Bioinformatics

Research outputs

  1. 2018
  2. Published

    snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions

    Nousiainen, K., Kanduri, K., Ricaño-Ponce, I., Wijmenga, C., Lahesmaa, R., Kumar, V. & Lähdesmäki, H., 1 Dec 2018, In : Bioinformatics (Oxford, England). 34, 23, p. 4112-4114 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    Liquid-chromatography retention order prediction for metabolite identification

    Bach, E., Szedmak, S., Brouard, C., Boecker, S. & Rousu, J., 1 Sep 2018, In : Bioinformatics. 34, 17, p. 875-883 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Published

    GOLabeler: Improving sequence-based large-scale protein function prediction by learning to rank

    You, R., Zhang, Z., Xiong, Y., Sun, F., Mamitsuka, H. & Zhu, S., 15 Jul 2018, In : Bioinformatics. 34, 14, p. 2465-2473 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Published

    Bacmeta: Simulator for genomic evolution in bacterial metapopulations

    Sipola, A., Marttinen, P. & Corander, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. 2308-2310 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  6. Published

    Learning with multiple pairwise kernels for drug bioactivity prediction

    Cichonska, A., Pahikkala, T., Szedmak, S., Julkunen, H., Airola, A., Heinonen, M., Aittokallio, T. & Rousu, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i509-i518

    Research output: Contribution to journalArticleScientificpeer-review

  7. Published

    MGPfusion: Predicting protein stability changes with Gaussian process kernel learning and data fusion

    Jokinen, E., Heinonen, M. & Lähdesmäki, H., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i274-i283

    Research output: Contribution to journalArticleScientificpeer-review

  8. Published

    SIMPLE Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra

    Nguyen, D. H., Nguyen, C. H. & Mamitsuka, H., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i323-i332 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Published

    Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge

    Sundin, I., Peltola, T., Micallef, L., Afrabandpey, H., Soare, M., Majumder, M. M., Daee, P., He, C., Serim, B., Havulinna, A. & 4 othersHeckman, C., Jacucci, G., Marttinen, P. & Kaski, S., 27 Jun 2018, In : Bioinformatics. 34, 13, p. i395-i403

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    Global proteomics profiling improves drug sensitivity prediction : results from a multi-omics, pan-cancer modeling approach

    Ali, M., Khan, S. A., Wennerberg, K. & Aittokallio, T., 15 Apr 2018, In : Bioinformatics. 34, 8, p. 1353-1362 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

    Principal metabolic flux mode analysis

    Bhadra, S., Blomberg, P., Castillo, S. & Rousu, J., 2018, In : Bioinformatics. 34, 14, p. 2409-2417

    Research output: Contribution to journalArticleScientificpeer-review

  12. Published

    ViraPipe: Scalable Parallel Pipeline for Viral Metagenome Analysis from Next Generation Sequencing Reads

    Maarala, A., Bzhalava, Z., Dillner, J., Heljanko, K. & Bzhalava, D., 2018, In : Bioinformatics. 34, 6, p. 928-935 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. 2017
  14. Published

    Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression

    Ammad-Ud-Din, M., Khan, S. A., Wennerberg, K. & Aittokallio, T., 15 Jul 2017, In : Bioinformatics. 33, 14, p. i359-i368

    Research output: Contribution to journalArticleScientificpeer-review

  15. Published

    Fast motif matching revisited: high-order PWMs, SNPs and indels

    Korhonen, J. H., Palin, K., Taipale, J. & Ukkonen, E., 15 Feb 2017, In : Bioinformatics. 33, 4, p. 514-521

    Research output: Contribution to journalArticleScientificpeer-review

  16. Published

    biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements

    Pirinen, M., Benner, C., Marttinen, P., Järvelin, M-R., Rivas, M. A. & Ripatti, S., 2017, In : Bioinformatics. 33, 15, p. 2405-2407 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  17. 2016
  18. Published

    A subpopulation model to analyze heterogeneous cell differentiation dynamics

    Chan, Y. H., Intosalmi, J., Rautio, S. & Lähdesmäki, H., 1 Nov 2016, In : Bioinformatics. 32, 21, p. 3306-3313 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Published

    Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

    Ammad-ud-din, M., Khan, S. A., Malani, D., Murumägi, A., Kallioniemi, O., Aittokallio, T. & Kaski, S., 3 Sep 2016, In : Bioinformatics. 32, 17, p. i455-i463 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    LuxGLM: A probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs

    Äijö, T., Yue, X., Rao, A. & Lähdesmäki, H., 1 Sep 2016, In : Bioinformatics. 32, 17, p. i511-i519

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Sparse group factor analysis for biclustering of multiple data sources

    Bunte, K., Leppäaho, E., Saarinen, I. & Kaski, S., 15 Aug 2016, In : Bioinformatics. 32, 16, p. 2457-2463 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis

