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---
---
References
==========
@Misc{Lahti2006biopax,
author = {Leo Lahti},
title = {A brief overview on the BioPAX and SBML standards},
howpublished = {arXiv},
status = {thesis},
year = 2006,
note = {Overview of machine-readable representations of
cell-biological processes. CC-BY licence.},
language = {Finnish},
note = {(in Finnish)}
}
@Misc{Lahti2001,
author = {Leo Lahti},
title = {Julian joukko iteraatioden valuma-altaan reunana},
status = {thesis},
year = 2001,
url = {https://github.com/antagomir/thesis/tree/master/julia01},
language = {Finnish},
pdf =
{https://github.com/antagomir/thesis/blob/master/julia01/julia.pdf},
note = {Special assignment in Mathematics (in Finnish)}
}
@Misc{Lahti2002,
author = {Leo Lahti},
title = {Itsesimilaaristen joukkojen Hausdorffin dimension
määrittäminen},
status = {thesis},
year = 2002,
url =
{https://github.com/antagomir/thesis/tree/master/hausdorff02},
language = {Finnish},
pdf =
{https://github.com/antagomir/thesis/blob/master/hausdorff02/similar.pdf},
note = {Special assignment in Mathematics (in Finnish)}
}
@TechReport{Bjork2018,
author = {Anna Björk and Juho-Matti Paavolainen and Teemu
Ropponen and Mikael Laakso and Leo Lahti},
title = {Opening academic publishing: development and
application of systematic evaluation criteria},
year = 2018,
publisher = {Open Science and Research Initiative (ATT)},
month = {January},
note = {Report on the openness of major scientific
publishers commissioned by Finnish Ministry of Education and Culture.},
status = {highlight},
url = {http://www.avointiede.fi/keskeiset-julkaisut},
pdf = {publications/papers/2018-Bjork-ATT.pdf}
}
@Article{Timmis2018,
author = {Timmis, Kenneth and Jebok, Franziska and Molinari,
Gabriellaand Rohde, Manfred and Lahti, Leo},
title = {Microbiome Yarns: human biome reproduction,
evolution and visual acuity},
journal = {Microbial Biotechnology},
year = 2018,
volume = 11,
number = 1,
pages = {149--159},
status = {other},
month = {January},
doi = {10.1111/1751-7915.13037},
note = {Comics piece for the popularization of microbiome
research.},
keywords = {popular}
}
@Article{Buelow2017,
author = {Elena Buelow and Teresita {d.J.} Bello González and
Susana Fuentes and Wouter A.A. {de Steenhuijsen
Piters} and Leo Lahti and Jumamurat R. Bayjanov and
Eline A.M. Majoor and Johanna C. Braat and Maaike
S. van Mourik and Evelien A.N. Oostdijk and Rob
J.L. Willems and Marc J.M. Bonten and Mark W.J. van
Passel and Hauke Smidt and Willem van Schaik},
title = {Comparative gut microbiota and resistome profiling
of intensive care patients receiving selective
digestive tract decontamination and healthy
subjects},
journal = {Microbiome},
year = 2017,
volume = 5,
number = 1,
pages = 88,
month = {Aug},
doi = {10.1186/s40168-017-0309-z}
}
@Article{Lahti17phos,
author = {Leo Lahti and Filipe da Silva and Markus Petteri
Laine and Viivi Lähteenoja and Mikko Tolonen},
title = {Alchemy & algorithms: perspectives on the philosophy
and history of open science},
journal = {RIO Journal},
year = 2017,
volume = 3,
pages = {e13593},
month = {May},
status = {highlight},
url = {http://riojournal.com/articles.php?id=13593},
doi = {10.3897/rio.3.e13593},
keywords = {dh},
note = {Review of the international conference, including
electronic material (video interviews, lectures and
podcasts.}
}
@Article{Faust2017,
author = {Karoline Faust and Didier Gonze and Leo Lahti and
Jeroen Raes},
title = {Multi-stability and the origin of microbial
community types},
