ecol. (2018) 27(22)4387-4416).

25. Yurgel ME, Shah KD, Brown EB, Burns C, Bennick RA, DiAngelo JR, and Keene AC. Ade2 functions in the Drosophila fat body to promote sleep.  G3 (Bethesda) (2018)  8(11):3385-3395.

26. Keene AC, Duboue ER. The origins and evolution of sleep. (2018) J Exp Biol. 12;221(pt11).

27. Chin JSR, Gassant CE, Amaral P, Lloyd E, Stahl BA, Jaggard JB, Keene AC, and Duboue ER. Convergence on reduced stress in the Mexican Blind Cavefish. Dev Biol. (2018). 441(2):319-327.

28. Lloyd E, Olive C, Stahl BA, Jaggard JB, Amaral P, Duboue ER, and Keene AC.  Evolutionary shift towards lateral line dependent prey-capture behavior in the blind Mexican cavefish.  Dev Biol. (2018). 441(2):328-337.

29. Yurgel ME and Keene AC.  Sleep: Helicon Cells Charge the Circuit.  Current Biology. (2018). 28 (7) R317-319.

30. Jaggard JB, Stahl BA, Lloyd E, Prober DA, Duboue ER and Keene AC. Hypocretin underlies the evolution of sleep loss in the Mexican cavefish. (2017)  eLife, 10 (1101) 122903.

31.  Brown E, Torres J, Bennick RA, Rozzo V, Kerbs A, DiAngelo JR and Keene AC. Geographic variation in sleep and metabolic function is associated with latitude and temperature. (2017) Ecology and Evolution 10(1101) 182790.

32. Tauber JM, Brown E, Li Y, Yurgel ME, Masek P and Keene AC. A subset of sweet-sensing neurons identified by Ir56d are necessary and sufficient for fatty acid taste. (2017) Plos Genetics. 13(11):e1007059.

33. Stahl BA and Keene AC.  To rebound or not to rebound. (2017) Elife, 6, e31646v.

34. Stahl BA,  Slocumb ME, Chaitin H, DiAngelo JR and Keene AC.  Sleep-Dependent Modulation of Metabolic Rate in Drosophila. (2017) Sleep. 40(8) zsx084.

35. Jaggard JB, Robinson B, Stahl BA, Oh I, Masek P, Yoshizawa M, and Keene AC.  The lateral line confers evolutionarily derived sleep loss in the Mexican cavefish.  J. Experimental Biology. 220(2)284-93.

36. Murphy KR, Deshpande SA, Yurgel ME, Quinn JP, Weissbach JL, Keene AC, Dawson-Scully K, Huber R, Tomchik SM, Ja WW (2016). Postprandial Sleep Mechanics in Drosophila. (2016). Elife 5. pii: e19334.

37. Masek P and Keene AC.  Gustatory processing and taste memory in Drosophila. (2016). J. Neurogenetics. 30(2) 112-21.

38. Murakami K, Yurgel ME, Stahl BA, Masek P, Mehta A, Heidker R, Bollinger W, Gingras RM, Kim YJ, Ja WW, Suter B, DiAngelo JR, Keene AC. translin is required for metabolic regulation of sleep (2016). Current Biology. 26(7):972-80.

39. Arble DM, Bass J, Behn CD, Butler MP, Challet E, Czeisler C, Depner CM, Elmquist J, Franken P, Grandner MA, Hanlon EC, Keene AC, Joyner MJ, Karatsoreos I, Kern PA, Klein S, Morris CJ, Pack AI, Panda S, Ptacek LJ, Punjabi NM, Sassone-Corsi P, Scheer FA, Saxena R, Seaquest ER, Thimgan MS, Van Cauter E, Wright KP.  Impact of sleep and circadian disruption on energy balance and diabetes: A summary of workshop discussions (2015) Sleep. 38(12):1849-60.

