Publications by authors named "Sonja Prohaska"

55Publications

Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in .

Int J Mol Sci 2020 Jul 23;21(15). Epub 2020 Jul 23.

Institute for Biochemistry, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany.

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July 2020

Divergent Evolution of Eukaryotic CC- and A-Adding Enzymes.

Int J Mol Sci 2020 Jan 10;21(2). Epub 2020 Jan 10.

Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.

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January 2020

Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration.

J Exp Zool B Mol Dev Evol 2018 01 22;330(1):5-14. Epub 2018 Jan 22.

Santa Fe Institute, Santa Fe, New Mexico.

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January 2018

Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem.

J Math Biol 2018 08 19;77(2):313-341. Epub 2017 Dec 19.

Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany.

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August 2018

Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes.

BMC Evol Biol 2017 07 6;17(1):163. Epub 2017 Jul 6.

Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.

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July 2017

Design specifications for cellular regulation.

Theory Biosci 2016 Dec 18;135(4):231-240. Epub 2016 Nov 18.

Bioinformatics Group at the Department of Computer Science, Interdisciplinary Center for Bioinformatics, ScaDS, Competence Center for Scalable Data services and Solutions, and German Center for Integrative Biodiversity Research, University Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany.

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December 2016

The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies.

Algorithms Mol Biol 2016 24;11. Epub 2016 Feb 24.

Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany ; Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.

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February 2016

The relativity of biological function.

Theory Biosci 2015 Dec 8;134(3-4):143-7. Epub 2015 Oct 8.

TFome Research Group at Department of Computer Science, Paul-Flechsig-Institute for Brain Research, and Interdisciplinary Center of Bioinformatics, University Leipzig, Härtelstraβe 16-18, 04107, Leipzig, Germany.

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December 2015

The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer.

Nucleic Acids Res 2015 Aug 27;43(14):6739-46. Epub 2015 Jun 27.

Computational EvoDevo Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany

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August 2015

Orthology detection combining clustering and synteny for very large datasets.

PLoS One 2014 19;9(8):e105015. Epub 2014 Aug 19.

Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark; The Santa Fe Institute, Santa Fe, New Mexico, United States of America; RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Leipzig, Germany.

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May 2015

The CHR site: definition and genome-wide identification of a cell cycle transcriptional element.

Nucleic Acids Res 2014 8;42(16):10331-50. Epub 2014 Aug 8.

Molecular Oncology, Medical School, University of Leipzig, Semmelweisstr. 14, 04103 Leipzig, Germany.

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January 2015

Chromatin computation: epigenetic inheritance as a pattern reconstruction problem.

J Theor Biol 2013 Nov 20;336:61-74. Epub 2013 Jul 20.

Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Harvard University, Department of Human Evolutionary Biology, 11 Divinity Avenue, Cambridge, MA 02138, USA. Electronic address:

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November 2013

The African coelacanth genome provides insights into tetrapod evolution.

Nature 2013 Apr;496(7445):311-6

Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA.

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April 2013

Transcriptional regulation by histone modifications: towards a theory of chromatin re-organization during stem cell differentiation.

Phys Biol 2013 Apr 12;10(2):026006. Epub 2013 Mar 12.

Interdisciplinary Centre for Bioinformatics, University of Leipzig, D-04107 Leipzig, Härtelstr. 16-18, Germany.

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April 2013

A global genome segmentation method for exploration of epigenetic patterns.

PLoS One 2012 12;7(10):e46811. Epub 2012 Oct 12.

Junior Professorship for Computational EvoDevo, Institute of Computer Science, University of Leipzig, Leipzig, Germany.

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March 2013

Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin.

Epigenomics 2012 Apr;4(2):205-19

Interdisciplinary Centre for Bioinformatics, University Leipzig, D-04107 Leipzig, Härtelstr. 16-18, Germany.

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April 2012

"Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity.

Orig Life Evol Biosph 2011 Dec 10;41(6):587-607. Epub 2012 Feb 10.

Computational EvoDevo Group, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany.

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December 2011

Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids.

Biochimie 2011 Nov 31;93(11):2019-23. Epub 2011 Jul 31.

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.

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November 2011

Proteinortho: detection of (co-)orthologs in large-scale analysis.

BMC Bioinformatics 2011 Apr 28;12:124. Epub 2011 Apr 28.

RNA Bioinformatics Group, Department of Pharmaceutical Chemistry, Philipps-University Marburg, Germany.

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April 2011

The use and abuse of -omes.

Methods Mol Biol 2011 ;719:173-96

Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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June 2011

Evolution and quantitative comparison of genome-wide protein domain distributions.

Genes (Basel) 2011 Nov 9;2(4):912-24. Epub 2011 Nov 9.

Computational EvoDevo Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.

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November 2011

Genomic organization of eukaryotic tRNAs.