journal = {ISME Journal},
year = 2017,
status = {highlight},
volume = 11,
pages = {2159--2166},
month = {may},
doi = {10.1038/ismej.2017.60}
}
@Article{Tolonen15EnnenNyt,
author = {Mikko Tolonen and Leo Lahti},
title = {Aatehistoria ja digitaalisten aineistojen
mahdollisuudet},
journal = {Ennen \& Nyt 2},
year = 2015,
volume = 2,
language = {Finnish},
month = {8},
keywords = {dh},
url =
{http://www.ennenjanyt.net/2015/08/aatehistoria-ja-digitaalisten-aineistojen-mahdollisuudet}
}
@InProceedings{Tolonen16dh,
author = {Mikko Tolonen and Niko Ilom{\"a}ki and Hege
Roivainen and Leo Lahti},
title = {Printing in a Periphery: a Quantitative Study of
Finnish Knowledge Production, 1640-1828},
booktitle = {Digital Humanities 2016: Conference Abstracts},
year = 2016,
publisher = {Jagiellonian University & Pedagogical University,
Kraków},
address = {Krakow, Poland},
pages = {383--385},
month = 7,
keywords = {dh}
}
@Article{Lahti15LIBER,
author = {Leo Lahti and Niko Ilom{\"a}ki and Mikko Tolonen},
title = {A quantitative study of history in the English
short-title catalogue (ESTC) 1470-1800},
journal = {LIBER Quarterly},
year = 2015,
volume = 25,
number = 2,
pages = {87-116},
month = {12},
issn = {2213-056X},
keywords = {dh},
url =
{http://liber.library.uu.nl/index.php/lq/article/view/10112}
}
@Article{Ritari15,
author = {Jarmo Ritari and Jarkko Salojärvi and Leo Lahti and
Willem M. de Vos},
title = {Improved taxonomic assignment of human intestinal
16S rRNA sequences by a dedicated reference
database},
journal = {BMC Genomics},
year = 2015,
volume = 16,
pages = 1056,
month = {12},
doi = {10.1186/s12864-015-2265-y},
url = {http://www.biomedcentral.com/1471-2164/16/1056}
}
@InProceedings{Laine15,
author = {Heidi Laine and Leo Lahti and Anne Lehto and Samuli
Ollila and Markus Miettinen},
title = {Beyond Open Access - The Changing Culture of
Producing and Disseminating Scientific Knowledge},
booktitle = {Proceedings of the 19th International Academic
Mindtrek Conference in Tampere, Finland — September
22 - 24, 2015},
year = 2015,
address = {ACM New York, NY, USA},
organization = {AcademicMindTrek'15: Proceedings of the 19th
International Academic Mindtrek Conference},
publisher = {ACM},
address = {New York, NY, USA},
location = {Tampere, Finland},
isbn = {978-1-4503-3948-3},
keywords = {dh, openscience},
pdf = {publications/papers/2015-Laine-Mindtrek.pdf},
url = {http://dl.acm.org/citation.cfm?id=2818187}
}
@Article{Su2015,
author = {Jing Su and Carl Ekman and Nikolay Oskolkov and Leo
Lahti and Kristoffer Ström and Alvis Brazma and Leif
Groop and Johan Rung and and Ola Hansson},
title = {A novel atlas of gene expression in human skeletal
muscle reveals molecular changes associated with
aging},
journal = {Skeletal Muscle},
year = 2015,
volume = 5,
number = 35,
doi = {10.1186/s13395-015-0059-1},
month = {10}
}
@Misc{Lahti13icml,
author = {Leo Lahti, Juuso Parkkinen, Joona Lehtomäki and
Markus Kainu},
title = {rOpenGov: open source ecosystem for computational
social sciences and digital humanities},
keywords = {dh, openscience},
howpublished = {software},
month = 12,
year = 2013,
url = {http://ropengov.github.io},
note = {Presentation at ICML/MLOSS workshop (Int'l Conf. on
Machine Learning - Open Source Software workshop).}
}
@Article{Siavash15,
author = {S Atashgahi and R Aydin and MR Dimitrov and D
Sipkema and K Hamonts and L Lahti and F Maphosa and
T Cruse and D Springael and W Dejonghe and H Smidt},
title = {Impact of a wastewater treatment plant on microbial
community composition and function in a hyporheic
