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    Alisha Holloway, PhD

    TitleAssistant Professor
    SchoolUCSF School of Medicine
    DepartmentEpidemiology & Biostatistics
    Address550 16th. Street
    San Francisco CA 94158
    Phone415-734-2723
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      Collapse Biography 
      Collapse Awards and Honors
      Colorado State University1995Colorado Graduate Fellowship
      Colorado State University1996University Graduate Fellowship
      University of Texas-Austin2000 - 2002Graduate Program in Zoology Research Awards
      University of Texas-Austin2002 - 2004NSF-IGERT Fellowship
      University of Texas-Austin2003 - 2004NSF Doctoral Dissertation Improvement Grant
      University of California-Davis2005 - 2007NSF Biological Informatics Postdoctoral Fellowship
      University of California-Davis2007Award for Excellence in Postdoctoral Research
      Gladstone Institutes2009Anne H. Snyder Award of Excellence

      Collapse Overview 
      Collapse Overview
      Dr. Holloway is an expert in comparative genomics and statistical analysis of high-throughput sequence data. Her postdoctoral work focused on integrating population genomic data with gene expression data to understand the underlying genetic basis for gene expression variation. Dr. Holloway’s research focuses on using comparative and population genomics to understand the evolution of mammalian traits and of gene regulatory networks in developing vertebrate hearts. Dr. Holloway is the founding director of the Gladstone Bioinformatics Core and directs a team of staff scientists who are experts in high-throughput data analysis and biostatistics. She also serves as Informatics Leader for the NHLBI Bench to Bassinet program, whose mission is to accelerate scientific discovery to clinical practice through collaborations of basic, translational and clinical research into congenital heart disease. In that role, she directs efforts to evaluate tools for high throughput sequence analysis, develop bioinformatics tools, and integrate analysis of orthogonal data sets.


