Selected Publications

Full list at Google scholar

Kabir, Muhammad; Ahmed, Saeed; Zhang, Haoyang; Rodríguez-Rodríguez, Ignacio; Najibi, Seyed Morteza; Vihinen, M. PON-P3: Accurate Prediction of Pathogenicity of Amino Acid Substitutions. International Journal of Molecular Sciences. 2025.
Johansson, Josefin; Lidéus, Sarah; Frykholm, Carina; Gunnarsson, Cecilia; Mihalic, Filip; Gudmundsson, Sanna; Ekvall, Sara; Molin, Anna-Maja; Pham, Mai; Vihinen, M. Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions. European Journal of Human Genetics. 2024.
Zhang, Haoyang; Kabir, Muhammad; Ahmed, Saeed; Vihinen, M. There will always be variants of uncertain significance. Analysis of VUSs. NAR Genomics and Bioinformatics. 2024.
Schaafsma, Gerard CP; Väliaho, Jouni; Wang, Qing; Berglöf, Anna; Zain, Rula; Smith, CI Edvard; Vihinen, M. BTKbase, Bruton Tyrosine Kinase Variant Database in X‐Linked Agammaglobulinemia: Looking Back and Ahead. Human Mutation. 2023.
Vihinen, M. Nonsynonymous synonymous variants demand for a paradigm shift in genetics. Current Genomics. 2023.
Yang, Yang; Chong, Zhang; Vihinen, M. PON-Fold: prediction of substitutions affecting protein folding rate. International Journal of Molecular Sciences. 2023.
Vihinen, M. Systematic errors in annotations of truncations, loss-of-function and synonymous variants. Frontiers in Genetics. 2023.
Shirvanizadeh, Niloofar; Vihinen, M. VariBench, new variation benchmark categories and data sets. Frontiers in Bioinformatics. 2023.
Mauno, Vihinen. Generic model for biological regulation. F1000Research. 2022.
Vihinen, M. Generic model for biological regulation. F1000Research. 2022.
Vihinen, M. Individual genetic heterogeneity. Genes. 2022.
Yang, Yang; Shao, Aibin; Vihinen, M. PON-All: Amino Acid Substitution Tolerance Predictor for All Organisms. Frontiers in Molecular Biosciences. 2022.
Yang, Yang; Zhao, Jianjun; Zeng, Lianjie; Vihinen, M. ProTstab2 for prediction of protein thermal stabilities. International journal of molecular sciences. 2022.
Vihinen, M. When a synonymous variant is nonsynonymous. Genes. 2022.
Vihinen, M. Functional effects of protein variants. Biochimie. 2021.
Vihinen, M. Guidelines for reporting protein modelling studies. Authorea Preprints. 2021.
Vihinen, M. Measuring and interpreting pervasive heterogeneity, poikilosis. FASEB BioAdvances. 2021.
Yang, Yang; Zeng, Lianjie; Vihinen, M. PON-Sol2: Prediction of effects of variants on protein solubility. International Journal of Molecular Sciences. 2021.
Zain, Rula; Vihinen, M. Structure-function relationships of covalent and non-covalent BTK inhibitors. Frontiers in immunology. 2021.
Vihinen, M. Guidelines for systematic reporting of sequence alignments. Biology Methods and Protocols. 2020.
Vihinen, M. Poikilosis–pervasive biological variation. F1000Research. 2020.
Vihinen, M. Problems in variation interpretation guidelines and in their implementation in computational tools. Molecular Genetics & Genomic Medicine. 2020.
Vihinen, M. Solubility of proteins. ADMET and DMPK. 2020.
Vihinen, M. Strategy for Disease Diagnosis, Progression Prediction, Risk Group Stratification and Treatment—Case of COVID-19. Frontiers in Medicine. 2020.
Sarkar, Anasua; Yang, Yang; Vihinen, M. Variation benchmark datasets: update, criteria, quality and applications. Database. 2020.
Orioli, Tommaso; Vihinen, M. Benchmarking subcellular localization and variant tolerance predictors on membrane proteins. BMC genomics. 2019.
Ekong, Rosemary; Vihinen, M. Checklist for gene/disease‐specific variation database curators to enable ethical data management. Human Mutation. 2019.
Niroula, Abhishek; Vihinen, M. How good are pathogenicity predictors in detecting benign variants?. PLoS computational biology. 2019.
Niroula, A; Orioli, T; Vihinen, M. How good are variant pathogenicity predictors?. EUROPEAN JOURNAL OF HUMAN GENETICS. 2019.
Yang, Yang; Ding, Xuesong; Zhu, Guanchen; Niroula, Abhishek; Lv, Qiang; Vihinen, M. ProTstab–predictor for cellular protein stability. BMC genomics. 2019.
Teku, Gabriel N; Vihinen, M. Pan-cancer analysis of neoepitopes. Scientific Reports. 2018.
Yang, Yang; Urolagin, Siddhaling; Niroula, Abhishek; Ding, Xuesong; Shen, Bairong; Vihinen, M. PON-tstab: protein variant stability predictor. Importance of training data quality. International journal of molecular sciences. 2018.
Schaafsma, Gerard CP; Vihinen, M. Representativeness of variation benchmark datasets. BMC bioinformatics. 2018.
Teku, Gabriel Ndipagbornchi; Vihinen, M. Simulation of the dynamics of primary immunodeficiencies in B cells. Frontiers in Immunology. 2018.
Vihinen, M. Systematics for types and effects of DNA variations. BMC genomics. 2018.
