Francisco S Domingues

Francisco S Domingues

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Francisco S Domingues

Publications by authors named "Francisco S Domingues"

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Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants.

J Mol Biol 2019 May 30;431(12):2354-2368. Epub 2019 Apr 30.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany; Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836193024
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http://dx.doi.org/10.1016/j.jmb.2019.04.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554042PMC
May 2019

Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees.

Bioinformatics 2019 01;35(1):69-76

Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.

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http://dx.doi.org/10.1093/bioinformatics/bty541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298062PMC
January 2019

A network-based meta-analysis for characterizing the genetic landscape of human aging.

Biogerontology 2018 02 21;19(1):81-94. Epub 2017 Dec 21.

Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy.

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http://dx.doi.org/10.1007/s10522-017-9741-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765210PMC
February 2018

A Web Resource for Levodopa-Induced Dyskinesia Genetics in Parkinson's Disease.

Neuroinformatics 2017 07;15(3):297-300

Institute for Biomedicine, Eurac Research, Eurac Research, Bolzano, Italy.

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http://dx.doi.org/10.1007/s12021-017-9327-zDOI Listing
July 2017

Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework.

Sci Rep 2017 03 23;7(1):381. Epub 2017 Mar 23.

Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.

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http://dx.doi.org/10.1038/s41598-017-00465-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5428484PMC
March 2017

Computational assessment of feature combinations for pathogenic variant prediction.

Mol Genet Genomic Med 2016 Jul 14;4(4):431-46. Epub 2016 Mar 14.

Center for BiomedicineEuropean Academy of Bozen/Bolzano (EURAC)Viale Druso 139100BolzanoItaly; Affiliated Institute of the University of LübeckLübeckGermany.

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http://dx.doi.org/10.1002/mgg3.214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947862PMC
July 2016

FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees.

Bioinformatics 2016 05 22;32(10):1583-5. Epub 2016 Jan 22.

Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Bolzano 39100, Italy and.

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http://dx.doi.org/10.1093/bioinformatics/btw019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866523PMC
May 2016

Dintor: functional annotation of genomic and proteomic data.

BMC Genomics 2015 Dec 21;16:1081. Epub 2015 Dec 21.

Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), (Affiliated to the University of Lübeck, Lübeck, Germany), Viale Druso 1, 39100, Bolzano, Italy.

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http://dx.doi.org/10.1186/s12864-015-2279-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687148PMC
December 2015

Overexpression of blood microRNAs 103a, 30b, and 29a in L-dopa-treated patients with PD.

Neurology 2015 Feb 16;84(7):645-53. Epub 2015 Jan 16.

From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany.

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http://dx.doi.org/10.1212/WNL.0000000000001258DOI Listing
February 2015

Integrative visual analysis of protein sequence mutations.

BMC Proc 2014 28;8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S2. Epub 2014 Aug 28.

University Medicine Greifswald, 17475 Greifswald, Germany ; Graz University of Technology, 8010 Graz, Austria ; BioTechMed-Graz, 8010 Graz, Austria.

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http://dx.doi.org/10.1186/1753-6561-8-S2-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155609PMC
September 2014

Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage.

PLoS Comput Biol 2013 21;9(3):e1002977. Epub 2013 Mar 21.

Max Planck Institute for Computer Science, Saarbrucken, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1002977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605109PMC
November 2013

Seventy-five genetic loci influencing the human red blood cell.

