Alisha Holloway, PhD

Title(s)Assistant Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
Address550 16th. Street, #357
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. to make corrections and additions.
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    1. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nat Ecol Evol. 2019 08; 3(8):1241-1252. Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR, Ciofi C, Kwok PY, Pollard KS, Bruneau BG. PMID: 31358948; PMCID: PMC6668926.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    2. Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages. Mol Biol Evol. 2018 08 01; 35(8):2034-2045. Kostka D, Holloway AK, Pollard KS. PMID: 29897475; PMCID: PMC6063267.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimals
    3. Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform. 2017 05 01; 18(3):441-450. Thomas R, Thomas S, Holloway AK, Pollard KS. PMID: 27169896; PMCID: PMC5429005.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    4. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell. 2016 Feb 25; 164(5):999-1014. 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. PMID: 26875865; PMCID: PMC4769693.
      View in: PubMed   Mentions: 98     Fields:    Translation:AnimalsCells
    5. Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor. Mol Biol Evol. 2016 Apr; 33(4):1008-18. Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. PMID: 26715627; PMCID: PMC4776709.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    6. From scientific discovery to cures: bright stars within a galaxy. Cell. 2015 Sep 24; 163(1):21-3. Williams RS, Lotia S, Holloway AK, Pico AR. PMID: 26406364.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimals
    7. motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. Stat Interface. 2015; 8(4):463-476. Kostka D, Friedrich T, Holloway AK, Pollard KS. PMID: 26709360; PMCID: PMC4689439.
      View in: PubMed   Mentions: 2  
    8. RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis. Curr Protoc Hum Genet. 2014 Oct 01; 83:11.13.1-20. Williams AG, Thomas S, Wyman SK, Holloway AK. PMID: 25271838; PMCID: PMC4230301.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    9. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS One. 2014; 9(4):e94650. Thomas S, Underwood JG, Tseng E, Holloway AK, Bench To Basinet CvDC Informatics Subcommittee. PMID: 24736250; PMCID: PMC3988055.
      View in: PubMed   Mentions: 36     Fields:    Translation:Animals
    10. 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. Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. PMID: 23867016; PMCID: PMC4054837.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    11. 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. 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. PMID: 23537068; PMCID: PMC4054807.
      View in: PubMed   Mentions: 127     Fields:    Translation:HumansAnimalsCells
    12. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20. 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. PMID: 22981692; PMCID: PMC3462286.
      View in: PubMed   Mentions: 356     Fields:    Translation:HumansAnimalsCells
    13. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 2012 Oct; 192(2):533-98. 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. PMID: 22673804; PMCID: PMC3454882.
      View in: PubMed   Mentions: 188     Fields:    Translation:AnimalsCells
    14. The microRNA expression changes associated with malignancy and SDHB mutation in pheochromocytoma. Endocr Relat Cancer. 2012 Apr; 19(2):157-66. Patterson E, Webb R, Weisbrod A, Bian B, He M, Zhang L, Holloway AK, Krishna R, Nilubol N, Pacak K, Kebebew E. PMID: 22241719; PMCID: PMC4716660.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    15. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12; 478(7370):476-82. 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, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, 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, Genome Institute at Washington University, 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. PMID: 21993624; PMCID: PMC3207357.
      View in: PubMed   Mentions: 593     Fields:    Translation:HumansAnimals
    16. MiR-886-3p regulates cell proliferation and migration, and is dysregulated in familial non-medullary thyroid cancer. PLoS One. 2011; 6(10):e24717. Xiong Y, Zhang L, Holloway AK, Wu X, Su L, Kebebew E. PMID: 21998631; PMCID: PMC3187745.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    17. Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet. 2011 Sep 09; 89(3):382-97. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF. PMID: 21855840; PMCID: PMC3169815.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    18. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genet. 2011 Apr; 7(4):e1002053. He BZ, Holloway AK, Maerkl SJ, Kreitman M. PMID: 21572512; PMCID: PMC3084208.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    19. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS One. 2011 Mar 18; 6(3):e17753. Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P. PMID: 21445258; PMCID: PMC3060818.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    20. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nat Commun. 2011 Feb 08; 2:187. 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. PMID: 21304516; PMCID: PMC3096875.
      View in: PubMed   Mentions: 112     Fields:    Translation:AnimalsCells
    21. Identification of differentially expressed microRNA in parathyroid tumors. Ann Surg Oncol. 2011 Apr; 18(4):1158-65. Rahbari R, Holloway AK, He M, Khanafshar E, Clark OH, Kebebew E. PMID: 21086055; PMCID: PMC3449317.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    22. MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy. Cancer. 2011 Apr 15; 117(8):1630-9. Patterson EE, Holloway AK, Weng J, Fojo T, Kebebew E. PMID: 21472710; PMCID: PMC3051015.
      View in: PubMed   Mentions: 87     Fields:    
    23. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics. 2011 Jan; 187(1):245-60. Kolaczkowski B, Kern AD, Holloway AK, Begun DJ. PMID: 21059887; PMCID: PMC3018305.
      View in: PubMed   Mentions: 116     Fields:    Translation:HumansAnimalsCells
    24. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science. 2010 Oct 22; 330(6003):512-4. 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. PMID: 20966253; PMCID: PMC3674514.
