Thomas A. Hopf

PhD student at Rostlab (TUM Computer Science) and Debora Marks lab (Harvard Medical School)

Publications

Hopf T.A., Morinaga S., Ihara S., Touhara K., Marks D.S., Benton R. (2015). Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors. Nature Communications 6:6077.
[paper] [pubmed]
Hopf T.A.*, Schärfe C.P.I.*, Rodrigues J.P.G.L.M.*, Green A.G., Kohlbacher O., Sander C., Bonvin A.M.J.J., Marks D.S. (2014). Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife Sep 25;3.
[paper] [pubmed]
Kajan L., Hopf T.A., Kalas M., Marks D.S., Rost B. (2014). FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics 15 (1), 85.
[paper] [pubmed]
Marks D.S., Hopf T.A., Sander C. (2012). Protein structure prediction from sequence variation. Nature Biotechnology 30 (11), 1072-80.
[paper] [pubmed]
Hopf T.A., Colwell L. J., Sheridan R., Rost B., Sander C., Marks D.S. (2012). Three-dimensional structures of membrane proteins from genomic sequencing. Cell 149 (7), 1607-21.
[paper] [data sets] [pubmed] [preview article]
Marks D.S., Colwell L.J., Sheridan R., Hopf T.A., Pagnani A., Zecchina R., Sander C. (2011): Protein 3D structure computed from evolutionary sequence variation. PLoS ONE e6(12): 28766.
[paper] [data sets] [pubmed]
Hopf T., Kramer S.: Mining Class-Correlated Patterns for Sequence Labeling (2010). In: Proceedings of the 13th International Conference on Discovery Science, Springer.
[paper] [source code and data sets]

11/2009-03/2012: M.Sc. in Bioinformatics, LMU and TU München
Master's thesis: Membrane protein 3D structure prediction from sequence alone
10/2006-11/2009: B.Sc. in Bioinformatics, LMU and TU München
Bachelor's thesis: Conditional random fields over sequence patterns