Matthew P Davis

Matthew P Davis

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Matthew P Davis

Matthew P Davis

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Morphology and evolution of bioluminescent organs in the glowbellies (Percomorpha: Acropomatidae) with comments on the taxonomy and phylogeny of Acropomatiformes.

Authors:
Michael J Ghedotti Josephine N Gruber Ryan W Barton Matthew P Davis W Leo Smith

J Morphol 2018 11 22;279(11):1640-1653. Epub 2018 Oct 22.

Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas.

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http://doi.wiley.com/10.1002/jmor.20894
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http://dx.doi.org/10.1002/jmor.20894DOI Listing
November 2018

Light in the darkness: New perspective on lanternfish relationships and classification using genomic and morphological data.

Authors:
Rene P Martin Emily E Olson Matthew G Girard Wm Leo Smith Matthew P Davis

Mol Phylogenet Evol 2018 04 2;121:71-85. Epub 2018 Jan 2.

Department of Biological Sciences, 720 Fourth Avenue South, St. Cloud State University, St. Cloud, MN 56301, United States.

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http://dx.doi.org/10.1016/j.ympev.2017.12.029DOI Listing
April 2018

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.

Authors:
Dimitrios M Vitsios Elissavet Kentepozidou Leonor Quintais Elia Benito-Gutiérrez Stijn van Dongen Matthew P Davis Anton J Enright

Nucleic Acids Res 2017 Dec;45(21):e177

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://academic.oup.com/nar/article/45/21/e177/4210935
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http://dx.doi.org/10.1093/nar/gkx836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716205PMC
December 2017

A high-resolution mRNA expression time course of embryonic development in zebrafish.

Authors:
Richard J White John E Collins Ian M Sealy Neha Wali Christopher M Dooley Zsofia Digby Derek L Stemple Daniel N Murphy Konstantinos Billis Thibaut Hourlier Anja Füllgrabe Matthew P Davis Anton J Enright Elisabeth M Busch-Nentwich

Elife 2017 11 16;6. Epub 2017 Nov 16.

Wellcome Trust Sanger Institute, Hinxton, United Kingdom.

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http://dx.doi.org/10.7554/eLife.30860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690287PMC
November 2017

Repeated and Widespread Evolution of Bioluminescence in Marine Fishes.

Authors:
Matthew P Davis John S Sparks W Leo Smith

PLoS One 2016 8;11(6):e0155154. Epub 2016 Jun 8.

University of Kansas, Lawrence, KS 66045, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155154PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898709PMC
July 2017

Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.

Authors:
Matthew P Davis Claudia Carrieri Harpreet K Saini Stijn van Dongen Tommaso Leonardi Giovanni Bussotti Jack M Monahan Tania Auchynnikava Angelo Bitetti Juri Rappsilber Robin C Allshire Alena Shkumatava Dónal O'Carroll Anton J Enright

EMBO Rep 2017 07 12;18(7):1231-1247. Epub 2017 May 12.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK

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http://dx.doi.org/10.15252/embr.201744059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5494522PMC
July 2017

The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae).

Authors:
Michael J Ghedotti Matthew P Davis

Zootaxa 2017 Apr 10;4250(6):577-586. Epub 2017 Apr 10.

Regis University, Department of Biology, 3333 Regis Boulevard, Denver, Colorado 80221, USA..

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http://dx.doi.org/10.11646/zootaxa.4250.6.5DOI Listing
April 2017

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.

Authors:
Dimitrios M Vitsios Matthew P Davis Stijn van Dongen Anton J Enright

Nucleic Acids Res 2017 02;45(3):1079-1090

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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https://academic.oup.com/nar/article/45/3/1079/2605688
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http://dx.doi.org/10.1093/nar/gkw1031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388392PMC
February 2017

Evolution of Venomous Cartilaginous and Ray-Finned Fishes.

Authors:
W Leo Smith Jennifer H Stern Matthew G Girard Matthew P Davis

Integr Comp Biol 2016 11 3;56(5):950-961. Epub 2016 Jul 3.

Department of Biological Sciences, St. Cloud State University, Saint Cloud, MN 56301, USA.

