Vincent Moulton

Vincent Moulton

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Vincent Moulton

Publications by authors named "Vincent Moulton"

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INDISIM-Denitrification, an individual-based model for study the denitrification process.

J Ind Microbiol Biotechnol 2019 Nov 5. Epub 2019 Nov 5.

School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s10295-019-02245-8DOI Listing
November 2019

Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks.

Bull Math Biol 2019 Oct 11;81(10):3823-3863. Epub 2019 Jul 11.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s11538-019-00641-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764941PMC
October 2019

Reconciling event-labeled gene trees with MUL-trees and species networks.

J Math Biol 2019 Oct 13;79(5):1885-1925. Epub 2019 Aug 13.

School of Computing Sciences, University of East Anglia, Norwich, UK.

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http://dx.doi.org/10.1007/s00285-019-01414-8DOI Listing
October 2019

Exploring and Visualizing Spaces of Tree Reconciliations.

Syst Biol 2019 07;68(4):607-618

Inria Grenoble - Rhône-Alpes; Inovallée 655, Avenue de l'Europe, Montbonnot, 38334 Saint Ismier Cedex, France.

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https://academic.oup.com/sysbio/advance-article/doi/10.1093/
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http://dx.doi.org/10.1093/sysbio/syy075DOI Listing
July 2019

Phylogenetic Flexibility via Hall-Type Inequalities and Submodularity.

Bull Math Biol 2019 02 27;81(2):598-617. Epub 2018 Mar 27.

Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.

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http://dx.doi.org/10.1007/s11538-018-0419-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342847PMC
February 2019

Recovering normal networks from shortest inter-taxa distance information.

J Math Biol 2018 09 24;77(3):571-594. Epub 2018 Feb 24.

School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand.

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http://dx.doi.org/10.1007/s00285-018-1218-xDOI Listing
September 2018

Quarnet Inference Rules for Level-1 Networks.

Bull Math Biol 2018 08 4;80(8):2137-2153. Epub 2018 Jun 4.

School of Computing Sciences, University of East Anglia, Norwich, UK.

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http://dx.doi.org/10.1007/s11538-018-0450-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061523PMC
August 2018

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution.

J Theor Biol 2018 06 13;446:160-167. Epub 2018 Mar 13.

School of Computing Sciences, University of East Anglia, Norwich, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2018.03.011DOI Listing
June 2018

Bounds for phylogenetic network space metrics.

J Math Biol 2018 04 23;76(5):1229-1248. Epub 2017 Aug 23.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s00285-017-1171-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829221PMC
April 2018

SPECTRE: a suite of phylogenetic tools for reticulate evolution.

Bioinformatics 2018 03;34(6):1056-1057

School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860355PMC
March 2018

The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

Methods Mol Biol 2017 ;1580:193-224

School of Computing Sciences, University of East Anglia, Norwich, UK.

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http://dx.doi.org/10.1007/978-1-4939-6866-4_14DOI Listing
February 2018

miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.

Bioinformatics 2017 Aug;33(16):2446-2454

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870699PMC
August 2017

Binets: Fundamental Building Blocks for Phylogenetic Networks.

Bull Math Biol 2017 05 6;79(5):1135-1154. Epub 2017 Apr 6.

School of Computing Sciences, University of East Anglia, Norwich, UK.

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http://dx.doi.org/10.1007/s11538-017-0275-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5488434PMC
May 2017

MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect.

Sci Rep 2017 03 31;7:45674. Epub 2017 Mar 31.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.

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http://dx.doi.org/10.1038/srep45674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374498PMC
March 2017

Folding and unfolding phylogenetic trees and networks.

J Math Biol 2016 12 23;73(6-7):1761-1780. Epub 2016 Apr 23.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s00285-016-0993-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061860PMC
December 2016

Transforming phylogenetic networks: Moving beyond tree space.

J Theor Biol 2016 09 22;404:30-39. Epub 2016 May 22.

School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.05.030DOI Listing
September 2016

INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium.

J Theor Biol 2016 08 11;403:45-58. Epub 2016 May 11.

School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ - United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.05.017DOI Listing
August 2016

TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories.

Mol Biol Evol 2016 08 15;33(8):2151-62. Epub 2016 Apr 15.

School of Computing Sciences, University of East Anglia, Norwich, United Kingdom

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http://dx.doi.org/10.1093/molbev/msw068DOI Listing
August 2016

Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations.