40. Garbe DS, Bollinger WL, Vigderman A, Masek P, Gertowski J, Sehgal A and Keene AC. Context specific comparison of sleep acquisition system in Drosophila (2015).  Biology open. 4(11):1558-68

41. Seidner G, Robinson JE, Wu M, Worden K, Masek P, Roberts SW, Keene AC and Joiner WJ. Identification of privileged neurons with a privileged role in sleep homeostasis in Drosophila melanogaster (2015). Current Biology. (22):2928-38.

42. Slocumb ME, Regalado JM, Yoshizawa M, Neely GG, Masek P, Gibbs AG, and Keene AC.  Enhanced sleep in an evolutionarily adaptive response to starvation stress in Drosophila (2015). Plos One. 10(7)eo131275.

43. Masek P, Worden K, Aso Y, Rubin GM, and Keene AC.  A dopamine-modulated neural circuit regulating aversive taste memory in Drosophila (2015) Current Biology. 25(11):1535-41.

44. Keene AC and Joiner WJ.  Neurodegeneration: paying it off with sleep. Current Biology. (2015). 25(6):R234-6.

45. Yoshizawa M, Robinson BG, Duboue ER, Masek P, Jaggard, JB, O’Quin KE, Borowsky RL, Jeffery WR and . Distinct genetic architecture underlies the emergence of foraging traits in the Mexican cavefish (2015) 20 (13):15.

46. Yurgel ME, Masek P, DiAngelo JR and Keene AC. Genetic dissection of sleep-metabolism interactions (2014) J Comp Physiol A. 201 (9):869-77.

47. McGaugh SE, Gross JB, Aken B,, Blin M, Borowsky RB, Chalopin C, Hinaux H, Jeffery WR, Keene AC, Ma L, Minx P, Murphy D, O’Quin KE, Retaux S, Rohner N, Searle SM, Stah BA, Tabin C, Volf JN, Yoshizawa M, and Warren WC.  The cavefish genome reveals candidate genes for eye loss. (2014) Nature Communications. 20(5):5307.

48. Murakami M and Keene AC. Development: Better sleep on it, children. (2014) Current Biology.  24(12):R569-71.

49. Masek P, Reynolds L, Bollinger WL, Moody C, Mehta A, Yoshizawa M, Gibbs A, and Keene AC. Altered sleep and feeding contribute to starvation resistance in Drosophila. (2014) J. Exp. Biol. 1(217):3122-32.

50. Masek, P and Keene AC. Drosophila Fatty Acid Taste Signals through the PLC Pathway in Sugar-Sensing Neurons (2013). Plos Genetics. 9(9): e1003710. 

51. Robertson M and Keene AC.  Molecular Mechanisms of Age-Related Sleep Loss. (2013) Gerontology. 9(4):334-9.

52. Sassu ED, McDermott JE, Keys BJ, Esmaeilli M, Keene AC, Birnbaum MJ, and Diangelo JR. Mio/dChREBP coordinately increasees fat mass by regulation lipid synthesis and feeding behavior in Drosophila. (2012) Biochem Biophys Res Commun. 426 (1):42-8.

53. Masek, P and Keene AC.  Dopamine: On the threshold of sleep.  (2012) Current Biology. 11(22):R949-51.

54. Duboue ER, Borowsky RB, and Keene AC. ß-adrenergic signaling regulates evolutionarily derived sleep loss in the Mexican Cavefish. (2012)  Brain, Behavior, Evolution. 21(80):233-43.

55. Keene AC and Masek P.  Optogenetic induction of aversive taste memory. (2012) Neuroscience. 11(222):173-80.

56. Keene AC and Sprecher SG.  Seeing the light: Photobehavior in fruit fly larvae. (2011)  Trends in Neuroscience. 35(2):104-110. 

57. Neely, GG*, Keene AC*, Duchek P, Chang EC, Wang QP, Aksoy YA, Rosenzweig M, Costigan M, Garrity P, and Penninger JM.  TRPA1 regulates thermal nociception in Drosophila.  (2011)  Plos One, 6(8);e24343.

58. Dus M, Min SH, Lee GY, Keene AC, and Suh GB. Taste-independent detection of the caloric content of sugar in Drosophila. (2011) Proc. Natl. Acad. Sci. USA. 108(28);11644-9.

