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Protein Structure and
Bioinformatics Group

Prof. Mauno Vihinen

Lund University

Publications

2017
 
Schaafsma G, Vihinen M
Large differences in proportions of harmful and benign amino acid substitutions between proteins and diseases. Hum Mutat doi: 10.1002/humu.23236
PUBMED
Niroula A, Vihinen M
PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned. Hum Mutat doi: 10.1002/humu.23199
PUBMED
Niroula A, Vihinen M
Predicting severity of disease-causing variants. Hum Mutat 38: 357-364
PUBMED
Vihinen M
How to define pathogenicity, health, and disease? Hum Mutat 38: 129-136
PUBMED
Viennas E, Komianou A, Mizzi C, Stojiljkovic M, Mitropoulou C, Muilu J, Vihinen M, Grypioti P, Papadaki S, Pavlidis C, Zukic B, Katsila T, van der Spek PJ, Pavlovic S, Tzimas G, Patrinos GP.
Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies. Nucleic Acids Res. 45: D846-D853
PUBMED
Hamasy A, Wang Q, Blomberg KE, Mohammad DK, Yu L, Vihinen M, Berglöf A, Smith CI.
Substitution scanning identifies a novel, catalytically active ibrutinib-resistant BTK cysteine 481 to threonine (C481T) variant. Leukemia 31: 177-185
PUBMED
2016
 
Vihinen M
Establishment of an international database for genetic variants in esophageal cancer. Ann NY Acad Sci 1381: 45-49
PUBMED
Vihinen M
Both generic and protein-specific tolerance predictors are needed. Hum Mutat 37: 989
PUBMED
Niroula A, Vihinen M
Variation interpretation predictors: Methods, principles, performance and choice.
Hum Mutat. 37: 579-597. doi: 10.1002/humu.22987
PUBMED
Vihinen, M, Hancock, J, Maglott, D, Landrum, M, Schaafsma, G, Taschner, P
Human Variome Project Quality Assessment Criteria for Variation Databases.
Hum Mutat. 37: 549-558. doi: 10.1002/humu.22976.
PUBMED
Schaafsma GCP, Vihinen M
VariOtator, a software tool for variation annotation with the Variation Ontology.
Hum Mutat. 37: 344-349. doi: 10.1002/humu.22954.
PUBMED
Niroula A, Vihinen M
PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations.
Nucleic Acids Res 44 2020-2027 doi: 10.1093/nar/gkw046
PUBMED
Yang, Y, Niroula, A, Shen, B, and Vihinen, M
PON-Sol: prediction of effects of variants on protein solubility.
Bioinformatics 32: 2032-2034
PUBMED
2015
 
Schaafsma GCP, Vihinen M
Genetic variation in Bruton tyrosine kinase.
In: Agammaglobulinemia. Rare Diseases of the Immune System 4. Edited by Allessandro Plebani and Vassilios Lougaris. Chapter 5: pages 75-85
Niroula A, Vihinen M
Classification of amino acid substitutions in mismatch repair proteins using PON-MMR2.
Hum Mutat. 36: 1128-1134 doi: 10.1002/humu.22900.
PUBMED
Wuttge DM, Carlsen AL, Teku G, Steen SO, Wildt M, Vihinen M, Hesselstrand R, Heegaard NH
Specific autoantibody profiles and disease subgroups correlate with circulating micro-RNA in systemic sclerosis.
Rheumatology (Oxford). 2015 Jul 10. pii: kev234.
PUBMED
Niroula A, Vihinen M
Harmful somatic amino acid substitutions affect key pathways in cancers.
BMC Med Genomics: 8(1):53 doi:10.1186/s12920-015-0125-x
PUBMED
Vihinen M
No more hidden solutions in bioinformatics.
Nature 521: 261 doi:10.1038/521261a
www.nature.com/news/
PUBMED
Vihinen M
Muddled genetic terms miss and mess the message.
Trends Genet. 31:423-425. doi: 10.1016/j.tig.2015.05.008
ScienceDirect
PUBMED
Vihinen M
The Importance of Proper Testing of Predictor Performance.
Hum Mutat. 2015 May; 36(5):iii-iv
DOI: 10.1002/humu.22651
Väliaho J, Faisal I, Ortutay, C, Smith, CIE, Vihinen M
Characterization of all possible single nucleotide change-caused amino acid substitutions in the kinase domain of Bruton tyrosine kinase.
Hum Mutat. 2015 Mar; 10.1002/humu.22791
onlinelibrary.wiley.com
PUBMED
Smith, TD, Vihinen M
Standard development at the Human Variome Project.
Database (2015) Vol. 2015: article ID bav024; doi:10.1093/database/bav024
Database 2015 bav024
PUBMED
Niroula, A, Urolagin, S, Vihinen M
PON-P2: Prediction method for fast and reliable identification of harmful variants.
PLoS ONE 10(2): e0117380. doi:10.1371/journal.pone.0117380
doi:10.1371/journal.pone.0117380
PUBMED
Vihinen M
Types and effects of protein variations.
Hum Genet. 2015 Apr;134(4):405-421
doi: 10.1007/s00439-015-1529-6
PUBMED