Vihinen, M. How to define pathogenicity, health, and disease?. Human mutation. 2017.
Schaafsma, Gerard CP; Vihinen, M. Large differences in proportions of harmful and benign amino acid substitutions between proteins and diseases. Human mutation. 2017.
Vihinen, M. One Gene, Several Diseases: The Characteristics of Pleiotropic Proteins. Human Mutation. 2017.
Niroula, Abhishek; Vihinen, M. PON‐P and PON‐P2 predictor performance in CAGI challenges: Lessons learned. Human mutation. 2017.
Čalyševa, Jelena; Vihinen, M. PON-SC–program for identifying steric clashes caused by amino acid substitutions. BMC bioinformatics. 2017.
Niroula, Abhishek; Vihinen, M. Predicting severity of disease‐causing variants. Human mutation. 2017.
Teku, Gabriel N; Vihinen, M. Simulation of the dynamics of primary immunodeficiencies in CD4+ T-cells. Plos one. 2017.
Vihinen, M. Both Generic and Protein‐Specific Tolerance Predictors Are Needed. Human Mutation. 2016.
Vihinen, M. Establishment of an international database for genetic variants in esophageal cancer. Annals of the New York Academy of Sciences. 2016.
Vihinen, M; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard CP; Taschner, Peter. Human variome project quality assessment criteria for variation databases. Human Mutation. 2016.
Niroula, Abhishek; Vihinen, M. PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations. Nucleic acids research. 2016.
Yang, Yang; Niroula, Abhishek; Shen, Bairong; Vihinen, M. PON-Sol: prediction of effects of amino acid substitutions on protein solubility. Bioinformatics. 2016.
Niroula, Abhishek; Vihinen, M. Variation interpretation predictors: principles, types, performance, and choice. Human mutation. 2016.
Schaafsma, Gerard CP; Vihinen, M. VariOtator, a software tool for variation annotation with the variation ontology. Human Mutation. 2016.
Väliaho, Jouni; Faisal, Imrul; Ortutay, Csaba; Smith, CI Edvard; Vihinen, M. Characterization of all possible single‐nucleotide change caused amino acid substitutions in the kinase domain of Bruton tyrosine kinase. Human Mutation. 2015.
Niroula, Abhishek; Vihinen, M. Classification of amino acid substitutions in mismatch repair proteins using PON‐MMR2. Human mutation. 2015.
Schaafsma, Gerard CP; Vihinen, M. Genetic variation in Bruton tyrosine kinase. Agammaglobulinemia. 2015.
Niroula, Abhishek; Vihinen, M. Harmful somatic amino acid substitutions affect key pathways in cancers. BMC medical genomics. 2015.
Vihinen, M. Immunodeficiency, primary: affecting the adaptive immune system. eLS. 2015.
Vihinen, M. Muddled genetic terms miss and mess the message. Trends in Genetics. 2015.
Vihinen, M. No more hidden solutions in bioinformatics. Nature. 2015.
Niroula, Abhishek; Urolagin, Siddhaling; Vihinen, M. PON-P2: prediction method for fast and reliable identification of harmful variants. PloS one. 2015.
Smith, Timothy D; Vihinen, M. Standard development at the human Variome project. Database. 2015.
Vihinen, M. The importance of proper testing of predictor performance. Human Mutation. 2015.
Vihinen, M. Types and effects of protein variations. Human Genetics. 2015.
Schaafsma, Gerard CP; Vihinen, M. V ari SNP, a benchmark database for variations from db SNP. Human mutation. 2015.
Tiirikka, Timo; Siermala, Markku; Vihinen, M. Clustering of gene ontology terms in genomes. Gene. 2014.
Vihinen, M. Contribution of pseudogenes to sequence diversity. Pseudogenes: Functions and Protocols. 2014.
Teku, Gabriel N; Ortutay, Csaba; Vihinen, M. Identification of core T cell network based on immunome interactome. BMC systems biology. 2014.
Vihinen, M. Interpreting Disease Relevance of Amino Acid Substitutions. eLS. 2014.
Vihinen, M. Majority vote and other problems when using computational tools. Human Mutation. 2014.
Ali, Heidi; Urolagin, Siddhaling; Gurarslan, Ömer; Vihinen, M. Performance of protein disorder prediction programs on amino acid substitutions. Human mutation. 2014.
Vihinen, M. Proper reporting of predictor performance.. nature methods. 2014.
Vihinen, M. Variation Ontology for annotation of variation effects and mechanisms. Genome research. 2014.
Vihinen, M. Variation ontology: annotator guide. Journal of Biomedical Semantics. 2014.
Vihinen, M. Guidelines for reporting and using prediction tools for genetic variation analysis. Human mutation. 2013.
Vihinen, M. Making Sense of Unclassified Missense Substitutions in MMR Genes. Human Mutation. 2013.
Salonen, Johanna; Rönnholm, Gunilla; Kalkkinen, Nisse; Vihinen, M. Proteomic changes during B cell maturation: 2D-DIGE approach. PLoS One. 2013.
Nair, Preethy Sasidharan; Vihinen, M. V ari b ench: A benchmark database for variations. Human mutation. 2013.
Ali, Heidi; Olatubosun, Ayodeji; Vihinen, M. Classification of mismatch repair gene missense variants with PON‐MMR. Human Mutation. 2012.
Ortutay, Csaba; Vihinen, M. Conserved and quickly evolving immunome genes have different evolutionary paths. Human mutation. 2012.
Vihinen, M; den Dunnen, Johan T; Dalgleish, Raymond; Cotton, Richard GH. Guidelines for establishing locus specific databases. Human mutation. 2012.