59. Keene AC, Mazzocchi EO, Blau J, Desplan C and Sprecher SG.  Distinct photoreceptor neurons mediate Drosophila light avoidance and circadian clock entrainment.  (2011) J. Neuroscience. 31(17):6527-34. 

60. Duboue ER, Keene AC, and Borowsky RB.  Evolutionary convergence on sleep loss in cavefish populations. (2011) Current Biology 8; 671-76.

61.  McDonald DM and Keene AC. The sleep-feeding conflict:  Understanding behavioral integration through genetic analysis in Drosophila. (2010) Aging, 2(8):1-4.

62. Keene AC, Duboue ER, McDonald DM, Dus, M, Suh GB, Waddell, S and Blau J.  Clock and cycle limit starvation-induced sleep loss in Drosophila. (2010) Current Biology, 20(13):1209-15.

63. Neely GG, Hess A, Costigan M, Keene AC, Goulas S, Langeslag M,  Griffith RS, Belfer I, Smith, SB, Gupta V, Xia X, Aman S, Arora S, Sarangi R, Debasis D, Novatchkova M, Pospisilik JA, Rosenzwig M, Truong D, Elling U, Schramek D, Angjeli B, Zoranovic T, Cronin S, Dietzl G, , Subramaniam S, Garrity PA, Bellen HJ Woolf CJ and Penninger JM et al.  A genome wide Drosophila screen for heat nociception identifies A2D3 as an evolutionarily-conserved pain gene. (2010) Cell. 143 (4);628-38.

64. Neely GG, Kuba K, Amann S, Isobe K, Zhang L, Cammarato A, Elmen L, Gupta V, Arora S, Srangi R, Dan D, Fuijisawa S, Usami T, Xia C, Keene AC, Pospisilik A, Elling U, Berger C, Novatchkova M, Koglgruber R, Isobe M, Imai Y, Subramaniam S, Kimura A, Bodmer R, and Penninger JM.  A global in vivo Drosophila RNAi screen identifies NOT3 as a key regulator of heart function. (2010) Cell. 14 (1): 142-153.

65. Keene AC and Waddell S.  Drosophila olfactory memory: single genes to complex neural circuits. (2007) Nature Neuroscience Reviews. 8(5):341-54.

66. Krashes MJ*, Keene AC*, Leung B, Armstrong JD, and Waddell S. Sequential use of mushroom body neuron subsets during Drosophila odor memory processing. (2007) Neuron  53(1):103-15.

67. Keene AC*, Krashes MJ*, Leung B, Bernard JA, and Waddell S. Drosophila Dorsal Paired Medial neurons provide a general mechanism for memory consolidation. (2006) Current Biology. 16(15):1524-30.

68. Yu D, Keene AC, Srivatsan A, Waddell S and Davis RL.  Drosophila DPM neurons form a delayed and branch-specific memory trace after olfactory classical conditioning. (2005) Cell  123 (5): 945-57.

69. Keene AC and Waddell S.  Drosophila olfactory memory: Dopamine signals punishment? (2005) Current Biology. 15(22):R932-4.

70. Keene AC, Stratmann M, Keller A, Perrat PN, Vosshall LB, and Waddell, S.  A benzaldehyde odor memory in Drosophila requires uniquely timed Dorsal Paired Medial neuron output. (2004) Neuron  44(3):521-33.

71. Ding H, Schwartz DS, Keene A, Affar E, Fenton L, Shi Y, Zamore PD, and Xu Z.  Selective silencing by RNAi of a dominant allele that causes amytrophic lateral sclerosis. (2003) Aging Cell  2(4):209-17.

72. Keene AC, Jones JE, Wade GN, and Corp ES.  Forebrain sites of NPY action on estrous behavior in Syrian hamsters. (2003) Physiology and Behavior    78(4-5):711-6.

73. Jones JE, Pick RR, Davenport MD, Keene AC, Corp ES, and Wade GN.  Disinhibition of female sexual behavior by a CRH receptor antagonist in Syrian hamsters. (2002) American Journal of  Physiology- Regulatory, Integrative and Comparative Physiology  283(3):R591-7.

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