zone of a eutrophic river},
journal = {Scientific Reports},
year = 2015,
volume = 5,
number = 17284,
month = {11},
doi = {10.1038/srep17284}
}
@Article{Faust15,
author = {Karoline Faust and Leo Lahti and Didier Gonze and
Willem M de Vos and Jeroen Raes},
title = {Metagenomics meets time series analysis: unraveling
microbial community dynamics},
journal = {Current Opinion in Microbiology},
year = 2015,
volume = 25,
keywords = {review},
status = {highlight},
pages = {56--66},
month = {6},
url =
{http://www.sciencedirect.com/science/article/pii/S1369527415000478},
doi = {10.1016/j.mib.2015.04.004},
annote = {Shared first author.}
}
@Article{OKeefe15,
author = {SJD O'Keefe and JV Li and L Lahti and J Ou and F
Carbonero and K Mohammed and JM Posma and J Kinross
and E Wahl and E Ruder and K Vipperla and V Naidoo
and L Mtshali and S Tims and PGB Puylaert, J DeLany
and A Krasinskas and AC Benefiel and HO Kaseb and K
Newton and JK Nicholson and WM de Vos and HR Gaskins
and EG Zoetendal},
title = {Fat, Fiber and Cancer Risk in African, Americans and
Rural Africans},
journal = {Nature Communications},
year = 2015,
volume = 6,
pages = 6342,
keywords = {gut},
status = {highlight},
month = {Apr},
doi = {10.1038/ncomms7342},
note = {Top science article in Guardian on the release day.},
pdf = {publications/papers/2015-OKeefe-NComms.pdf},
annote = {Guardian:
http://www.theguardian.com/science/2015/apr/28/bowel-cancer-risk-may-be-reduced-by-rural-african-diet-study-finds}
}
@Article{Aleksic14,
author = {Jelena Aleksic and Adrian Alexa and Teresa K Attwood
and Neil Chue Hong and Martin Dahl{\"o} and Robert
Davey and Holger Dinkel and Konrad U F{\"o}rstner
and Ivo Grigorov and Jean-Karim Hériché and Leo
Lahti and Dan MacLean and Michael L Markie and Jenny
Molloy and Maria Victoria Schneider and Camille
Scott and Richard Smith-Unna and Bruno Miguel
Vieira},
keywords = {openscience},
status = {other},
title = {The Open Science Peer Review Oath},
journal = {F1000Research},
year = 2015,
volume = 3,
pages = 271,
note = {As part of the AllBio: Open Science &
Reproducibility Best Practice Workshop},
doi = {10.12688/f1000research.5686.2}
}
@Article{Niini12,
author = {Tarja Niini and Ilari Scheinin and Leo Lahti and
Suvi Savola and Fredrik Mertens and Jaakko Hollmén
and Tom Böhling and Aarne Kivioja and Karolin H
Nord and Sakari Knuutila},
title = {Homozygous Deletions of Cadherin Genes in
Chondrosarcoma – an Array CGH Study},
journal = {Cancer Genetics},
year = 2012,
volume = 205,
number = 11,
pages = {588-93},
month = {11},
url = {http://www.ncbi.nlm.nih.gov/pubmed?term=23146407}
}
@Article{Lahti12cmi,
author = {Anne Salonen and Jarkko Saloj{\"a}rvi and Leo Lahti
and and Willem M. de Vos},
title = {The adult intestinal core microbiota is determined
by analysis depth and health status},
journal = {Clinical Microbiology and Infection},
year = 2012,
volume = 18,
number = {Suppl. 4},
pages = {16–20},
url =
{http://onlinelibrary.wiley.com/doi/10.1111/j.1469-0691.2012.03855.x/abstract}
}
@Article{Mosakhani12,
author = {Neda Mosakhani and Leo Lahti and Ioana Borze and
Marja-Liisa Karjalainen-Lindsberg and Jari Sundstrom
and Raija Ristamaki and Pia Osterlund and Sakari
Knuutila and and Virinder Kaur Sarhadi},
title = {MicroRNA profiling predicts survival in anti-EGFR
treated chemorefractory metastatic colorectal cancer
patients with wild-type KRAS and BRAF},
journal = {Cancer Genetics},
year = 2012,
volume = 205,
number = 11,
pages = {545-51},
month = {11},
url =
