2017
Tripathi SK, Chen Z, Larjo A, Kanduri K, Nousiainen K, Äijö T,
Ricano-Ponce I, Hrdlickova B, Tuomela S, Laajala E, Salo V, Kumar V,
Wijmenga C, Lähdesmäki H and Lahesmaa R,
Genome-wide analysis of STAT3-mediated transcription during early human Th17 cell differentiation,
Cell Reports, Vol. 19, pp. 1888-1901, 2017.
[pubmed, abstract, html, pdf, suppl. materials]
Lund RJ, Rahkonen N, Malonzo M, Kauko L, Emani MR, Kivinen V, Närvä
E, Kemppainen E, Laiho A, Skottman H, Hovatta O, Rasool O, Nykter M,
Lähdesmäki H, Lahesmaa R,
RNA polymerase III subunit POLR3G regulates a specific subset of
polyA+ and smallRNA transcriptomes and splicing in human pluripotent
stem cells,
Stem Cell Reports, Vol. 8, pp. 1442-1454, 2017.
[pubmed, abstract, html, pdf, suppl. materials]
Tsagaratou A, Gonzalez-Avalos E, Rautio S, Scott-Browne J, Togher S, Pastor WA, Rothenberg EV, Chavez L, Lähdesmäki H, Rao A,
TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells,
Nature Immunology, Vol. 18, No. 1, pp. 45-53, 2017.
[pubmed, abstract, html, pdf, suppl. materials]
2016
Chan YH, Intosalmi J, Rautio S, Lähdesmäki H,
A subpopulation model to analyze heterogeneous cell differentiation dynamics,
Bioinformatics, Vol. 32, No. 21, pp. 3306-3313, 2016.
[pubmed, abstract, html, pdf, suppl. materials]
[Software]
Äijö T, Yue X, Rao A, Lähdesmäki H,
LuxGLM: A probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs,
Bioinformatics (ECCB2016), Vol. 32, No. 17, pp. i511-i519, 2016.
[pubmed, abstract, html, pdf, suppl. materials]
[Software]
Intosalmi J, Nousiainen K, Ahlfors H, Lähdesmäki H,
Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks,
Bioinformatics (ISMB2016), Vol. 32, No. 12, pp. i288-i296, 2016.
[pubmed, abstract, html, pdf]
[Software]
Rahkonen N, Stubb A, Malonzo M, Edelman S, Emani MR, Närvä E, Lähdesmäki, Baker-Ruokola H, Lahesmaa R, Lund R,
Mature Let-7 miRNAs fine tune expression of LIN28B proteins in pluripotent human embryonic stem cells,
Stem Cell Research, Vol. 17, No. 3, pp. 498-503, 2016.
[pubmed, abstract, html, pdf]
Vatanen T, Kostic AD, d’Hennezel E, Siljander H, Franzosa EA,
Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen A-M, Peet A,
Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM,
Szabo SJ, Porter J, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW,
Knip M on behalf of the DIABIMMUNE Study Group, Xavier RJ,
Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans,
Cell, Vol. 165, No. 4, pp. 842-853, 2016.
[pubmed, abstract, html, pdf]
[project website]
Äijö T, Huang Y, Mannerström H, Chavez L, Tsagaratou A, Rao A, Lähdesmäki H,
A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways,
Genome Biology, 17:49, 2016.
[pubmed, html, pdf, suppl. materials]
[Software]
Yue X, Trifari S, Äijö T, Tsagaratou A, Pastor W, Zepeda-Martinez JA, Huang Y, Vijayanand P, Lähdesmäki H, Rao A,
Control of Foxp3 stability through modulation of TET activity,
Journal of Experimental Medicine, Vol. 213, No. 3, pp. 377-397, 2016.
[pubmed, abstract, html, pdf]
Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D,
Synthetic transcription amplifier system for orthogonal control of gene expression in Saccharomyces cerevisiae,
PLoS ONE, Vol. 11, No. 2, e0148320, 2016.
[pubmed, html, pdf]
Tuomela S, Rautio S, Ahlfors H, Öling V, Salo V, Chen Z, Hämälistö
S, Tripathi SK, Ullah U, Äijö T, Soueidan H, Wessels L, Stockinger B,
Lähdesmäki H, Lahesmaa R,
Comparative analysis of human and mouse transcriptomes of Th17 cell priming,
Oncotargets, Vol. 7, No. 12, pp. 13416-13428, 2016.
[pubmed, abstract, html, pdf]
Konki M, Pasumarthy K, Malonzo M, Sainio A, Valensisi C, Söderström
M, Emani MR, Stubb A, Närvä E, Ghimire B, Laiho A, Järveläinen H,
Lahesmaa R, Lähdesmäki H, Hawkins RD, Lund RJ,
Epigenetic silencing of the key antioxidant enzyme catalase in karyotypically abnormal human pluripotent stem cells,
Scientific Reports, Vol. 6, No. 22190, 2016.
