User Profile

micha


Name
Michael Sammeth
Status:
Post-doc
Location:
Barcelona (Catalunya)
Research Interests:
Alignment, Multiple Alignments, Repeats, Tandem Repeats, Splicing, Alternative Splicing, Splice Graphs, Short Read Sequencing, New Sequencing Technologies, Next Generation Sequencing, Protein Domains, Protein Interaction Networks, Vizualization, Algorithms, Phylogeny, Metrics
Publications in PubMed
  1. Sammeth M, Foissac S, Guigó R. A general definition and nomenclature for alternative splicing events. PLoS computational biology 2008 4(8). DOI:10.1371/journal.pcbi.1000147.
  2. Mellmann A, Weniger T, Berssenbrügge C, Rothgänger J, Sammeth M, Stoye J, Harmsen D. Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms. BMC microbiology 2007 7. DOI:10.1186/1471-2180-7-98.
  3. Foissac S, Sammeth M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic acids research 2007 35. DOI:10.1093/nar/gkm311.
  4. Sammeth M, Stoye J. Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 3(4). DOI:10.1109/TCBB.2006.46.
  5. Sammeth M, Heringa J. Global multiple-sequence alignment with repeats. Proteins 2006 64(1). DOI:10.1002/prot.20957.
  6. Sammeth M, Griebel T, Tille F, Stoye J. Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinformatics (Oxford, England) 2006 22(7). DOI:10.1093/bioinformatics/btl007.
  7. Harmsen D, Dostal S, Roth A, Niemann S, Rothgänger J, Sammeth M, Albert J, Frosch M, Richter E. RIDOM: comprehensive and public sequence database for identification of Mycobacterium species. BMC infectious diseases 2003 3. DOI:10.1186/1471-2334-3-26.
  8. Sammeth M, Morgenstern B, Stoye J. Divide-and-conquer multiple alignment with segment-based constraints. Bioinformatics (Oxford, England) 2003 19 Suppl 2. DOI:10.1186/1471-2334-3-26.
  9. Sammeth M, Rothgänger J, Esser W, Albert J, Stoye J, Harmsen D. QAlign: quality-based multiple alignments with dynamic phylogenetic analysis. Bioinformatics (Oxford, England) 2003 19(12). DOI:10.1186/1471-2334-3-26.
  10. Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R. Nucleosome positioning as a determinant of exon recognition. Nature structuralmolecular biology 2009 16(9). DOI:10.1038/nsmb.1658.
  11. Sammeth M. Complete alternative splicing events are bubbles in splicing graphs. Journal of computational biology : a journal of computational molecular cell biology 2009 16(8). DOI:10.1089/cmb.2009.0108.
  12. Horner DS, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Briefings in bioinformatics 2009. DOI:10.1093/bib/bbp046.
Publications
Michael Sammeth, Gabriel Valiente, Roderic Guigó: Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs. RECOMB 2008: 372-395

Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye: Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). WABI 2005: 276-290

History of Education and Employment
Biology
Bioinformatics
Computational Biology

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Feb 23, 2009
Reconstruction of Alternative Splice...
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Aug 12, 2008
A General Definition and Nomenclature...