User:Leo Lahti/Publications

Publications by Leo Lahti (order RSS feed)

''Formalisms blindly followed induce blindness. Intelligently adopted, however, they improve vision. Being obliged to spell out the argument, check its logical implications, and examine whether the evidence conforms to the argument promotes both visual acuity and intellectual responsibility.'' (Charles Tilly, 2004)

Journal articles

 * 1) Intestinal microbiota in healthy adults: Temporal analysis reveals individual and common core and relation to digestive symptoms. Jonna Jalanka-Tuovinen, Anne Salonen, Janne Nikkilä, Outi Immonen, Riina Kekkonen, Leo Lahti, Airi Palva and Willem M. de Vos. PLoS One. In press.
 * 2) Integrative Analysis of microRNA, mRNA and aCGH Data Reveals Asbestos- and Histology-Related Changes in Lung Cancer. Penny Nymark, Mohamed Guled, Ioana Borze, Ali Faisal, Leo Lahti, Kaisa Salmenkivi, Eeva Kettunen, Sisko Anttila and Sakari Knuutila. Genes, Chromosomes and Cancer. In press.
 * 3) Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays. Leo Lahti, Laura L. Elo, Tero Aittokallio, and Samuel Kaski. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(1):217-225, 2011. (abstract; preprint (pdf); R/BioConductor package (RPA)).
 * 4) Global modeling of transcriptional responses in interaction networks. Leo Lahti, Juha E.A. Knuuttila, and Samuel Kaski. Bioinformatics 26(21):2713-2720, 2010. abstract; preprint with supplementary figures (pdf); implementation in R and Matlab)
 * 5) Array Comparative Genomic Hybridization Reveals Frequent Alterations of G1/S Checkpoint Genes in Undifferentiated Pleomorphic Sarcoma of Bone. Tarja Niini, Leo Lahti, Francesca Michelacci, Shinsuke Ninomiya, Claudia Maria Hattinger, Mohamed Guled, Tom B&ouml;hling, Piero Picci, Massimo Serra, and Sakari Knuutila. Genes, Chromosomes and Cancer 50(5)291-306, 2011.
 * 6) MicroRNA microarrays on archive bone marrow core biopsies of leukemias - method validation. Ioana Borze, Mohamed Guled, Suad Musse, Anna Raunio, Erkki Elonen, Ulla Saarinen-Pihkala, Marja-Liisa Karjalainen-Lindsberg, Leo Lahti, and Sakari Knuutila. Leukemia Research 35(2)188-195, 2011.
 * 7) Unique microRNA profile in Dupuytren's contracture supports deregulation of &#x03B2;-catenin pathway. Neda Mosakhani, Mohamed Guled, Leo Lahti, Ioana Borze, Minna Forsman, Jorma Ryh&auml;nen, and Sakari Knuutila. Modern Pathology 23:1544-1522, 2010.
 * 8) CDKN2A, NF2 and JUN Are Dysregulated Among Other Genes by miRNAs in Malignant Mesothelioma - a miRNA Microarray Analysis. Mohamed Guled, Leo Lahti, Pamela M Lindholm, Kaisa Salmenkivi, Izhar Bagwan, Andrew G Nicholson and Sakari Knuutila. Genes, Chromosomes and Cancer 48:615-23, 2009. (full text)
 * 9) Specific Gene Expression Profiles in Asbestos-exposed Epithelial and Mesothelial Lung Cell Lines. Penny Nymark, Pamela M Lindholm, Mikko V Korpela, Leo Lahti, Salla Ruosaari, Samuel Kaski, Jaakko Hollmen, Sisko Anttila, Vuokko L Kinnula, and Sakari Knuutila.  BMC Genomics 8:62, 2007 (abstract)
 * 10) Integrating probe-level expression changes across generations of Affymetrix arrays. Laura L. Elo, Leo Lahti, Heli Skottman, Minna Kyläniemi, Riitta Lahesmaa and Tero Aittokallio. Nucleic Acids Research 2005 33(22):e193 (abstract, full text, pdf, check also R package written by L. Elo)
 * 11) Associative clustering for exploring dependencies between functional genomics data sets. Samuel Kaski, Janne Nikkilä, Janne Sinkkonen, Leo Lahti, Juha E.A. Knuuttila, and Christophe Roos. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Special Issue on Machine Learning for Bioinformatics -- Part 2, 2(3):203-216, 2005 (abstract, pdf. This is the most thorough description of associative clustering, including two bioinformatics case studies.)