[pubmed, html, pdf]
Heinonen M, Mannerström H, Rousu J, Kaski S, Lähdesmäki H,
Non-stationary Gaussian process regression with Hamiltonian Monte Carlo,
In Proceedings of the Eighteenth International Conference on Artificial Intelligence and Statistics (AISTATS) 2016, to appear.
[abstract, pdf, suppl]
[Software]
2015
Rautio S, Lähdesmäki H,
MixChIP: A probabilistic method for cell type specific protein-DNA binding analysis,
BMC Bioinformatics, Vol. 16, No. 413, 2015.
[pubmed, abstract, html, pdf]
[software]
Intosalmi J, Ahlfors H, Rautio S, Mannerström H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H,
Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data,
BMC Systems Biology, Vol. 9, No. 81, 2015.
[pubmed, abstract, html, pdf]
Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins D, Ren B, Lähdesmäki, Lahesmaa R,
Identification of global regulators of T-helper cell lineage specification,
Genome Medicine, 7:122, 2015.
[pubmed, abstract, html, pdf]
Balasubramani A, Larjo A, Chang X, Hastie R, Togher S, Bassein J, Lähdesmäki, Rao A,
Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex,
Nature Communications, Vol. 6, No. 7307, 2015.
[abstract, html, pdf]
Larjo A and Lähdesmäki H,
Using multi-step proposal distribution for improved MCMC convergence in Bayesian network structure learning,
EURASIP Journal on Bioinformatics and Systems Biology, Vol. 6, 2015.
[abstract, html, pdf]
Kähärä J, Lähdesmäki H,
BinDNase: A discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data,
Bioinformatics, Vol. 31, No. 17, pp. 2852-2859, 2015.
[abstract, html, pdf]
[software]
Moulder R, Bhosale SD, Erkkilä T, Laajala E, Salmi J, Nguyen EV,
Kallionpää H, Mykkänen J, Vähä-Mäkilä M, Hyöty H, Veijola R,
Ilonen J, Simell T, Toppari J, Knip M, Goodlett DR, Lähdesmäki H,
Simell O, Lahesmaa R,
Serum proteomes distinguish type-1 diabetes developing children in a cohort with HLA-conferred susceptibility,
Diabetes, Vol. 64, No. 6, pp. 2265-2278, 2015.
[abstract, html, pdf]
Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T,
Hämäläinen A-M, Peet A, Tillman V, Pöho P, Mattila I, Lähdesmäki
H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J,
Virtanen S, Clish CB, Oresic M, Huttenhower C, Knip M on
behalf of the DIABIMMUNE Study Group, Xavier RJ,
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes,
Cell Host & Microbe, Vol. 17, No. 2, pp. 260-273, 2015.
[abstract, html, pdf] [pdf]
Martinez GJ, Pereira RM, Äijö T, Kim EY, Marangoni F, Pipkin
ME, Togher S, Heissmeyer V, Zhang YC, Crotty S, Lamperti ED, Ansel KM,
Mempel TR, Lähdesmäki H, Hogan PG, Rao A,
The transcription factor NFAT promotes exhaustion of activated CD8+ T cells,
Immunity, Vol. 42, No. 2, pp. 265-278, 2015.
[abstract, html, pdf]
Kantojärvi K, Kanduri C, Salo PM, Vanhala R, Buck G, Blancher C Lähdesmäki H, Järvelä I,
The landscape of copy number variations in Finnish families with autism spectrum disorders,
Autism Research, Vol. 9, No. 1, pp. 9-16, 2016.
[abstract, html, pdf]
Heinonen M, Laine A-P, Söderhäll C, Gruzieva O, Rautio S, Melen E,
Pershagen G, Lähdesmäki H, Knip M, Ilonen J, Henttinen T, Kere J,
Lahesmaa R, The Finnish Pediatric Diabetes Registry,
Gimap GTPase family genes -- potential modifiers in autoimmune diabetes, asthma and allergy,
The Journal of Immunology, Vol. 194, No. 12, pp. 5885-5594.
[abstract, html, pdf]
Kanduri C, Kuusi T, Ahvenainen M, Philips AK, Lähdesmäki H, Järvelä I,
The effect of music performance on the transcriptome of professional musicians,
Scientific Reports, Vol. 5, No. 9506, 2015.
[abstract, html, pdf]
Kanduri C, Raijas P, Ahvenainen M, Philips AK, Ukkola-Vuoti L, Lähdesmäki H, Järvelä I,
The effect of listening to music on human transcriptome,
PeerJ, Vol. 3, e830, 2015.