Schaafsma GCP, Vihinen M
VariSNP, a benchmark database for variations from dbSNP.
Hum Mutat. 2015 Feb; 36(2):161-166; doi: 10.1002/humu.22727
PUBMED

Deans, AR et al.
Finding our way through phenotypes.
PLoS Biol. 2015 13(1); e1002033 doi: 10.1371/journal.pbio.1002033
PUBMED

2014
 
Vihinen M
Interpreting disease relevance of amino acid substitutions.
In: eLS. John Wiley & Sons, Ltd: Chichester. http://www.els.net doi: 10.1002/9780470015902.a0025177

Vihinen M
Majority vote and other problems when using computational tools.
Hum Mutat. 2014 Aug; 35(8):912-914 doi: 10.1002/humu.22600
PUBMED

Vihinen M
Proper reporting of predictor performance.
Nat Methods. 2014 Jul 30;11(8):781 doi: 10.1038/nmeth.3032
PUBMED

Tiirikka T, Siermala M, Vihinen M
Clustering of gene ontology terms in genomes.
Gene. 2014 Jul 1. pii: S0378-1119(14)00740-9. doi: 10.1016/j.gene.2014.06.060. [Epub ahead of print]
PUBMED

Ali H, Urolagin S, Gurarslan O, Vihinen M
Performance of protein disorder prediction programs on amino acid substitutions.
Hum Mutat. 2014 Apr 21 doi: 10.1002/humu.22564
PUBMED

Ekvall S, Sjörs K, Jonzon A, Vihinen M, Annerén G, Bondeson ML
Novel association of neurofibromatisis type 1-causing mutations in families with neurofibromatosis-Noonan syndrome.
Am J Med Genet A. 2014 Mar;164A(3)579-87
PUBMED

Lee YN, Frugoni F, Dobbs K, Walter JE, Giliani S, Gennery AR, Al-Herz W, Haddad E, LeDeist F, Bleesing JH, Henderson LA, Pai SY, Nelson RP, El-Ghoneimy DH, El-Feky RA, Reda SM, Hossny E, Soler-Palacin P, Fuleihan RL, Patel NC, Massaad MJ, Geha RS, Puck JM, Palma P, Cancrini C, Chen K, Vihinen M, Alt FW, Notarangelo LD
A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency.
J Allergy Clin Immunol. 2014 Apr;133(4)1099-108
PUBMED

Teku G, Ortutay C, Vihinen M
Identification of core T cell network based on immunome interactome.
BMC Syst Biol 2014 Feb 15; 8(1):17
PUBMED

Vihinen M
Variation ontology: annotator guide.
J Biomed Semantics 2014 Feb 17;5(1):9
  PUBMED  

Vihinen M
Variation Ontology for annotation of variation effects and mechanisms.
Genome Res. 2014 Feb;24(2):356-64
  PUBMED  

Vihinen M
Contribution of pseudogenes to sequence diversity.
Methods Mol Biol. 2014;1167:15-24 doi: 10.1007/978-1-4939-0835-6_2
PUBMED

2013
 
Salonen J, Rönnholm G, Kalkkinen N, Vihinen M
Proteomic changes during B cell maturation: 2D-DIGE approach.
PLoS ONE 2013 Oct 29;8(10): e77894
PLoS ONE