Vihinen, M. How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. BMC genomics. 2012.
Samarghitean, C; Iltanen, K; Helminen, M; Vihinen, M. PIDEXPERT-DECISION SUPPORT SYSTEM FOR PRIMARY IMMUNODEFICIENCIES-AN UPDATE. JOURNAL OF CLINICAL IMMUNOLOGY. 2012.
Olatubosun, Ayodeji; Väliaho, Jouni; Härkönen, Jani; Thusberg, Janita; Vihinen, M. PON‐P: Integrated predictor for pathogenicity of missense variants. Human mutation. 2012.
Klein, Artjom; Riazanov, Alexandre; Al-Rababah, Khaleel; Baker, CJ; Vihinen, M. Towards a next generation protein mutation grounding system for full texts. Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine. 2012.
Dalgleish, Raymond; Oetting, William S; Auerbach, Arleen D; Beckmann, Jacques S; Cambon-Thomsen, Anne; Devereau, Andrew; Greenblatt, Marc S; Patrinos, George P; Taylor, Graham R; Vihinen, M. Clarity and claims in variation/mutation databasing. Nature biotechnology. 2011.
Thusberg, Janita; Olatubosun, Ayodeji; Vihinen, M. Performance of mutation pathogenicity prediction methods on missense variants. Human mutation. 2011.
Samarghitean, Crina; Ortutay, Csaba; Vihinen, M. Primary Immunodeficiencies Network. SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2011.
Laurila, Kirsti; Vihinen, M. PROlocalizer: integrated web service for protein subcellular localization prediction. Amino Acids. 2011.
Jaaskelainen, Satu; Riikonen, Pentti; Salakoski, Tapio; Vihinen, M. Accuracy of protein hydropathy predictions. International journal of data mining and bioinformatics. 2010.
Khan, Sofia; Vihinen, M. Performance of protein stability predictors. Human mutation. 2010.
Samarghitean, Crina; Vihinen, M. Bioinformatics services related to diagnosis of primary immunodeficiencies. Current opinion in allergy and clinical immunology. 2009.
Stenberg, Kaj AE; Vihinen, M. Crystal structure of a 1.6‐hexanediol bound tetrameric form of Escherichia coli Lac‐repressor refined to 2.1 Å resolution. Proteins: Structure, Function, and Bioinformatics. 2009.
Khan, S; Vihinen, M. Evaluation of accuracy and applicability of protein models: retrospective analysis of biological and biomadical predictions. In Silico Biology. An International Journal On Computational Molecular Medicine. 2009.
Khan, Sofia; Vihinen, M. Evaluation of accuracy and applicability of protein models: Retrospective analysis of biological and biomedical predictions. In silico biology. 2009.
Ortutay, Csaba; Vihinen, M. Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies. Nucleic acids research. 2009.
Vihinen, M. Immunodeficiencies and Immunome: Diseases and Information Services. Clinical Applications of Immunomics. 2009.
Ortutay, Csaba; Vihinen, M. Immunome knowledge base (IKB): an integrated service for immunome research. BMC immunology. 2009.
Thusberg, Janita; Vihinen, M. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Human mutation. 2009.
Laurila, Kirsti; Vihinen, M. Prediction of disease-related mutations affecting protein localization. BMC genomics. 2009.
Vihinen, M. Problems with anti-plagiarism database. Nature. 2009.
Samarghitean, Crina; Ortutay, Csaba; Vihinen, M. Systematic classification of primary immunodeficiencies based on clinical, pathological, and laboratory parameters. The Journal of Immunology. 2009.
Kivioja, Teemu; Tiirikka, Timo; Siermala, Markku; Vihinen, M. Dynamic covariation between gene expression and genome characteristics. Gene. 2008.
Ortutay, Csaba; Vihinen, M. Efficiency of the immunome protein interaction network increases during evolution. Immunome Research. 2008.
Fan, Yue-Mei; Karhunen, Pekka J; Levula, Mari; Ilveskoski, Erkki; Mikkelsson, Jussi; Kajander, Olli A; Järvinen, Otso; Oksala, Niku; Thusberg, Janita; Vihinen, M. 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. Thrombosis Journal. 2008.
Lappalainen, Ilkka; Thusberg, Janita; Shen, Bairong; Vihinen, M. Genome wide analysis of pathogenic SH2 domain mutations. Proteins: Structure, Function, and Bioinformatics. 2008.
Samarghitean, C; Valiaho, J; Vihinen, M. IDdiagnostics-database for genetic and clinical test laboratories on primary immunodeficiencies, an update. CLINICAL AND EXPERIMENTAL IMMUNOLOGY. 2008.
Samarghitean, C; Valiaho, J; Vihinen, M. IDR knowledge for primary immunodeficiencies an update. CLINICAL AND EXPERIMENTAL IMMUNOLOGY. 2008.
Valiaho, J; Vihinen, M. Immunodeficiency mutation databases (IDbases) review. CLINICAL AND EXPERIMENTAL IMMUNOLOGY. 2008.
Vihinen, M; Samarghitean, Crina. Medical expert systems. Current Bioinformatics. 2008.
Riikonen, Pentti; Vihinen, M. National research contributions: A case study on Finnish biomedical research. Scientometrics. 2008.
Samarghitean, C; Ortutay, C; Vihinen, M. New classification of primary immunodeficiencies. CLINICAL AND EXPERIMENTAL IMMUNOLOGY. 2008.