{http://www.sciencedirect.com/science/article/pii/S2210776212002293}
}
@Article{Lahti2012intcomp,
author = {Leo Lahti and Martin Sch{\"a}fer and Hans-Ulrich
Klein and Silvio Bicciato and Martin Dugas},
title = {Cancer gene prioritization by integrative analysis
of mRNA expression and DNA copy number data: a
comparative review},
journal = {Briefings in Bioinformatics},
year = 2013,
volume = 14,
number = 1,
pages = {27--35},
url =
{http://bib.oxfordjournals.org/content/14/1/27.abstract.html?etoc},
annote = {Implementation available at
http://intcomp.r-forge.r-project.org}
}
@Article{Lahti13provasI,
author = {Leo Lahti and Anne Salonen and Riina A. Kekkonen and
Jarkko Salojärvi and Jonna Jalanka-Tuovinen and
Airi Palva and Matej Orešič and Willem M. de Vos},
title = {Associations between the human intestinal
microbiota, Lactobacillus rhamnosus GG and
serum lipids indicated by integrated analysis of
high-throughput profiling data},
journal = {PeerJ},
year = 2013,
volume = 1,
pages = {e32},
url = {http://dx.doi.org/10.7717/peerj.32},
pmid = 23638368
}
@Article{Sarhadi13,
author = {Virinder Kaur Sarhadi and Leo Lahti and Ilari
Scheinin and Anne Tyyb{\"a}kinoja and Suvi Savola
and Anu Usvasalo and Riikka R{\"a}ty and Erkki
Elonen and Pekka Ellonen and Ulla M Saarinen-Pihkala
and Sakari Knuutila},
title = {Targeted Resequencing of 9p in Acute Lymphoblastic
Leukemia Yields Concordant Results with Array CGH
and Reveals Novel Genomic Alterations},
journal = {Genomics},
year = 2013,
volume = 102,
number = 3,
pages = {182--188},
url = {http://www.sciencedirect.com/science/article/pii/S0888754313000025},
annote = {Shared first author.}
}
@Article{Mosakhani12LL,
author = {N Mosakhani and VK Sarhadi and A Usvasalo and ML
Karjalainen-Lindsberg and L Lahti and K Tuononen and
UM Saarinen-Pihkala and S Knuutila},
title = {MicroRNA profiling in pediatric acute lymphoblastic
leukemia: novel prognostic tools},
journal = {Leukemia \& Lymphoma},
year = 2012,
volume = 53,
number = 12,
pages = {2517-20},
month = {Dec},
url =
{http://informahealthcare.com/doi/abs/10.3109/10428194.2012.685731}
}
@Article{Harris17,
author = {Keith Harris and Todd L Parsons and Umer Z Ijaz and
Leo Lahti and Ian Holmes and Christopher Quince},
title = {Linking statistical and ecological theory: Hubbell's
unified neutral theory of biodiversity as a
hierarchical Dirichlet process},
journal = {Proceedings of the IEEE},
status = {highlight},
year = 2017,
volume = 105,
number = 3,
pages = {516--529},
month = {March},
url = {http://arxiv.org/abs/1410.4038}
}
@Article{Alneberg14,
author = {Johannes Alneberg and Brynjar Smári Bjarnason and
Ino de Bruijn and Melanie Schirmer and Joshua Quick
and Umer Z Ijaz and Leo Lahti and Nicholas J Loman
and Anders F Andersson and Christopher Quince},
title = {Binning metagenomic contigs by coverage and
composition},
journal = {Nature Methods},
year = 2014,
status = {highlight},
volume = 11,
number = {1144--1146},
doi = {10.1038/nmeth.3103},
annote = {CONCOCT method}
}
@Article{lahti14natcomm,
author = {Leo Lahti and Jarkko Saloj{\"a}rvi and Anne Salonen
and Marten Scheffer and Willem M. de Vos},
title = {Tipping elements in the human intestinal ecosystem},
journal = {Nature Communications},
year = 2014,
volume = 5,
pages = 4344,
month = {7},
status = {highlight},
doi = {10.1038/ncomms5344}
}
@Article{salonen14,
author = {Anne Salonen and Leo Lahti and Jarkko Saloj{\"a}rvi
and Grietje Holtrop and Katri Korpela and Sylvia
Duncan and Priya Date and Alexandra Johnstone and
Gerald Lobley and Petra Louis and Harry Flint and
