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Dr. Francisco Domingues, Staff Scientist

Dr. Francisco Domingues, Staff Scientist

Max-Planck-Institut für Informatik
Computational Biology and Applied Algorithmics

Campus E1 4
66123 Saarbrücken, Germany
email:   francisco.domingues@eurac.edu
phone:   +39 0471 055 539
fax:   +39 0471 055 599
room:   0 (Building E1 4)
2nd homepage:  http://www.eurac.edu/de/eurac/people/staff/default.html?searchByLetter=D

Publications

S. Susser, C. Welsch, Y. Wang, M. Zettler, F. S. Domingues, U. Karey, E. Hughes, R. Ralston, X. Tong, E. Herrmann, S. Zeuzem, C. Sarrazin
Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus infected patients
Hepatology 2009, 50:1709-1718. (PubMed)

K. Kono, K. Bozek, F. S. Domingues, T. Shioda, E. E. Nakayama.
Impact of a single amino acid in the variable region 2 of the Old World monkey TRIM5alpha SPRY (B30.2) domain on anti-human immunodeficiency virus type 2 activity.
Virology 2009, 388:160-168. (PubMed)

A. Franke, T. Balschun, T. H. Karlsen, J. Sventoraityte, S. Nikolaus, G. Mayr, F. S. Domingues, M. Albrecht, M. Nothnagel, D. Ellinghaus, C. Sina, C. M. Onnie, R. K. Weersma, P. C. F. Stokkers, C. Wijmenga, M. Gazouli, D. Strachan, W. L. McArdle, S. Vermeire, P. Rutgeerts, P. Rosenstiel, M. Krawczak, M. H. Vatn, the IBSEN study group, C. G. Mathew, S. Schreiber.
Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility.
Nat Genet 2008, 40:1319-1323. (PubMed) (Nature Genetics)

N. Weinhold, O. Sander, F. S. Domingues, T. Lengauer, I. Sommer
Local Function Conservation in Sequence and Structure Space
PLoS Computational Biology 2008, 4:e1000105. (PubMed) (Open Access)

H. Zhu, I. Sommer, T. Lengauer, F. S. Domingues
Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
PLoS ONE 2008, 3:e1926. (PubMed) (Open Access)

C. Welsch, F. S. Domingues, S. Susser, I. Antes, C. Hartmann, G. Mayr, A. Schlicker, C. Sarrazin, M. Albrecht, S. Zeuzem, T. Lengauer
Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of HCV.
Genome Biology 2008, 9:R16. (PubMed) (Open Access)

F. S. Domingues, J. Rahnenführer, T. Lengauer
Conformational analysis of alternative protein structures.
Bioinformatics 2007, 23:3131-3138. (PubMed) (Open Access)

I. Sommer, O. Müller, F. S. Domingues, O. Sander, J. Weickert, T. Lengauer
Moment invariants as shape recognition technique for comparing protein binding sites.
Bioinformatics 2007, 23:3139-3146. (PubMed)

G. Mayr, F. S. Domingues, P. Lackner
Comparative analysis of protein structure alignments.
BMC Structural Biology 2007, 7:50. (PubMed) (Open Access)

O. Sander, T. Sing, I. Sommer, A. J. Low, P. K. Cheung, P. R. Harrigan, T. Lengauer, F. S. Domingues
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
PLoS Computational Biology 2007, 3:e58. (PubMed) (Open Access)

T. Sing, A. J. Low, N. Beerenwinkel, O. Sander, P. K. Cheung, F. S. Domingues, J. Büch, M. Däumer, R. Kaiser, T. Lengauer, P. R. Harrigan
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates.
Antivir Ther 2007, 12:1097-1106. (PubMed)

A. Schlicker, J. Rahnenführer, M. Albrecht, T. Lengauer, F. S. Domingues
GOTax: investigating biological processes and biochemical activities along the taxonomic tree
Genome Biology 2007, 8:R33. (PubMed) (Open Access)

A. Schlicker, F. S. Domingues, J. Rahnenführer, T. Lengauer
A new measure for functional similarity of gene products based on Gene Ontology
BMC Bioinformatics 2006, 7:302. (PubMed) (Open Access)

H. Zhu, F. S. Domingues, I. Sommer, T. Lengauer
NOXclass: prediction of protein-protein interaction types
BMC Bioinformatics 2006, 7:27. (PubMed) (Open Access)

F. S. Domingues, J. Rahnenführer, T. Lengauer
Automated clustering of ensembles of alternative models in protein structure databases
Protein Engineering Design and Selection 2004, 17:537-543. (PubMed)