Shen, Bairong; Bai, Jinwei; Vihinen, M. Physicochemical feature-based classification of amino acid mutations. Protein Engineering, Design & Selection. 2008.
Samarghitean, Crina; Iltanen, Kati; Varpa, Kirsi; Helminen, Merja; Juhola, Martti; Vihinen, M. PIDexpert-decision support system for primary immunodeficiencies. CLINICAL AND EXPERIMENTAL IMMUNOLOGY. 2008.
Ortutay, Csaba; Vihinen, M. PseudoGeneQuest–Service for identification of different pseudogene types in the human genome. BMC bioinformatics. 2008.
Jaaskelainen, Satu; Riikonen, Pentti; Salakoski, Tapio; Vihinen, M. Evaluation of protein hydropathy scales. 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007). 2007.
Samarghitean, Crina; Väliaho, Jouni; Vihinen, M. IDR knowledge base for primary immunodeficiencies. Immunome research. 2007.
Ortutay, Csaba; Siermala, Markku; Vihinen, M. ImmTree: database of evolutionary relationships of genes and proteins in the human immune system. Immunome Research. 2007.
Rannikko, Kathryn; Ortutay, Csaba; Vihinen, M. Immunity genes and their orthologs: a multi-species database. International immunology. 2007.
Ollila, Juha; Vihinen, M. Immunological systems biology: gene expression analysis of B-cell development in Ramos B-cells. Molecular immunology. 2007.
Ortutay, Csaba; Siermala, Markku; Rannikko, Kathryn; Vihinen, M. Immunome, Immtree and Immunity: Databases for Systems Biology of Immune System. 2007 IEEE International Workshop on Genomic Signal Processing and Statistics. 2007.
Ortutay, Csaba; Siermala, Markku; Vihinen, M. Molecular characterization of the immune system: emergence of proteins, processes, and domains. Immunogenetics. 2007.
Khan, Sofia; Vihinen, M. Spectrum of disease-causing mutations in protein secondary structures. BMC Structural Biology. 2007.
Thusberg, J; Vihinen, M. The structural basis of hyper IgM deficiency–CD40L mutations. Protein Engineering, Design & Selection. 2007.
Thusberg, Janita; Vihinen, M. Bioinformatic analysis of protein structure–function relationships: case study of leukocyte elastase (ELA2) missense mutations. Human mutation. 2006.
Vihinen, M. BIOINFORMATICS ON POST GENOMIC ERA: FROM GENOMES TO SYSTEMS BIOLOGY. Biotechnology,[Eds. Horst W. Doelle, Stefan Rokem, Marin Berovic], in Encyclopedia of Life Support Systems (EOLSS). Developed under the Auspices of the UNESCO, Eolss Publishers, Oxford, UK,[http: www. eolss. net]. 2006.
Väliaho, Jouni; Smith, CI Edvard; Vihinen, M. BTKbase: the mutation database for X‐linked agammaglobulinemia. Human mutation. 2006.
Vihinen, M. Focus on immunogenetics: diagnosis, molecular genetics, mutations, and diseases. Human Mutation. 2006.
Samarghitean, C; Väliaho, J; Piirilä, H; Pusa, M; Vihinen, M. Immunodeficiency information services. Primary immunodeficiency diseases. 2006.
Piirilä, Hilkka; Väliaho, Jouni; Vihinen, M. Immunodeficiency mutation databases (IDbases). Human mutation. 2006.
Ortutay, Csaba; Vihinen, M. Immunome: a reference set of genes and proteins for systems biology of the human immune system. Cellular immunology. 2006.
Ortutay, Csaba; Siermala, Markku; Vihinen, M. IMMUNOME: COLLECTION OF GENES AND PROTEINS FOR SYSTEMS BIOLOGICAL STUDIES ON HUMAN IMMUNE SYSTEM. 4th TICSP WORKSHOP ON COMPUTATIONAL SYSTEMS BIOLOGY, WCSB 2006. 2006.
Vihinen, M; Durandy, Anne. Primary immunodeficiencies: genotype–phenotype correlations. Immunogenetics and human disease. Hoboken, NJ: John Wiley & Sons. p. 2006.
Salonen, Johanna M; Valmu, Leena; Rönnholm, Gunilla; Kalkkinen, Nisse; Vihinen, M. Proteome analysis of B‐cell maturation. Proteomics. 2006.
Kim, Chang Sik; Salakoski, Tapio; Vihinen, M. Reverse engineering for gene regulatory networks by Bayesian orthogonal least squares (BOLS) algorithm. 2006 IEEE International Workshop on Genomic Signal Processing and Statistics. 2006.
Vihinen, M; Smith, CI Edvard. Authors’ addresses Jessica M. Lindvall1 K. Emelie M. Blomberg1 Jouni Väliaho2 Leonardo Vargas1 Juhana E. Heinonen1 Anna Berglöf1 Abdalla J. Mohamed1 Beston F. Nore1. Immunological Reviews. 2005.
Ollila, Juha; Vihinen, M. B cells. The international journal of biochemistry & cell biology. 2005.
Hilvo, Mika; Tolvanen, Martti; Clark, Amy; Shen, Bairong; Shah, Gul N; Waheed, Abdul; Halmi, Piia; Hänninen, Milla; Hämäläinen, Jonna M; Vihinen, M. Characterization of CA XV, a new GPI-anchored form of carbonic anhydrase. Biochemical journal. 2005.
Väliaho, Jouni; Riikonen, Pentti; Vihinen, M. Distribution of immunodeficiency fact files with XML–from Web to WAP. BMC Medical Informatics and Decision Making. 2005.