Willem M. de Vos},
title = {Impact of diet and individual variation on
intestinal microbiota composition and fermentation
products in obese men},
journal = {ISME Journal},
year = 2014,
volume = 8,
pages = {2218--2230},
url =
{http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201463a.html},
doi = {10.1038/ismej.2014.63}
}
@Article{bender13,
author = {Leo Lahti},
title = {Intestinal microbiota, individuality and
health. In: Computational Methods Aiding Early-Stage
Drug Design (Dagstuhl Seminar 13212)},
pages = {78--94},
journal = {Dagstuhl Reports},
ISSN = {2192-5283},
year = 2013,
volume = 3,
number = 5,
status = {abstract},
editor = {Andreas Bender and Hinrich G{\"o}hlmann and Sepp
Hochreiter and Ziv Shkedy},
publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
address = {Dagstuhl, Germany},
URL = {http://drops.dagstuhl.de/opus/volltexte/2013/4179},
URN = {urn:nbn:de:0030-drops-41791},
doi = {http://dx.doi.org/10.4230/DagRep.3.5.78},
annote = {Keywords: Bioinformatics, Chemoinformatics, Machine
learning, Statistics, Interdisciplinary
applications. Short abstract for the Dagstuhl
seminar.}
}
@Article{Salonen12,
author = {Anne Salonen and Jarkko Saloj{\"a}rvi and Leo Lahti
and Willem M. de Vos},
title = {The Adult Intestinal Core Microbiota Is Determined
by Analysis Depth and Health Status},
journal = {Clinical Microbiology and Infection},
year = 2012,
volume = 18,
issue = S4,
pages = {16-20}
}
@article{Lahti11rpa,
author = {Leo Lahti and Laura L. Elo and Tero Aittokallio and
Samuel Kaski},
title = {Probabilistic Analysis of Probe Reliability in
Differential Gene Expression Studies with Short
Oligonucleotide Arrays},
journal = {IEEE/ACM Transactions on Computational Biology and
Bioinformatics},
year = 2011,
volume = 8,
number = 1,
pages = {217--225},
month = {Jan.-Mar.},
doi = {10.1109/TCBB.2009.38},
pdf = {https://www.researchgate.net/publication/224439493_Probabilistic_Analysis_of_Probe_Reliability_in_Differential_Gene_Expression_Studies_with_Short_Oligonucleotide_Arrays/file/9fcfd4fbe8b3e5387a.pdf},
url =
{http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2009.38},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
annote = {Open source implementation:
http://bioconductor.org/packages/release/bioc/html/RPA.html}
}
@Misc{Lahti11-louhos,
author = {Juuso Parkkinen and Leo Lahti},
title = {Louhos blog},
howpublished = {blog},
url = {http://louhos.wordpress.com/},
note = {Regular blog with case studies on the analysis of
open government and other public data sources with a
particular focus on Finland}
}
@Misc{Lahti11intcomp,
author = {Leo Lahti and Martin Sch{\"a}fer and Hans-Ulrich
Klein and Silvio Bicciato and Martin Dugas},
title = {intcomp: a benchmarking pipeline for integrative
cancer gene detection algorithms},
howpublished = {software},
month = 2,
year = 2011,
url = {http://intcomp.r-forge.r-project.org/},
note = {R-forge}
}
@Article{Jalanka-Tuovinen11,
author = {Jonna Jalanka-Tuovinen and Anne Salonen and Janne
Nikkil{\"a} and Outi Immonen and Riina Kekkonen and
Leo Lahti and Airi Palva and Willem M. de Vos},
title = {Intestinal microbiota in healthy adults: Temporal
analysis reveals individual and common core and
relation to intestinal symptoms},
journal = {PLoS One},
year = 2011,
volume = 6,
number = 7,
pages = {e23035},
url =
{http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023035}
}
@InProceedings{Louhimo11camda,
author = {Riku Louhimo and Viljami Aittom{\"a}ki and Ali
Faisal and Marko Laakso and Ping Chen and Kristian