Tuohimaa P, Wang J-H, Khan S, Kuuslahti M, Qian K, Manninen T, Auvinen P, Vihinen M, Lou Y-R
Gene Expression Profiles in Human and Mouse Primary Cells Provide New Insights into the Differential Actions of Vitamin D3 Metabolites.
PLoS ONE 2013;8(10): e75338
PLoS ONE

Yang Y, Chen B, Tan G, Vihinen M, Shen B
Structure-based prediction of the effects of a missense variant on protein stability.
Amino Acids. 2013 Mar;44(3):847-55
  PUBMED  

Aspatwar A, Tolvanen ME, Jokitalo E, Parikka M, Ortutay C, Harjula SK, Rämet M, Vihinen M, Parkkila S
Abnormal cerebellar development and ataxia in CARP VIII morphant zebrafish.
Hum Mol Genet. 2013 Feb 1;22(3):417-32
  PUBMED  

Vihinen M
Guidelines for establishing locus specific databases.
Hum Mutat. 2013 Feb;34(2):275-82
  PUBMED  

Sasidharan Nair P, Vihinen M
VariBench: a benchmark database for variations.
Hum Mutat. 2013 Jan;34(1):42-9
  PUBMED  

Kuusisto KM, Akinrinade O, Vihinen M, Kankuri-Tammilehto M, Laasanen SL, Schleutker J
Copy Number Variation Analysis in Familial BRCA1/2-Negative Finnish Breast and Ovarian Cancer.
PLoS ONE 2013;8(8):e71802
  PUBMED  

2012
 
Ali H, Olatubosun A, Vihinen M
Classification of mismatch repair gene missense variants with PON-MMR.
Hum Mutat 2012 Apr;33(4):642-50
  PUBMED  

Byrne M, Fokkema IF, Lancaster O, Adamusiak T, Ahonen-Bishopp A, Atlan D, Béroud C, Cornell M, Dalgleish R, Devereau A, Patrinos GP, Swertz MA, Taschner PE, Thorisson GA, Vihinen M, Brookes AJ, Muilu J
VarioML framework for comprehensive variation data representation and exchange.
BMC Bioinformatics 2012 Oct 3;13:254
  PUBMED  

Celli J, Dalgleish R, Vihinen M, Taschner PE, den Dunnen JT
Curating gene variant databases (LSDBs): toward a universal standard.
Hum Mutat 2012 Feb;33(2):291-7
  PUBMED  

Olatubosun A, Väliaho J, Härkönen J, Thusberg J, Vihinen M
PON-P: Integrated predictor for pathogenicity of missense variants.
Hum Mutat 2012 Aug;33(8):1166-74
  PUBMED  

Ortutay C, Vihinen M
Conserved and quickly evolving immunome genes have different evolutionary paths.
Hum Mutat 2012 Oct;33(10):1456-63
  PUBMED  

Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RG, Rimoin D; International Confederation of Countries Advisory Council.
Human Variome Project country nodes: documenting genetic information within a country.
Hum Mutat 2012 Nov;33(11):1513-9
  PUBMED  

Rasila TS, Vihinen M, Paulin L, Haapa-Paananen S, Savilahti H
Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues.
PLoS ONE 2012;7(5):e37922
  PUBMED  

Teittinen KJ, Kärkkäinen P, Salonen J, Rönnholm G, Korkeamäki H, Vihinen M, Kalkkinen N, Lohi O
Nucleolar proteins with altered expression in leukemic cell lines.
Leuk Res 2012 Feb;36(2):232-6
  PUBMED  

Vihinen M
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis.
BMC Genomics 2012 Jun 18;13 Suppl 4:S2
  PUBMED  

Vihinen M, den Dunnen JT, Dalgleish R, Cotton RG
Guidelines for establishing locus specific databases.
Hum Mutat 2012 Feb;33(2):298-305
  PUBMED  