[abstract, html, pdf]
Vatanen T, Osmala M, Raiko T, Lagus K, Sysi-Aho M, Oresic M, Honkela T, Lähdesmäki H,
Self-organization and missing values in SOM and GTM,
Neurocomputing, Vol. 147, pp. 60-70, 2015.
[abstract, html, pdf]
Kumar V, Gutierrez-Achury J, Kanduri K, Almeida R, Hrdlickova B,
Zhernakova DV, Westra H-J, Karjalainen J, Ricaño-Ponce I, Li Y, Stachurska A, Tigchelaar EF, Abdulahad WH,
Lähdesmäki H, Hofker MH, Zhernakova A, Franke L, Lahesmaa R, Wijmenga
C, Withoff S,
Systematic annotation of celiac
disease loci refines pathological pathways and suggests a genetic
explanation for increased interferon-gamma levels,
Human Molecular Genetics, Vol. 24, No. 2, pp. 397-409, 2015.
[abstract, html, pdf, supp.]
Heinonen M, Kandury K, Lähdesmäki H, Lahesmaa R, Henttinen T,
Tubulin- and actin-associating GIMAP4 is required for IFN-γ secretion during Th cell differentiation,
Immunology and Cell Biology, Vol. 93, pp. 158-166, 2015.
[abstract, html, pdf, supp.]
Halla-aho V, Mannerström H, Lähdesmäki H,
A probabilistic method for quantifying chromatin interactions,
In Machine Learning in Computational Biology, Montreal, Canada, December 12, 2015.
[pdf]
2014
Hawkins RD¶*, Larjo A*, Tripathi SK*, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H¶, Lahesmaa R¶,
Global chromatin state analysis
reveals lineage-specific enhancers during the initiation of human T
helper 1 and T helper 2 cell polarization,
Immunity, Vol. 38, No. 6, pp. 1271-1284, 2013.
[abstract, html, pdf, suppl.] [pdf]
Närvä E, Pursiheimo J-P, Laiho A, Rahkonen N, Emania MR, Viitala M,
Laurila K, Sahla R, Lund R, Lähdesmäki H, Jaakkola P and Lahesmaa R,
Continuous hypoxic culturing of human embryonic stem cells enhances Ssea-3 and Myc levels,
PLoS ONE, Vol. 8, No. 11, e78847, 2013.
[abstract, html, pdf] [pdf]
Ko M, An J, Bandukwala HS, Chavez L, Äijö T, Pastor WA, Segal MF, Li H, Koh KP, Lähdesmäki H, Hogan PG, Aravind L, Rao A,
Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX,
Nature, Vol. 497, No. 7447, pp. 122-126, 2013.
[abstract, html, pdf] [pdf]
Kähärä J, Lähdesmäki H,
Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data,
BMC Bioinformatics, 14(Suppl 10):S2, 2013.
[abstract, html, pdf] [pdf]
Äijö T, Granberg K, Lähdesmäki H,
Sorad: A systems biology approach to
predict and modulate dynamic signaling pathway response from
phosphoproteome time-course measurements,
Bioinformatics, Vol. 29, No. 10, pp. 1283-1291, 2013.
[abstract, html, pdf, suppl.] [pdf]
[software]
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TJ,
Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 consortium,
Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR,
Evaluation of methods for modeling transcription factor sequence specificity,
Nature Biotechnology, Vol. 31, No. 2, pp. 126-134, 2013.
[abstract, html, pdf, suppl.] [pdf]
Tahvanainen J, Kyläniemi MK, Kanduri K, Gupta B, Lähteenmäki H,
Kallonen T, Rajavuori A, Rasool O, Koskinen PJ, Rao KVS, Lähdesmäki H,
Lahesmaa R,
Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation,
The Journal of Biological Chemistry, Vol. 288, No. 5, pp. 3048-3058, 2013.
[abstract, html, pdf] [pdf]
Kanduri C, Ukkola-Vuoti L, Oikkonen J, Buck G, Blancher C, Raijas P, Karma K, Lähdesmäki H, Järvelä I,
The genome wide landscape of copy
number variations in the isolated Finnish population: the MUSGEN study
provides evidence for a founder effect,
European Journal of Human Genetics, Vol. 288, No. 5, pp. 3048-3058, 2013.
[abstract, html, pdf] [pdf]
Ukkola-Vuoti L, Kanduri C, Oikkonen J, Buck G, Blancher C, Raijas P, Karma K, Lähdesmäki H, Järvelä I,
Genome-wide copy number variation
analysis in extended families and unrelated individuals characterized
for musical aptitude and creativity in music,
PLoS ONE, Vol. 8, No. 2, e56356, 2013.
[abstract+html] [pdf]
Lehmusvaara S, Erkkilä T, Urbanucci A, Jalava S, Seppälä J, Kaipia
A, Kujala P, Lähdesmäki H, Tammela TLJ and Visakorpi T,
Goserelin and bicalutamide treatments
alter the expression of microRNAs in prostate,
The Prostate, Vol. 73, No. 1, pp. 101-112, 2013.