J Math Biol 2016 Feb 3;72(3):699-725. Epub 2015 Jun 3.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s00285-015-0899-7DOI Listing
February 2016

The minimum evolution problem is hard: a link between tree inference and graph clustering problems.

Bioinformatics 2016 Feb 24;32(4):518-22. Epub 2015 Oct 24.

School of Computing Sciences, University of East Anglia, Norwich, UK and.

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http://dx.doi.org/10.1093/bioinformatics/btv623DOI Listing
February 2016

Erratum to: Neighborhoods of trees in circular orderings.

Bull Math Biol 2015 Mar;77(3):579

The Genome Analysis Centre, Norwich, UK,

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http://dx.doi.org/10.1007/s11538-015-0071-yDOI Listing
March 2015

How much information is needed to infer reticulate evolutionary histories?

Syst Biol 2015 Jan 18;64(1):102-11. Epub 2014 Sep 18.

School of Computing Sciences, University of East Anglia, Norwich, UK, and Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands.

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http://dx.doi.org/10.1093/sysbio/syu076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265143PMC
January 2015

Neighborhoods of trees in circular orderings.

Bull Math Biol 2015 Jan 5;77(1):46-70. Epub 2014 Dec 5.

The Genome Analysis Centre, Norwich, UK,

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http://dx.doi.org/10.1007/s11538-014-0049-1DOI Listing
January 2015

Prioritizing populations for conservation using phylogenetic networks.

PLoS One 2014 28;9(2):e88945. Epub 2014 Feb 28.

Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada ; Interdisciplinary Research in the Mathematical and Computational Sciences (IRMACS) Centre, Simon Fraser University, Burnaby, British Columbia, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088945PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938429PMC
November 2014

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation.

BMC Genomics 2014 Oct 15;15:901. Epub 2014 Oct 15.

School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.

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http://dx.doi.org/10.1186/1471-2164-15-901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209020PMC
October 2014

Trinets encode tree-child and level-2 phylogenetic networks.

J Math Biol 2014 Jun 17;68(7):1707-29. Epub 2013 May 17.

Centrum Wiskunde & Informatica (CWI), P.O. Box 94079, 1090 GB , Amsterdam, The Netherlands,

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http://dx.doi.org/10.1007/s00285-013-0683-5DOI Listing
June 2014

Constructing and drawing regular planar split networks.

IEEE/ACM Trans Comput Biol Bioinform 2012 4;9(2):395-407. Epub 2011 Aug 4.

University of Greifswald, Greifswald.

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http://dx.doi.org/10.1109/TCBB.2011.115DOI Listing
May 2014

FlatNJ: a novel network-based approach to visualize evolutionary and biogeographical relationships.

Syst Biol 2014 May 15;63(3):383-96. Epub 2014 Jan 15.

Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany and School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1093/sysbio/syu001DOI Listing
May 2014

SuperQ: computing supernetworks from quartets.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jan-Feb;10(1):151-60

CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1109/TCBB.2013.8DOI Listing
January 2014

Modeling the effect of copper availability on bacterial denitrification.

Microbiologyopen 2013 Oct 30;2(5):756-65. Epub 2013 Jul 30.

School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, U.K.

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http://dx.doi.org/10.1002/mbo3.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3831637PMC
October 2013

Orthology relations, symbolic ultrametrics, and cographs.

J Math Biol 2013 Jan 29;66(1-2):399-420. Epub 2012 Mar 29.

Center for Bioinformatics, Saarland University, Building E 2.1, 66041, Saarbrücken, Germany.

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http://dx.doi.org/10.1007/s00285-012-0525-xDOI Listing
January 2013

Novel distances for dollo data.

Syst Biol 2013 Jan 22;62(1):62-77. Epub 2012 Aug 22.

School of Mathematics and Physics, CRC for Forestry, School of Plant Science, University of Tasmania, Private Bag 55, Hobart 7001, Australia.

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https://academic.oup.com/sysbio/article/62/1/62/1656728
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http://dx.doi.org/10.1093/sysbio/sys071DOI Listing
January 2013

Computational modeling of the regulatory network organizing the wound response in Arabidopsis thaliana.

Artif Life 2012 31;18(4):445-60. Epub 2012 Aug 31.

University of East Anglia, UK.

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http://dx.doi.org/10.1162/ARTL_a_00076DOI Listing
January 2013

MirPlex: a tool for identifying miRNAs in high-throughput sRNA datasets without a genome.