    Cichonska, A., Rousu, J., Marttinen, P., Kangas, A. J., Soininen, P., Lehtimaki, T., Raitakari, O., Jarvelin, M-R., Salomaa, V., Ala-Korpela, M. & 2 othersRipatti, S. & Pirinen, M., 1 Jul 2016, In : Bioinformatics. 32, 13, p. 1981-1989 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Published

    Analysis of differential splicing suggests different modes of short-term splicing regulation

    Topa, H. & Honkela, A., 15 Jun 2016, In : Bioinformatics. 32, 12, p. i147-i155

    Research output: Contribution to journalArticleScientificpeer-review

  24. Published

    Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

    Intosalmi, J., Nousiainen, K., Ahlfors, H. & Lähdesmäki, H., 15 Jun 2016, In : Bioinformatics. 32, 12, p. 288-296

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    DeepMeSH: Deep semantic representation for improving large-scale MeSH indexing

    Peng, S., You, R., Wang, H., Zhai, C., Mamitsuka, H. & Zhu, S., 15 Jun 2016, In : Bioinformatics. 32, 12, p. i70-i79 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

    DrugE-Rank: Improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank

    Yuan, Q., Gao, J., Wu, D., Zhang, S., Mamitsuka, H. & Zhu, S., 15 Jun 2016, In : Bioinformatics. 32, 12, p. i18-i27 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    Fast metabolite identification with Input Output Kernel Regression

    Brouard, C., Shen, H., Dührkop, K., d'Alché-Buc, F., Böcker, S. & Rousu, J., 15 Jun 2016, In : Bioinformatics. 32, 12, p. 28-36

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    Modelling-based experiment retrieval: A case study with gene expression clustering

    Blomstedt, P., Dutta, R., Seth, S., Brazma, A. & Kaski, S., 1 May 2016, In : Bioinformatics. 32, 9, p. 1388-1394 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  29. 2015
  30. Published

    Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction

    Heinonen, M., Guipaud, O., Milliat, F., Buard, V., Micheau, B., Tarlet, G., Benderitter, M., Zehraoui, F. & d'Alche-Buc, F., 1 Mar 2015, In : Bioinformatics. 31, 5, p. 728-735 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  31. Published

    BinDNase: A discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

    Kähärä, J. & Lähdesmäki, H., 2015, In : Bioinformatics. 31, 17, p. 2852-2859

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Gaussian process test for high-throughput sequencing time series: application to experimental evolution

    Topa, H., Jònàs, À., Kofler, R., Kosiol, C. & Honkela, A., 2015, In : Bioinformatics. 31, 11, p. 1762-1770

    Research output: Contribution to journalArticleScientificpeer-review

  33. 2014
  34. Published

    Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

    Marttinen, P., Pirinen, M., Sarin, A-P., Gillberg, J., Kettunen, J., Surakka, I., Kangas, A. J., Soininen, P., "O'Reilly", P., Kaakinen, M. & 8 othersKähönen, M., Lehtimäki, T., Ala-Korpela, M., Raitakari, O. T., Salomaa, V., Järvelin, M-R., Ripatti, S. & Kaski, S., 2014, In : Bioinformatics. 30, 14, p. 2026-2034

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Exploration and retrieval of whole-metagenome sequencing samples

    Seth, S., Välimäki, N., Kaski, S. & Honkela, A., 2014, In : Bioinformatics. 30, 17, p. 2471-2479

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    Identification of structural features in chemicals associated with cancer drug response: A systematic data-driven analysis

    Khan, S. A., Virtanen, S., Kallioniemi, O. P., Wennerberg, K., Poso, A. & Kaski, S., 2014, In : Bioinformatics. 30, 17, p. pp. i497-i504

    Research output: Contribution to journalArticleScientificpeer-review

  37. Published

    Metabolite identification through multiple kernel learning on fragmentation trees

    Shen, H., Dührkop, K., Böcker, S. & Rousu, J., 2014, In : Bioinformatics. 30, 12, p. pp. i157-i164

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

    Äijö, T., Butty, V., Chen, JZ., Salo, V., Tripathi, S., Burge, C. B., Lahesmaa, R. & Lähdesmäki, H., 2014, In : Bioinformatics. 30, 12, p. pp. i113-i120

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

    PconsFold: improved contact predictions improve protein models

    Michel, M., Hayat, S., Skwark, M. J., Sander, C., Marks, D. S. & Elofsson, A., 2014, In : Bioinformatics. 30, 17, p. pp. i482-i488

    Research output: Contribution to journalArticleScientificpeer-review

  40. Published

    SEK: sparsity exploiting k-mer-based estimation of bacterial community composition

    Chatterjee, S., Koslicki, D., Dong, S., Innocenti, N., Cheng, L., Lan, Y., Vehkaperä, M., Skoglund, M., Rasmussen, L. K., Aurell, E. & 1 othersCorander, J., 2014, In : Bioinformatics. 30, 17, p. 24232431