[abstract,
pdf]
2012
Äijö T, Edelman S, Lönnberg T, Larjo A, Järvenpää H, Tuomela S,
Engström E, Lahesmaa R and Lähdesmäki H,
An integrative
computational systems biology approach identifies lineage specific
dynamic transcriptome signatures which drive the initiation of human T
helper cell differentiation,
BMC Genomics, 13:572, 2012.
[abstract,
html, pdf,
suppl.] [pdf]
[software]
Benson MJ, Äijö T, Chang X,
Gagnon J, Pape UJ, Anantharaman V, Aravind L, Pursiheimo J-P,
Oberdoerffer S, Liu XS, Lahesmaa R, Lähdesmäki H and Rao A,
Heterogeneous
nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA
polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma
cells,
Proceedings
of the National Academy of Sciences of the USA, Vol. 109, No. 40, pp. 16252-16257, 2012.
[abstract,
pdf,
suppl.]
[pdf]
Tuomela S, Salo V, Tripathi SK, Chen Z, Laurila K, Äijö T, Gupta B,
Oikari L, Stockinger B, Lähdesmäki H and Lahesmaa R,
Identification of early gene
expression changes during human Th17 cell differentiation,
Blood, Vol. 119, No. 23, pp.
e151-160, 2012.
[abstract,
pdf,
suppl.]
[pdf]
Lehmusvaara
S, Erkkilä T, Urbanucci A, Waltering K, Seppälä J, Tuominen V,
Isola J, Kujala P, Lähdesmäki H, Kaipia A, Tammela TLJ and Visakorpi T,
Chemical castration and antiandrogens
induce differential gene expression in prostate cancer,
The Journal of Pathology, Vol.
227, No. 3, pp. 336--345, 2012.
[abstract,
html,
pdf,
suppl.]
[pdf]
Jalava SE, Urbanucci A, Latonen LM, Waltering KK, Sahu B, Jänne OA,
Seppälä J, Lähdesmäki H, Tammela TLJ and Visakorpi T,
Androgen-regulated miR-32 targets BTG2
and is overexpressed in castration-resistant prostate cancer,
Oncogene, Vol. 31, No. 41, pp.
4460-4471, 2012.
[abstract,
html,
pdf,
suppl.]
[pdf]
Urbanucci A, Sahu B,
Seppälä J, Larjo A, Latonen LM, Waltering KK, Tammela TLJ, Vessella RL,
Lähdesmäki H, Jänne OA and Visakorpi T,
Overexpression of androgen receptor
enhances the binding of the receptor to the chromatin in prostate cancer,
Oncogene, Vol. 31, No. 17, pp.
2153-2163, 2012.
[abstract,
html,
pdf,
suppl.]
[pdf]
Närvä E,
Rahkonen N, Emani MR, Lund R, Pursiheimo J-P, Nästi J, Autio R, Rasool
O, Denessiouk K, Lähdesmäki H, Rao A and Lahesmaa R,
RNA binding protein L1TD1
interacts with LIN28 via RNA and is required for human embryonic stem
cell self-renewal and cancer cell proliferation,
Stem Cells, Vol. 30, No. 3,
pp. 452-460, 2012.
[abstract,
pdf]
[pdf]
2011
Annala, M., Laurila, K., Lähdesmäki, H., and Nykter, M.,
A linear model for transcription
factor binding affinity prediction in protein binding microarrays,
PLoS ONE, 6(5): e20059, 2011.
[html,
pdf]
[pdf]
[software]
Porkka, K. P., Ogg, E.-L.,
Saramäki, O. R., Vessella, R. L., Pukkila, H., Lähdesmäki, H., van
Weerden, W. M., Wolf, M., Kallioniemi, O. P., Jenster, G. and
Visakorpi, T.,
The miR-15a-miR-16-1 locus is
homozygously deleted in a subset of prostate cancers,
Genes, Chromosomes and Cancer,
Vol. 50, No. 7, pp. 499-509, 2011.
[abstract,
html,
pdf]
[pdf]
2010
Erkkilä, T., Lehmusvaara, S., Ruusuvuori, P., Visakorpi, T.,
Shmulevich, I. and Lähdesmäki, H.,
Probabilistic analysis of gene
expression measurements from heterogeneous tissues,
Bioinformatics, Vol. 26, No.
20, pp. 2571-2577, 2010.