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      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Thomas R, Thomas S, Holloway AK, Pollard KS. Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform. 2016 May 11. PMID: 27169896.
        View in: PubMed
      2. Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MA, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Müller CW, Bruneau BG. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell. 2016 Feb 25; 164(5):999-1014. PMID: 26875865.
        View in: PubMed
      3. Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor. Mol Biol Evol. 2016 Apr; 33(4):1008-18. PMID: 26715627.
        View in: PubMed
      4. Williams RS, Lotia S, Holloway AK, Pico AR. From Scientific Discovery to Cures: Bright Stars within a Galaxy. Cell. 2015 Sep 24; 163(1):21-3. PMID: 26406364.
        View in: PubMed
      5. Kostka D, Friedrich T, Holloway AK, Pollard KS. motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. Stat Interface. 2015; 8(4):463-476. PMID: 26709360.
        View in: PubMed
      6. Williams AG, Thomas S, Wyman SK, Holloway AK. RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis. Curr Protoc Hum Genet. 2014; 83:11.13.1-11.13.20. PMID: 25271838; PMCID: PMC4230301.
      7. Thomas S, Underwood JG, Tseng E, Holloway AK. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS One. 2014; 9(4):e94650. PMID: 24736250; PMCID: PMC3988055.
      8. Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol. 2013; 14(7):R72. PMID: 23867016; PMCID: PMC4054837.
      9. Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 2013; 14(3):R28. PMID: 23537068; PMCID: PMC4054807.
      10. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20. PMID: 22981692; PMCID: PMC3462286.
      11. Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, Song YS, Hahn MW, Begun DJ. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 2012 Oct; 192(2):533-98. PMID: 22673804; PMCID: PMC3454882.
      12. Patterson E, Webb R, Weisbrod A, Bian B, He M, Zhang L, Holloway AK, Krishna R, Nilubol N, Pacak K, Kebebew E. The microRNA expression changes associated with malignancy and SDHB mutation in pheochromocytoma. Endocr Relat Cancer. 2012 Apr; 19(2):157-66. PMID: 22241719.
        View in: PubMed
      13. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 27; 478(7370):476-82. PMID: 21993624; PMCID: PMC3207357.
      14. Xiong Y, Zhang L, Holloway AK, Wu X, Su L, Kebebew E. MiR-886-3p regulates cell proliferation and migration, and is dysregulated in familial non-medullary thyroid cancer. PLoS One. 2011; 6(10):e24717. PMID: 21998631; PMCID: PMC3187745.
      15. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF. Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet. 2011 Sep 9; 89(3):382-97. PMID: 21855840; PMCID: PMC3169815.
      16. He BZ, Holloway AK, Maerkl SJ, Kreitman M. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genet. 2011 Apr; 7(4):e1002053. PMID: 21572512; PMCID: PMC3084208.
      17. Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS One. 2011; 6(3):e17753. PMID: 21445258; PMCID: PMC3060818.
      18. Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y, Zhou YQ, Yeh RF, Henkelman RM, Harvey RP, Metzger D, Chambon P, Stainier DY, Pollard KS, Scott IC, Bruneau BG. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nat Commun. 2011; 2:187. PMID: 21304516; PMCID: PMC3096875.
      19. Rahbari R, Holloway AK, He M, Khanafshar E, Clark OH, Kebebew E. Identification of differentially expressed microRNA in parathyroid tumors. Ann Surg Oncol. 2011 Apr; 18(4):1158-65. PMID: 21086055; PMCID: PMC3449317.
      20. Patterson EE, Holloway AK, Weng J, Fojo T, Kebebew E. MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy. Cancer. 2011 Apr 15; 117(8):1630-9. PMID: 21472710; PMCID: PMC3051015.
      21. Kolaczkowski B, Kern AD, Holloway AK, Begun DJ. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics. 2011 Jan; 187(1):245-60. PMID: 21059887; PMCID: PMC3018305.
      22. Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, Kyung K, Walenz BP, Garcia-Hernandez E, Aguiar M, Viswanathan LD, Rogers YH, Strausberg RL, Saski CA, Lawson D, Collins FH, Kafatos FC, Christophides GK, Clifton SW, Kirkness EF, Besansky NJ. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science. 2010 Oct 22; 330(6003):512-4. PMID: 20966253; PMCID: PMC3674514.
      23. Li YF, Costello JC, Holloway AK, Hahn MW. "Reverse ecology" and the power of population genomics. Evolution. 2008 Dec; 62(12):2984-94. PMID: 18752601; PMCID: PMC2626434.
      24. Lawniczak MK, Holloway AK, Begun DJ, Jones CD. Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biol. 2008; 9(8):R125. PMID: 18700012; PMCID: PMC2575515.
      25. Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res. 2008 Oct; 18(10):1592-601. PMID: 18583644; PMCID: PMC2556263.
      26. Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 2007 Nov 6; 5(11):e310. PMID: 17988176; PMCID: PMC2062478.
      27. Levine MT, Holloway AK, Arshad U, Begun DJ. Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster. Genetics. 2007 Nov; 177(3):1959-62. PMID: 18039888; PMCID: PMC2147993.
      28. Holloway AK, Begun DJ. Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. PLoS One. 2007; 2(10):e1113. PMID: 17971876; PMCID: PMC2040203.
      29. Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD. Adaptive gene expression divergence inferred from population genomics. PLoS Genet. 2007 Oct; 3(10):2007-13. PMID: 17967066; PMCID: PMC2042001.
      30. Holloway AK, Palzkill T, Bull JJ. Experimental evolution of gene duplicates in a bacterial plasmid model. J Mol Evol. 2007 Feb; 64(2):215-22. PMID: 17211548.
        View in: PubMed
      31. Holloway AK, Cannatella DC, Gerhardt HC, Hillis DM. Polyploids with different origins and ancestors form a single sexual polyploid species. Am Nat. 2006 Apr; 167(4):E88-101. PMID: 16670990.
        View in: PubMed
      32. Begun DJ, Lindfors HA, Thompson ME, Holloway AK. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics. 2006 Mar; 172(3):1675-81. PMID: 16361246; PMCID: PMC1456303.
      33. Holloway AK, Begun DJ. Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila. Mol Biol Evol. 2004 Sep; 21(9):1625-8. PMID: 15215320.
        View in: PubMed
      34. Holder MT, Anderson JA, Holloway AK. Difficulties in detecting hybridization. Syst Biol. 2001 Nov-Dec; 50(6):978-82. PMID: 12116644.
        View in: PubMed
      35. Adams RM, Mueller UG, Holloway AK, Green AM, Narozniak J. Garden sharing and garden stealing in fungus-growing ants. Naturwissenschaften. 2000 Nov; 87(11):491-3. PMID: 11151668.
        View in: PubMed
      36. Holloway AK, Strand MR, Black WC, Antolin MF. Linkage analysis of sex determination in Bracon sp. near hebetor (Hymenoptera: Braconidae). Genetics. 2000 Jan; 154(1):205-12. PMID: 10628981; PMCID: PMC1460894.
      37. Hamilton MT, Etienne J, McClure WC, Pavey BS, Holloway AK. Role of local contractile activity and muscle fiber type on LPL regulation during exercise. Am J Physiol. 1998 Dec; 275(6 Pt 1):E1016-22. PMID: 9843744.
        View in: PubMed
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