Authors:
Pim van der Harst Weihua Zhang Irene Mateo Leach Augusto Rendon Niek Verweij Joban Sehmi Dirk S Paul Ulrich Elling Hooman Allayee Xinzhong Li Aparna Radhakrishnan Sian-Tsung Tan Katrin Voss Christian X Weichenberger Cornelis A Albers Abtehale Al-Hussani Folkert W Asselbergs Marina Ciullo Fabrice Danjou Christian Dina Tõnu Esko David M Evans Lude Franke Martin Gögele Jaana Hartiala Micha Hersch Hilma Holm Jouke-Jan Hottenga Stavroula Kanoni Marcus E Kleber Vasiliki Lagou Claudia Langenberg Lorna M Lopez Leo-Pekka Lyytikäinen Olle Melander Federico Murgia Ilja M Nolte Paul F O'Reilly Sandosh Padmanabhan Afshin Parsa Nicola Pirastu Eleonora Porcu Laura Portas Inga Prokopenko Janina S Ried So-Youn Shin Clara S Tang Alexander Teumer Michela Traglia Sheila Ulivi Harm-Jan Westra Jian Yang Jing Hua Zhao Franco Anni Abdel Abdellaoui Antony Attwood Beverley Balkau Stefania Bandinelli François Bastardot Beben Benyamin Bernhard O Boehm William O Cookson Debashish Das Paul I W de Bakker Rudolf A de Boer Eco J C de Geus Marleen H de Moor Maria Dimitriou Francisco S Domingues Angela Döring Gunnar Engström Gudmundur Ingi Eyjolfsson Luigi Ferrucci Krista Fischer Renzo Galanello Stephen F Garner Bernd Genser Quince D Gibson Giorgia Girotto Daniel Fannar Gudbjartsson Sarah E Harris Anna-Liisa Hartikainen Claire E Hastie Bo Hedblad Thomas Illig Jennifer Jolley Mika Kähönen Ido P Kema John P Kemp Liming Liang Heather Lloyd-Jones Ruth J F Loos Stuart Meacham Sarah E Medland Christa Meisinger Yasin Memari Evelin Mihailov Kathy Miller Miriam F Moffatt Matthias Nauck Maria Novatchkova Teresa Nutile Isleifur Olafsson Pall T Onundarson Debora Parracciani Brenda W Penninx Lucia Perseu Antonio Piga Giorgio Pistis Anneli Pouta Ursula Puc Olli Raitakari Susan M Ring Antonietta Robino Daniela Ruggiero Aimo Ruokonen Aude Saint-Pierre Cinzia Sala Andres Salumets Jennifer Sambrook Hein Schepers Carsten Oliver Schmidt Herman H W Silljé Rob Sladek Johannes H Smit John M Starr Jonathan Stephens Patrick Sulem Toshiko Tanaka Unnur Thorsteinsdottir Vinicius Tragante Wiek H van Gilst L Joost van Pelt Dirk J van Veldhuisen Uwe Völker John B Whitfield Gonneke Willemsen Bernhard R Winkelmann Gerald Wirnsberger Ale Algra Francesco Cucca Adamo Pio d'Adamo John Danesh Ian J Deary Anna F Dominiczak Paul Elliott Paolo Fortina Philippe Froguel Paolo Gasparini Andreas Greinacher Stanley L Hazen Marjo-Riitta Jarvelin Kay Tee Khaw Terho Lehtimäki Winfried Maerz Nicholas G Martin Andres Metspalu Braxton D Mitchell Grant W Montgomery Carmel Moore Gerjan Navis Mario Pirastu Peter P Pramstaller Ramiro Ramirez-Solis Eric Schadt James Scott Alan R Shuldiner George Davey Smith J Gustav Smith Harold Snieder Rossella Sorice Tim D Spector Kari Stefansson Michael Stumvoll W H Wilson Tang Daniela Toniolo Anke Tönjes Peter M Visscher Peter Vollenweider Nicholas J Wareham Bruce H R Wolffenbuttel Dorret I Boomsma Jacques S Beckmann George V Dedoussis Panos Deloukas Manuel A Ferreira Serena Sanna Manuela Uda Andrew A Hicks Josef Martin Penninger Christian Gieger Jaspal S Kooner Willem H Ouwehand Nicole Soranzo John C Chambers

Nature 2012 Dec 5;492(7429):369-75. Epub 2012 Dec 5.

Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands.

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http://dx.doi.org/10.1038/nature11677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623669PMC
December 2012

Ketoamide resistance and hepatitis C virus fitness in val55 variants of the NS3 serine protease.

Antimicrob Agents Chemother 2012 Apr 17;56(4):1907-15. Epub 2012 Jan 17.

Division of Infectious Diseases, Department of Medicine and the Lineberger Comprehensive Cancer Center, Chapel Hill, University of North Carolina at Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1128/AAC.05184-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318394PMC
April 2012

Peptidomimetic escape mechanisms arise via genetic diversity in the ligand-binding site of the hepatitis C virus NS3/4A serine protease.

Gastroenterology 2012 Mar 7;142(3):654-63. Epub 2011 Dec 7.

Division of Infectious Diseases, Department of Medicine, Inflammatory Diseases Institute, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599--7292, USA.

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http://dx.doi.org/10.1053/j.gastro.2011.11.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288278PMC
March 2012

Topological analysis and interactive visualization of biological networks and protein structures.

Nat Protoc 2012 Mar 15;7(4):670-85. Epub 2012 Mar 15.

Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1038/nprot.2012.004DOI Listing
March 2012

Analyzing and visualizing residue networks of protein structures.

Trends Biochem Sci 2011 Apr 21;36(4):179-82. Epub 2011 Feb 21.

Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S096800041100013
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http://dx.doi.org/10.1016/j.tibs.2011.01.002DOI Listing
April 2011

Predicting interactions between T cell receptors and MHC-peptide complexes.

Mol Immunol 2011 Jan 23;48(4):553-62. Epub 2010 Nov 23.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbruecken, Germany.

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http://dx.doi.org/10.1016/j.molimm.2010.10.014DOI Listing
January 2011

Towards optimal alignment of protein structure distance matrices.

Bioinformatics 2010 Sep 17;26(18):2273-80. Epub 2010 Jul 17.

CWI, Life Sciences Group, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btq420DOI Listing
September 2010

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 May 1;388(1):160-8. Epub 2009 Apr 1.

Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita-shi, Osaka, Japan.

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http://dx.doi.org/10.1016/j.virol.2009.03.004DOI Listing
May 2009

Local function conservation in sequence and structure space.

PLoS Comput Biol 2008 Jul 4;4(7):e1000105. Epub 2008 Jul 4.

Max Planck Institute for Informatics, Saarbrücken, Germany.

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https://dx.plos.org/10.1371/journal.pcbi.1000105
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http://dx.doi.org/10.1371/journal.pcbi.1000105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427199PMC
July 2008

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus.

Genome Biol 2008 Jan 23;9(1):R16. Epub 2008 Jan 23.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1186/gb-2008-9-1-r16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395260PMC
January 2008

Conformational analysis of alternative protein structures.

Bioinformatics 2007 Dec 12;23(23):3131-8. Epub 2007 Oct 12.

Max-Planck-Institut Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btm499DOI Listing
December 2007

Moment invariants as shape recognition technique for comparing protein binding sites.

Bioinformatics 2007 Dec 31;23(23):3139-46. Epub 2007 Oct 31.

Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btm503DOI Listing
December 2007

Comparative analysis of protein structure alignments.

BMC Struct Biol 2007 Jul 26;7:50. Epub 2007 Jul 26.

Department of Molecular Biology, University of Salzburg, Salzburg, Austria.

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http://dx.doi.org/10.1186/1472-6807-7-50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1959231PMC
July 2007

GOTax: investigating biological processes and biochemical activities along the taxonomic tree.

Genome Biol 2007 ;8(3):R33

Department of Computational Biology and Applied Algorithmics, Max-Planck-Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1186/gb-2007-8-3-r33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868936PMC
June 2007

A new measure for functional similarity of gene products based on Gene Ontology.

BMC Bioinformatics 2006 Jun 15;7:302. Epub 2006 Jun 15.

Department of Computational Biology and Applied Algorithmics, Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1471-2105-7-302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559652PMC
June 2006

Calculating the statistical significance of changes in pathway activity from gene expression data.

Stat Appl Genet Mol Biol 2004 22;3:Article16. Epub 2004 Jun 22.

Max-Planck-Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.2202/1544-6115.1055DOI Listing
May 2006

Protein function from sequence and structure data.

Appl Bioinformatics 2003 ;2(1):3-12

Max-Planck-Institut für Informatik, Saarbrücken, Germany.

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March 2006

NOXclass: prediction of protein-protein interaction types.

BMC Bioinformatics 2006 Jan 19;7:27. Epub 2006 Jan 19.

Max-Planck-lnstitut für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1186/1471-2105-7-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1386716PMC
January 2006

Automated clustering of ensembles of alternative models in protein structure databases.

Protein Eng Des Sel 2004 Jun 19;17(6):537-43. Epub 2004 Aug 19.

Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/protein/gzh063DOI Listing
June 2004

WILMA-automated annotation of protein sequences.

Bioinformatics 2004 Jan;20(1):127-8

Center of Applied Molecular Engineering, Institute for Chemistry and Biochemistry, University of Salzburg, Jakob-Haringerstr. 5, A-5020 Salzburg, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btg380DOI Listing
January 2004

Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2.

FEBS Lett 2003 Nov;554(3):520-8

Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1016/s0014-5793(03)01222-5DOI Listing
November 2003

Identification of mammalian orthologs associates PYPAF5 with distinct functional roles.

FEBS Lett 2003 Mar;538(1-3):173-7

Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1016/s0014-5793(03)00161-3DOI Listing
March 2003