Publications

The complete bibliography is available as BibTex and RSS feed. Copies of most papers and other outputs are available here, or I can send PDF copies also by email, just ask !

Peer-reviewed articles

Alchemy & algorithms: perspectives on the philosophy and history of open science Leo Lahti and Filipe da Silva and Markus Petteri Laine and Viivi Lähteenoja and Mikko Tolonen. RIO Journal 3:e13593, 2017. html. Preprint awaiting post-publication review.

Retrieval and Analysis of Eurostat Open Data with the eurostat Package Leo Lahti, Janne Huovari, Markus Kainu and Przemysław Biecek. R Journal 2017. html

Multi-stability and the origin of microbial community types Karoline Faust, Didier Gonze, Leo Lahti, Jeroen Raes. ISME Journal 2017. In press.

Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies. Sudarshan Shetty, Floor Hugenholtz, Leo Lahti, Hauke Smidt, Willem M de Vos, Antoine Danchin. FEMS Microbiology Reviews fuw045, 2017 html; pdf

A Quantitative Study of History in the English Short-Title Catalogue (ESTC) 1470-1800 Leo Lahti, Niko Ilomäki, Mikko Tolonen. LIBER Quarterly 25(2):87-116, 2015. html

Beyond Open Access - The Changing Culture of Producing and Disseminating Scientific Knowledge Heidi Laine, Leo Lahti, Anne Lehto, Samuli Ollila, Markus Miettinen. Proc. 19th International Academic Mindtrek Conference 2015 in Tampere, Finland — September 22 - 24, 2015. ACM New York, NY, USA. html PDF

Aatehistoria ja digitaalisten aineistojen mahdollisuudet Mikko Tolonen, Leo Lahti. Ennen & Nyt 2, 2015. html

Metagenomics meets time series analysis: unraveling microbial community dynamics Karoline Faust, Leo Lahti, Didier Gonze, Willem M de Vos, Jeroen Raes. Current Opinion in Microbiology 15:56-66 2015. html

Fat, Fiber and Cancer Risk in African, Americans and Rural Africans Stephen O’Keefe, Jia V. Li, Leo Lahti, Junhai Ou, Franck Carbonero, Khaled Mohammed, Joram M. Posma, James Kinross, Elaine Wahl, Elizabeth Ruder, Kishore Vipperla, Vasudevan Naidoo, Lungile Mtshali, Sebastian Tims, Philippe G. B. Puylaert, James DeLany, Alyssa Krasinskas, Ann C. Benefiel, Hatem O. Kaseb, Keith Newton, Jeremy K. Nicholson, Willem M. de Vos, H. Rex Gaskins, Erwin G. Zoetendal. Nature Communications 6:6342, 2015. html; PDF; data; Guardian article

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river Atashgahi S, Aydin R, Dimitrov MR, Sipkema D, Hamonts K, Lahti L, Maphosa F, Cruse T, Springael D, Dejonghe W & Smidt H. Scientific Reports. 5:17284, 2015. html

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database Jarmo Ritari, Jarkko Salojärvi, Leo Lahti, Willem M. de Vos. BMC Genomics 16:1056, 2015. html pdf

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J Hansson O. Skeletal Muscle 5:35, 2015. html

Tipping elements in the human intestinal ecosystem Leo Lahti, Jarkko Salojärvi, Anne Salonen, Marten Scheffer, Willem M. de Vos. Nature Communications 5:4344, 2014. html data

Linking statistical and ecological theory: Hubbell’s unified neutral theory of biodiversity as a hierarchical Dirichlet process Keith Harris, Todd L Parsons, Umer Z Ijaz, Leo Lahti, Ian Holmes, Christopher Quince. Proc. IEEE In press. PDF; Code

Binning metagenomic contigs by coverage and composition (CONCOCT) Johannes Alneberg, Brynjar Smári Bjarnason, Ino de Bruijn, Melanie Schirmer, Joshua Quick, Umer Z Ijaz, Leo Lahti, Nicholas J Loman, Anders F Andersson, Christopher Quince Nature Methods 11:1144-6, 2014. html; CONCOCT @ Github