Ovaska and Erkka Valo and Leo Lahti and Vladimir
Rogojin and Samuel Kaski and Sampsa Hautaniemi. },
title = {Systematic Use of Computational Methods Allows
Stratifying Treatment Responders in Glioblastoma
Multiforme},
booktitle = {Proc. Critical Assessment of Massive Data Analysis
(CAMDA) workshop},
year = 2011,
status = {abstract},
month = 7,
address = {Vienna, Austria}
}
@Misc{Lahti11ismb,
author = {Leo Lahti and Samuel Kaski},
title = {Probabilistic dependency models for data integration
in functional genomics},
status = {abstract},
pdf =
{https://lahtilab.github.io/files/publications/papers/2011-MLSB-Lahti.pdf},
month = {July},
year = 2011,
note = {Machine Learning for Systems Biology workshop, ISMB,
Vienna, Austria}
}
@article{Louhimo14,
author = {Riku Louhimo and Viljami Aittom{\"a}ki and Ali
Faisal and Marko Laakso and Ping Chen and Kristian
Ovaska and Erkka Valo and Leo Lahti and Vladimir
Rogojin and Samuel Kaski and Sampsa Hautaniemi},
journal = {Systems Biomedicine},
language = {eng},
pages = {130-136},
title = {Systematic use of computational methods allows
stratification of treatment responders in
glioblastoma multiforme},
volume = 1,
number = 2,
year = 2014,
doi = {10.4161/sysb.28904}
}
@Article{Nymark11,
author = {Penny Nymark and Mohamed Guled and Ioana Borze and
Ali Faisal and Leo Lahti and Kaisa Salmenkivi and
Eeva Kettunen and Sisko Anttila and Sakari Knuutila},
title = {Integrative Analysis of microRNA, mRNA and aCGH Data
Reveals Asbestos- and Histology-Related Changes in
Lung Cancer},
journal = {Genes, Chromosomes and Cancer},
year = 2011,
volume = 50,
number = 8,
pages = {585--597},
url =
{http://onlinelibrary.wiley.com/doi/10.1002/gcc.20880/full}
}
@Article{Niini11mfh,
author = {Tarja Niini and Leo Lahti and Francesca Michelacci
and Shinsuke Ninomiya and Claudia Maria Hattinger
and Mohamed Guled and Tom B{\"o}hling and Piero
Picci and Massimo Serra and Sakari Knuutila},
title = {Array Comparative Genomic Hybridization Reveals
Frequent Alterations of G1/S Checkpoint Genes in
Undifferentiated Pleomorphic Sarcoma of Bone},
journal = {Genes, Chromosomes and Cancer},
year = 2011,
volume = 50,
number = 5,
pages = {291--306},
url =
{http://onlinelibrary.wiley.com/doi/10.1002/gcc.20851/abstract},
doi = {10.1002/gcc.20851}
}
@article{Elo05,
author = {Elo, Laura L. and Lahti, Leo and Skottman, Heli and
Kyl{\"a}niemi, Minna and Lahesmaa, Riitta and
Aittokallio, Tero},
title = {Integrating probe-level expression changes across
generations of Affymetrix arrays},
journal = {Nucleic Acids Research},
volume = 33,
number = 22,
pages = {e193},
doi = {10.1093/nar/gni193},
URL =
{http://nar.oxfordjournals.org/cgi/content/abstract/33/22/e193
},
pdf =
{http://nar.oxfordjournals.org/cgi/reprint/33/22/e193.pdf},
year = 2005
}
@Article{Kaski05,
author = {Samuel Kaski and Janne Nikkil{\"a} and Janne
Sinkkonen and Leo Lahti and Juha Knuuttila and
Christophe Roos},
title = {Associative clustering for exploring dependencies
between functional genomics data sets},
journal = {IEEE/ACM Transactions on Computational Biology and
Bioinformatics},
year = 2005,
volume = 2,
number = 3,
pages = {203--216},
note = {Special Issue on Machine Learning for Bioinformatics
-- Part 2},
url =
{http://www.cis.hut.fi/projects/mi/abstracts/tcbb05.html},
pdf =
{https://www.researchgate.net/publication/6751780_Associative_clustering_for_exploring_dependencies_between_functional_genomics_data_sets/file/9fcfd505af3fa6d1b8.pdf}
}
@MastersThesis{Lahti03,
author = {Lahti, Leo},