J. Rahnenführer, F. S. Domingues, J. Maydt, T. Lengauer
Calculating the statistical significance of changes in pathway activity from gene expression data
Statistical Applications in Genetics and Molecular Biology 2004, 3:Article16. (PubMed)

I. Sommer, J. Rahnenführer, F. S. Domingues, U. de Lichtenberg, T. Lengauer
Predicting Protein Structure Classes from Function Predictions
Bioinformatics 2004, 20:770-776. (PubMed)

A. Prlic, F. S. Domingues, P. Lackner, M. J. Sippl
WILMA-automated annotation of protein sequences
Bioinformatics 2004, 20:127-128. (PubMed)

M. Albrecht, F.S. Domingues, S. Schreiber, T. Lengauer
Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2.
FEBS Lett. 2003, 554:520-528. (PubMed)

M. Albrecht, F.S. Domingues, S. Schreiber, T. Lengauer
Identification of mammalian orthologs associates PYPAF5 with distinct functional roles.
FEBS Lett. 2003, 538:173-177. (PubMed)

F.S. Domingues, T. Lengauer
Protein function from sequence and structure data
Applied Bioinformatics 2003, 2:3-12. (Paper as PDF, PubMed)

M.J. Sippl, P. Lackner, F.S. Domingues, A. Prlic, R. Malik, A. Andreeva, M. Wiederstein
Assessment of the CASP4 Fold Recognition Category
Proteins 2001, Suppl. 5:55-67. (PubMed)

P. Lackner, W.A. Koppensteiner, M.J. Sippl, F.S. Domingues
ProSup: a refined tool for protein structure alignment
Protein Eng. 2000, 13:745-752. (PubMed)

A. Prlic, F.S. Domingues, M.J. Sippl
Structure-derived substitution matrices for alignment of distantly related sequences
Protein Eng. 2000, 13:545-550. (PubMed)

F.S. Domingues, W.A. Koppensteiner, M.J. Sippl
The role of protein structure in genomics
FEBS Lett. 2000, 476:98-102. (PubMed)

F.S. Domingues, P. Lackner, A. Andreeva, M.J. Sippl
Structure-based evaluation of sequence comparison and fold recognition alignment accuracy
J. Mol. Biol. 2000, 297:1003-1013. (PubMed)

M.J. Sippl, P. Lackner, F.S. Domingues, W.A. Koppensteiner
An attempt to analyse progress in fold recognition from CASP1 to CASP3
Proteins 1999, Suppl.3:226-230. (PubMed)

F.S. Domingues, W.A. Koppensteiner, M. Jaritz, A. Prlic, C. Weichenberger, M. Wiederstein, H. Floeckner, P. Lackner, M.J. Sippl
Sustained performance of knowledge-based potentials in fold recognition
Proteins 1999, Suppl.3:112-120. (PubMed)

P. Lackner, W.A. Koppensteiner, F.S. Domingues, M.J. Sippl
Automated large scale evaluation of protein structure predictions
Proteins 1999, Suppl.3:7-14. (PubMed)

H. Inouye, F.S. Domingues, A.M. Damas, M.J. Saraiva, E. Lundgren, O. Sandgren, D.A. Kirschner
Analysis of x-ray diffraction patterns from amyloid of biopsied vitreous humor and kidney of transthyretin (TTR) Met30 familial amyloidotic polyneuropathy (FAP) patients: axially arrayed TTR monomers constitute the protofilament
Amyloid 1998, 5:163-174. (PubMed)

H. Flockner, F.S. Domingues, M.J. Sippl
Protein folds from pair interactions: a blind test in fold recognition
Proteins 1997, Suppl 1:129-133. (PubMed)

A.M. Damas, M.P. Sebastiao, F.S. Domingues, P.P. Costa, M.J. Saraiva
Structural studies on FAP fibrils
Amyloid 1995, 2:173-178.

Book Contributions

J. D. Watson, J. M. Thornton, M. L. Tress, G. Lopez, A. Valencia, O. Redfern, C. A. Orengo, I. Sommer, F. S. Domingues
Structure to function
In: Modern Genome Annotation. The Biosapiens Network. 2009, 239-262.

F. S. Domingues, T. Lengauer
Inferring Protein Function from Protein Structure
In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function 2007, 1211-1252.

F. S. Domingues, I. Sommer, T. Lengauer
Protein Structure Prediction and Databases
In: Encyclopedia of Life Sciences 2004.