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men Anne Salonen, Leo Lahti, Jarkko Salojärvi, Grietje Holtrop, Katri Korpela, Sylvia Duncan, Priya Date, Alexandra Johnstone, Gerald Lobley, Petra Louis, Harry. Flint, Willem M. de Vos. ISME Journal 8:2218-30, 2014. html

Open Science Peer Review Oath J Aleksic, A Alexa, TK Attwood, D Bolser, M Dahlö, R Davey, H Dinkel, K Förstner, I Grigorov, J-K Hèriché, N Chue Hong, L Lahti, D MacLean, ML Markie, J Molloy, MV Schneider, C Scott, R Smith-Unna, BM Vieira. F1000Research 3:271, 2014. AllBio: Open Science & Reproducibility Best Practice Workshop 2014 html

Copy Number Alterations and Neoplasia Specific Mutations in MELK, PDCD1LG2, TLN1, and PAX5 at 9p in Different Neoplasias Virinder Sarhadi, Leo Lahti, Ilari Scheinin, Pekka Ellonen, Eeva Kettunen, Massimo Serra, Katia Scotlandi, Pierro Picci, Sakari Knuutila. Genes, Chromosomes and Cancer. 53(7):579-588, 2014. html

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. Systems Biomedicine 1(2):130-136, 2014. html

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases Leo Lahti, Aurora Torrente, Laura L Elo, Alvis Brazma, Johan Rung. Nucleic Acids Research 41(10):e110, 2013. html; R/Bioconductor; usage examples

Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data Leo Lahti, Anne Salonen, Riina A. Kekkonen, Jarkko Salojärvi, Jonna Jalanka-Tuovinen, Airi Palva, Matej Orešič, Willem M. de Vos. PeerJ 1:e32, 2013. html

Targeted Resequencing of 9p in Acute Lymphoblastic Leukemia Yields Concordant Results with Array CGH and Reveals Novel Genomic Alterations Virinder Kaur Sarhadi, Leo Lahti, Ilari Scheinin, Anne Tyybäkinoja, Suvi Savola, Anu Usvasalo, Riikka Räty, Erkki Elonen, Pekka Ellonen, Ulla M Saarinen-Pihkala, Sakari Knuutila. Genomics 102(3):182-8, 2013. Abstract

Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review Leo Lahti, Martin Schäfer, Hans-Ulrich Klein, Silvio Bicciato and Martin Dugas. Briefings in Bioinformatics 14(1): 27-35, 2013. html; Source code

Homozygous Deletions of Cadherin Genes in Chondrosarcoma – an Array CGH Study Tarja Niini, Ilari Scheinin, Leo Lahti, Suvi Savola, Fredrik Mertens, Jaakko Hollmén, Tom Böhling, Aarne Kivioja, Karolin H Nord, Sakari Knuutila. Cancer Genetics 205(11):588-93, 2012. Abstract

MicroRNA profiling predicts survival in anti-EGFR treated chemorefractory metastatic colorectal cancer patients with wild-type KRAS and BRAF Neda Mosakhani, Leo Lahti, Ioana Borze, Marja-Liisa Karjalainen-Lindsberg, Jari Sundstrom, Raija Ristamaki, Pia Osterlund, Sakari Knuutila, and Virinder Kaur Sarhadi. Cancer Genetics. 205(11):545-51, 2012. Abstract

The adult intestinal core microbiota is determined by analysis depth and health status Anne Salonen, Jarkko Salojärvi, Leo Lahti, and Willem M. de Vos. Clinical Microbiology and Infection 18(S4):16 20, 2012. Abstract

miRNA profiling in pediatric acute lymphoblastic leukemia: novel prognostic tools Neda Mosakhani, Virinder Kaur Sarhadi, Anu Usvasalo, Marja-Liisa Karjalainen-Lindsberg, Leo Lahti, Katja Tuononen, Ulla M Saarinen-Pihkala and Sakari Knuutila. Leukemia & lymphoma 53(12)2517-20, 2012. html

