Publications by authors named "Giddy Landan"

35Publications

The order of trait emergence in the evolution of cyanobacterial multicellularity.

Genome Biol Evol 2020 Nov 24. Epub 2020 Nov 24.

Genomic Microbiology Group, Institute of Microbiology, Kiel University, Kiel, Germany.

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http://dx.doi.org/10.1093/gbe/evaa249DOI Listing
November 2020

New views on an old enzyme: allosteric regulation and evolution of archaeal pyruvate kinases.

FEBS J 2019 07 26;286(13):2471-2489. Epub 2019 Apr 26.

Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany.

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https://onlinelibrary.wiley.com/doi/abs/10.1111/febs.14837
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http://dx.doi.org/10.1111/febs.14837DOI Listing
July 2019

Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction.

Syst Biol 2019 01;68(1):117-130

Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.

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http://dx.doi.org/10.1093/sysbio/syy036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657586PMC
January 2019

Phylogenetic rooting using minimal ancestor deviation.

Nat Ecol Evol 2017 06 19;1:193. Epub 2017 Jun 19.

Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel 24118, Germany.

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http://dx.doi.org/10.1038/s41559-017-0193DOI Listing
June 2017

Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis.

Nat Plants 2017 May 15;3:17066. Epub 2017 May 15.

Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.

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http://dx.doi.org/10.1038/nplants.2017.66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5438061PMC
May 2017

Late Mitochondrial Origin Is an Artifact.

Genome Biol Evol 2017 02;9(2):373-379

Institute of Microbiology, Christian-Albrechts-University of Kiel, Germany.

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https://academic.oup.com/gbe/article/9/2/373/2986798
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http://dx.doi.org/10.1093/gbe/evx027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516564PMC
February 2017

Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction.

ISME J 2017 02 20;11(2):543-554. Epub 2016 Sep 20.

Institute of General Microbiology, Christian-Albrechts University of Kiel, Kiel, Germany.

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http://dx.doi.org/10.1038/ismej.2016.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5183456PMC
February 2017

DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes.

Genome Biol Evol 2016 06 3;8(5):1590-9. Epub 2016 Jun 3.

Institute of General Microbiology, Christian-Albrechts Universtiy of Kiel, Kiel, Germany

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http://dx.doi.org/10.1093/gbe/evw102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898814PMC
June 2016

Endosymbiotic origin and differential loss of eukaryotic genes.

Nature 2015 Aug 19;524(7566):427-32. Epub 2015 Aug 19.

Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1038/nature14963DOI Listing
August 2015

The Contribution of Genetic Recombination to CRISPR Array Evolution.

Genome Biol Evol 2015 Jun 16;7(7):1925-39. Epub 2015 Jun 16.

Institute of General Microbiology, Christian-Albrechts-University Kiel, Germany.

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http://dx.doi.org/10.1093/gbe/evv113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524480PMC
June 2015

Concatenated alignments and the case of the disappearing tree.

BMC Evol Biol 2014 Dec 30;14:266. Epub 2014 Dec 30.

Institute of Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.

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http://dx.doi.org/10.1186/s12862-014-0266-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302582PMC
December 2014

The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes.

BMC Genomics 2014 Oct 17;15:906. Epub 2014 Oct 17.

Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.

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http://dx.doi.org/10.1186/1471-2164-15-906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223856PMC
October 2014

Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Nature 2015 Jan 15;517(7532):77-80. Epub 2014 Oct 15.

1] Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany [2] Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.

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http://dx.doi.org/10.1038/nature13805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285555PMC
January 2015

Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis.

Mol Biol Evol 2014 Feb 4;31(2):410-8. Epub 2013 Nov 4.

Institute of Microbiology, Christian-Albrechts-University of Kiel, Kiel, Germany.

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http://dx.doi.org/10.1093/molbev/mst212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907059PMC
February 2014

Early bioenergetic evolution.

Philos Trans R Soc Lond B Biol Sci 2013 Jul 10;368(1622):20130088. Epub 2013 Jun 10.

Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1098/rstb.2013.0088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685469PMC
July 2013

Deep sequencing of Trichomonas vaginalis during the early infection of vaginal epithelial cells and amoeboid transition.

Int J Parasitol 2013 Aug 18;43(9):707-19. Epub 2013 May 18.

Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1016/j.ijpara.2013.04.002DOI Listing
August 2013

Detecting negative selection on recurrent mutations using gene genealogy.

BMC Genet 2013 May 7;14:37. Epub 2013 May 7.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.

