Working Papers and Datasets

 

2013

Kressing, F, Fangerau, H, Krischel, M: The "Global Phylogeny" and its Historical Legacy - A Critical Review of a Unified Theory of Human Biological and Linguistic Co-Evolution. Medicine Studies, Februar (2013) online DOI 10.1007/s12376_013_0081-8.

 

2012

List, J-M (2012a): Improving phonetic alignment by handling secondary sequence structures. In: Hinrichs, E. and Jäger, G. (eds.): Computational approaches to the study of dialectal and typological variation. Working papers submitted for the workshop organized as part of the ESSLLI 2012.

List, J-M (2012b): SCA: Phonetic alignment based on sound classes. In Slavkovik, M. & Lassiter, D. (eds.): New directions in logic, language, and computation. Springer, Berlin and Heidelberg. 32-51.

List, J-M (2012c): LexStat: Automatic detection of cognates in multilingual wordlists. In Proceedings of EACL, Joint Workshop of LINGVIS and UNCLH, April 23-24, Avignon, France. 117-125.

List, J-M (2012d): Multiple sequence alignment in historical linguistics. A sound class based approach. Proceedings of ConSOLE XIX (2011) 241-260.

Martin WF, Roettger M, Kloesges T, Thiergart T, Woehle C, Gould SB, Dagan T: Modern endosymbiotic theory: Getting lateral gene transfer into the equation. Endocytobiosis Cell Res 23:1-5 (2012)

Thiergart T, Landan G, Schenk M, Dagan T, Martin WF: An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol Evol 4:466-85 (2012). Pubmed

 

2011

Dagan T: Phylogenomic networks. Trends Microbiol 19:483-91 (2011).

Wagele H, Deusch O, Handeler K, Martin R, Schmitt V, Christa G, Pinzger B, Gould SB, Dagan T, Klussmann-Kolb A, Martin W: Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plackobranchus ocellatus does not entail lateral transfer of algal nuclear genes. Mol Biol Evol 28:699-706 (2011). Pubmed

Geisler, H List, J-M (to appear in 2011): Beautiful trees on unstable ground: Notes on the data problem in lexicostatistics. In: Hettrich, Heinrich (ed.): Die Ausbreitung des Indogermanischen. Thesen aus Sprachwissenschaft, Archäologie und Genetik, Akten der Arbeitstagung der Indogermanischen Gesellschaft Würzburg, 24.-26. September 2009. Wiesbaden: Reichert.

Krischel, M; Kressing, F; Fangerau, H (2011): Die Entwicklung der Deszendenztheorie in Biologie, Linguistik und Anthropologie als Austauschprozess zwischen Geistes- und Naturwissenschaften. In: H.-K. Keul, M. Krischel (eds.), Deszendenztheorie und Darwinismus in den Wissenschaften vom Menschen. Steiner: Stuttgart 2011, 107-121.

Kloesges T, Popa O, Martin W, Dagan T: Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28:1057-74 (2011). pdf Pubmed

Martin W: Early evolution without a tree of life.
Biol Direct 6:36 (2011).

Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T: Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599-609 (2011). pdf [see Supplementary resources]

Popa O, Dagan T: Trends and barriers to lateral gene transfer in prokaryotes.  Curr Opin Microbiol in press (2011).

 

2010

Ahmadinejad N, Dagan T, Gruenheit N, Martin W, Gabaldon T: Evolution of spliceosomal introns following endosymbiotic gene transfer. BMC Evolutionary BMC Evol Biol 10:57 (2010). Pubmed

Dagan T, Roettger M, Bryant D, Martin W: Genome Networks Root the Tree of Life between Prokaryotic Domains. Genome Biol Evol 2:379-392 (2010). Pubmed

Fangerau H (2010): Spinning the Scientific Web: Jacques Loeb (1859-1924) und sein Programm einer internationalen biomedizinischen Grundlagenforschung. Berlin. Akademie Verlag.

Krischel M (2010): "Perceived Hereditary Effect of World War I: A Study of the Positions of Friedrich von Bernhardi and Vernon Kellogg", Medicine Studies 2 (2), 139-150.

Krischel M (2010): "Kritik an Charles Darwin und der Evolutionstheorie in der islamischen Welt", in: Uni Ulm intern - das Ulmer Universitätsmagazin, 302, 32-33.

List, J (2010): Phonetic alignment based on sound classes. A new method for sequence comparison in historical linguistics. In: Slavkovik, Marija (ed.): Proceedings of the 15th Student Session of the European Summer School for Logic, Language and Information. August 9-20, Copenhagen, Denmark. 192-202. [pdf]

Wichmann, Søren; Holman, Eric W.; Müller, André; Velupillai, Viveka; List, Johann-Mattis; Belyaev, Oleg; Urban, Matthias & Bakker, Dik (2010): Glottochronology as a heuristic for genealogical language relationships. Journal of Quantitative Linguistics 17.4. 303-316. [abstract]

Nelson-Sathi S, List JM, Geisler H, Fangerau H, Gray RD, Martin W, Dagan T: Networks uncover hidden lexical borrowing in Indo-European language evolution. Proc Biol Sci 278:1794-803 (2011). pdf Pubmed

Martin W (2010): Evolutionary origins of metabolic compartmentalization in eukaryotes. In: Philos Trans R Soc Lond B Biol Sci 365:847-55. Pubmed

Lane, N & Martin, W (2010) The energetics of genome complexity. Nature, 467: 929-934. DOI: 10.1038/nature09486

2009

Dagan T, Martin W (2009): Getting a better picture of microbial evolution en route to a network of genomes. Phil. Trans Roy. Soc. Lond. B 364: 2187–2196. Pubmed

Roettger M, Martin W, Dagan T: A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies. Mol Biol Evol. 26:1931-9 (2009). Pubmed

Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupre J, Dagan T, Boucher Y, Martin W: Prokaryotic evolution and the tree of life are two different things Biol Direct. 4:34 (2009). Pubmed

Fangerau H (2009): From Mephistopheles to Iesajah: Jacques Loeb, Science and Modernism. Social Studies of Science 39:229-256. Pubmed

Fangerau H, Halling T (eds.) (2009): Netzwerke: Eine allgemeine Theorie oder die Anwendung einer Universalmetapher in den Wissenschaften. Bielefeld. Transcript. 

Krischel M, Kressing F, Fangerau H (2009): Computergestützte Analyse in Biologie, Sprach- und Geschichtswissenschaft, in: Hegering H-G, Lehmann A, Ohlbach H-J, Scheideler C (Hrsg.) Informatik 2009 Im Focus das Leben. Beiträge der 38. Jahrestagung der Gesellschaft für Informatik e.V., 582-594

Kressing F, Krischel M (2009): Evolution in Biologie, Linguistik und Wissenschaftsgeschichte – Spannende Fragen zu Stammbaum-Modell und Sprachenvielfalt. Uni Ulm Intern – Forschung  298: 30-31.

List, J (2009): Sprachvariation im modernen Chinesischen. CHUN – Chinesisch-Unterricht. 123-140. [pdf]

2008

Dagan T, Artzy-Randrup Y, Martin W (2008): Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc. Natl. Acad. Sci. USA 105:10039–10044. Pubmed

Geisler H (2008): Konvergenz und Divergenzphänomene in der Romania: Lautentwicklung. In: Gerhard Ernst et al. (eds.): HSK Romanische Sprachgeschichte. Vol. 3:255-265.