Sharabiani, Mansour Taghavi Azar; Siermala, Markku; Lehtinen, Tommi O; Vihinen, M. Dynamic covariation between gene expression and proteome characteristics. Bmc Bioinformatics. 2005.
Hyyrö, Heikki; Juhola, Martti; Vihinen, M. Genome-wide selection of unique and valid oligonucleotides. Nucleic Acids Research. 2005.
Piirilä, Hilkka; Samarghitean, Crina; Väliaho, Jouni; Vihinen, M. Immunodeficiency information services. Central European Journal of Immunology. 2005.
Ortutay, Csaba; Väliaho, Jouni; Stenberg, Kaj; Vihinen, M. KinMutBase: a registry of disease‐causing mutations in protein kinase domains. Human mutation. 2005.
Hyyrö, Heikki; Juhola, Martti; Vihinen, M. On exact string matching of unique oligonucleotides. Computers in Biology and Medicine. 2005.
Shen, Bairong; 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 Engineering Design and Selection. 2004.
Giurcărneanu, Ciprian Doru; Tăbuş, Ioan; Astola, Jaakko; Ollila, Juha; Vihinen, M. Fast iterative gene clustering based on information theoretic criteria for selecting the cluster structure. Journal of Computational Biology. 2004.
Vihinen, M; Tolvanen, Martti. Fjärrinlärning i bioinformatik. FINSKA LÄKARESÄLLSKAPETS HANDLINGAR. 2004.
Vihinen, M. Immunodeficiencies-From genotype to phenotype. TISSUE ANTIGENS. 2004.
Samarghitean, Crina; Väliaho, Jouni; Vihinen, M. Online registry of genetic and clinical immunodeficiency diagnostic laboratories, IDdiagnostics. Journal of Clinical Immunology. 2004.
Ahola, Virpi; Aittokallio, Tero; Uusipaikka, Esa; Vihinen, M. Statistical methods for identifying conserved residues in multiple sequence alignment. Statistical applications in genetics and molecular biology. 2004.
Vihinen, M. The diverse genetic basis. Susceptibility to infectious diseases: the importance of host genetics. 2004.
Tolvanen, Martti; Vihinen, M. Virtual bioinformatics distance learning suite. Biochemistry and Molecular Biology Education. 2004.
Vihinen, M. Bioinformatics in proteomics. Handbook of Proteomic Methods. 2003.
Ahola, Virpi; Aittokallio, Tero; Uusipaikka, Esa; Vihinen, M. Efficient estimation of emission probabilities in profile hidden Markov models. Bioinformatics. 2003.
Siermala, Markku; Juhola, Martti; Vihinen, M. On postprocessing of neural network prediction of polyproline type II secondary structures: network spectrum, response analysis, and scattering. Neural Computing & Applications. 2003.
Shen, Bairong; Vihinen, M. RankViaContact: ranking and visualization of amino acid contacts. Bioinformatics. 2003.
Vihinen, M. Signal transduction-related bioinformatics services. Briefings in bioinformatics. 2003.
Ollila, J; Vihinen, M. Stimulation-induced gene expression in Ramos B-cells. Genes & Immunity. 2003.
Väliaho, Jouni; Pusa, Marianne; Ylinen, Tuomo; Vihinen, M. IDR: the immunodeficiency resource. Nucleic acids research. 2002.
Okoh, Michael P; Vihinen, M. Interaction between Btk TH and SH3 domain. Biopolymers: Original Research on Biomolecules. 2002.
Ollila, Juha; Vihinen, M. Microarray analysis of B-cell stimulation. Vitam Horm. 2002.
Riikonen, Pentti; Boberg, Jorma; Salakoski, Tapio; Vihinen, M. Mobile access to biological databases on the Internet. IEEE transactions on biomedical engineering. 2002.
Okoh, Michael P; Kainulainen, Leena; Heiskanen, Kaarina; Isa, M Nizam; Varming, Kim; Ruuskanen, Olli; Vihinen, M. Novel insertions of Bruton tyrosine kinase in patients with X‐linked agammaglobulinemia. Human Mutation. 2002.
Lappalainen, Ilkka; Vihinen, M. Structural basis of ICF-causing mutations in the methyltransferase domain of DNMT3B. Protein engineering. 2002.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarström, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lähdesmäki, Aleksi. 4 Primary immunodeficiency mutation databases. Advances in Genetics. 2001.
Siermala, Markku; Juhola, Martti; Vihinen, M. Binary vector or real value coding for secondary structure prediction? A case study of polyproline type II prediction. Medical Data Analysis: Second International Symposium, ISMDA 2001 Madrid, Spain, October 8–9, 2001 Proceedings 2. 2001.
Vihinen, M. Bioinformatics in proteomics. Biomolecular engineering. 2001.
Riikonen, Pentti; Boberg, Jorma; Salakoski, Tapio; Vihinen, M. BioWAP, mobile Internet service for bioinformatics. Bioinformatics. 2001.
Nars, Martin; Vihinen, M. Coevolution of the domains of cytoplasmic tyrosine kinases. Molecular biology and evolution. 2001.
Vihinen, M. Mixed T and B Lymphocyte Deficiency Disorders. e LS. 2001.
Norberg, Jan; Vihinen, M. Molecular dynamics simulation of the effects of cytosine methylation on structure of oligonucleotides. Journal of Molecular Structure: THEOCHEM. 2001.
Siermala, Markku; Juhola, Martti; Vihinen, M. On preprocessing of protein sequences for neural network prediction of polyproline type II secondary structures. Computers in biology and medicine. 2001.