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http://dx.doi.org/10.1186/1471-2156-14-37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3661350PMC
May 2013

Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.

Proc Natl Acad Sci U S A 2012 Dec 26;109(50):20537-42. Epub 2012 Nov 26.

Institute of Molecular Evolution, Heinrich Heine University, 40225 Düsseldorf, Germany.

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http://dx.doi.org/10.1073/pnas.1209119109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528564PMC
December 2012

Chaperones divide yeast proteins into classes of expression level and evolutionary rate.

Genome Biol Evol 2012 14;4(5):618-25. Epub 2012 Mar 14.

Institute of Molecular Evolution, Heinrich-Heine University Düsseldorf, Germany.

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http://dx.doi.org/10.1093/gbe/evs025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3381671PMC
August 2012

An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.

Genome Biol Evol 2012 21;4(4):466-85. Epub 2012 Feb 21.

Institute of Molecular Evolution, Heinrich-Heine University Düsseldorf, Germany.

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http://dx.doi.org/10.1093/gbe/evs018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342870PMC
July 2012

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes.

Genome Res 2011 Apr 26;21(4):599-609. Epub 2011 Jan 26.

Institute of Botany III, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.

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http://dx.doi.org/10.1101/gr.115592.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065707PMC
April 2011

Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm.

Nucleic Acids Res 2010 Aug 22;38(15):e158. Epub 2010 Jun 22.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/nar/gkq532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926622PMC
August 2010

GUIDANCE: a web server for assessing alignment confidence scores.

Nucleic Acids Res 2010 Jul 23;38(Web Server issue):W23-8. Epub 2010 May 23.

Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1093/nar/gkq443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896199PMC
July 2010

An alignment confidence score capturing robustness to guide tree uncertainty.

Mol Biol Evol 2010 Aug 5;27(8):1759-67. Epub 2010 Mar 5.

Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

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http://www.tau.ac.il/~talp/publications/GuidanceAlgorithm.pd
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http://guidance.tau.ac.il/An_alignment_confidence_score_capt
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msq066
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http://dx.doi.org/10.1093/molbev/msq066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908709PMC
August 2010

Can GC content at third-codon positions be used as a proxy for isochore composition?

Mol Biol Evol 2009 Aug 14;26(8):1829-33. Epub 2009 May 14.

Department of Biology and Biochemistry, University of Houston, TX, USA.

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http://dx.doi.org/10.1093/molbev/msp100DOI Listing
August 2009

A method for the simultaneous estimation of selection intensities in overlapping genes.

PLoS One 2008 22;3(12):e3996. Epub 2008 Dec 22.

Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003996PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2601044PMC
June 2009

Same-strand overlapping genes in bacteria: compositional determinants of phase bias.

Biol Direct 2008 Aug 21;3:36. Epub 2008 Aug 21.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

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http://dx.doi.org/10.1186/1745-6150-3-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2542354PMC
August 2008

Characterization of pairwise and multiple sequence alignment errors.

Gene 2009 Jul 3;441(1-2):141-7. Epub 2008 Jun 3.

Department of Biology & Biochemistry, University of Houston, Houston, TX 77204-5001, USA.

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http://dx.doi.org/10.1016/j.gene.2008.05.016DOI Listing
July 2009

The genome of the model beetle and pest Tribolium castaneum.