[abstract,
html,
pdf,
supplementary
material] [pdf, supplementary material]
[software, web tool]
Elo,
L. L., Järvenpää, H., Tuomela, S., Raghav, S., Ahlfors, H., Laurila,
K., Gupta, B., Lund, R. J., Tahvanainen, J., Hawkins, D., Oresic, M.,
Lähdesmäki, H., Rasool, O., Rao, K. V., Aittokallio, T. and Lahesmaa,
R.,
Genome-wide Profiling of Interleukin-4
and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming,
Immunity, Vol. 32, No. 6, pp.
727-862, 2010.
[abstract,
html,
pdf,
supplementary
material] [pdf]
Aho,
T., Almusa, H., Matilainen, J., Larjo, A., Ruusuvuori, P., Aho, K.-L.,
Wilhelm, T., Lähdesmäki, H., Beyer, A., Harju, M., Chowdhury, S.,
Leinonen, K, Roos, C. and Yli-Harja, O.,
Reconstruction and validation of
RefRec: a global model for the yeast molecular interaction network,
PLoS ONE, 5(5):e10662, 2010.
[html,
pdf]
[pdf]
Dai,
X. and Lähdesmäki, H.,
Novel data fusion method and
exploration of multiple information sources for transcription factor
target gene prediction,
EURASIP Journal on Advances in Signal
Processing, Special issue on Genomic Signal Processing, Vol.
2010, Article ID 235795, 2010.
[abstract,
html,
pdf]
[pdf]
2009
Laurila, K. and
Lähdesmäki, H.,
A protein-protein
interaction guided method for competitive transcription factor binding
improves target predictions,
Nucleic Acids Research, Vol.
37, No. 22, e146, 2009.
[abstract,
html,
pdf, supplementary
material: pdf]
[software]
Äijö, T. and
Lähdesmäki, H.,
Learning gene regulatory
networks from gene expression measurements using non-parametric
molecular kinetics,
Bioinformatics, Vol. 25, No.
22, pp. 2937-2944, 2009.
[abstract,
pdf]
[pdf, supplementary material: pdf]
[software]
Laurila, K. and
Lähdesmäki, H.,
Systematic analysis of
disease-related regulatory mutation classes reveals distinct effects on
transcription factor binding,
In Silico Biology,
Vol. 9, 0018, 2009.
[abstract,
html]
[pdf-preprint]
Dai, X., Erkkilä, T.,
Yli-Harja, O. and Lähdesmäki, H.,
A joint mixture model for
clustering genes from Gaussian and beta distributed data,
BMC Bioinformatics
10:165, 2009.
[abstract,
html, pdf]
[pdf]
Dai, X.,
Lähdesmäki, H. and Yli-Harja, O.,
A stratified beta-Gaussian
mixture model for clustering genes with multiple data sources,
International Journal
on Advances in Life Sciences, Vol. 1, No. 1, pp. 14-25, 2009.
[pdf]
Nykter,
M., Lähdesmäki, H., Rust, A. G., Thorsson, V.
and Shmulevich, I.,
A data integration
framework for prediction of transcription factor targets: a BCL6 case
study,
Annals of the New York
Academy of Sciences, Vol. 1158, pp. 205-214, 2009.
[abstract,
html,
pdf]
[pdf]
2008
Lähdesmäki, H.,
Rust, A. G. and Shmulevich, I.,
Probabilistic inference of transcription factor binding from multiple
data sources,
PLoS ONE, Vol. 3,
No. 3, e1820, 2008.
[pdf,
html]
[pdf]
[web tool, software]
Lähdesmäki, H.
and Shmulevich, I.,
Learning the structure of
dynamic Bayesian networks from time series and steady state measurements,
Machine Learning, Vol. 71, No. 2-3,
pp. 185-217, 2008.
[abstract,
pdf]
[pdf]
[software]
Liu, W.,
Lähdesmäki, H., Dougherty, E. R. and Shmulevich, I.,
Inference of Boolean networks using
sensitivity regularization,
EURASIP
Journal on Bioinformatics and Systems Biology,
Vol. 2008, Article ID 780541, 12 pages, 2008.
[abstract,
pdf]
[pdf]
2007
Ahdesmäki, M.,
Lähdesmäki, H., Gracey, A., Shmulevich, I. and Yli-Harja O.,
Robust regression for periodicity detection in
non-uniformly sampled time-course gene expression data,
BMC Bioinformatics,
8:233, 2007.
[abstract,
html,
pdf]
[pdf, supplementary
material and software]
2006
Lähdesmäki, H.,
Hautaniemi,
S., Shmulevich, I. and Yli-Harja, O.,
Relationships between probabilistic Boolean networks and
dynamic Bayesian networks as models of gene regulatory networks,
Signal Processing , Vol. 86, No. 4, pp. 814-834,
April 2006.
[pdf]
[html, pdf]
2005
Ahdesmäki, M.,*
Lähdesmäki, H.,* Pearson, R., Huttunen, H. and Yli-Harja, O.,
Robust detection of periodic time series measured from
biological systems,
BMC Bioinformatics, 6:117, 2005.