2011
 
Auerbach AD, Burn J, Cassiman JJ, Claustres M, Cotton RG, Cutting G, den Dunnen JT, El-Ruby M, Vargas AF, Greenblatt MS, Macrae F, Matsubara Y, Rimoin DL, Vihinen M, Van Broeckhoven C
Mutation (variation) databases and registries: a rationale for coordination of efforts.
Nat Rev Genet 2011 ;12(12)881; discussion 881
  PUBMED  

Dalgleish R, Oetting WS, Auerbach AD, Beckmann JS, Cambon-Thomsen A, Devereau A, Greenblatt MS, Patrinos GP, Taylor GR, Vihinen M, Brookes AJ
Clarity and claims in variation/mutation databasing.
Nat Biotechnol 2011 ;29(9)790-2; author reply 792-4
  PUBMED  

Mattila H, Schindler M, Isotalo J, Ikonen T, Vihinen M, Oja H, Tammela TL, Wahlfors T, Schleutker J
NMD and microRNA expression profiling of the HPCX1 locus reveal MAGEC1 as a candidate prostate cancer predisposition gene.
BMC Cancer 2011 ;11327
  PUBMED  

Khanna A, Okkeri J, Bilgen T, Tiirikka T, Vihinen M, Visakorpi T, Westermarck J
ETS1 mediates MEK1/2-dependent overexpression of cancerous inhibitor of protein phosphatase 2A (CIP2A) in human cancer cells.
PLoS ONE 2011 ;6(3)e17979
  PUBMED  

Thusberg J, Olatubosun A, Vihinen M
Performance of mutation pathogenicity prediction methods on missense variants.
Hum Mutat 2011 ;32(4)358-68
  PUBMED  

Kuusisto KM, Bebel A, Vihinen M, Schleutker J, Sallinen SL
Screening for BRCA1, BRCA2, CHEK2, PALB2, BRIP1, RAD50, and CDH1 mutations in high-risk Finnish BRCA1/2-founder mutation-negative breast and/or ovarian cancer individuals.
Breast Cancer Res 2011 ;13(1)R20
  PUBMED  

Laurila K, Vihinen M
PROlocalizer: integrated web service for protein subcellular localization prediction.
Amino Acids 2011 ;40(3)975-80
  PUBMED  

2010
 
Kohonen-Corish MR, Al-Aama JY, Auerbach AD, Axton M, Barash CI, Bernstein I, Béroud C, Burn J, Cunningham F, Cutting GR, den Dunnen JT, Greenblatt MS, Kaput J, Katz M, Lindblom A, Macrae F, Maglott D, Möslein G, Povey S, Ramesar R, Richards S, Seminara D, Sobrido MJ, Tavtigian S, Taylor G, Vihinen M, Winship I, Cotton RG,
How to catch all those mutations--the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010.
Hum Mutat 2010 ;31(12)1374-81
  PUBMED  

Lanzi G, Ferrari S, Vihinen M, Caraffi S, Kutukculer N, Schiaffonati L, Plebani A, Notarangelo LD, Fra AM, Giliani S
Different molecular behavior of CD40 mutants causing hyper-IgM syndrome.
Blood 2010 ;116(26)5867-74
  PUBMED  

Khan S, Vihinen M
Performance of protein stability predictors.
Hum Mutat 2010 ;31(6)675-84
  PUBMED  

Howard HJ, Horaitis O, Cotton RG, Vihinen M, Dalgleish R, Robinson P, Brookes AJ, Axton M, Hoffmann R, Tuffery-Giraud S
The Human Variome Project (HVP) 2009 Forum "Towards Establishing Standards".
Hum Mutat 2010 ;31(3)366-7
  PUBMED  

Jääskeläinen S, Riikonen P, Salakoski T, Vihinen M
Accuracy of protein hydropathy predictions.
Int J Data Min Bioinform 2010 ;4(6)735-54
  PUBMED  

2009
 
Cotton RG, Al Aqeel AI, Al-Mulla F, Carrera P, Claustres M, Ekong R, Hyland VJ, Macrae FA, Marafie MJ, Paalman MH, Patrinos GP, Qi M, Ramesar RS, Scott RJ, Sijmons RH, Sobrido MJ, Vihinen M,
Capturing all disease-causing mutations for clinical and research use: toward an effortless system for the Human Variome Project.
Genet Med 2009 ;11(12)843-9
  PUBMED  

