Nicholas Putnam

Nicholas Putnam

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Nicholas Putnam

Nicholas Putnam

Publications by authors named "Nicholas Putnam"

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33Publications

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Deeply conserved synteny resolves early events in vertebrate evolution.

Nat Ecol Evol 2020 Apr 20. Epub 2020 Apr 20.

Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.

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http://dx.doi.org/10.1038/s41559-020-1156-zDOI Listing
April 2020

Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue.

J Mol Diagn 2019 05 31;21(3):375-383. Epub 2018 Dec 31.

Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15251578183017
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http://dx.doi.org/10.1016/j.jmoldx.2018.11.003DOI Listing
May 2019

Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis.

Gigascience 2016 10;5:20. Epub 2016 May 10.

Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080 USA ; Department of Biology, University of Florida, Gainesville, FL 32611-8525 USA.

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http://dx.doi.org/10.1186/s13742-016-0125-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863316PMC
October 2017

Genome evolution in the allotetraploid frog Xenopus laevis.

Nature 2016 10;538(7625):336-343

University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.

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http://dx.doi.org/10.1038/nature19840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313049PMC
October 2016

Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.

Genome Biol Evol 2016 08 25;8(8):2387-405. Epub 2016 Aug 25.

Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California

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http://dx.doi.org/10.1093/gbe/evw158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010895PMC
August 2016

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

Genome Res 2016 Mar 4;26(3):342-50. Epub 2016 Feb 4.

Dovetail Genomics LLC, Santa Cruz, California 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, California 95066, USA;

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http://dx.doi.org/10.1101/gr.193474.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772016PMC
March 2016

Evolution of the perlecan/HSPG2 gene and its activation in regenerating Nematostella vectensis.

PLoS One 2015 15;10(4):e0124578. Epub 2015 Apr 15.

Department of BioSciences, Rice University, Houston, Texas, United States; Department of Bioengineering, Rice University, Houston, Texas, United States.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124578PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398486PMC
January 2016

Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida.

Genome Biol Evol 2015 Dec 10;8(1):271-81. Epub 2015 Dec 10.

Whitney Laboratory for Marine Bioscience, University of Florida Department of Biology, University of Florida

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http://dx.doi.org/10.1093/gbe/evv243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758240PMC
December 2015

Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals.

BMC Evol Biol 2014 Oct 4;14:212. Epub 2014 Oct 4.

Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research, National Institutes of Health, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1186/s12862-014-0212-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4219131PMC
October 2014

The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution.

Genome Biol Evol 2014 Sep 19;6(10):2681-96. Epub 2014 Sep 19.

Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego

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http://dx.doi.org/10.1093/gbe/evu212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224339PMC
September 2014

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication.

Gigascience 2014 14;3. Epub 2014 May 14.

Department of Ecology and Evolutionary Biology, Rice University, P.O. Box 1892, Houston, TX 77251-1892, USA ; Department of Biochemistry and Cell Biology, Rice University, P.O. Box 1892, Houston, TX 77251-1892, USA.

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http://dx.doi.org/10.1186/2047-217X-3-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066314PMC
July 2014

Phytozome: a comparative platform for green plant genomics.

Nucleic Acids Res 2012 Jan 22;40(Database issue):D1178-86. Epub 2011 Nov 22.

US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1093/nar/gkr944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245001PMC
January 2012

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.

BMC Bioinformatics 2011 Oct 5;12 Suppl 9:S11. Epub 2011 Oct 5.

Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77098, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-S9-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283319PMC
October 2011

The dynamic genome of Hydra.

Nature 2010 Mar 14;464(7288):592-6. Epub 2010 Mar 14.

US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature08830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479502PMC
March 2010

Domain shuffling and the evolution of vertebrates.

Genome Res 2009 Aug 14;19(8):1393-403. Epub 2009 May 14.

Okinawa Institute of Science and Technology, Uruma, Okinawa, Japan.

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http://dx.doi.org/10.1101/gr.087072.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720177PMC
August 2009

Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes.

Genome Inform 2007 ;19:50-60

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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July 2008