John Malone


Assistant Professor

University of Connecticut
Deptment of Molecular and Cell Biology
67 North Eagleville Road, Unit 3197
Engineering Science Building 306D
Storrs, CT 06269 -3197

Telephone: 860-486-1899
Fax: 860-486-1936

Visit Assistant Professor Malone’s Website.


Education: Postdoctoral, Florida State University, The National Institutes of Health; PhD, Quantitative Biology, University of Texas at Arlington; MS, Zoology, The University of Oklahoma; BS, Wildlife and Fisheries Sciences, Texas A&M University

Research Interests: Gene dosage, dosage compensation, sex determination, sex chromosomes, genome balance, and genome evolution.

Selected Publications:

Malone JH. 2015. Dosage compensation in frogs and toads. In: Epigenetics: Current Research and Emerging Trends, BP Chadwick editor. Caister Academic Press, pp. 167-183.

Malone JH. 2015. Widespread rescue of Y-linked genes by gene movement to autosomes. Genome Biology 16:121.

Malone JH. 2015. Balancing copy number in ribosomal DNA. Proceedings of the National Academies of Sciences USA 112:2635-2636.

Malcom JW, Kudra RS, Malone JH. 2014. The sex chromosomes of frogs: variability and tolerance offer clues to genome evolution and function. Journal of Genomics 2:68-76.pdf.

Malcom JW, Malone JH. 2014. Analysis of deep sequencing data: insights and challenges. In: Fundamentals of  Advanced Omics Technologies: From Genes to Metabolites, C. Simó, A. Cifuentes, and V. García-Cañas, eds. Comprehensive Analytical Chemistry 63:325-354.

Chen Z-X, Sturgill D, Carson JQ, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki D, Fitzgerald P, Artieri C, Atallah J, Barmina O, Brown JB, Blankenburg K, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kovar C, Lee S, Li Mingmei, Malley J, Malone JH, Matthew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Pu L-L, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner C, Worley KC, Wu Y-Q, Zou X, Cherbas P, Kellis M, Eisen M, Piano F, Kionte K, Fitch D, Sternberg P, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs R, Bicket PJ, Kopp AK, Carninci P, Celniker SE, Oliver B, Richards S. 2014. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research 24:1209-1223.

Streicher JW, Devitt TJ, Goldberg CS, Malone JH, Blackmon H, Fujita MK. 2014. Diversification and asymmetrical gene flow across a heterogeneous landscape: lineage sorting dynamics in polytypic barking frogs. Molecular Ecology 23:3273-3291.

Malone JH, Ribado J, Lemmon EM. 2014. Sensory drive does not explain reproductive character displacement of male acoustic signals in the Upland Chorus Frog (Pseudacris feriarum). Evolution 68:1306-1319.

Sturgill D, Malone JH*, Sun X*, Smith HE, Rabinow L, Samson M-L, Oliver B. 2013. Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data. BMC Bioinformatics 14:320.

Malone JH*, Cho DY*, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, Smith HE, McDaniel J, Munro S, Salit M, Andrews J, Przytycka TM, Oliver B. 2012. Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biology 13:R28. *Editor’s Choice*

Meisel, RP*, Malone JH*, Clark AG. 2012. Disentangling the relationship between sex-biased gene expression and X-linkage. Genome Research 22:1255-1256.

Meisel, RP, Malone JH, Clark AG. 2012. Faster-X evolution of gene expression in Drosophila. PLoS Genetics 8: e1003013.

Malone JH, Oliver B. 2011. Microarrays and deep sequencing for measuring the transcriptome. BMC Biology 9:34.

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471:473-479.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone JH, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. 2010. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330:1787-1797.

Parisi M, Gupta V, Sturgill D Warren JT, Jallon JM, Malone JH, Zhang Y, Gilbert LI, Oliver B. 2010. Germline-dependent gene expression in distant nongonadal somatic tissues of Drosophila. BMC Genomics 11:346.

Zhang Y, Malone JH, Powell SK, Periwal V, Spana E, MacAlpine DM, Oliver B. 2010. Expression in aneuploid Drosophila S2 cells. PLoS Biology 8(2):e1000320. *Selected for Epigenetics 2010, evaluated as a “Must Read” by Faculty1000*

Malone JH, Oliver B. 2009. The genomic “inner fish” and a regulatory enigma in the vertebrates. Journal of Biology 8:32.

Malone JH, Fontenot B. 2008. Patterns of reproductive isolation in toads. PLoS ONE 3:e3900.

Malone JH, Oliver B. 2008. The sex chromosome that refused to die. Bioessays 30:409-411.

Malone JH, Michalak P. 2008. Gene expression analysis of the ovary of hybrid females of Xenopus laevis and X. muelleri. BMC Evolutionary Biology 8:82.

Michalak P, Malone JH. 2008. Testis-derived microRNA profiles of African Clawed Frogs (Xenopus) and their sterile hybrids. Genomics 91:158-164.

Malone JH, Michalak P. 2008. Physiological sex predicts hybrid sterility regardless of genotype. Science 319:59.

Malone JH, Chrzanowski TH, Michalak P. 2007. Sterility and gene expression in hybrid males of Xenopus laevis and X. muelleri. PLoS ONE 2:e781.

Michalak P, Malone JH, Lee IT, Hoshino D, Ma D. 2007. Gene expression polymorphism in Drosophila populations. Molecular Ecology 16:1179-1189.

Malone JH, Hawkins DL Jr, Michalak P. 2006. Sex-biased gene expression in a ZW sex determination system. Journal of Molecular Evolution 63:427-436. *Cover*