J Exp Zool B Mol Dev Evol 2013 Jan 26;320(1):47-56. Epub 2012 Nov 26.

University of East Anglia, Norwich, United Kingdom.

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http://dx.doi.org/10.1002/jez.b.22483DOI Listing
January 2013

The 'Butterfly effect' in Cayley graphs with applications to genomics.

J Math Biol 2012 Dec 4;65(6-7):1267-84. Epub 2011 Dec 4.

School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s00285-011-0498-1DOI Listing
December 2012

Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions.

Planta 2012 Dec 26;236(6):1875-87. Epub 2012 Aug 26.

School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s00425-012-1734-7DOI Listing
December 2012

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing.

Nucleic Acids Res 2012 Jul 29;40(13):e103. Epub 2012 Mar 29.

School of Computing Sciences and School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1093/nar/gks277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401462PMC
July 2012

Reducing ligation bias of small RNAs in libraries for next generation sequencing.

Silence 2012 May 30;3(1). Epub 2012 May 30.

School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1186/1758-907X-3-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489589PMC
May 2012

mRNA expression profiling reveals conserved and non-conserved miR-140 targets.

RNA Biol 2011 Jul-Aug;8(4):607-15. Epub 2011 Jul 1.

School of Biological Sciences, University of East Anglia, Norwich, UK.

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http://dx.doi.org/10.4161/rna.8.4.15390DOI Listing
April 2012

Computing evolutionary distinctiveness indices in large scale analysis.

Algorithms Mol Biol 2012 Apr 13;7. Epub 2012 Apr 13.

IRMACS and BioSciences, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6 Canada.

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http://dx.doi.org/10.1186/1748-7188-7-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353162PMC
April 2012

Small RNA discovery and characterisation in eukaryotes using high-throughput approaches.

Adv Exp Med Biol 2011 ;722:239-54

School of Computing Sciences, University of East Anglia, Norwich, UK.

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http://dx.doi.org/10.1007/978-1-4614-0332-6_16DOI Listing
October 2011

Metrics on multilabeled trees: interrelationships and diameter bounds.

IEEE/ACM Trans Comput Biol Bioinform 2011 Jul-Aug;8(4):1029-40

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1109/TCBB.2010.122DOI Listing
September 2011

Identifying and reconstructing lateral transfers from distance matrices by combining the minimum contradiction method and neighbor-net.

J Bioinform Comput Biol 2011 Aug;9(4):453-70

School of Computing Sciences, University of East Anglia, Norwich NR47TJ, UK.

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http://dx.doi.org/10.1142/s0219720011005409DOI Listing
August 2011

Revealing biological information using data structuring and automated learning.

Recent Pat DNA Gene Seq 2010 Nov;4(3):181-91

School of Computing Sciences, University of East Anglia, NR4 7TJ, Norwich, UK.

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http://dx.doi.org/10.2174/187221510794751668DOI Listing
November 2010

RDP3: a flexible and fast computer program for analyzing recombination.

Bioinformatics 2010 Oct 26;26(19):2462-3. Epub 2010 Aug 26.

Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Centre for High Performance Computing, Rosebank, Cape Town, South Africa.

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http://dx.doi.org/10.1093/bioinformatics/btq467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944210PMC
October 2010

Species, clusters and the 'Tree of life': a graph-theoretic perspective.

J Theor Biol 2010 Aug 2;265(4):535-42. Epub 2010 Jun 2.

CAS-MPG Partner Institute for Computational Biology, Shanghai, China.

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http://dx.doi.org/10.1016/j.jtbi.2010.05.031DOI Listing
August 2010

Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis.

Plant J 2010 Jun;62(6):960-76

Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy.

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http://dx.doi.org/10.1111/j.0960-7412.2010.04208.xDOI Listing
June 2010

Structural and functional analysis of viral siRNAs.

PLoS Pathog 2010 Apr 1;6(4):e1000838. Epub 2010 Apr 1.

School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.

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http://dx.plos.org/10.1371/journal.ppat.1000838
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http://dx.doi.org/10.1371/journal.ppat.1000838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848561PMC
April 2010

Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity.

Algorithms Mol Biol 2010 Mar 20;5:19. Epub 2010 Mar 20.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://almob.biomedcentral.com/articles/10.1186/1748-7188-5-
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http://dx.doi.org/10.1186/1748-7188-5-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853546PMC
March 2010

Finding sRNA generative locales from high-throughput sequencing data with NiBLS.