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http://dx.doi.org/10.1093/icb/icw070DOI Listing
November 2016

Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology.

Authors:
David F Gruber Ellis R Loew Dimitri D Deheyn Derya Akkaynak Jean P Gaffney W Leo Smith Matthew P Davis Jennifer H Stern Vincent A Pieribone John S Sparks

Sci Rep 2016 04 25;6:24751. Epub 2016 Apr 25.

American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY 10024, USA.

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http://dx.doi.org/10.1038/srep24751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843165PMC
April 2016

The first report of luminescent liver tissue in fishes: evolution and structure of bioluminescent organs in the deep-sea naked barracudinas (Aulopiformes: Lestidiidae).

Authors:
Michael J Ghedotti Ryan W Barton Andrew M Simons Matthew P Davis

J Morphol 2015 Mar 18;276(3):310-8. Epub 2014 Nov 18.

Department of Biology, Regis University, Denver, Colorado, 80221.

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http://dx.doi.org/10.1002/jmor.20341DOI Listing
March 2015

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.

Authors:
Chiara Cossetti Nunzio Iraci Tim R Mercer Tommaso Leonardi Emanuele Alpi Denise Drago Clara Alfaro-Cervello Harpreet K Saini Matthew P Davis Julia Schaeffer Beatriz Vega Matilde Stefanini CongJian Zhao Werner Muller Jose Manuel Garcia-Verdugo Suresh Mathivanan Angela Bachi Anton J Enright John S Mattick Stefano Pluchino

Mol Cell 2014 Oct 18;56(2):193-204. Epub 2014 Sep 18.

John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, and NIHR Biomedical Research Centre, University of Cambridge, CB2 0PY Cambridge, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, Cambridge, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.08.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578249PMC
October 2014

The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon.

Authors:
John S Sparks Robert C Schelly W Leo Smith Matthew P Davis Dan Tchernov Vincent A Pieribone David F Gruber

PLoS One 2014 8;9(1):e83259. Epub 2014 Jan 8.

Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America ; Department of Natural Sciences, Baruch College, City University of New York, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083259PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885428PMC
September 2014

Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae).

Authors:
Caleb D McMahan Prosanta Chakrabarty John S Sparks W M Leo Smith Matthew P Davis

PLoS One 2013 19;8(8):e71162. Epub 2013 Aug 19.

LSU Museum of Natural Science (Ichthyology), Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071162PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747193PMC
April 2014

Species-specific bioluminescence facilitates speciation in the deep sea.

Authors:
Matthew P Davis Nancy I Holcroft Edward O Wiley John S Sparks W Leo Smith

Mar Biol 2014 21;161(5):1139-1148. Epub 2014 Feb 21.

University of Kansas, Lawrence, KS 66045 USA.

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http://dx.doi.org/10.1007/s00227-014-2406-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996283PMC
February 2014

Kraken: a set of tools for quality control and analysis of high-throughput sequence data.

Authors:
Matthew P A Davis Stijn van Dongen Cei Abreu-Goodger Nenad Bartonicek Anton J Enright

Methods 2013 Sep 29;63(1):41-9. Epub 2013 Jun 29.

EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.ymeth.2013.06.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991327PMC
September 2013

MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs.

Authors:
Dong Lu Matthew P A Davis Cei Abreu-Goodger Wei Wang Lia S Campos Julia Siede Elena Vigorito William C Skarnes Ian Dunham Anton J Enright Pentao Liu

PLoS One 2012 17;7(8):e40938. Epub 2012 Aug 17.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040938PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422229PMC
April 2013

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.

Authors:
Matthew P A Davis Cei Abreu-Goodger Stijn van Dongen Dong Lu Peri H Tate Nenad Bartonicek Claudia Kutter Pentao Liu William C Skarnes Anton J Enright Ian Dunham

PLoS One 2012 17;7(8):e41762. Epub 2012 Aug 17.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041762PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422281PMC
April 2013

The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites.

Authors:
Prosanta Chakrabarty Matthew P Davis John S Sparks

PLoS One 2012 28;7(8):e44083. Epub 2012 Aug 28.

