Laura F Landweber

Laura F Landweber

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Laura F Landweber

Laura F Landweber

Publications by authors named "Laura F Landweber"

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77Publications

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Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms.

BMC Genomics 2019 Dec 30;20(1):1037. Epub 2019 Dec 30.

Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA.

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http://dx.doi.org/10.1186/s12864-019-6189-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6937825PMC
December 2019

Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA.

Nucleic Acids Res 2019 10;47(18):9741-9760

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

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http://dx.doi.org/10.1093/nar/gkz725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765146PMC
October 2019

Programmed Chromosome Deletion in the Ciliate .

G3 (Bethesda) 2019 10 7;9(10):3105-3118. Epub 2019 Oct 7.

Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY and

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http://dx.doi.org/10.1534/g3.118.200930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778801PMC
October 2019

Transformation with Artificial Chromosomes in and Their Applications.

G3 (Bethesda) 2019 10 7;9(10):3119-3127. Epub 2019 Oct 7.

Departments of Biochemistry and Molecular Biophysics and Biological Sciences, Columbia University, New York, NY,

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http://dx.doi.org/10.1534/g3.119.400298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778790PMC
October 2019

Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.

Cell 2019 Jun 16;177(7):1781-1796.e25. Epub 2019 May 16.

Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.04.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6570567PMC
June 2019

Russian Doll Genes and Complex Chromosome Rearrangements in .

G3 (Bethesda) 2018 05 4;8(5):1669-1674. Epub 2018 May 4.

University of South Florida; Department of Mathematics and Statistics

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http://dx.doi.org/10.1534/g3.118.200176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940158PMC
May 2018

Small RNA-mediated regulation of DNA dosage in the ciliate .

RNA 2018 01 27;24(1):18-29. Epub 2017 Oct 27.

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA

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http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.061333.11
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http://dx.doi.org/10.1261/rna.061333.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733567PMC
January 2018

Chromosome fusions triggered by noncoding RNA.

RNA Biol 2017 05 7;14(5):620-631. Epub 2016 Jun 7.

e Department of Ecology & Evolutionary Biology , Princeton University , NJ , USA.

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http://dx.doi.org/10.1080/15476286.2016.1195940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449082PMC
May 2017

What Is a Genome?

PLoS Genet 2016 07 21;12(7):e1006181. Epub 2016 Jul 21.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4956268PMC
July 2016

: a database of ciliate genome rearrangements.

Nucleic Acids Res 2016 Jan 19;44(D1):D703-9. Epub 2015 Nov 19.

Department of Ecology and Evolutionary Biology, Princeton University, NJ 08544, USA

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv1190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702850PMC
January 2016

The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism.

J Mol Evol 2016 Jan 5;82(1):17-26. Epub 2016 Jan 5.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.

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http://dx.doi.org/10.1007/s00239-015-9722-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709378PMC
January 2016

Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha.

Mob DNA 2016 25;7. Epub 2016 Jan 25.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544 USA.

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http://dx.doi.org/10.1186/s13100-016-0057-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724952PMC
January 2016

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.

Genome Res 2015 Nov 1;25(11):1727-38. Epub 2015 Sep 1.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA;

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http://dx.doi.org/10.1101/gr.188516.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617968PMC
November 2015

Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates.

Genome Biol Evol 2015 Sep 2;7(10):2859-70. Epub 2015 Sep 2.

Department of Ecology and Evolutionary Biology, Princeton University

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http://dx.doi.org/10.1093/gbe/evv172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684698PMC
September 2015

Where Next for Genetics and Genomics?

PLoS Biol 2015 Jul 30;13(7):e1002216. Epub 2015 Jul 30.

The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pbio.1002216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520474PMC
July 2015

Programmed Genome Rearrangements in the Ciliate Oxytricha.

Microbiol Spectr 2014 Dec;2(6)

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544.

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http://dx.doi.org/10.1128/microbiolspec.MDNA3-0025-2014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480583PMC
December 2014

Transposon domestication versus mutualism in ciliate genome rearrangements.

PLoS Genet 2013 1;9(8):e1003659. Epub 2013 Aug 1.

Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.

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http://dx.doi.org/10.1371/journal.pgen.1003659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731211PMC
March 2014

RNA-mediated genome rearrangement: hypotheses and evidence.

Bioessays 2013 Feb 20;35(2):84-7. Epub 2012 Dec 20.

Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1002/bies.201200140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821980PMC
February 2013

LUCApedia: a database for the study of ancient life.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D1079-82. Epub 2012 Nov 27.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08542, USA.

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http://academic.oup.com/nar/article/41/D1/D1079/1069131/LUCA
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http://dx.doi.org/10.1093/nar/gks1217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531223PMC
January 2013

Genomes on the edge: programmed genome instability in ciliates.