BMC Bioinformatics 2010 Feb 18;11:93. Epub 2010 Feb 18.

The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR47UH, UK.

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http://dx.doi.org/10.1186/1471-2105-11-93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837031PMC
February 2010

Deciphering the diversity of small RNAs in plants: the long and short of it.

Brief Funct Genomic Proteomic 2009 Nov 29;8(6):472-81. Epub 2009 Jul 29.

School of Computing Sciences, University of East Anglia, Norwich, UK.

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http://dx.doi.org/10.1093/bfgp/elp024DOI Listing
November 2009

Maximum parsimony for tree mixtures.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jan-Mar;6(1):97-102

Department of Combinatorics and Geometry, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 YueYang Road, Shanghai 200031.

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http://ieeexplore.ieee.org/document/4585356/
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http://dx.doi.org/10.1109/TCBB.2008.75DOI Listing
August 2009

Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jan-Mar;6(1):110-7

Department of Computer Science, University of Durham, Science Laboratories, South Road, DH13LE Durham, UK.

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http://dx.doi.org/10.1109/TCBB.2008.37DOI Listing
August 2009

Refining phylogenetic trees given additional data: an algorithm based on parsimony.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jan-Mar;6(1):118-25

Department of Computer Science and School of Mathematical Sciences, Queen Mary, University of London, London.

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http://dx.doi.org/10.1109/TCBB.2008.100DOI Listing
August 2009

Special section: phylogenetics.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jan-Mar;6(1):4-6

University of Tübingen, Sand 14, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1109/tcbb.2009.21DOI Listing
August 2009

Inferring polyploid phylogenies from multiply-labeled gene trees.

BMC Evol Biol 2009 Aug 28;9:216. Epub 2009 Aug 28.

School of Computing Sciences, University of East Anglia, Norwich, UK.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-9-216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748082PMC
August 2009

PADRE: a package for analyzing and displaying reticulate evolution.

Bioinformatics 2009 May 5;25(9):1199-200. Epub 2009 Mar 5.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp133DOI Listing
May 2009

High throughput sequencing of microRNAs in chicken somites.

FEBS Lett 2009 May 27;583(9):1422-6. Epub 2009 Mar 27.

School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

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http://doi.wiley.com/10.1016/j.febslet.2009.03.048
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http://dx.doi.org/10.1016/j.febslet.2009.03.048DOI Listing
May 2009

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning.

BMC Bioinformatics 2009 Apr 27;10:126. Epub 2009 Apr 27.

Rega Institute, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.

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http://www.biomedcentral.com/1471-2105/10/126
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http://dx.doi.org/10.1186/1471-2105-10-126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684544PMC
April 2009

The complexity of deriving multi-labeled trees from bipartitions.

J Comput Biol 2008 Jul-Aug;15(6):639-51

School of Computing Sciences, University of East Anglia, Norwich, United Kingdom.

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http://dx.doi.org/10.1089/cmb.2008.0088DOI Listing
October 2008

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.

Genome Res 2008 Oct 24;18(10):1602-9. Epub 2008 Jul 24.

School of Computing, University of East Anglia, Norwich NR4 7TJ, United Kingdom.

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http://dx.doi.org/10.1101/gr.080127.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556272PMC
October 2008

A toolkit for analysing large-scale plant small RNA datasets.

Bioinformatics 2008 Oct 19;24(19):2252-3. Epub 2008 Aug 19.

School of Computing Sciences, School of Biological Sciences, University of East Anglia, Norwich NR47TJ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn428DOI Listing
October 2008

Computing phylogenetic diversity for split systems.

IEEE/ACM Trans Comput Biol Bioinform 2008 Apr-Jun;5(2):235-44

School of Computer Sciences, University of East Anglia, Norwich, Uk.

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http://dx.doi.org/10.1109/TCBB.2007.70260DOI Listing
July 2008

Using supernetworks to distinguish hybridization from lineage-sorting.

BMC Evol Biol 2008 Jul 14;8:202. Epub 2008 Jul 14.

Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-8-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2500029PMC
July 2008

Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update.

BMC Res Notes 2008 Jul 21;1:49. Epub 2008 Jul 21.

Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, S-751, 24 Uppsala, Sweden; Department of Clinical Microbiology, Clinical Bacteriology, Umeå University, 901 85 Umeå, Sweden.