Samarghitean C, Ortutay C, Vihinen M
Systematic classification of primary immunodeficiencies based on clinical, pathological, and laboratory parameters.
J Immunol 2009 ;183(11)7569-75
  PUBMED  

Samarghitean C, Vihinen M
Bioinformatics services related to diagnosis of primary immunodeficiencies.
Curr Opin Allergy Clin Immunol 2009 ;9(6)531-6
  PUBMED  

Qi CJ, Zheng L, Ma HB, Fei M, Qian KQ, Shen BR, Wu CP, Vihinen M, Zhang XG
A novel mutation in CD40 and its functional characterization.
Hum Mutat 2009 ;30(6)985-94
  PUBMED  

Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, Nelson WG, Yegnasubramanian S, Luo J, Wang Y, Xu J, Isaacs WB, Visakorpi T, Bova GS
Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer.
Nat Med 2009 ;15(5)559-65
  PUBMED  

Laurila K, Vihinen M
Prediction of disease-related mutations affecting protein localization.
BMC Genomics 2009 ;10122
  PUBMED  

Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS,
Planning the human variome project: the Spain report.
Hum Mutat 2009 ;30(4)496-510
  PUBMED  

den Dunnen JT, Sijmons RH, Andersen PS, Vihinen M, Beckmann JS, Rossetti S, Talbot CC, Hardison RC, Povey S, Cotton RG
Sharing data between LSDBs and central repositories.
Hum Mutat 2009 ;30(4)493-5
  PUBMED  

Mohamed AJ, Yu L, Bäckesjö CM, Vargas L, Faryal R, Aints A, Christensson B, Berglöf A, Vihinen M, Nore BF, Smith CI
Bruton's tyrosine kinase (Btk): function, regulation, and transformation with special emphasis on the PH domain.
Immunol Rev 2009 ;228(1)58-73
  PUBMED  

Thusberg J, Vihinen M
Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods.
Hum Mutat 2009 ;30(5)703-14
  PUBMED  

Ortutay C, Vihinen M
Immunome knowledge base (IKB): an integrated service for immunome research.
BMC Immunol 2009 ;103
  PUBMED  

Vihinen M
Problems with anti-plagiarism database.
Nature 2009 ;457(7225)26
  PUBMED  

Ortutay C, Vihinen M
Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.
Nucleic Acids Res 2009 ;37(2)622-8
  PUBMED  

Stenberg KA, Vihinen M
Crystal structure of a 1.6-hexanediol bound tetrameric form of Escherichia coli lac-repressor refined to 2.1 A resolution.
Proteins 2009 ;75(3)748-59
  PUBMED  

2008
 
Ortutay C, Nore BF, Vihinen M, Smith CI
Phylogeny of Tec family kinases identification of a premetazoan origin of Btk, Bmx, Itk, Tec, Txk, and the Btk regulator SH3BP5.
Adv Genet 2008 ;6451-80
  PUBMED  

Fan YM, Karhunen PJ, Levula M, Ilveskoski E, Mikkelsson J, Kajander OA, Järvinen O, Oksala N, Thusberg J, Vihinen M, Salenius JP, Kytömäki L, Soini JT, Laaksonen R, Lehtimäki T
Expression of sterol regulatory element-binding transcription factor (SREBF) 2 and SREBF cleavage-activating protein (SCAP) in human atheroma and the association of their allelic variants with sudden cardiac death.
Thromb J 2008 ;617
  PUBMED  

Ahola V, Aittokallio T, Vihinen M, Uusipaikka E
Model-based prediction of sequence alignment quality.
Bioinformatics 2008 ;24(19)2165-71
  PUBMED  

Ortutay C, Vihinen M
PseudoGeneQuest - service for identification of different pseudogene types in the human genome.
BMC Bioinformatics 2008 ;9299
  PUBMED  

Ortutay C, Vihinen M
Efficiency of the immunome protein interaction network increases during evolution.
Immunome Res 2008 ;44
  PUBMED  

Lappalainen I, Thusberg J, Shen B, Vihinen M
Genome wide analysis of pathogenic SH2 domain mutations.
Proteins 2008 ;72(2)779-92
  PUBMED  