Intestinal microbiota in healthy adults: Temporal analysis reveals individual and common core and relation to intestinal symptoms Jonna Jalanka-Tuovinen, Anne Salonen, Janne Nikkilä, Outi Immonen, Riina Kekkonen, Leo Lahti, Airi Palva and Willem M. de Vos. PLoS One 6(7):e23035, 2011. html

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 50(8):585-97, 2011 html

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):217-25, 2011. abstract; PDF (preprint); R/Bioconductor (RPA)

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 Böhling, Piero Picci, Massimo Serra, and Sakari Knuutila. Genes, Chromosomes and Cancer 50(5)291-306, 2011. Abstract

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)188-95, 2011. Abstract

Global modeling of transcriptional responses in interaction networks Leo Lahti, Juha E.A. Knuuttila, and Samuel Kaski. Bioinformatics 26(21):2713-20, 2010. Abstract; PDF; ArXiv; R/Matlab source code

Unique microRNA profile in Dupuytren’s contracture supports deregulation of β-catenin pathway Neda Mosakhani, Mohamed Guled, Leo Lahti, Ioana Borze, Minna Forsman, Jorma Ryhänen, and Sakari Knuutila. Modern Pathology 23:1544-52, 2010. The International Dupuytren Award 2011 Abstract

Dependency detection with similarity constraints Leo Lahti, Samuel Myllykangas, Sakari Knuutila, and Samuel Kaski. In Tülay Adali, Jocelyn Chanussot, Christian Jutten, and Jan Larsen, editors, Proceedings of the 2009 IEEE International Workshop on Machine Learning for Signal Processing XIX, pages 198–203. IEEE, Piscataway, NJ, USA, 2009. PDF arXiv R/Bioconductor (pint)

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. Article

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. html

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 33(22):e193, 2005. Abstract; R package

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):203-16, 2005. Abstract; PDF

Associative Clustering Janne Sinkkonen, Janne Nikkilä, Leo Lahti and Samuel Kaski. In: Boulicaut, Esposito, Giannotti, Pedreschi (eds.): ECML2004 Proceedings of 15th European Conference on Machine Learning, Lecture Notes in Computer Science 3201, pages 396-406, 2004. Abstract PDF

Theses and Assignments

For source material (LaTeX code, figures etc.) of these theses, see Github.

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. Thesis introduction released with CC-BY license. Väitöstiedote Electronic version LaTeX/GitHub PDF.

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|LaTeX/Github

B.Sc thesis (in Finnish). Simon Blackburnin kvasi-realismi ja moraalisen keskustelun turvaaminen / Concerning Blackburn’s quasi-realism in securing moral discussion. University of Helsinki, Faculty of political sciences, 2009. CC-BY license. LaTeX/Github PDF.

A brief overview on the BioPAX and SBML standards
Overview of machine-readable representations of cell-biological processes. arXiv. CC-BY licence.

Julian joukko iteraatioden valuma-altaan reunana
Matematiikan erikoistyö, 2001. PDF LaTeX/Github. CC-BY licence.

Itsesimilaaristen joukkojen Hausdorffin dimension määrittäminen
Matematiikan erikoistyö, 2002. PDF LaTeX/Github. CC-BY licence.

Technical Reports and Workshop papers

Biomarker discovery via dependency analysis of multi-view functional genomics data A Faisal, R Louhimo, L Lahti, S Kaski, S Hautaniemi. Personalized medicine workshop, NIPS 2011, Granada, Spain, December 2011. Spotlight presentation by A Faisal.

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. PDF

Associative Clustering (AC): Technical Details J Sinkkonen, S Kaski, J Nikkilä, and L Lahti. Technical Report A84, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, April 2005. PDF

Associative Clustering by Maximizing a Bayes Factor J Sinkkonen, J Nikkilä, L Lahti and S Kaski. Technical Report A68, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, June 2003. Postscript

Scientific data and open source software

See the separate code and data pages.

The material is presented to ensure timely dissemination of scholarly and technical work. While I aim to grant CC or other open source/copyleft licenses for the content wherever possible, kindly note that copyright in the external links and all rights therein are retained by authors or by other copyright holders.