BMC Genomics 2010 Apr 28;11:270. Epub 2010 Apr 28.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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April 2010

Innovation in gene regulation: the case of chromatin computation.

J Theor Biol 2010 Jul 18;265(1):27-44. Epub 2010 Mar 18.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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July 2010

PROCESS FLOW FOR CLASSIFICATION AND CLUSTERING OF FRUIT FLY GENE EXPRESSION PATTERNS.

Proc Int Conf Image Proc 2008 Dec;1(1):721-724

Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, 04107 Leipzig.

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December 2008

Defining genes: a computational framework.

Theory Biosci 2009 Aug 26;128(3):165-70. Epub 2009 Jun 26.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany.

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August 2009

Evolution of vault RNAs.

Mol Biol Evol 2009 Sep 2;26(9):1975-91. Epub 2009 Jun 2.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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September 2009

Conserved introns reveal novel transcripts in Drosophila melanogaster.

Genome Res 2009 Jul 20;19(7):1289-300. Epub 2009 May 20.

Bioinformatics Group, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany.

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July 2009

SynBlast: assisting the analysis of conserved synteny information.

BMC Bioinformatics 2008 Aug 24;9:351. Epub 2008 Aug 24.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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August 2008

Noisy: identification of problematic columns in multiple sequence alignments.

Algorithms Mol Biol 2008 Jun 24;3. Epub 2008 Jun 24.

Department of Combinatorics and Geometry (DCG), MPG/CAS Partner Institute for Computational Biology (PICB), Shanghai Institutesfor Biological Sciences (SIBS), Shanghai, PR China.

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June 2008

Transcriptional regulation of the human CD97 promoter by Sp1/Sp3 in smooth muscle cells.

Gene 2008 Apr 9;413(1-2):67-75. Epub 2008 Feb 9.

Department of Surgery, Research Laboratories, University of Leipzig, Leipzig, Germany.

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April 2008

"Genes".

Theory Biosci 2008 Aug 5;127(3):215-21. Epub 2008 Mar 5.

Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA.

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August 2008

The duplication of the Hox gene clusters in teleost fishes.

Theory Biosci 2004 Jun;123(1):89-110

Lehrstuhl für Bioinformatik am Institut für Informatik, Universität Leipzig, Kreuzstraße 7b, D-04103, Leipzig, Germany.

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June 2004

Computational RNomics of drosophilids.

BMC Genomics 2007 Nov 8;8:406. Epub 2007 Nov 8.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, Leipzig, Germany.

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November 2007

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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November 2007

Multiple sequence alignment with user-defined anchor points.

Algorithms Mol Biol 2006 Apr 19;1(1). Epub 2006 Apr 19.

Universität Göttingen, Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Goldschmidtstrasse, 1, D-37077 Göttingen, Germany.

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April 2006

Evolution of the vertebrate ParaHox clusters.

J Exp Zool B Mol Dev Evol 2006 Sep;306(5):481-7

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany.

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September 2006

Multiple sequence alignment with user-defined constraints at GOBICS.

Bioinformatics 2005 Apr 16;21(7):1271-3. Epub 2004 Nov 16.

Institut für Mikrobiologie und Genetik, Universität Göttingen, Abteilung für Bioinformatik Goldschmidtstrasse 1, D-37077 Göttingen, Germany.

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April 2005

Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii.

Mol Phylogenet Evol 2004 Sep;32(3):686-94

Lehrstuhl für Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstrasse 7b, D-04103 Leipzig, Germany.

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September 2004

Divergence of conserved non-coding sequences: rate estimates and relative rate tests.

Mol Biol Evol 2004 Nov 28;21(11):2116-21. Epub 2004 Jul 28.

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

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November 2004

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications.

Mol Phylogenet Evol 2004 May;31(2):581-604

Lehrstuhl für Bioinformatik, Institut für Informatik, Uniersitäat Leipzig, Germany.

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May 2004

Exclusion of repetitive DNA elements from gnathostome Hox clusters.

J Exp Zool B Mol Dev Evol 2004 Mar;302(2):165-73

Bioinformatics Group, Department of Computer Science, University of Leipzig Kreuzstrabetae 7b, D-04103 Leipzig, Germany.

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March 2004

The shark HoxN cluster is homologous to the human HoxD cluster.

J Mol Evol 2004 Feb;58(2):212-7

Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstrassse 7b, D-04103 Leipzig, Germany.

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February 2004

The footprint sorting problem.

J Chem Inf Comput Sci 2004 Mar-Apr;44(2):332-8

Bioinformatics, Department of Computer Science, University of Leipzig, Germany.

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December 2004

Independent Hox-cluster duplications in lampreys.

J Exp Zool B Mol Dev Evol 2003 Oct;299(1):18-25

Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstrasse 7b, D-04103 Leipzig, Germany.

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October 2003