Alisha K. Holloway, Ph.D. - Publications

University of California, San Francisco, San Francisco, CA 
Molecular evolution, computational biology

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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, et al. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nature Ecology & Evolution. 3: 1241-1252. PMID 31358948 DOI: 10.1038/s41559-019-0945-8  0.44
2018 Kostka D, Holloway AK, Pollard KS. Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages. Molecular Biology and Evolution. PMID 29897475 DOI: 10.1093/molbev/msy109  0.44
2016 Thomas R, Thomas S, Holloway AK, Pollard KS. Features that define the best ChIP-seq peak calling algorithms. Briefings in Bioinformatics. PMID 27169896 DOI: 10.1093/bib/bbw035  0.44
2016 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. PMID 26875865 DOI: 10.1016/j.cell.2016.01.004  1
2015 Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. Accelerated evolution of enhancer hotspots in the mammal ancestor. Molecular Biology and Evolution. PMID 26715627 DOI: 10.1093/molbev/msv344  0.44
2015 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. Statistics and Its Interface. 8: 463-476. PMID 26709360 DOI: 10.4310/SII.2015.v8.n4.a6  1
2015 Williams RS, Lotia S, Holloway AK, Pico AR. From Scientific Discovery to Cures: Bright Stars within a Galaxy. Cell. 163: 21-3. PMID 26406364 DOI: 10.1016/j.cell.2015.09.007  1
2014 Thomas S, Underwood JG, Tseng E, Holloway AK. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. Plos One. 9: e94650. PMID 24736250 DOI: 10.1371/journal.pone.0094650  1
2013 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 Biology. 14: R72. PMID 23867016 DOI: 10.1186/gb-2013-14-7-r72  1
2013 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, ... ... Holloway AK, et al. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 14: R28. PMID 23537068 DOI: 10.1186/gb-2013-14-3-r28  1
2012 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, ... ... Holloway AK, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 151: 206-20. PMID 22981692 DOI: 10.1016/j.cell.2012.07.035  0.44
2012 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, et al. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 192: 533-98. PMID 22673804 DOI: 10.1534/genetics.112.142018  1
2012 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. Endocrine-Related Cancer. 19: 157-66. PMID 22241719 DOI: 10.1530/ERC-11-0308  1
2011 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. 6: e24717. PMID 21998631 DOI: 10.1371/journal.pone.0024717  1
2011 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, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/nature10530  1
2011 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. American Journal of Human Genetics. 89: 382-97. PMID 21855840 DOI: 10.1016/j.ajhg.2011.07.023  1
2011 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 Genetics. 7: e1002053. PMID 21572512 DOI: 10.1371/journal.pgen.1002053  1
2011 Patterson EE, Holloway AK, Weng J, Fojo T, Kebebew E. MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy. Cancer. 117: 1630-9. PMID 21472710 DOI: 10.1002/cncr.25724  1
2011 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. 6: e17753. PMID 21445258 DOI: 10.1371/journal.pone.0017753  1
2011 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, et al. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nature Communications. 2: 187. PMID 21304516 DOI: 10.1038/ncomms1187  0.44
2011 Rahbari R, Holloway AK, He M, Khanafshar E, Clark OH, Kebebew E. Identification of differentially expressed microRNA in parathyroid tumors. Annals of Surgical Oncology. 18: 1158-65. PMID 21086055 DOI: 10.1245/s10434-010-1359-7  1
2011 Kolaczkowski B, Kern AD, Holloway AK, Begun DJ. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics. 187: 245-60. PMID 21059887 DOI: 10.1534/genetics.110.123059  1
2010 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, et al. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science (New York, N.Y.). 330: 512-4. PMID 20966253 DOI: 10.1126/science.1195755  1
2008 Li YF, Costello JC, Holloway AK, Hahn MW. "Reverse ecology" and the power of population genomics. Evolution; International Journal of Organic Evolution. 62: 2984-94. PMID 18752601 DOI: 10.1111/j.1558-5646.2008.00486.x  1
2008 Lawniczak MK, Holloway AK, Begun DJ, Jones CD. Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biology. 9: R125. PMID 18700012 DOI: 10.1186/gb-2008-9-8-r125  1
2008 Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Research. 18: 1592-601. PMID 18583644 DOI: 10.1101/gr.077131.108  1
2007 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. 177: 1959-62. PMID 18039888 DOI: 10.1534/genetics.107.079459  1
2007 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 Biology. 5: e310. PMID 17988176 DOI: 10.1371/journal.pbio.0050310  1
2007 Holloway AK, Begun DJ. Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. Plos One. 2: e1113. PMID 17971876 DOI: 10.1371/journal.pone.0001113  1
2007 Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD. Adaptive gene expression divergence inferred from population genomics. Plos Genetics. 3: 2007-13. PMID 17967066 DOI: 10.1371/journal.pgen.0030187  1
2007 Holloway AK, Palzkill T, Bull JJ. Experimental evolution of gene duplicates in a bacterial plasmid model. Journal of Molecular Evolution. 64: 215-22. PMID 17211548 DOI: 10.1007/s00239-006-0087-x  1
2006 Holloway AK, Cannatella DC, Gerhardt HC, Hillis DM. Polyploids with different origins and ancestors form a single sexual polyploid species. The American Naturalist. 167: E88-101. PMID 16670990 DOI: 10.1086/501079  1
2006 Begun DJ, Lindfors HA, Thompson ME, Holloway AK. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics. 172: 1675-81. PMID 16361246 DOI: 10.1534/genetics.105.050336  1
2004 Holloway AK, Begun DJ. Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila. Molecular Biology and Evolution. 21: 1625-8. PMID 15215320 DOI: 10.1093/molbev/msh195  1
2001 Holder MT, Anderson JA, Holloway AK. Difficulties in detecting hybridization. Systematic Biology. 50: 978-82. PMID 12116644 DOI: 10.1080/106351501753462911  1
2001 Antolin MF, Van Horne B, Berger J, Holloway AK, Roach JL, Weeks J. Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population Canadian Journal of Zoology. 79: 26-34. DOI: 10.1139/cjz-79-1-26  1
2000 Adams RM, Mueller UG, Holloway AK, Green AM, Narozniak J. Garden sharing and garden stealing in fungus-growing ants. Die Naturwissenschaften. 87: 491-3. PMID 11151668 DOI: 10.1007/s001140050765  1
2000 Holloway AK, Strand MR, Black WC, Antolin MF. Linkage analysis of sex determination in Bracon sp. near hebetor (Hymenoptera: Braconidae). Genetics. 154: 205-12. PMID 10628981  1
1999 Holloway AK, Heimpel GE, Strand MR, Antolin MF. Survival of diploid males in Bracon sp. near hebetor (Hymenoptera: Braconidae) Annals of the Entomological Society of America. 92: 110-116.  1
1998 Hamilton MT, Etienne J, McClure WC, Pavey BS, Holloway AK. Role of local contractile activity and muscle fiber type on LPL regulation during exercise. The American Journal of Physiology. 275: E1016-22. PMID 9843744  1
1997 Holloway AK, Schnell GD. Relationship between numbers of the endangered american burying beetle Nicrophorus americanus Olivier (Coleoptera: Silphidae) and available food resources Biological Conservation. 81: 145-152. DOI: 10.1016/S0006-3207(96)00158-9  1
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