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A
Human Proteinpedia enables sharing of human protein data.
Nat Biotechnol 2008 ;26(2)164-7
  PUBMED  

Kivioja T, Tiirikka T, Siermala M, Vihinen M
Dynamic covariation between gene expression and genome characteristics.
Gene 2008 ;410(1)53-66
  PUBMED  

Shen B, Bai J, Vihinen M
Physicochemical feature-based classification of amino acid mutations.
Protein Eng Des Sel 2008 ;21(1)37-44
  PUBMED  

Pärssinen J, Alarmo EL, Khan S, Karhu R, Vihinen M, Kallioniemi A
Identification of differentially expressed genes after PPM1D silencing in breast cancer.
Cancer Lett 2008 ;259(1)61-70
  PUBMED  

Wehr C, Kivioja T, Schmitt C, Ferry B, Witte T, Eren E, Vlkova M, Hernandez M, Detkova D, Bos PR, Poerksen G, von Bernuth H, Baumann U, Goldacker S, Gutenberger S, Schlesier M, Bergeron-van der Cruyssen F, Le Garff M, Debré P, Jacobs R, Jones J, Bateman E, Litzman J, van Hagen PM, Plebani A, Schmidt RE, Thon V, Quinti I, Espanol T, Webster AD, Chapel H, Vihinen M, Oksenhendler E, Peter HH, Warnatz K
The EUROclass trial: defining subgroups in common variable immunodeficiency.
Blood 2008 ;111(1)77-85
  PUBMED  

2007
 
Rannikko K, Ortutay C, Vihinen M
Immunity genes and their orthologs: a multi-species database.
Int Immunol 2007 ;19(12)1361-70
  PUBMED  

Khan S, Vihinen M
Spectrum of disease-causing mutations in protein secondary structures.
BMC Struct Biol 2007 ;756
  PUBMED  

Pajunen M, Turakainen H, Poussu E, Peränen J, Vihinen M, Savilahti H
High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.
Nucleic Acids Res 2007 ;35(16)e103
  PUBMED  

Ollila J, Vihinen M
Immunological systems biology: gene expression analysis of B-cell development in Ramos B-cells.
Mol Immunol 2007 ;44(14)3537-51
  PUBMED  

Samarghitean C, Väliaho J, Vihinen M
IDR knowledge base for primary immunodeficiencies.
Immunome Res 2007 ;36
  PUBMED  

Ortutay C, Siermala M, Vihinen M
ImmTree: database of evolutionary relationships of genes and proteins in the human immune system.
Immunome Res 2007 ;34
  PUBMED  

Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, Chui D, Scriver C, Phommarinh M, Patnaik SK, Blumenfeld O, Gottlieb B, Vihinen M, Väliaho J, Kent J, Miller W, Hardison RC
PhenCode: connecting ENCODE data with mutations and phenotype.
Hum Mutat 2007 ;28(6)554-62
  PUBMED  

Ortutay C, Siermala M, Vihinen M
Molecular characterization of the immune system: emergence of proteins, processes, and domains.
Immunogenetics 2007 ;59(5)333-48
  PUBMED  

2006
 
Ortutay C, Vihinen M
Immunome: a reference set of genes and proteins for systems biology of the human immune system.
Cell Immunol 2006 ;244(2)87-9
  PUBMED  

Ahola V, Aittokallio T, Vihinen M, Uusipaikka E
A statistical score for assessing the quality of multiple sequence alignments.
BMC Bioinformatics 2006 ;7484
  PUBMED  

Piirilä H, Väliaho J, Vihinen M
Immunodeficiency mutation databases (IDbases).
Hum Mutat 2006 ;27(12)1200-8
  PUBMED  

Thusberg J, Vihinen M
Bioinformatic analysis of protein structure-function relationships: case study of leukocyte elastase (ELA2) missense mutations.
Hum Mutat 2006 ;27(12)1230-43
  PUBMED  

Väliaho J, Smith CI, Vihinen M
BTKbase: the mutation database for X-linked agammaglobulinemia.
Hum Mutat 2006 ;27(12)1209-17
  PUBMED  