Lappalainen¹, Ilkka; Vihinen, M. STRUCTURAL BASIS FOR IMMUNODEFICIENCY-CAUSING MUTATIONS IN THE SH2 DOMAINS OF. Protein Modules in Cellular Signalling. 2001.
Smith, CI Edvard; Islam, Tahmina C; Mattsson, Pekka T; Mohamed, Abdalla J; Nore, Beston F; Vihinen, M. The Tec family of cytoplasmic tyrosine kinases: mammalian Btk, Bmx, Itk, Tec, Txk and homologs in other species. Bioessays. 2001.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-I Introduction. Advances in Genetics. 2000.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-II Antibody Deficiencies. Advances in Genetics. 2000.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-III T-Cell Deficiencies. Advances in Genetics. 2000.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-IV Combined Immunodeficiencies. Advances in Genetics. 2000.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-References. Advances in Genetics. 2000.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-V Other Well-Defined Immunodeficiencies. Advances in Genetics. 2000.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-VI Phagocytic Immunodeficiencies. Advances in Genetics. 2000.
Vihinen, M; Arredondo-Vega, Francisco X; Casanova, Jean-Laurent; Etzioni, Amos; Giliani, Silvia; Hammarstrom, Lennart; Hershfield, Michael S; Heyworth, Paul G; Hsu, Amy P; Lahdesmaki, Aleksi. 4 Primary Immunodeficiency Mutation Databases-VII Discussion. Advances in Genetics. 2000.
Vihinen, M; Mattsson, Pekka T; Smith, CI. Bruton tyrosine kinase (BTK) in X-linked agammaglobulinemia (XLA). Front Biosci. 2000.
Vihinen, M; Lehväslaiho, H. Geenitietokannat ja niiden käyttö. Duodecim. 2000.
Pitkanen, Jukka; Doucas, Vassilis; Sternsdorf, Thomas; Nakajima, Toshihiro; Aratani, Satoko; Jensen, Kirsten; Will, Hans; Vahamurto, Perttu; Ollila, Juha; Vihinen, M. GENES: STRUCTURE AND REGULATION-The autoimmune regulator protein has transcriptional transactivating properties and interacts with the common coactivator CREB-binding protein. Journal of Biological Chemistry. 2000.
Vihinen, M; Lehväslaiho, H. Genetic databases and their use. Duodecim; Laaketieteellinen Aikakauskirja. 2000.
Valiaho, J; Hershfield, M; Notarangelo, LD; Regueiro, JR; Roos, D; Smith, CIE; Villa, A; Vihinen, M. Immunodeficiency mutation databases. IXth Meeting of the European-Society-for-Immunodeficiencies. 2000.
Stenberg, Kaj AE; Riikonen, Pentti T; Vihinen, M. KinMutBase, a database of human disease-causing protein kinase mutations. Nucleic Acids Research. 2000.
SIERMALA, Markku; JUHOLA, Martti; Vihinen, M. Medical Infobahn for Europe 475 A. Hasman et al.(Eds.) IOS Press, 2000. Medical Infobahn for Europe: Proceedings of MIE2000 and GMDS2000. 2000.
Vihinen, M; Villa, Anna; Mella, Patrizia; Schumacher, R Fabian; Savoldi, Gianfranco; O’Shea, John J; Candotti, Fabio; Notarangelo, Luigi D. Molecular modeling of the Jak3 kinase domains and structural basis for severe combined immunodeficiency. Clinical Immunology. 2000.
Siermala, Markku; Juhola, Martti; Vihinen, M. Neural network prediction of polyproline type II secondary structures. Medical Infobahn for Europe. 2000.
Väliaho, Jouni; Riikonen, Pentti; Vihinen, M. Novel immunodeficiency data servers.. Immunological reviews. 2000.
Lappalainen, Ilkka; Giliani, Silvia; Franceschini, Roberta; Bonnefoy, Jean-Yves; Duckett, Colin; Notarangelo, Luigi D; Vihinen, M. Structural basis for SH2D1A mutations in X-linked lymphoproliferative disease. Biochemical and Biophysical Research Communications. 2000.
Rong, Suo-Bao; Väliaho, Jouni; Vihinen, M. Structural basis of Bloom syndrome (BS) causing mutations in the BLM helicase domain. Molecular medicine. 2000.
Rong, Suo-Bao; Vihinen, M. Structural basis of Wiskott-Aldrich syndrome causing mutations in the WH1 domain. Journal of molecular medicine. 2000.
Korpi; Väliaho; Vihinen. Structure‐function effects in primary immunodeficiencies. Scandinavian Journal of Immunology. 2000.
Pitkänen, Jukka; Doucas, Vassilis; Sternsdorf, Thomas; Nakajima, Toshihiro; Aratani, Satoko; Jensen, Kirsten; Will, Hans; Vähämurto, Perttu; Ollila, Juha; Vihinen, M. The autoimmune regulator protein has transcriptional transactivating properties and interacts with the common coactivator CREB-binding protein. Journal of Biological Chemistry. 2000.
Stenberg, Kaj AE; Riikonen, Pentti T; Vihinen, M. KinMutBase, a database of human disease-causing protein kinase mutations. Nucleic acids research. 1999.
Vihinen, M; Kwan, Sau‐Ping; Lester, Tracy; Ochs, Hans D; Resnick, Igor; Väliaho, Jouni; Conley, Mary Ellen; Smith, CI Edvard. Mutations of the human BTK gene coding for bruton tyrosine kinase in X‐linked agammaglobulinemia. Human mutation. 1999.