[abstract,
html,
pdf]
[pdf, supplementary
material and software]
(*equally contributing authors)
Lähdesmäki, H.,
Shmulevich, I., Dunmire, V., Yli-Harja O. and Zhang, W.,
In silico microdissection of microarray data from
heterogeneous cell populations,
BMC Bioinformatics, 6:54, 2005.
[abstract,
html,
pdf] [pdf]
2004
Lähdesmäki, H.,
Hao, X., Sun, B.,
Hu, L., Yli-Harja, O., Shmulevich, I. and Zhang, W.,
Distinguishing key biological pathways between primary
breast cancers and their lymph node metastases by gene function-based
clustering analysis,
International
Journal of Oncology, Vol. 24, No. 6, pp. 1589-1596, June 2004.
[pdf]
Hao, X., Sun, B., Hu, L.,
Lähdesmäki, H., Dunmire, V., Feng, Y., Zhang, S.-W., Wang,
H., Wu, C.,
Wang, H., Fuller, G. N., Symmans, W. F., Shmulevich, I. and Zhang, W.,
Differential gene and protein expression in primary
breast malignancies and their lymph node metastases as revealed by
combined cDNA microarray and tissue microarray analysis,
Cancer, Vol.
100, No. 6, pp. 1110-1122, 2004.
[pdf]
[abstract,
html,
pdf]
Shmulevich, I.
Lähdesmäki, H. and Egiazarian, K.
Spectral methods for testing membership in certain Post
classes and the class of forcing functions,
IEEE Signal
Processing Letters, Vol. 11, No. 2, pp. 289-292, 2004.
[pdf]
[abstract,
pdf]
2003
Shmulevich, I.,
Lähdesmäki, H.,
Dougherty, E. R., Astola, J. and Zhang, W.,
The role of certain Post classes in Boolean network
models of genetic networks,
Proceedings
of the National Academy of Sciences of the USA, Vol. 100, No. 19,
pp. 10734-10739, 2003.
[pdf]
[abstract,
html,
pdf]
Lähdesmäki, H.,
Shmulevich, I.
and Yli-Harja, O.,
On learning gene regulatory networks under the Boolean
network model,
Machine Learning, Vol. 52, No. 1-2, pp. 147-167,
June
- August 2003.
[pdf]
[abstract,
pdf]
Lähdesmäki, H.,
Huttunen, H.,
Aho, T., Linne, M.-L., Niemi, J., Kesseli, J., Pearson, R. and
Yli-Harja, O.,
Estimation and inversion of the effects of cell
population asynchrony in gene expression time-series,
Signal
Processing, Vol. 83, No. 4, pp. 835-858, April 2003.
[pdf]
[abstract, html,
pdf]
2016
Heinonen M, Mannerström H, Rousu J, Kaski S, Lähdesmäki H,
Non-stationary Gaussian process regression with Hamiltonian Monte Carlo,
In Proceedings of the Eighteenth International Conference on Artificial Intelligence and Statistics (AISTATS) 2016, to appear.
[abstract, pdf, suppl]
[Software]
2015
Halla-aho V, Mannerström H, Lähdesmäki H,
A probabilistic method for quantifying chromatin interactions,
In Machine Learning in Computational Biology, Montreal, Canada, December 12, 2015.
[pdf]
2013
Larjo A, Lähdesmäki H,
Active learning for Bayesian network models of biological networks using structure priors,
In IEEE International Workshop on Genomic Signal Processing and Statistics, Houston, TX, USA, November 17-19, 2013.
[pdf]
2010
Erkkilä, T., Thorsson, V., Lähdesmäki, H. and Shmulevich, I.,
Inferring genetic regulatory interactions from time-collapsed Boolean summary variables,
In Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010.
[pdf]
2009
Laurila, K.
and Lähdesmäki, H.,
A probabilistic model for
competitive binding of transcription factors,
In Sixth International
Workshop on Computational Systems Biology, WCSB 2009,
Århus, Denmark, June 10-12, 2009.
[pdf]
Dai, X. and
Lähdesmäki, H.,
A unified probabilistic
framework for clustering genes from gene expression and protein-protein
interaction data,
In Sixth International
Workshop on Computational Systems Biology, WCSB 2009, Århus,
Denmark, June 10-12, 2009.
[pdf]
2008
Dai, X.,
Lähdesmäki, H. and Yli-Harja, O.,
sBGMM: a stratified
Beta-Gaussian mixture model for clustering genes with multiple data
sources,
In International Conference on
Biocomputation, Bioinformatics, and Biomedical Technologies, BIOTECHNO
2008, June 29 - July 5, 2008 - Bucharest, Romania.