    Research output: Contribution to journalArticleScientificpeer-review

  41. Published

    SeqPig: Simple and scalable scripting for large sequencing data sets in Hadoop

    Schumacher, A., Pireddu, L., Niemenmaa, M., Kallio, A., Korpelainen, E., Zanetti, G. & Heljanko, K., 2014, In : Bioinformatics. 30, 1, p. 119-120

    Research output: Contribution to journalArticleScientificpeer-review

  42. Published

    Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations

    Suvitaival, T., Rogers, S. & Kaski, S., 2014, In : Bioinformatics. 30, 17, p. pp. i461-i467

    Research output: Contribution to journalArticleScientificpeer-review

  43. 2013
  44. Published

    Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements

    Äijö, T., Granberg, K. & Lähdesmäki, H., 2013, In : Bioinformatics. 29, 10, p. 1283-1291

    Research output: Contribution to journalArticleScientificpeer-review

  45. 2012
  46. Published

    Data-Driven Information Retrieval in Heterogeneous Collections of Transcriptomics Data Links SIM2s to Malignant Pleural Mesothelioma

    Caldas, J., Gehlenborg, N., Kettunen, E., Faisal, A., Rönty, M., Nicholson, A. G., Knuutila, S., Brazma, A. & Kaski, S., 2012, In : Bioinformatics. 28, 2, p. 246-253

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    Hadoop-BAM: Directly manipulating next generation sequencing data in the cloud

    Niemenmaa, M., Kallio, A., Schumacher, A., Klemelä, P., Korpelainen, E. & Heljanko, K., 2012, In : Bioinformatics. 28, 6, p. 876-877

    Research output: Contribution to journalArticleScientificpeer-review

  48. Published

    Metabolite identification and molecular fingerprint prediction through machine learning

    Heinonen, M., Shen, H., Zamboni, N. & Rousu, J., 2012, In : Bioinformatics. 28, 18, p. 2333-2341

    Research output: Contribution to journalArticleScientificpeer-review

  49. Published

    Predicting Drug-Target Interactions from Chemical and Genomic Kernels Using Bayesian Matrix Factorization

    Gönen, M., 2012, In : Bioinformatics. 28, 18, p. 2304-2310

    Research output: Contribution to journalArticleScientificpeer-review

  50. Published

    Targeted Retrieval of Gene Expression Measurements Using Regulatory Models

    Georgii, E., Salojärvi, J., Brosché, M., Kangasjärvi, J. & Kaski, S., 2012, In : Bioinformatics. 28, 18, p. 2349-2356

    Research output: Contribution to journalArticleScientificpeer-review

  51. 2011
  52. Published

    tigre: Transcription factor inference through Gaussian process reconstruction of expression for bioconductor

    Honkela, A., Gao, P., Ropponen, J., Rattray, M. & Lawrence, N. D., Apr 2011, In : Bioinformatics. 27, 7, p. 1026-1027 2 p., btr057.

    Research output: Contribution to journalArticleScientificpeer-review

  53. 2010
  54. Published

    Global modeling of transcriptional responses in interaction networks

    Lahti, L., Knuuttila, J. E. A. & Kaski, S., 2010, In : Bioinformatics. 26, 21, p. 2713-2720

    Research output: Contribution to journalArticleScientificpeer-review

  55. Published

    Multivariate multi-way analysis of multi-source data

    Huopaniemi, I., Suvitaival, T., Nikkilä, J., Oresic, M. & Kaski, S., 2010, In : Bioinformatics. 26, 12, p. pp. i391-i398

    Research output: Contribution to journalArticleScientificpeer-review

  56. Published

    Probabilistic analysis of gene expression measurements from heterogeneous tissues

    Erkkilä, T., Lehmusvaara, S., Ruusuvuori, P., Visakorpi, T., Shmulevich, I. & Lähdesmäki, H., 2010, In : Bioinformatics. 26, 20, p. 2571-2577

    Research output: Contribution to journalArticleScientificpeer-review

  57. 2009
  58. Published

    Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

    Äijö, T. & Lähdesmäki, H., 2009, In : Bioinformatics. 25, p. 2937-2944

    Research output: Contribution to journalArticleScientificpeer-review

  59. Published

    Probabilistic retrieval and visualization of biologically relevant microarray experiments

    Caldas, J., Gehlenborg, N., Faisal, A., Brazma, A. & Kaski, S., 2009, In : Bioinformatics. 25, p. pp. i145-i153

    Research output: Contribution to journalArticleScientificpeer-review

  60. 2008
  61. Published

    Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities

    Gao, P., Honkela, A., Rattray, M. & Lawrence, N. D., 2008, In : Bioinformatics. 24, 16, p. pp. i70-i75

    Research output: Contribution to journalArticleScientificpeer-review

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