Salonen JM, Valmu L, Rönnholm G, Kalkkinen N, Vihinen M
Proteome analysis of B-cell maturation.
Proteomics 2006 ;6(19)5152-68
  PUBMED  

Mononen N, Seppälä EH, Duggal P, Autio V, Ikonen T, Ellonen P, Saharinen J, Saarela J, Vihinen M, Tammela TL, Kallioniemi O, Bailey-Wilson JE, Schleutker J
Profiling genetic variation along the androgen biosynthesis and metabolism pathways implicates several single nucleotide polymorphisms and their combinations as prostate cancer risk factors.
Cancer Res 2006 ;66(2)743-7
  PUBMED  

2005
 
Sharabiani MT, Siermala M, Lehtinen TO, Vihinen M
Dynamic covariation between gene expression and proteome characteristics.
BMC Bioinformatics 2005 ;6215
  PUBMED  

Hilvo M, Tolvanen M, Clark A, Shen B, Shah GN, Waheed A, Halmi P, Hänninen M, Hämäläinen JM, Vihinen M, Sly WS, Parkkila S
Characterization of CA XV, a new GPI-anchored form of carbonic anhydrase.
Biochem J 2005 ;392(Pt 1)83-92
  PUBMED  

Hyyrö H, Juhola M, Vihinen M
Genome-wide selection of unique and valid oligonucleotides.
Nucleic Acids Res 2005 ;33(13)e115
  PUBMED  

Väliaho J, Riikonen P, Vihinen M
Distribution of immunodeficiency fact files with XML--from Web to WAP.
BMC Med Inform Decis Mak 2005 ;521
  PUBMED  

Ortutay C, Väliaho J, Stenberg K, Vihinen M
KinMutBase: a registry of disease-causing mutations in protein kinase domains.
Hum Mutat 2005 ;25(5)435-42
  PUBMED  

Lindvall JM, Blomberg KE, Väliaho J, Vargas L, Heinonen JE, Berglöf A, Mohamed AJ, Nore BF, Vihinen M, Smith CI
Bruton's tyrosine kinase: cell biology, sequence conservation, mutation spectrum, siRNA modifications, and expression profiling.
Immunol Rev 2005 ;203200-15
  PUBMED  

Ollila J, Vihinen M
B cells.
Int J Biochem Cell Biol 2005 ;37(3)518-23
  PUBMED  

Hyyrö H, Juhola M, Vihinen M
On exact string matching of unique oligonucleotides.
Comput Biol Med 2005 ;35(2)173-81
  PUBMED  

2004
 
Ahola V, Aittokallio T, Uusipaikka E, Vihinen M
Statistical methods for identifying conserved residues in multiple sequence alignment.
Stat Appl Genet Mol Biol 2004 ;3Article28
  PUBMED  

Giurcăneanu CD, Tăbuş I, Astola J, Ollila J, Vihinen M
Fast iterative gene clustering based on information theoretic criteria for selecting the cluster structure.
J Comput Biol 2004 ;11(4)660-82
  PUBMED  

Ferrer A, Ollila J, Tobin G, Nagy B, Thunberg U, Aalto Y, Vihinen M, Vilpo J, Rosenquist R, Knuutila S
Different gene expression in immunoglobulin-mutated and immunoglobulin-unmutated forms of chronic lymphocytic leukemia.
Cancer Genet Cytogenet 2004 ;153(1)69-72
  PUBMED  

Shen B, Vihinen M
Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain.
Protein Eng Des Sel 2004 ;17(3)267-76
  PUBMED  

Poussu E, Vihinen M, Paulin L, Savilahti H
Probing the alpha-complementing domain of E. coli beta-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition.
Proteins 2004 ;54(4)681-92
  PUBMED  

Samarghitean C, Väliaho J, Vihinen M
Online registry of genetic and clinical immunodeficiency diagnostic laboratories, IDdiagnostics.
J Clin Immunol 2004 ;24(1)53-61
  PUBMED  

Vitikainen M, Lappalainen I, Seppala R, Antelmann H, Boer H, Taira S, Savilahti H, Hecker M, Vihinen M, Sarvas M, Kontinen VP
Structure-function analysis of PrsA reveals roles for the parvulin-like and flanking N- and C-terminal domains in protein folding and secretion in Bacillus subtilis.
J Biol Chem 2004 ;279(18)19302-14
  PUBMED  