Cell 2013 Jan;152(3):406-16

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.cell.2013.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725814PMC
January 2013

Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement.

Cell 2012 Dec;151(6):1243-55

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.cell.2012.10.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678556PMC
December 2012

Detection of a common chimeric transcript between human chromosomes 7 and 16.

Biol Direct 2012 Dec 29;7:49. Epub 2012 Dec 29.

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/1745-6150-7-49DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538553PMC
December 2012

Oxytricha as a modern analog of ancient genome evolution.

Trends Genet 2012 Aug 21;28(8):382-8. Epub 2012 May 21.

Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ 08544, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01689525120005
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http://dx.doi.org/10.1016/j.tig.2012.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401270PMC
August 2012

RNA-Mediated Epigenetic Programming of Genome Rearrangements.

Annu Rev Genomics Hum Genet 2011 ;12:367-89

Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.

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http://dx.doi.org/10.1146/annurev-genom-082410-101420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518427PMC
October 2011

A chimeric chromosome in the ciliate oxytricha resulting from duplication.

J Mol Evol 2011 Oct 22;73(3-4):70-3. Epub 2011 Oct 22.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA

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http://dx.doi.org/10.1007/s00239-011-9464-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494457PMC
October 2011

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes.

Nucleic Acids Res 2011 Sep 28;39(17):7529-47. Epub 2011 Jun 28.

Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn VA 20147, USA.

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http://dx.doi.org/10.1093/nar/gkr501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177221PMC
September 2011

RNA-mediated epigenetic regulation of DNA copy number.

Proc Natl Acad Sci U S A 2010 Dec 15;107(51):22140-4. Epub 2010 Nov 15.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1012236107
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http://dx.doi.org/10.1073/pnas.1012236107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009799PMC
December 2010

Epigenetic inheritance in ciliates.

Curr Opin Microbiol 2009 Dec 31;12(6):638-43. Epub 2009 Oct 31.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.mib.2009.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868311PMC
December 2009

A functional role for transposases in a large eukaryotic genome.

Science 2009 May 16;324(5929):935-8. Epub 2009 Apr 16.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1126/science.1170023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491810PMC
May 2009

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns.

BMC Genomics 2008 Dec 5;9:587. Epub 2008 Dec 5.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Nijmegen, the Netherlands.

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http://dx.doi.org/10.1186/1471-2164-9-587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633312PMC
December 2008

RNA-mediated epigenetic programming of a genome-rearrangement pathway.

Nature 2008 Jan 28;451(7175):153-8. Epub 2007 Nov 28.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.

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http://www.nature.com/articles/nature06452
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http://dx.doi.org/10.1038/nature06452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647009PMC
January 2008

RNA-guided DNA assembly.

J Theor Biol 2007 Oct 12;248(4):706-20. Epub 2007 Jun 12.

Department of Mathematics and Statistics, University of South Florida, USA.

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http://dx.doi.org/10.1016/j.jtbi.2007.06.007DOI Listing
October 2007

Genetics. Why genomes in pieces?

Science 2007 Oct;318(5849):405-7

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1126/science.1150280DOI Listing
October 2007

BLASTO: a tool for searching orthologous groups.

Nucleic Acids Res 2007 Jul 5;35(Web Server issue):W678-82. Epub 2007 May 5.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1093/nar/gkm278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933156PMC
July 2007

Hypothesis: RNA editing of microRNA target sites in humans?

RNA 2007 Apr 25;13(4):463-7. Epub 2007 Jan 25.

Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1261/rna.296407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1831856PMC
April 2007

Conservation of tandem stop codons in yeasts.

Genome Biol 2005 15;6(4):R31. Epub 2005 Mar 15.

Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1186/gb-2005-6-4-r31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088959PMC
August 2006

Interconversion of germline-limited and somatic DNA in a scrambled gene.

J Mol Evol 2006 Jul 3;63(1):69-73. Epub 2006 Jun 3.

Institute of Cell Biology, Witten/Herdecke University, 58448, Witten, Germany.

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http://dx.doi.org/10.1007/s00239-005-0166-4DOI Listing
July 2006

SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W382-4

Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1093/nar/gkl272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538794PMC
July 2006

On the paucity of duplicated genes in Caenorhabditis elegans operons.

J Mol Evol 2006 Jun 28;62(6):765-71. Epub 2006 Apr 28.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1007/s00239-005-0203-3DOI Listing
June 2006

Evolution of programmed DNA rearrangements in a scrambled gene.

Mol Biol Evol 2006 Apr 23;23(4):756-63. Epub 2006 Jan 23.