Conference Proceedings

 * 1) Dependency detection with similarity constraints. Leo Lahti, Samuel Myllykangas, Sakari Knuutila, and Samuel Kaski. In T&uuml;lay Adali, Jocelyn Chanussot, Christian Jutten, and Jan Larsen, editors, Proceedings of the 2009 IEEE International Workshop on Machine Learning for Signal Processing XIX, pages 89--94. IEEE, Piscataway, NJ, USA, 2009. (pdf; arXiv preprint; R/BioConductor package (pint))
 * 2) Associative Clustering. Janne Sinkkonen, Janne Nikkil&auml;, Leo Lahti and Samuel Kaski. ECML 2004, Pisa, Italy.  In: Boulicaut, Esposito, Giannotti, Pedreschi (eds.): Machine Learning: ECML2004 (Proceedings of 15th European Conference on Machine Learning), Lecture Notes in Computer Science 3201, pages 396-406, 2004. (abstract, pdf) ©Springer-Verlag

Theses

 * D.Sc. (Tech.), Probabilistic analysis of the human transcriptome with side information, PhD thesis; Aalto University School of Science and Technology, Faculty of Information and Natural Sciences, Espoo, Finland, 2010. (V&auml;it&ouml;stiedote (pdf), Summary, electronic version, LaTeX sources, pdf). Thesis introduction released with CC-BY license.


 * M.Sc. (Tech.), Comparative functional genome analysis using associative clustering (M.Sc. thesis; in Finnish), Helsinki University of Technology, Department of Engineering Physics and Mathematics, 2003. (pdf)


 * B.Sc. Simon Blackburnin kvasi-realismi ja moraalisen keskustelun turvaaminen (Concerning Blackburn's quasi-realism in securing moral discussion; B.Sc. thesis, in Finnish), University of Helsinki, Faculty of political sciences, 2009. (LaTex; pdf). CC-BY license.

Scientific Open Source Software

 * Functional network analysis (netresponse). R/BioConductor, Matlab Probabilistic algorithms for global modeling of context-specific network activation patterns. Provides tools to study transcriptional responses in genome-scale interaction networks across organism-wide collections of gene expression data.


 * Probabilistic data integration for functional genomics (pint) R/BioConductor Particular tools to integrate measurements of RNA and DNA levels to investigate functional effects of chromosomal mutations.


 * Robust probabilistic averaging (RPA): R/BioConductor for probe reliability analysis and gene expression preprocessing. In AffyComp comparisons, the average ranking of RPA across the various tests was ranked as 1/65 (hgu95) and 4/95 (hgu133; as of March 13, 2011). This confirms the superior performance of the probabilistic RPA method to other preprocessing algorithms. Recommended preprocessing method for Affymetrix data.


 * Dependency modeling toolkit (DMT) R/CRAN. Unified framework for probabilistic dependency models. Probabilistic versions of PCA, factor analysis and CCA, their regularized variants, dependency-based dimensionality reduction etc.

Technical Reports and Workshop papers

 * Probabilistic dependency models for data integration in functional genomics. L Lahti and S Kaski. Machine Learning for Systems Biology workshop, ISMB, Vienna, Austria, July 2011.


 * Systematic Use of Computational Methods Allows Stratifying Treatment Responders in Glioblastoma Multiforme. R Louhimo, V Aittomäki, A Faisal, M Laakso, P Chen, K Ovaska, E Valo, L Lahti, V Rogojin, S Kaski and S Hautaniemi. Critical Assessment of Massive Data Analysis (CAMDA) workshop, ISMB, Vienna, Austria, July 2011.


 * Associative Clustering (AC): Technical Details. J Sinkkonen, S Kaski, J Nikkil&auml;, and L Lahti. Technical Report A84, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, April 2005. (ps, pdf; accompanying report including only additional technical details and derivations of the method.)


 * Associative Clustering by Maximizing a Bayes Factor. J Sinkkonen, J Nikkil&auml;, L Lahti and S Kaski. Technical Report A68, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, June 2003. (postscript)

Selected Posters

 * Combining multiple data sources in functional genomics for improving genome-wide inferences L Lahti, S Myllykangas, S Knuutila, J Hollmen, E Castren and S Kaski. In SYSBIO symposium, Helsinki, Finland 2007.


 * Modeling gene expression in biological networks L Lahti, JEA Knuuttila and S Kaski. In ECCB 2008, Cagliari, September 2008.


 * Probabilistic analysis of probe performance on short nucleotide arrays L Lahti, LL Elo, T Aittokallio and S Kaski. In ISMB 2007, Vienna, July 21-25, 2007.


 * Method for exploring dependencies in the expression of orthologous man-mouse gene pairs L Lahti, JEA Knuuttila, J Nikkil&auml; and S Kaski. In SYSBIO Symposium, Meripuisto, Finland, 2005. Best poster award.

Other material

 * Comparative overview on the BioPAX and SBML standards for machine-readable representations of cell-biological processes. (Special assignment, 2007; pdf) CC-BY licence.


 * A quantum computing survey (Quantum computing course essay, 2001 (doc)).


 * Julian joukko iteraatioden valuma-altaan reunana (Matematiikan erikoistyö, 2001 pdf, tex). CC-BY licence.


 * Itsesimilaaristen joukkojen Hausdorffin dimension m&auml;&auml;ritt&auml;minen (Matematiikan erikoistyö, 2002 pdf, tex). CC-BY licence.

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