Alisha Holloway, PhD

TitleAssistant Professor
InstitutionUniversity of California San Francisco
DepartmentEpidemiology & Biostatistics
Address550 16th. Street
San Francisco CA 94158
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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 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.
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    1. Kostka D, Holloway A, Pollard KS. Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages. Mol Biol Evol. 2018 Jun 12. PMID: 29897475.
      View in: PubMed
    2. Thomas R, Thomas S, Holloway A, Pollard KS. Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform. 2017 05 01; 18(3):441-450. PMID: 27169896.
      View in: PubMed
    3. Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MA, He D, Small EM, Mileikovsky M, Nagy A, Holloway A, 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; PMCID: PMC4769693 [Available on 02/25/17].
    4. Holloway A, 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
    5. Williams RS, Lotia S, Holloway A, 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
    6. Kostka D, Friedrich T, Holloway A, 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
    7. Williams AG, Thomas S, Wyman SK, Holloway A. RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis. Curr Protoc Hum Genet. 2014 Oct 01; 83:11.13.1-20. PMID: 25271838; PMCID: PMC4230301.
    8. Thomas S, Underwood JG, Tseng E, Holloway A. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS One. 2014; 9(4):e94650. PMID: 24736250; PMCID: PMC3988055.
    9. Smith RP, Riesenfeld SJ, Holloway A, 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 Jul 18; 14(7):R72. PMID: 23867016; PMCID: PMC4054837.
    10. 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 A, 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 Mar 28; 14(3):R28. PMID: 23537068; PMCID: PMC4054807.
    11. 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 A, 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.
    12. 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 A, 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.
    13. Patterson E, Webb R, Weisbrod A, Bian B, He M, Zhang L, Holloway A, 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
    14. 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 A, 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. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12; 478(7370):476-82. PMID: 21993624.
      View in: PubMed
    15. Xiong Y, Zhang L, Holloway A, 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.
    16. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway A, 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 09; 89(3):382-97. PMID: 21855840; PMCID: PMC3169815.
    17. He BZ, Holloway A, 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.
    18. Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway A, 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 Mar 18; 6(3):e17753. PMID: 21445258; PMCID: PMC3060818.
    19. Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway A, 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 Feb 08; 2:187. PMID: 21304516; PMCID: PMC3096875.
    20. Rahbari R, Holloway A, 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.
      View in: PubMed
    21. Patterson EE, Holloway A, 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.
      View in: PubMed
    22. Kolaczkowski B, Kern AD, Holloway A, Begun DJ. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics. 2011 Jan; 187(1):245-60. PMID: 21059887; PMCID: PMC3018305.
    23. Lawniczak MK, Emrich SJ, Holloway A, 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.
    24. Li YF, Costello JC, Holloway A, Hahn MW. "Reverse ecology" and the power of population genomics. Evolution. 2008 Dec; 62(12):2984-94. PMID: 18752601; PMCID: PMC2626434.
    25. Lawniczak MK, Holloway A, 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.
    26. Holloway A, 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.
    27. Begun DJ, Holloway A, 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 06; 5(11):e310. PMID: 17988176; PMCID: PMC2062478.
    28. Levine MT, Holloway A, 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.
    29. Holloway A, Begun DJ. Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. PLoS One. 2007 Oct 31; 2(10):e1113. PMID: 17971876; PMCID: PMC2040203.
    30. Holloway A, 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.
    31. Holloway A, 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
    32. Holloway A, 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
    33. Begun DJ, Lindfors HA, Thompson ME, Holloway A. 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.
    34. Holloway A, 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
    35. Holder MT, Anderson JA, Holloway A. Difficulties in detecting hybridization. Syst Biol. 2001 Nov-Dec; 50(6):978-82. PMID: 12116644.
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    36. Adams RM, Mueller UG, Holloway A, 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
    37. Holloway A, 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.
    38. Hamilton MT, Etienne J, McClure WC, Pavey BS, Holloway A. 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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