title = {Comparative functional genome analysis using
associative clustering},
school = {Helsinki University of Technology},
year = 2003,
language = {Finnish},
url =
{https://github.com/antagomir/thesis/tree/master/msc03},
pdf =
{https://github.com/antagomir/thesis/blob/master/msc03/dtyo.pdf},
status = {thesis},
note = {(in Finnish)}
}
@Misc{Lahti09bsc,
author = {Leo Lahti},
title = {Concerning Blackburn's quasi-realism in securing
moral discussion},
howpublished = {B.Sc. thesis. University of Helsinki, Faculty of
Political Sciences},
month = {7},
year = 2009,
language = {Finnish},
status = {thesis},
pdf =
{http://www.roihu.info/publications/theses/LeoLahti-BSc-2008.pdf},
note = {(In Finnish)}
}
@Article{Nymark07,
author = {Penny Nymark and Pamela M. Lindholm and Mikko
V. Korpela and Leo Lahti and Salla Ruosaari and
Samuel Kaski and Jaakko Hollmen and Sisko Anttila
and Vuokko L. Kinnula and Sakari Knuutila},
title = {Gene Expression Profiles in Asbestos-exposed
Epithelial and Mesothelial Lung Cell Lines},
journal = {BMC Genomics},
year = 2007,
volume = 8,
number = 62,
url =
{http://www.biomedcentral.com/1471-2164/8/62/abstract},
annote = {Includes CCA application on two asbestos-exposed
cell lines.}
}
@TechReport{Sinkkonen05tr,
author = {Janne Sinkkonen and Samuel Kaski and Janne
Nikkil{\"a} and Leo Lahti},
title = {Associative Clustering (AC): Technical Details},
institution = {Helsinki University of Technology},
year = 2005,
number = {A84},
address = {Espoo, Finland},
month = {April},
pdf = {http://www.cis.hut.fi/projects/mi/papers/tr84.pdf},
note = {Publications in Computer and Information Science}
}
@InCollection{Sinkkonen04ecml,
author = {Janne Sinkkonen and Janne Nikkil\"{a} and Leo Lahti
and Samuel Kaski},
title = {Associative Clustering},
booktitle = {Machine Learning: ECML2004 (Proceedings of the
ECML'04, 15th European Conference on Machine
Learning)},
editor = {Boulicaut and Esposito and Giannotti and Pedreschi},
pages = {396--406},
publisher = {Springer},
address = {Berlin},
status = {abstract},
year = 2004,
url =
{http://www.cis.hut.fi/projects/mi/abstracts/ecml04.html},
pdf =
{http://www.researchgate.net/publication/225904975_Associative_Clustering}
}
@Misc{Lahti04socbin,
author = {Leo Lahti and Juha Knuuttila and Janne Nikkil{\"a}
and Samuel Kaski},
title = {Exploring dependencies in the expression of
orthologous man-mouse gene pairs},
year = 2004,
status = {poster},
note = {In Bioinformatics 2004, Link\"oping, Sweden, 6 3-6,
2004. A poster.}
}
@TechReport{Sinkkonen03tr,
author = {Janne Sinkkonen and Janne Nikkil\"{a} and Leo Lahti
and Samuel Kaski},
title = {Associative Clustering by Maximizing a {B}ayes
Factor},
institution = {Helsinki University of Technology, Laboratory of
Computer and Information Science},
year = 2003,
number = {A68},
address = {Espoo, Finland}
}
@article{Lahti17eurostat,
author = {Leo Lahti and Janne Huovari and Markus Kainu and
Przemysław Biecek},
title = {Retrieval and Analysis of Eurostat Open Data with
the eurostat Package},
year = 2017,
journal = {The R Journal},
url =
{https://journal.r-project.org/archive/2017/RJ-2017-019/index.html},
pages = {385--392},
keywords = {dh},
software = {yes},
volume = 9,
number = 1,
annote = {R package homepage URL:
http://ropengov.github.io/eurostat/}
}
@Article{Shetty2017,
author = {Shetty, SA and Hugenholtz, F and Lahti, L and Smidt,
H and de Vos, WM and Danchin, A},
title = {Intestinal microbiome landscaping: Insight in
community assemblage and implications for microbial
modulation strategies},