[pdf]
Laurila, K. and
Lähdesmäki, H.,
Effects of disease-related mutations on transcription factor binding,
In Fifth International Workshop on
Computational Systems Biology (WCSB08), Leipzig, Germany, June
11-13, 2008.
[pdf]
Larjo, A.,
Lähdesmäki, H., Facciotti, M., Baliga, N., Yli-Harja, O. and
Shmulevich, I.,
Active learning of
Bayesian network structure in a realistic setting,
In Fifth International Workshop on
Computational Systems Biology (WCSB08), Leipzig, Germany, June
11-13, 2008.
[pdf]
Nikkilä,
J., Erkkilä, T. and Lähdesmäki, H.,
Decomposing gene
expression into regulatory and differential parts with Bayesian data
fusion,
In Fifth International Workshop on
Computational Systems Biology (WCSB08), Leipzig, Germany, June
11-13, 2008.
[pdf]
Erkkilä,
T., Nykter, M., Lähdesmäki, H., Ahdesmäki, M and
Yli-Harja, O.,
Testing for differential
expression in simulated and real cDNA microarray data using frequentist
and Bayesian methods,
In Fifth International Workshop on
Computational Systems Biology (WCSB08), Leipzig, Germany, June
11-13, 2008.
[pdf]
Dai, X.,
Lähdesmaki, H. and Yli-Harja, O.,
BGMM: a Beta-Gaussian
mixture model for clustering genes with multiple data sources,
In Fifth International Workshop on
Computational Systems Biology (WCSB08), Leipzig, Germany, June
11-13, 2008.
[pdf]
2007
Lähdesmäki, H.
and Shmulevich, I.,
Probabilistic framework for transcription factor binding
prediction,
In Fifth IEEE International
Workshop on Genomic Signal
Processing and Statistics (Gensips'07), Tuusula, FINLAND, June
10-12, 2007.
[pdf]
Ahdesmäki,
M., Lähdesmäki, H. and Yli-Harja O.,
Robust Fisher's test for
periodicity detection in noisy biological time series,
In Fifth IEEE International
Workshop on Genomic Signal
Processing and Statistics (Gensips'07),
Tuusula, FINLAND, June 10-12, 2007.
[pdf]
2005
Lähdesmäki, H.,
Yli-Harja, O., Zhang, W. and Shmulevich, I.,
Intrinsic dimensionality in gene expression analysis,
In IEEE International Workshop on Genomic Signal Processing and
Statistics (GENSIPS) 2005, Hyatt Regent Hotel, Newport, Rhode
Island, May 22 - 24, 2005.
[pdf]
2003
Pearson, R. K.,
Lähdesmäki, H., Huttunen, H. and Yli-Harja, O.,
Detecting periodicity in nonideal datasets,
In SIAM International Conference on Data Mining (2003),
Cathedral Hill Hotel, San Francisco, CA, May 1-3, 2003.
[pdf]
2001
Lähdesmäki,
H., Shmulevich, I., Pezzati, L. and Tozzi, A.,
Optimization of edge detectors for topographic maps of
cave inscriptions,
In 12th Scandinavian Conference on
Image Analysis (SCIA 2001), Bergen, Norway, June 11-14, 2001, pp.
280-287.
[pdf]
Kartiek Kanduri,
Integration of genome-wide datasets to understand regulation of human T-helper cell differentiation,
Ph.D., University of Turku, June 2020.
[pdf]
Rautio S,
Bioinformatic methods to understand gene expression and its regulation,
D.Sc. (Tech.) thesis, Aalto University School of Science, January 2019.
[pdf]
Timo Erkkilä,
Mixture models for probabilistic analysis of genomic data,
D.Sc. (Tech.) thesis, Tampere University of Technology, December 2018.
[pdf]
Vatanen T,
Metagenomic analyses of the human gut microbiome reveal connections to the immune system,
D.Sc. (Tech.) thesis, Aalto University School of Science, March 2017.
[pdf]
Larjo A,
Computational methods for modelling and analysing biological networks,
D.Sc. (Tech.) thesis, Tampere University of Technology, March 2015.
[pdf]
(Co-supervised with O. Yli-Harja from TUT.)
Äijö T,
Computational Methods for Analysis of
Dynamic Transcriptome and Its Regulation Through Chromatin Remodeling
and Intracellular Signaling,
D.Sc. (Tech.) thesis, Aalto University School of Science, October 2014.
[pdf]
Laurila K,
Computational Approaches for Analyzing Gene Regulatory Processes,
D.Sc. (Tech.) thesis, Tampere University of Technology, August 2011.
[pdf]
(Co-supervised with O. Yli-Harja from TUT. Accepted with distinction. The best PhD thesis in 2011 granted by the Finnish Society for Bioinformatics.)
Lähdesmäki,
H.,
Computational Methods for Systems Biology: Analysis
of High-Throughput Measurements and Modeling of Genetic Regulatory
Networks,
Ph.D. Thesis, Tampere University of Technology, October 2005.
