Alisha K Holloway

Alisha K Holloway

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Alisha K Holloway

Alisha K Holloway

Publications by authors named "Alisha K Holloway"

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33Publications

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Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.

Mol Biol Evol 2016 Apr 29;33(4):1008-18. Epub 2015 Dec 29.

Gladstone Institute of Cardiovascular Disease, San Francisco, CA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA Institute for Human Genetics, University of California, San Francisco, CA

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http://dx.doi.org/10.1093/molbev/msv344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776709PMC
April 2016

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

Cell 2016 Feb 11;164(5):999-1014. Epub 2016 Feb 11.

Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769693PMC
February 2016

From scientific discovery to cures: bright stars within a galaxy.

Cell 2015 Sep;163(1):21-3

Gladstone Institutes, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1016/j.cell.2015.09.007DOI Listing
September 2015

Long-read sequencing of chicken transcripts and identification of new transcript isoforms.

PLoS One 2014 15;9(4):e94650. Epub 2014 Apr 15.

The Gladstone Institutes, San Francisco, California, United States of America; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094650PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988055PMC
January 2015

motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences.

Stat Interface 2015;8(4):463-476

Gladstone Institutes, Institute for Human Genetics, Division of Biostatistics, University of California, 1650 Owens Street, San Francisco, CA 94158, USA.

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http://www.intlpress.com/site/pub/pages/journals/items/sii/c
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http://dx.doi.org/10.4310/SII.2015.v8.n4.a6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689439PMC
January 2015

RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.

Curr Protoc Hum Genet 2014 Oct 1;83:11.13.1-20. Epub 2014 Oct 1.

Gladstone Institute of Cardiovascular Disease, San Francisco, California.

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http://dx.doi.org/10.1002/0471142905.hg1113s83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230301PMC
October 2014

MiR-886-3p regulates cell proliferation and migration, and is dysregulated in familial non-medullary thyroid cancer.

PLoS One 2011 5;6(10):e24717. Epub 2011 Oct 5.

Endocrine Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024717PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187745PMC
February 2012

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

Identification of differentially expressed microRNA in parathyroid tumors.

Ann Surg Oncol 2011 Apr 18;18(4):1158-65. Epub 2010 Nov 18.

Endocrine Oncology Section, Surgery Branch, National Cancer Institute, Bethesda, MD, USA.

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http://dx.doi.org/10.1245/s10434-010-1359-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3449317PMC
April 2011

MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy.

Cancer 2011 Apr 8;117(8):1630-9. Epub 2010 Nov 8.

Endocrine Oncology Section, Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://doi.wiley.com/10.1002/cncr.25724
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http://dx.doi.org/10.1002/cncr.25724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051015PMC
April 2011

Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.

PLoS Genet 2011 Apr 28;7(4):e1002053. Epub 2011 Apr 28.

Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084208PMC
April 2011

"Reverse ecology" and the power of population genomics.

Evolution 2008 Dec 26;62(12):2984-94. Epub 2008 Aug 26.

School of Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2008.00486.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2626434PMC
December 2008

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.

Genome Res 2008 Oct 26;18(10):1592-601. Epub 2008 Jun 26.

Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95691, USA.

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http://dx.doi.org/10.1101/gr.077131.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556263PMC
October 2008

Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster.

Genetics 2007 Nov;177(3):1959-62

Section of Evolution and Ecology, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1534/genetics.107.079459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2147993PMC
November 2007

Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans.

PLoS One 2007 Oct 31;2(10):e1113. Epub 2007 Oct 31.

Section of Evolution and Ecology, University of California at Davis, Davis, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001113PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2040203PMC
October 2007

Experimental evolution of gene duplicates in a bacterial plasmid model.

J Mol Evol 2007 Feb 8;64(2):215-22. Epub 2007 Jan 8.

Section of Evolution and Ecology, Center for Population Biology, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1007/s00239-006-0087-xDOI Listing
February 2007

Polyploids with different origins and ancestors form a single sexual polyploid species.

Am Nat 2006 Apr 8;167(4):E88-101. Epub 2006 Mar 8.

Section of Integrative Biology, University of Texas, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1086/501079DOI Listing
April 2006

Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila.

Mol Biol Evol 2004 Sep 23;21(9):1625-8. Epub 2004 Jun 23.

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http://dx.doi.org/10.1093/molbev/msh195DOI Listing
September 2004