Department of Biological Sciences, Louisiana State University, Museum of Natural Science, Baton Rouge, Louisiana, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044083PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429432PMC
February 2013

Exploring power and parameter estimation of the BiSSE method for analyzing species diversification.

Authors:
Matthew P Davis Peter E Midford Wayne Maddison

BMC Evol Biol 2013 Feb 11;13:38. Epub 2013 Feb 11.

The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, USA.

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http://dx.doi.org/10.1186/1471-2148-13-38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583807PMC
February 2013

Resolution of ray-finned fish phylogeny and timing of diversification.

Authors:
Thomas J Near Ron I Eytan Alex Dornburg Kristen L Kuhn Jon A Moore Matthew P Davis Peter C Wainwright Matt Friedman W Leo Smith

Proc Natl Acad Sci U S A 2012 Aug 6;109(34):13698-703. Epub 2012 Aug 6.

Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1073/pnas.1206625109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427055PMC
August 2012

Is sexual selection driving diversification of the bioluminescent ponyfishes (Teleostei: Leiognathidae)?

Authors:
Prosanta Chakrabarty Matthew P Davis W Leo Smith Zachary H Baldwin John S Sparks

Mol Ecol 2011 Jul 30;20(13):2818-34. Epub 2011 May 30.

Museum of Natural Science (Ichthyology Section), Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2011.05112.xDOI Listing
July 2011

Evolution of the light organ system in ponyfishes (Teleostei: Leiognathidae).

Authors:
Prosanta Chakrabarty Matthew P Davis Wm Leo Smith Rachel Berquist Kristen M Gledhill Larry R Frank John S Sparks

J Morphol 2011 Jun 23;272(6):704-21. Epub 2011 Mar 23.

Ichthyology Section, Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA.

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http://dx.doi.org/10.1002/jmor.10941DOI Listing
June 2011

Estimating divergence times of lizardfishes and their allies (Euteleostei: Aulopiformes) and the timing of deep-sea adaptations.

Authors:
Matthew P Davis Christopher Fielitz

Mol Phylogenet Evol 2010 Dec 18;57(3):1194-208. Epub 2010 Sep 18.

Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.ympev.2010.09.003DOI Listing
December 2010

Recombinant VP4 of human rhinovirus induces permeability in model membranes.

Authors:
Matthew P Davis Graham Bottley Lucy P Beales Richard A Killington David J Rowlands Tobias J Tuthill

J Virol 2008 Apr 6;82(8):4169-74. Epub 2008 Feb 6.

Institute for Molecular and Cellular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds LS2 9JT, United Kingdom.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.01070-07
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http://dx.doi.org/10.1128/JVI.01070-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2293005PMC
April 2008

A genome annotation-driven approach to cloning the human ORFeome.

Authors:
John E Collins Charmain L Wright Carol A Edwards Matthew P Davis James A Grinham Charlotte G Cole Melanie E Goward Begoña Aguado Meera Mallya Younes Mokrab Elizabeth J Huckle David M Beare Ian Dunham

Genome Biol 2004 30;5(10):R84. Epub 2004 Sep 30.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2004-5-10-r84DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545604PMC
July 2005

Trends in antimicrobial prescribing for bronchitis and upper respiratory infections among adults and children.

Authors:
Arch G Mainous William J Hueston Matthew P Davis William S Pearson

Am J Public Health 2003 Nov;93(11):1910-4

Department of Family Medicine, Medical University of South Carolina, Charleston 29425, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448075PMC
http://dx.doi.org/10.2105/ajph.93.11.1910DOI Listing
November 2003

Use of complementary and alternative medicine by children in the United States.

Authors:
Matthew P Davis Paul M Darden

Arch Pediatr Adolesc Med 2003 Apr;157(4):393-6

Department of Pediatrics, the Academic Generalist Fellowship Program, and the Center for Health Care Research, Medical University of South Carolina, Charleston 29425, USA.

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http://archpedi.jamanetwork.com/article.aspx?doi=10.1001/arc
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http://dx.doi.org/10.1001/archpedi.157.4.393DOI Listing
April 2003