Sonja J Prohaska: search on Z-Library

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1

The challenges and scope of theoretical biology

David C. Krakauer, James P. Collins, Douglas Erwin, Jessica C. Flack, Walter Fontana, Manfred D. Laubichler, Sonja J. Prohaska, Geoffrey B. West, Peter F. Stadler

Journal:

Journal of Theoretical Biology

Year:

2011

Language:

english

File:

PDF, 245 KB

english, 2011

2

The relativity of biological function

Laubichler, Manfred D., Stadler, Peter F., Prohaska, Sonja J., Nowick, Katja

Journal:

Theory in Biosciences

Year:

2015

Language:

english

File:

PDF, 349 KB

english, 2015

3

Exclusion of repetitive DNA elements from gnathostome Hox clusters

Claudia Fried, Sonja J. Prohaska, Peter F. Stadler

Journal:

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Year:

2004

Language:

english

File:

PDF, 444 KB

english, 2004

4

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

Laubichler, Manfred D., Prohaska, Sonja J., Stadler, Peter F.

Journal:

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Year:

2018

Language:

english

File:

PDF, 635 KB

english, 2018

5

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

Lechner, Marcus, Hernandez-Rosales, Maribel, Doerr, Daniel, Wieseke, Nicolas, Thévenin, Annelyse, Stoye, Jens, Hartmann, Roland K., Prohaska, Sonja J., Stadler, Peter F., Ouzounis, Christos A.

Journal:

Year:

2014

Language:

english

File:

PDF, 433 KB

english, 2014

6

Transcriptional memory emerges from cooperative histone modifications

Binder, Hans, Steiner, Lydia, Rohlf, Thimo, Prohaska, Sonja, Galle, Joerg

Journal:

Nature Precedings

Year:

2011

Language:

english

File:

PDF, 681 KB

english, 2011

7

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

Sven Findeiß, Jan Engelhardt, Sonja J. Prohaska, Peter F. Stadler

Journal:

Year:

2011

Language:

english

File:

PDF, 540 KB

english, 2011

8

Complete HOX Cluster Characterization of the Coelacanth Provides Further Evidence for Slow Evolution of Its Genome

Chris T. Amemiya, Thomas P. Powers, Sonja J. Prohaska, Jane Grimwood, Jeremy Schmutz, Mark Dickson, Tsutomu Miyake, Michael A. Schoenborn, Richard M. Myers, Francis H. Ruddle and Peter F. Stadler

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.49 MB

english, 2010

9

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

Betat, Heike, Mede, Tobias, Tretbar, Sandy, Steiner, Lydia, Stadler, Peter F., Mörl, Mario, Prohaska, Sonja J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 250 KB

english, 2015

10

“Hypothesis for the Modern RNA World”: ApervasiveNon-coding RNA-Based Genetic Regulation is a Prerequisite for the Emergence of Multicellular Complexity

Irma Lozada-Chávez, Peter F. Stadler, Sonja J. Prohaska

Journal:

Origins of Life and Evolution of Biospheres

Year:

2011

Language:

english

File:

PDF, 585 KB

english, 2011

11

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

Indrischek, Henrike, Prohaska, Sonja J., Gurevich, Vsevolod V., Gurevich, Eugenia V., Stadler, Peter F.

Journal:

BMC Evolutionary Biology

Year:

2017

Language:

english

File:

PDF, 3.07 MB

english, 2017

12

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

Peter F. Stadler, Claudia Fried, Sonja J. Prohaska, Wendy J. Bailey, Bernhard Y. Misof, Frank H. Ruddle, Günter P. Wagner

Journal:

Molecular Phylogenetics and Evolution

Year:

2004

Language:

english

File:

PDF, 765 KB

english, 2004

13

Genomic organization of eukaryotic tRNAs

Clara Bermudez-Santana, Camille Stephan-Otto Attolini, Toralf Kirsten, Jan Engelhardt, Sonja J Prohaska, Stephan Steigele, Peter F Stadler

Journal:

Year:

2010

Language:

english

File:

PDF, 1.19 MB

english, 2010

14

Multiple sequence alignment with user-defined anchor points

Burkhard Morgenstern, Sonja J Prohaska, Dirk Pöhler…

Journal:

Algorithms for Molecular Biology

Year:

2006

Language:

english

File:

PDF, 291 KB

english, 2006

15

Algebraic Dynamic Programming over general data structures

Christian Höner zu Siederdissen,Sonja J Prohaska,Peter F Stadler

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.14 MB

english, 2015

16

Defining genes: a computational framework

Peter F. Stadler, Sonja J. Prohaska, Christian V. Forst, David C. Krakauer

Journal:

Theory in Biosciences

Year:

2009

Language:

english

File:

PDF, 293 KB

english, 2009

17

The amphioxus Hox cluster: characterization, comparative genomics, and evolution

Chris T. Amemiya, Sonja J. Prohaska, Alicia Hill-Force, April Cook, Jessica Wasserscheid, David E.K. Ferrier, Juan Pascual-Anaya, Jordi Garcia-Fernàndez, Ken Dewar, Peter F. Stadler

Journal:

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Year:

2008

Language:

english

File:

PDF, 370 KB

english, 2008

18

Discovering cis-regulatory modules by optimizing barbecues

Axel Mosig, Türker Bıyıkoğlu, Sonja J. Prohaska, Peter F. Stadler

Journal:

Discrete Applied Mathematics

Year:

2009

Language:

english

File:

PDF, 900 KB

english, 2009

19

Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased Synonymous Substitution Rate and Asymmetrical Co-divergence of Coding and Non-coding Sequences

Günter P. Wagner, Kazuhiko Takahashi, Vincent Lynch, Sonja J. Prohaska, Claudia Fried, Peter F. Stadler, Chris Amemiya

Journal:

Journal of Molecular Evolution

Year:

2005

Language:

english

File:

PDF, 189 KB

english, 2005

20

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

Sonja J. Prohaska, Claudia Fried, Christoph Flamm, Günter P. Wagner, Peter F. Stadler

Journal:

Molecular Phylogenetics and Evolution

Year:

2004

Language:

english

File:

PDF, 638 KB

english, 2004

21

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

Arnold, Christian, Stadler, Peter F., Prohaska, Sonja J.

Journal:

Journal of Theoretical Biology

Year:

2013

Language:

english

File:

PDF, 1.75 MB

english, 2013

22

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

Prohaska, Sonja J., Berkemer, Sarah J., Gärtner, Fabian, Gatter, Thomas, Retzlaff, Nancy, Höner zu Siederdissen, Christian, Stadler, Peter F.

Journal:

Journal of Mathematical Biology

Year:

2017

Language:

english

File:

PDF, 1.05 MB

english, 2017

23

Transcriptional memory emerges from cooperative histone modifications

Binder, Hans, Steiner, Lydia, Rohlf, Thimo, Prohaska, Sonja, Galle, Joerg

Journal:

Nature Precedings

Year:

2011

File:

PDF, 681 KB

2011

24

A STORY OF GROWING CONFUSION: GENES AND THEIR REGULATION

PROHASKA, SONJA J., STADLER, PETER F.

Journal:

Biophysical Reviews and Letters

Year:

2008

Language:

english

File:

PDF, 298 KB

english, 2008

25

Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny

Jeremy D. Raincrow, Ken Dewar, Claudia Stocsits, Sonja J. Prohaska, Chris T. Amemiya, Peter F. Stadler, Chi-Hua Chiu

Journal:

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Year:

2011

Language:

english

File:

PDF, 456 KB

english, 2011

26

SynBlast: Assisting the analysis of conserved synteny information

Jörg Lehmann, Peter F Stadler, Sonja J Prohaska

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 797 KB

english, 2008

27

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

Indrischek, Henrike, Wieseke, Nicolas, Stadler, Peter F., Prohaska, Sonja J.

Journal:

Algorithms for Molecular Biology

Year:

2016

Language:

english

File:

PDF, 2.14 MB

english, 2016

28

The duplication of theHoxgene clusters in teleost fishes

Sonja J. Prohaska, Peter F. Stadler

Journal:

Theory in Biosciences

Year:

2004

Language:

english

File:

PDF, 342 KB

english, 2004

29

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

Rohlf, Thimo, Steiner, Lydia, Przybilla, Jens, Prohaska, Sonja, Binder, Hans, Galle, Jörg

Journal:

Year:

2012

Language:

english

File:

PDF, 3.05 MB

english, 2012

30

[IEEE 2008 15th IEEE International Conference on Image Processing - San Diego, CA, USA (2008.10.12-2008.10.15)] 2008 15th IEEE International Conference on Image Processing - Process flow for classification and clustering of fruit fly gene expression patterns

Heffel, Andreas, Stadler, Peter F., Prohaska, Sonja J., Kauer, Gerhard, Kuska, Jens-Peer

Year:

2008

Language:

english

File:

PDF, 765 KB

english, 2008

31

A prioriassessment of data quality in molecular phylogenetics

Misof, Bernhard, Meusemann, Karen, von Reumont, Björn M, Kück, Patrick, Prohaska, Sonja J, Stadler, Peter F

Journal:

Algorithms for Molecular Biology

Year:

2014

Language:

english

File:

PDF, 1.54 MB

english, 2014

32

A Global Genome Segmentation Method for Exploration of Epigenetic Patterns

Steiner, Lydia, Hopp, Lydia, Wirth, Henry, Galle, Jörg, Binder, Hans, Prohaska, Sonja J., Rohlf, Thimo, Mariño-Ramírez, Leonardo

Journal:

Year:

2012

Language:

english

File:

PDF, 1003 KB

english, 2012

33

“Genes”

Sonja J. Prohaska, Peter F. Stadler

Journal:

Theory in Biosciences

Year:

2008

Language:

english

File:

PDF, 200 KB

english, 2008

34

Kiwi genome provides insights into evolution of a nocturnal lifestyle

Le Duc, Diana, Renaud, Gabriel, Krishnan, Arunkumar, Almén, Markus Sällman, Huynen, Leon, Prohaska, Sonja J., Ongyerth, Matthias, Bitarello, Bárbara D., Schiöth, Helgi B., Hofreiter, Michael, Stadler,

Journal:

Year:

2015

Language:

english

File:

PDF, 1.48 MB

english, 2015

35

Evolution of the vertebrate parahox clusters

Sonja J. Prohaska, Peter F. Stadler

Journal:

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Year:

2006

Language:

english

File:

PDF, 144 KB

english, 2006

36

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

Binder, Hans, Steiner, Lydia, Przybilla, Jens, Rohlf, Thimo, Prohaska, Sonja, Galle, Jörg

Journal:

Physical Biology

Year:

2013

Language:

english

File:

PDF, 1.78 MB

english, 2013

37

Design specifications for cellular regulation

Krakauer, David C., Müller, Lydia, Prohaska, Sonja J., Stadler, Peter F.

Journal:

Theory in Biosciences

Year:

2016

Language:

english

File:

PDF, 590 KB

english, 2016

38

Computational RNomics of Drosophilids

Dominic Rose, Jörg Hackermüller, Stefan Washietl, Kristin Reiche, Jana Hertel, Sven Findeiß, Peter F Stadler, Sonja J Prohaska

Journal:

Year:

2007

Language:

english

File:

PDF, 432 KB

english, 2007

39

Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions

Parikesit, Arli A., Stadler, Peter F., Prohaska, Sonja J.

Journal:

Year:

2011

Language:

english

File:

PDF, 120 KB

english, 2011

40

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F Stadler, Sonja J Prohaska

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 475 KB

english, 2011

41

RNAs everywhere: genome-wide annotation of structured RNAs

Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter

Journal:

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Year:

2007

Language:

english

File:

PDF, 1.18 MB

english, 2007

42

Innovation in gene regulation: The case of chromatin computation

Sonja J. Prohaska, Peter F. Stadler, David C. Krakauer

Journal:

Journal of Theoretical Biology

Year:

2010

Language:

english

File:

PDF, 831 KB

english, 2010

43

Are bacterial proteins part of the matrix of kidney stones?

Sasha Daskalova, Sonja Kostadinova, Diethelm Gauster, Reiner Prohaska, Alexander Ivanov

Journal:

Microbial Pathogenesis

Year:

1998

Language:

english

File:

PDF, 198 KB

english, 1998

44

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

Manja Wobus, Elke Wandel, Sonja Prohaska, Sven Findeiβ, Katrin Tschöp, Gabriela Aust

Journal:

Year:

2008

Language:

english

File:

PDF, 695 KB

english, 2008

45

Independent Hox-cluster duplications in lampreys

Claudia Fried, Sonja J. Prohaska, Peter F. Stadler

Journal:

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Year:

2003

Language:

english

File:

PDF, 225 KB

english, 2003

46

Evolutionary patterns of non-coding RNAs

Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M.R. Stadler, Peter F.

Journal:

Theory in Biosciences

Year:

2005

Language:

english

File:

PDF, 1.33 MB

english, 2005

47

Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in Dictyostelium discoideum

Erber, Lieselotte, Hoffmann, Anne, Fallmann, JÃ¶rg, Hagedorn, Monica, Hammann, Christian, Stadler, Peter F., Betat, Heike, Prohaska, Sonja, MÃ¶rl, Mario

Journal:

International Journal of Molecular Sciences

Year:

2020

File:

PDF, 2.59 MB

2020

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