Authors:
Stephen Richards Richard A Gibbs George M Weinstock Susan J Brown Robin Denell Richard W Beeman Richard Gibbs Richard W Beeman Susan J Brown Gregor Bucher Markus Friedrich Cornelis J P Grimmelikhuijzen Martin Klingler Marce Lorenzen Stephen Richards Siegfried Roth Reinhard Schröder Diethard Tautz Evgeny M Zdobnov Donna Muzny Richard A Gibbs George M Weinstock Tony Attaway Stephanie Bell Christian J Buhay Mimi N Chandrabose Dean Chavez Kerstin P Clerk-Blankenburg Andrew Cree Marvin Dao Clay Davis Joseph Chacko Huyen Dinh Shannon Dugan-Rocha Gerald Fowler Toni T Garner Jeffrey Garnes Andreas Gnirke Alica Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan LaRonda Jackson Christie Kovar Andrea Kowis Sandra Lee Lora R Lewis Jon Margolis Margaret Morgan Lynne V Nazareth Ngoc Nguyen Geoffrey Okwuonu David Parker Stephen Richards San-Juana Ruiz Jireh Santibanez Joël Savard Steven E Scherer Brian Schneider Erica Sodergren Diethard Tautz Selina Vattahil Donna Villasana Courtney S White Rita Wright Yoonseong Park Richard W Beeman Jeff Lord Brenda Oppert Marce Lorenzen Susan Brown Liangjiang Wang Joël Savard Diethard Tautz Stephen Richards George Weinstock Richard A Gibbs Yue Liu Kim Worley George Weinstock Christine G Elsik Justin T Reese Eran Elhaik Giddy Landan Dan Graur Peter Arensburger Peter Atkinson Richard W Beeman Jim Beidler Susan J Brown Jeffery P Demuth Douglas W Drury Yu-Zhou Du Haruhiko Fujiwara Marce Lorenzen Vincenza Maselli Mizuko Osanai Yoonseong Park Hugh M Robertson Zhijian Tu Jian-jun Wang Suzhi Wang Stephen Richards Henry Song Lan Zhang Erica Sodergren Doreen Werner Mario Stanke Burkhard Morgenstern Victor Solovyev Peter Kosarev Garth Brown Hsiu-Chuan Chen Olga Ermolaeva Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Donna Maglott Kim Pruitt Victor Sapojnikov Alexandre Souvorov Aaron J Mackey Robert M Waterhouse Stefan Wyder Evgeny M Zdobnov Evgeny M Zdobnov Stefan Wyder Evgenia V Kriventseva Tatsuhiko Kadowaki Peer Bork Manuel Aranda Riyue Bao Anke Beermann Nicola Berns Renata Bolognesi François Bonneton Daniel Bopp Susan J Brown Gregor Bucher Thomas Butts Arnaud Chaumot Robin E Denell David E K Ferrier Markus Friedrich Cassondra M Gordon Marek Jindra Martin Klingler Que Lan H Michael G Lattorff Vincent Laudet Cornelia von Levetsow Zhenyi Liu Rebekka Lutz Jeremy A Lynch Rodrigo Nunes da Fonseca Nico Posnien Rolf Reuter Siegfried Roth Joël Savard Johannes B Schinko Christian Schmitt Michael Schoppmeier Reinhard Schröder Teresa D Shippy Franck Simonnet Henrique Marques-Souza Diethard Tautz Yoshinori Tomoyasu Jochen Trauner Maurijn Van der Zee Michel Vervoort Nadine Wittkopp Ernst A Wimmer Xiaoyun Yang Andrew K Jones David B Sattelle Paul R Ebert David Nelson Jeffrey G Scott Richard W Beeman Subbaratnam Muthukrishnan Karl J Kramer Yasuyuki Arakane Richard W Beeman Qingsong Zhu David Hogenkamp Radhika Dixit Brenda Oppert Haobo Jiang Zhen Zou Jeremy Marshall Elena Elpidina Konstantin Vinokurov Cris Oppert Zhen Zou Jay Evans Zhiqiang Lu Picheng Zhao Niranji Sumathipala Boran Altincicek Andreas Vilcinskas Michael Williams Dan Hultmark Charles Hetru Haobo Jiang Cornelis J P Grimmelikhuijzen Frank Hauser Giuseppe Cazzamali Michael Williamson Yoonseong Park Bin Li Yoshiaki Tanaka Reinhard Predel Susanne Neupert Joachim Schachtner Peter Verleyen Florian Raible Peer Bork Markus Friedrich Kimberly K O Walden Hugh M Robertson Sergio Angeli Sylvain Forêt Gregor Bucher Stefan Schuetz Ryszard Maleszka Ernst A Wimmer Richard W Beeman Marce Lorenzen Yoshinori Tomoyasu Sherry C Miller Daniela Grossmann Gregor Bucher

Nature 2008 Apr 23;452(7190):949-55. Epub 2008 Mar 23.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature06784DOI Listing
April 2008

Local reliability measures from sets of co-optimal multiple sequence alignments.

Pac Symp Biocomput 2008 :15-24

Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA.

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March 2008

Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor.

Mol Biol Evol 2008 Apr 24;25(4):748-61. Epub 2008 Jan 24.

Institut für Botanik III, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany.

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http://dx.doi.org/10.1093/molbev/msn022DOI Listing
April 2008

Heads or tails: a simple reliability check for multiple sequence alignments.

Mol Biol Evol 2007 Jun 25;24(6):1380-3. Epub 2007 Mar 25.

Department of Biology & Biochemistry, University of Houston, TX, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msm060DOI Listing
June 2007