Riikonen, Pentti; Vihinen, M. MUTbase: maintenance and analysis of distributed mutation databases.. Bioinformatics (Oxford, England). 1999.
Okoh, Michael P; Vihinen, M. Pleckstrin homology domains of tec family protein kinases. Biochemical and biophysical research communications. 1999.
Vihinen, M; Brandau, Oliver; Brandén, Lars J; Kwan, Sau-Ping; Lappalainen, Ilkka; Lester, Tracy; Noordzij, Jeroen G; Ochs, Hans D; Ollila, Juha; Pienaar, Sandy M. BTKbase, mutation database for X-linked agammaglobulinemia (XLA). Nucleic acids research. 1998.
Vihinen, M. Immunodeficiency mutation databases (IDbases). Molecular Immunology. 1998.
Vihinen, M; Smith, CI Edvard. Interactions between SH2 and SH3 domains. Biochemical and biophysical research communications. 1998.
Tanhuanpää, Pirjo; Vilkki, Juha; Vihinen, M. Mapping and cloning of FAD2 gene to develop allele-specific PCR for oleic acid in spring turnip rape (Brassica rapa ssp. oleifera). Molecular Breeding. 1998.
Notarangelo, LD; Giliani, S; Jones, A; de Saint Basile, G; Florini, M; Toniati, P; Mella, P; Vihinen, M. Report of the ESID collaborative study on clinical features and molecular analysis in X-linked hyper-IgM syndrome. Molecular Immunology. 1998.
Ollila, Juha; Vihinen, M. Stimulation of B and T cells activates expression of transcription and differentiation factors. Biochemical and biophysical research communications. 1998.
Smaith, CIE; Bäckesjö, Carl-Magnus; Brandén, Lars J; Islam, Tahmina; Mattsson, Pekka T; Mohamed, Abdalla J; Nore, Beston F; Vargas, L; Vihinen, M. XLA-Studies on the Btk tyrosine kinase. Molecular Immunology. 1998.
Smith, CI Edvard; Bäckesjö, Carl-Magnus; Berglöf, Anna; Brandén, Lars J; Islam, Tahmina; Mattsson, Pekka T; Mohamed, Abdalla J; Müller, Susanne; Nore, Beston; Vihinen, M. X-linked agammaglobulinemia: lack of mature B lineage cells caused by mutations in the Btk kinase. Springer seminars in immunopathology. 1998.
Vihinen, M; Mattsson, Pekka T; Smith, CI Edvard. BTK, the tyrosine kinase affected in X-linked agammaglobulinemia. Front Biosci. 1997.
Vihinen, M; Belohradsky, BH; Haire, RN; Holinski-Feder, E; Kwan, S-P; Lappalainen, I; Lehväslaiho, H; Lester, T; Meindl, A; Ochs, H. BTKbase, mutation database for X-linked agammaglobulinemia. Nucleic Acids Research. 1997.
Vihinen, M; Belohradsky, Bernd H; Haire, Robert N; Holinski-Feder, Elke; Kwan, Sau-Ping; Lappalainen, Ilkka; Lehväslaiho, Heikki; Lester, Tracy; Meindl, Alfons; Ochs, Hans D. BTKbase, mutation database for X-linked agammaglobulinemia (XLA). Nucleic acids research. 1997.
Vihinen, M; Nore, Beston F; Mattsson, Pekka T; Bäckesjö, Carl-Magnus; Nars, Martin; Koutaniemi, Sanna; Watanabe, Chiaki; Lester, Tracy; Jones, Allison; Ochs, Hans D. Missense mutations affecting a conserved cysteine pair in the TH domain of Btk. FEBS letters. 1997.
Saha, Bratin K; Curtis, Sherill K; Vogler, Larry B; Vihinen, M. Molecular and structural characterization of five novel mutations in the Bruton’s tyrosine kinase gene from patients with X-linked agammaglobulinemia. Molecular Medicine. 1997.
Saha, BK; Curtis, SK; Vogler, LB; Vihinen, M. Molecular/structural characterization of novel mutations and identification of novel polymorphisms in the Bruton’s tyrosine kinase (Btk) gene from patients with X-linked agammaglobulinemia (XLA).. American Journal of Human Genetics. 1997.
Lappalainen, Ilkka; Ollila, Juha; Smith, CI Edvard; Vihinen, M. Registries of immunodeficiency patients and mutations. Human Mutation. 1997.
Vihinen, M; Iwata, Tsutomu; Kinnon, Christine; Kwan, Sau-Ping; Ochs, Hans D; Vorechovsky, Igor; Smith, CI Edvard. BTKbase, mutation database for X-linked agammaglobulinemia (XLA). Nucleic acids research. 1996.
Vihinen, M; Brooimans, Rik A; Kwan, Sau-Ping; Lehväslaiho, Heikki; Litman, Gary W; Ochs, Hans D; Resnick, Igor; Schwaber, Jerrold H; Vořechovsky, Igor; Smith, CI Edvard. BTKbase: XLA-mutation registry. Immunology today. 1996.
Vihinen, M; Smith, CI Edvard. Immunodeficiency mutation databases. 7th Meeting of the European-Society-of-Immunodeficiencies. 1996.
Smith, CI Edvard; Vihinen, M. Immunodeficiency mutation databases—a new research tool. Immunology today. 1996.
Ollila, Juha; Lappalainen, Ilkka; Vihinen, M. Sequence specificity in CpG mutation hotspots. FEBS letters. 1996.