Halonen M, Kangas H, Rüppell T, Ilmarinen T, Ollila J, Kolmer M, Vihinen M, Palvimo J, Saarela J, Ulmanen I, Eskelin P
APECED-causing mutations in AIRE reveal the functional domains of the protein.
Hum Mutat 2004 ;23(3)245-57
  PUBMED  

Lehtonen J, Shen B, Vihinen M, Casini A, Scozzafava A, Supuran CT, Parkkila AK, Saarnio J, Kivelä AJ, Waheed A, Sly WS, Parkkila S
Characterization of CA XIII, a novel member of the carbonic anhydrase isozyme family.
J Biol Chem 2004 ;279(4)2719-27
  PUBMED  

2003
 
Vihinen M
Signal transduction-related bioinformatics services.
Brief Bioinform 2003 ;4(4)325-31
  PUBMED  

Ahola V, Aittokallio T, Uusipaikka E, Vihinen M
Efficient estimation of emission probabilities in profile hidden Markov models.
Bioinformatics 2003 ;19(18)2359-68
  PUBMED  

Shen B, Vihinen M
RankViaContact: ranking and visualization of amino acid contacts.
Bioinformatics 2003 ;19(16)2161-2
  PUBMED  

Casas S, Ollila J, Aventín A, Vihinen M, Sierra J, Knuutila S
Changes in apoptosis-related pathways in acute myelocytic leukemia.
Cancer Genet Cytogenet 2003 ;146(2)89-101
  PUBMED  

Saharinen P, Vihinen M, Silvennoinen O
Autoinhibition of Jak2 tyrosine kinase is dependent on specific regions in its pseudokinase domain.
Mol Biol Cell 2003 ;14(4)1448-59
  PUBMED  

2002
 
Lappalainen I, Vihinen M
Structural basis of ICF-causing mutations in the methyltransferase domain of DNMT3B.
Protein Eng 2002 ;15(12)1005-14
  PUBMED  

Riikonen P, Boberg J, Salakoski T, Vihinen M
Mobile access to biological databases on the Internet.
IEEE Trans Biomed Eng 2002 ;49(12)1477-9
  PUBMED  

Okoh MP, Kainulainen L, Heiskanen K, Isa MN, Varming K, Ruuskanen O, Vihinen M
Novel insertions of Bruton tyrosine kinase in patients with X-linked agammaglobulinemia.
Hum Mutat 2002 ;20(6)480-1
  PUBMED  

Hyytinen ER, Haapala K, Thompson J, Lappalainen I, Roiha M, Rantala I, Helin HJ, Jänne OA, Vihinen M, Palvimo JJ, Koivisto PA
Pattern of somatic androgen receptor gene mutations in patients with hormone-refractory prostate cancer.
Lab Invest 2002 ;82(11)1591-8
  PUBMED  

Larramendy ML, Niini T, Elonen E, Nagy B, Ollila J, Vihinen M, Knuutila S
Overexpression of translocation-associated fusion genes of FGFRI, MYC, NPMI, and DEK, but absence of the translocations in acute myeloid leukemia. A microarray analysis.
Haematologica 2002 ;87(6)569-77
  PUBMED  

Ollila J, Vihinen M
Microarray analysis of B-cell stimulation.
Vitam Horm 2002 ;6477-99
  PUBMED  

Okoh MP, Vihinen M
Interaction between Btk TH and SH3 domain.
Biopolymers 2002 ;63(5)325-34
  PUBMED  

Väliaho J, Pusa M, Ylinen T, Vihinen M
IDR: the ImmunoDeficiency Resource.
Nucleic Acids Res 2002 ;30(1)232-4
  PUBMED  

Home

Databases:
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ImmunoDeficiency Resource (IDR)
Immunome Knowledge Base (IKB)
GOme

Bioinformatics services:
B-Cell Proteome
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PPSC
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VariO
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HVP Guidelines
Guidelines for prediction tools
Curating gene variant databases
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Recommendations for LSDBs

Research:
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Links:
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