[Table
of Contents: pdf][*pdf]
*The doctoral thesis consists of an introduction (94 pages) and nine
(9) original publications that are included as an appendix. Please note
that the original publications are not included into the pdf-file.
Most of the original publications can be found from this web page.
Michele Vantini,
Gaussian process modeling of gene expression time series from multi-condition paired experimental design,
M.Sc. thesis, Aalto University, 09/2020.
[pdf]
Saara Hiltunen,
Integrating multi-tube flow cytometry data via deep generative modelling,
M.Sc. thesis, Aalto University, 08/2020.
[pdf]
Valerii Iakovlev,
Learning partial differential equations from data,
M.Sc. thesis, Aalto University, June 2020.
[pdf]
Johanna Vikkula,
Modelling transcriptional velocities and latent dynamics of single cells,
M.Sc. thesis, Aalto University, May 2020.
[pdf]
Qianqian Qin,
Identifying phenotypes based on TCR repertoire using machine learning methods,
M.Sc. thesis, Aalto University, May 2020.
[pdf]
Ranchandran S,
Latent Gaussian processes with composite likelihoods for data-driven disease stratification,
M.Sc. thesis, Aalto University, August 2019.
[link]
Danmei Huang,
Statistical data analysis for biomarker discovery and type 1 diabetes
prediction,
M.Sc. thesis, University of Helsinki, December 2018.
[pdf]
Antikainen A,
Modeling protein-DNA binding specificities with random forest,
M.Sc. thesis, Aalto University, January 2018.
[pdf]
Timonen J,
An efficient strategy to infer biochemical networks by means of statistical calibration of mechanistic models,
M.Sc. thesis, Aalto University, November 2017.
[pdf]
Jokinen E,
Modeling protein stability with Gaussian processes,
M.Sc. thesis, Aalto University, August 2016.
[pdf]
Kari M,
A parallel forward selection wrapper for genome wide association studies,
M.Sc. thesis, Aalto University, June 2016.
[pdf]
Chan, Louis Yat Hin
Experimentally-based mathematical modeling to analyze T helper 17 cell differentiation in heterogeneous cell populations,
M.Sc. thesis, University of Helsinki, December 2015.
[pdf]
Halla-aho V,
A probabilistic method for quantifying chromatin interactions,
M.Sc. thesis, Aalto University, November 2015.
[pdf]
Khakipoor B,
Integrated data analysis pipeline for whole human genome transcription factor binding sites prediction,
M.Sc. thesis, Aalto University, June 2015.
[pdf]
Eraslan B,
A probabilistic model for competitive binding of DNA binding proteins using ChIP-seq and MNase-seq data,
M.Sc. thesis, Aalto University, May 2015.
[pdf]
Eraslan G,
A Dirichlet-multinomial mixture model for clustering heterogeneous epigenomics data,
M.Sc. thesis, Aalto University, September 2014.
[pdf]
Kähärä J,
Using DNase I hypersensitivity Data for Transcription Factor Binding Predictions,
M.Sc. thesis, Aalto University, May 2014.
[pdf]
Somani J,
Identifying associations between host genotype and gut microbiota using statistical and computational models,
M.Sc. thesis, Aalto University, October 2013.
[pdf]
Rautio S,
Analyzing time-series RNA-seq data for T helper cell differentiation in mouse and human,
M.Sc. thesis, Aalto University, December 2012.
[pdf]
Malonzo M,
RNA-seq analysis of stem cells for differential gene expression and alternative splicing,
M.Sc. thesis, Aalto University, October 2012.
[pdf]
Prakash K,
A binary combinatorial histone code,
M.Sc. thesis, Aalto University, March 2012.
[pdf]
Laajala E,
Type 1 diabetes biomarkers in human whole blood transcriptome,
M.Sc. thesis, Aalto University, November 2011.
[pdf]
Laurila K,
In silico analysis of point mutation effects on transcription factor binding and protein subcellular localization,
M.Sc. thesis, University of Tampere, April, 2010.
[pdf]
Äijö T,
Learning the structure of an in vitro gene regulatory network using Gaussian processes,
M.Sc. thesis, Tampere University of Technology, July 2009.
[pdf]
(Co-supervised with O. Yli-Harja from TUT.)
Sahla R,
Vaihtoehtoisen silmukoinnin tutkiminen RNA-sekvensointimittauksilla,
B.Sc. thesis, Aalto University, May 2012.
[pdf]
Somani J,
Systems biology methods to study naive T helper cell activation at a transcriptome level,
B.Sc. thesis, Aalto University, December 2010.
Äijö T,
Gaussin Prosessit Regressioanalyysissä,
B.Sc. thesis, Tampere University of Technology, May 2008.