Department of Molecular Biology, Princeton University, USA.

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http://dx.doi.org/10.1093/molbev/msj089DOI Listing
April 2006

Conserved linkage of two genes on the same macronuclear chromosome in spirotrichous ciliates.

Chromosoma 2006 Apr 7;115(2):129-38. Epub 2006 Mar 7.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1007/s00412-005-0040-6DOI Listing
April 2006

A new scrambled gene in the ciliate Uroleptus.

Gene 2006 Mar 28;368:72-7. Epub 2005 Nov 28.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.gene.2005.10.008DOI Listing
March 2006

A genome-wide study of dual coding regions in human alternatively spliced genes.

Genome Res 2006 Feb 19;16(2):190-6. Epub 2005 Dec 19.

Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1101/gr.4246506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361714PMC
February 2006

Complex germline architecture: two genes intertwined on two loci.

Mol Biol Evol 2006 Jan 14;23(1):4-6. Epub 2005 Sep 14.

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http://dx.doi.org/10.1093/molbev/msj017DOI Listing
January 2006

Are stop codons recognized by base triplets in the large ribosomal RNA subunit?

RNA 2005 Oct;11(10):1478-84

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1261/rna.2780505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370831PMC
October 2005

The evolutionary origin of a complex scrambled gene.

Proc Natl Acad Sci U S A 2005 Oct 10;102(42):15149-54. Epub 2005 Oct 10.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1073/pnas.0507682102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1257744PMC
October 2005

Molecular mimicry: quantitative methods to study structural similarity between protein and RNA.

RNA 2005 Aug;11(8):1167-72

Department of Chemistry, Princeton University, NJ 08544, USA.

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http://dx.doi.org/10.1261/rna.7207205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370800PMC
August 2005

The RNA world on ice: a new scenario for the emergence of RNA information.

J Mol Evol 2005 Aug 13;61(2):264-73. Epub 2005 Jul 13.

SomaGenics, Inc., 2161 Delaware Avenue, Santa Cruz, CA 95060, USA.

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http://dx.doi.org/10.1007/s00239-004-0362-7DOI Listing
August 2005

Decoding the decoding region: analysis of eukaryotic release factor (eRF1) stop codon-binding residues.

J Mol Evol 2005 Mar;60(3):337-44

Department of Chemistry, Princeton University, NJ 08544, USA.

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http://dx.doi.org/10.1007/s00239-004-0211-8DOI Listing
March 2005

MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates.

Nucleic Acids Res 2005 Jan;33(Database issue):D396-8

Department of Ecology and Evolutionary Biology, Princeton University, NJ 08544, USA.

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http://dx.doi.org/10.1093/nar/gki130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540084PMC
January 2005

Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project.

Chromosoma 2004 Sep 16;113(2):69-76. Epub 2004 Jul 16.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1007/s00412-004-0295-3DOI Listing
September 2004

Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences.

Protist 2004 Sep;155(3):311-22

Department of Ecology and Evolutionary Biology, Princeton University, NJ 08544, USA.

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http://dx.doi.org/10.1078/1434461041844196DOI Listing
September 2004

A micronuclear locus containing three protein-coding genes remains linked during macronuclear development in the spirotrichous ciliate Holosticha.

Protist 2004 Jun;155(2):245-55

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1078/143446104774199628DOI Listing
June 2004

Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world.

Nucleic Acids Res 2004 25;32(9):2966-74. Epub 2004 May 25.

SomaGenics, Inc., 2161 Delaware Avenue, Santa Cruz, CA 95060, USA.

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http://dx.doi.org/10.1093/nar/gkh601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC419604PMC
May 2004

Gene Unscrambler for detangling scrambled genes in ciliates.

Bioinformatics 2004 Mar 29;20(5):800-2. Epub 2004 Jan 29.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth003DOI Listing
March 2004

Genetic code.

Curr Biol 2004 Feb;14(4):R147

Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08544, USA.

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February 2004

Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

Genetics 2003 Dec;165(4):1761-77

Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462920PMC
December 2003

Genetic code: what nature missed.

Curr Biol 2003 Nov;13(22):R884-5

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.cub.2003.10.052DOI Listing
November 2003

Molecular computing revisited: a Moore's Law?

Trends Biotechnol 2003 Mar;21(3):98-101

Dept of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/S0167-7799(03)00007-6DOI Listing
March 2003

Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes.

Curr Opin Microbiol 2002 Dec;5(6):620-6

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/s1369-5274(02)00379-xDOI Listing
December 2002

Custom codons come in threes, fours, and fives.

Chem Biol 2002 Feb;9(2):143

Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/s1074-5521(02)00107-2DOI Listing
February 2002