Vihinen, M; Smith, CI Edward. Structural aspects of signal transduction in B-cells. Critical Reviews™ in Immunology. 1996.
Lamminmäki, Urpo; Vihinen, M. Structural consequences of neopullulanase mutations. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology. 1996.
Boberg, Jorma; Salakoski, Tapio; Vihinen, M. Accurate prediction of protein secondary structural class with fuzzy structural vectors. Protein Engineering, Design and Selection. 1995.
Vihinen, M. BTKbase: a database of XLA-causing mutations. Immunology today. 1995.
Boberg, Jorma; Salakoski, Tapio; Vihinen, M. Representative selection of proteins based on nuclear families. Protein Engineering, Design and Selection. 1995.
Vihinen, M; Zvelebil, Marketa JJM; Zhu, Qili; Brooimans, Rik A; Ochs, Hans D; Zegers, Ben JM; Nilsson, Lennart; Waterfield, Michael D; Smith, CI Edvard. Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia. Biochemistry. 1995.
Vihinen, M; Torkkila, Esa; Riikonen, Pentti. Accuracy of protein flexibility predictions. Proteins: Structure, Function, and Bioinformatics. 1994.
Vihinen, M; Peltonen, Taina; Iitiä, Antti; Suominen, Ilari; Mäntsälä, Pekka. C-terminal truncations of a thermostable Bacillus stearothermophilus α-amylase. Protein Engineering, Design and Selection. 1994.
Vihinen, M. Modeling of prostate-specific antigen and human glandular kallikrein structures. Biochemical and biophysical research communications. 1994.
Hakala, Juha ML; Vihinen, M. Modelling the structure of the calcitonin gene-related peptide. Protein Engineering, Design and Selection. 1994.
Vihinen, M; Vetrie, David; Maniar, Hina S; Ochs, Hans D; Zhu, Qili; Vorechovský, Igor; Webster, AD; Notarangelo, Luigi D; Nilsson, Lennart; Sowadski, Janusz M. Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease.. Proceedings of the National Academy of Sciences. 1994.
Vihinen, M; Nilsson, Lennart; Smith, CI Edvard. Structural basis of SH2 domain mutations in X-linked agammaglobulinemia. Biochemical and biophysical research communications. 1994.
Vihinen, M; Nilsson, Lennart; Smith, CI Edvard. Tec homology (TH) adjacent to the PH domain. FEBS letters. 1994.
Vihinen, M; Torkkila, Esa. HYDRO: a program for protein hydropathy predictions. Computer methods and programs in biomedicine. 1993.
Vihinen, M; Helin, Sari; Mlintstilli, Pekka. Active-Site Residues of Bacillus stearothermophilus a-Amy&e, Molecular Engineering 1: 267-273.1991. Please be informed that Figure 2B (bottom picture) on p. 271 should be rotated 180” to appear in the right position.. Molecular Engineering. 1992.
Vihinen, M; Lundin, Maria; Baltscheffsky, Herrick. Computer modeling of two inorganic pyrophosphatases. Biochemical and biophysical research communications. 1992.
Vihinen, M; Euranto, Antti; Luostarinen, Petri; Nevalainen, Olli. MULTICOMP: a program package for multiple sequence comparison. Bioinformatics. 1992.
Boberg, Jorma; Salakoski, Tapio; Vihinen, M. Selection of a representative set of structures from Brookhaven Protein Data Bank. Proteins: Structure, Function, and Bioinformatics. 1992.
Vihinen, M; Helin, Sari; Mäntsälä, Pekka. Site-directed mutagenesis of putative active-site residues of Bacillus stearothermophilus α-amylase. Molecular Engineering. 1991.
Vihinen, M. [28] Simultaneous comparison of several sequences. Methods Enzymol. 1990.
Vihinen, M; Mantsala, Pekka. Characterization of a thermostable Bacillus stearothermophilus alpha‐amylase. Biotechnology and Applied Biochemistry. 1990.
Vihinen, M; Mäntsälä, Pekka. Conserved residues of liquefying α-amylases are concentrated in the vicinity of active site. Biochemical and biophysical research communications. 1990.
Vihinen, M; Ollikka, Pauli; Niskanen, Jukka; Meyer, Peter; Suominen, Ilari; Karp, Matti; Holm, Liisa; Knowles, Jonathan; Mäntsälä, Pekka. Site-directed mutagenesis of a thermostable α-amylase from Bacillus stearothermophilus: putative role of three conserved residues. The Journal of Biochemistry. 1990.
Vihinen, M. Site-directed Mutagenesis of the Bacillus Stearothermophilus [alpha]-amylase Based on Sequence Analysis and Computer Modeling. . 1990.
Vihinen, M; Mantsala, P. Critical reviews in biochemistry and molecular biology [J]. Microbial amylolytic enzymes. 1989.
M Vihinen, P Mäntsälättt Microbial amylolytic enzymes. Microbial amylolytic enzymes. Crit Rev Biochem Mol Biol. 1989.
Vihinen, M; Mantsiila, Pekka. Microbial amylolytic enzyme. Critical reviews in biochemistry and molecular biology. 1989.
Vihinen, M. An algorithm for simultaneous comparison of several sequences. Bioinformatics. 1988.
Vihinen, M. SIMULTANEOUS COMPARISON OF SEVERAL PRIMARY SEQUENCES AND PREDICTED SECONDARY STRUCTURAL FEATURES. Journal of Protein Chemistry. 1988.
Vihinen, M. Relationship of protein flexibility to thermostability. Protein Engineering, Design and Selection. 1987.