      View in: PubMed   Mentions: 136     Fields:    Translation:Animals
    25. Parathyroid neoplasms have distinct microRNA gene expression profile. Journal of the American College of Surgeons. 2010 Sep 1; 211(3):s122. Rahbari RR, Holloway HA, He HM, Clark CO. .
      View in: Publisher Site   Mentions:
    26. "Reverse ecology" and the power of population genomics. Evolution. 2008 Dec; 62(12):2984-94. Li YF, Costello JC, Holloway AK, Hahn MW. PMID: 18752601; PMCID: PMC2626434.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansAnimalsCells
    27. Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biol. 2008; 9(8):R125. Lawniczak MK, Holloway AK, Begun DJ, Jones CD. PMID: 18700012; PMCID: PMC2575515.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    28. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res. 2008 Oct; 18(10):1592-601. Holloway AK, Begun DJ, Siepel A, Pollard KS. PMID: 18583644; PMCID: PMC2556263.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    29. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 2007 Nov 06; 5(11):e310. 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. PMID: 17988176; PMCID: PMC2062478.
      View in: PubMed   Mentions: 378     Fields:    Translation:AnimalsCells
    30. Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster. Genetics. 2007 Nov; 177(3):1959-62. Levine MT, Holloway AK, Arshad U, Begun DJ. PMID: 18039888; PMCID: PMC2147993.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    31. Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. PLoS One. 2007 Oct 31; 2(10):e1113. Holloway AK, Begun DJ. PMID: 17971876; PMCID: PMC2040203.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    32. Adaptive gene expression divergence inferred from population genomics. PLoS Genet. 2007 Oct; 3(10):2007-13. Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD. PMID: 17967066; PMCID: PMC2042001.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    33. Experimental evolution of gene duplicates in a bacterial plasmid model. J Mol Evol. 2007 Feb; 64(2):215-22. Holloway AK, Palzkill T, Bull JJ. PMID: 17211548.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    34. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics. 2007 Jan 1; 3:117693430700300016. Lapp LH, Bala BS, Balhoff BJ, Bouck BA, Goto GN, Holder HM, Holland HR, Holloway HA, Katayama KT, Lewis LP, Mackey MA, Osborne OB, Piel PW, Pond PS, Poon PA, Qiu QW, Stajich SJ, Stoltzfus SA, Thierer TT, Vilella VA, Vos VR, Zmasek ZC, Zwickl ZD, Vision VT. .
      View in: Publisher Site   Mentions:
    35. Polyploids with different origins and ancestors form a single sexual polyploid species. Am Nat. 2006 Apr; 167(4):E88-101. Holloway AK, Cannatella DC, Gerhardt HC, Hillis DM. PMID: 16670990.
      View in: PubMed   Mentions: 28     Fields:    Translation:Animals
    36. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics. 2006 Mar; 172(3):1675-81. Begun DJ, Lindfors HA, Thompson ME, Holloway AK. PMID: 16361246; PMCID: PMC1456303.
      View in: PubMed   Mentions: 73     Fields:    Translation:Animals
    37. Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila. Mol Biol Evol. 2004 Sep; 21(9):1625-8. Holloway AK, Begun DJ. PMID: 15215320.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    38. Difficulties in detecting hybridization. Syst Biol. 2001 Nov-Dec; 50(6):978-82. Holder MT, Anderson JA, Holloway AK. PMID: 12116644.
      View in: PubMed   Mentions: 26     Fields:    
    39. Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population. Canadian Journal of Zoology. 2001 Jan 1; 79(1):26-34. Antolin AM, Horne HB, Berger, Jr. BM, Holloway HA, Roach RJ, Weeks, Jr. WR. .
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    40. Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population. Canadian Journal of Zoology. 2001 Jan 1; 79(1):26-34. Antolin AM, Van Horne VB, Berger BM, Holloway HA, Roach RJ, Weeks WR. .
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    41. Garden sharing and garden stealing in fungus-growing ants. Naturwissenschaften. 2000 Nov; 87(11):491-3. Adams RM, Mueller UG, Holloway AK, Green AM, Narozniak J. PMID: 11151668.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    42. Linkage analysis of sex determination in Bracon sp. near hebetor (Hymenoptera: Braconidae). Genetics. 2000 Jan; 154(1):205-12. Holloway AK, Strand MR, Black WC, Antolin MF. PMID: 10628981; PMCID: PMC1460894.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    43. Survival of Diploid Males in Braconsp. near hebetor (Hymenoptera: Braconidae). Annals of the Entomological Society of America. 1999 Jan 1; 92(1):110-116. Holloway HA, Heimpel HG, Strand SM, Antolin AM. .
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    44. Role of local contractile activity and muscle fiber type on LPL regulation during exercise. Am J Physiol. 1998 12; 275(6):E1016-22. Hamilton MT, Etienne J, McClure WC, Pavey BS, Holloway AK. PMID: 9843744.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    45. Relationship between numbers of the endangered American burying beetle Nicrophorus americanus Olivier (Coleoptera : Silphidae) and available food resources. Biological Conservation. 1997 Jul 1; 81(1-2):145-152. Holloway HA, Schnell SG. .
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