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http://dx.doi.org/10.1186/1756-0500-1-49DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2551606PMC
July 2008

Exploring contradictory phylogenetic relationships in yeasts.

FEMS Yeast Res 2008 Jun 24;8(4):641-50. Epub 2008 Mar 24.

School of Computing Science, University of East Anglia, Norwich, UK.

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June 2008

Encoding phylogenetic trees in terms of weighted quartets.

J Math Biol 2008 Apr 21;56(4):465-77. Epub 2007 Sep 21.

CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China.

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April 2008

A scoring matrix approach to detecting miRNA target sites.

Algorithms Mol Biol 2008 Mar 31;3. Epub 2008 Mar 31.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2365947PMC
March 2008

Estimating parameters for generalized mass action models using constraint propagation.

Math Biosci 2007 Aug 8;208(2):607-20. Epub 2006 Dec 8.

Department of Mathematics, Uppsala University, Box 480, Uppsala, Sweden.

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http://dx.doi.org/10.1016/j.mbs.2006.11.009DOI Listing
August 2007

Identification of novel small RNAs in tomato (Solanum lycopersicum).

Planta 2007 Aug 6;226(3):709-17. Epub 2007 Apr 6.

School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1007/s00425-007-0518-yDOI Listing
August 2007

Boltzmann probability of RNA structural neighbors and riboswitch detection.

Bioinformatics 2007 Aug 14;23(16):2054-62. Epub 2007 Jun 14.

Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btm314DOI Listing
August 2007

RNAbor: a web server for RNA structural neighbors.

Nucleic Acids Res 2007 Jul 25;35(Web Server issue):W305-9. Epub 2007 May 25.

Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden.

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http://dx.doi.org/10.1093/nar/gkm255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933207PMC
July 2007

Untangling complex histories of genome mergings in high polyploids.

Syst Biol 2007 Jun;56(3):467-76

National Centre for Biosystematics, Natural History Museum, University of Oslo, Blindern, Oslo, Norway.

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June 2007

Consistency of the neighbor-net algorithm.

Algorithms Mol Biol 2007 Jun 28;2. Epub 2007 Jun 28.

Department of Mathematics, University of Auckland, Private Bag 92019, Auckland, NZ.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1948893PMC
June 2007

Optimizing phylogenetic diversity under constraints.

J Theor Biol 2007 May 22;246(1):186-94. Epub 2006 Dec 22.

School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

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http://dx.doi.org/10.1016/j.jtbi.2006.12.021DOI Listing
May 2007

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets.

Mol Biol Evol 2007 Feb 21;24(2):532-8. Epub 2006 Nov 21.

Chinese Academy of Science-Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China.

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February 2007

Reconstructing the evolutionary history of polyploids from multilabeled trees.

Mol Biol Evol 2006 Sep 23;23(9):1784-91. Epub 2006 Jun 23.

School of Computing Sciences, University of East Anglia, Norwich, United Kingdom.

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September 2006

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny.

Mol Biol Evol 2006 May 9;23(5):848-55. Epub 2005 Nov 9.

Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, New Zealand.

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http://dx.doi.org/10.1093/molbev/msj061DOI Listing
May 2006

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos.

Nucleic Acids Res 2006 9;34(3):905-16. Epub 2006 Feb 9.

Linnaeus Centre for Bioinformatics, Uppsala University Uppsala, Sweden.

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http://dx.doi.org/10.1093/nar/gkj478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1363773PMC
March 2006

Predicting RNA structure using mutual information.

Appl Bioinformatics 2005 ;4(1):53-9

The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.2165/00822942-200504010-00006DOI Listing
December 2005

A comparison of RNA folding measures.

BMC Bioinformatics 2005 Oct 3;6:241. Epub 2005 Oct 3.

The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1186/1471-2105-6-241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274297PMC
October 2005

Bounding the number of hybridisation events for a consistent evolutionary history.

J Math Biol 2005 Aug 2;51(2):171-82. Epub 2005 May 2.

Biomathematics Research Centre, Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand.

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August 2005

Biogeographic interpretation of splits graphs: least squares optimization of branch lengths.

Syst Biol 2005 Feb;54(1):56-65

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.

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February 2005

Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods.

Syst Biol 2005 Feb;54(1):66-76

The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11222, Palmerston North, New Zealand.

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February 2005