journal = {FEMS Microbiology Reviews},
volume = 41,
issue = 2,
month = {March},
status = {review},
pages = {182--199},
year = 2017,
pages = {fuw045},
doi = {10.1093/femsre/fuw045}
}
@Article{sarhadi14,
author = {Virinder Sarhadi and Leo Lahti and Ilari Scheinin and Pekka Ellonen and Eeva Kettunen and Massimo Serra and Katia Scotlandi and Pierro Picci and Sakari Knuutila},
title = {Copy Number Alterations and Neoplasia Specific
Mutations in MELK, PDCD1LG2, TLN1, and PAX5 at 9p in
Different Neoplasias},
journal = {Genes, Chromosomes and Cancer},
year = 2014,
volume = 53,
number = 7,
pages = {579--588},
month = 7,
doi = {10.1002/gcc.22168}
}
@Article{Lahti13nar,
author = {Leo Lahti and Aurora Torrente and Laura L Elo and
Alvis Brazma and Johan Rung},
title = {A fully scalable online pre-processing algorithm for
short oligonucleotide microarray atlases},
journal = {Nucleic Acids Research},
volume = 41,
number = 10,
year = 2013,
pages = {e110},
doi = {10.1093/nar/gkt229},
note = {Implementation available through Bioconductor RPA
package.}
}
@InProceedings{Faisal2011,
author = {Ali Faisal and Riku Louhimo and Leo Lahti and Sampsa
Hautaniemi and Samuel Kaski},
title = {Biomarker discovery via dependency analysis of
multi-view functional genomics data},
booktitle = {NIPS 2011 workshop From Statistical Genetics to
Predictive Models in Personalized Medicine},
status = {abstract},
year = 2011
}
@PhdThesis{Lahti10thesis,
author = {Leo Lahti},
title = {Probabilistic analysis of the human transcriptome
with side information},
school = {Aalto University School of Science and Technology,
Faculty of Information and Natural Sciences,
Department of Information and Computer Science},
year = 2010,
address = {Espoo},
month = 12,
series = {TKK Dissertations in Information and Computer
Science},
status = {thesis},
language = {Finnish},
number = {TKK-ICS-D19},
note = {The LaTeX sources and the pdf version are freely
available under cc-by license at
https://github.com/antagomir/thesis/tree/master/phd10 | Press release: https://github.com/antagomir/thesis/blob/master/phd10/Vaitostiedote-LeoLahti-20101207.pdf},
keywords = {probabilistic models, Bayesian analysis, data
integration, gene expression, microarrays,
computational science, data analysis, machine
learning, computational biology, open source, open
access, creative commons},
url = {http://lib.tkk.fi/Diss/2010/isbn9789526033686/},
pdf =
{https://github.com/antagomir/thesis/blob/master/phd10/sources/publications/thesis-LeoLahti-2010.pdf},
issn = {1797-5069},
abstract = {Recent advances in high-throughput measurement
technologies and efficient sharing of biomedical
data through community databases have made it
possible to investigate the complete collection of
genetic material, the genome, which encodes the
heritable genetic program of an organism. This has
opened up new views to the study of living organisms
with a profound impact on biological research.
Functional genomics is a subdiscipline of molecular
biology that investigates the functional
organization of genetic information. This thesis
develops computational strategies to investigate a
key functional layer of the genome, the
transcriptome. The time- and context-specific
transcriptional activity of the genes regulates the
function of living cells through protein
synthesis. Efficient computational techniques are
needed in order to extract useful information from
high-dimensional genomic observations that are
associated with high levels of complex
variation. Statistical learning and probabilistic