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Items: 1 to 50 of 90

1.

Bayesian metabolic flux analysis reveals intracellular flux couplings.

Heinonen M, Osmala M, Mannerström H, Wallenius J, Kaski S, Rousu J, Lähdesmäki H.

Bioinformatics. 2019 Jul 15;35(14):i548-i557. doi: 10.1093/bioinformatics/btz315.

2.

Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease.

Konki M, Malonzo M, Karlsson IK, Lindgren N, Ghimire B, Smolander J, Scheinin NM, Ollikainen M, Laiho A, Elo LL, Lönnberg T, Röyttä M, Pedersen NL, Kaprio J, Lähdesmäki H, Rinne JO, Lund RJ.

Clin Epigenetics. 2019 Sep 2;11(1):130. doi: 10.1186/s13148-019-0729-7.

3.

Early Detection of Peripheral Blood Cell Signature in Children Developing Beta-Cell Autoimmunity at a Young Age.

Kallionpää H, Somani J, Tuomela S, Ullah U, de Albuquerque R, Lönnberg T, Komsi E, Siljander H, Honkanen J, Härkönen T, Peet A, Tillmann V, Chandra V, Anagandula MK, Frisk G, Otonkoski T, Rasool O, Lund R, Lähdesmäki H, Knip M, Lahesmaa R.

Diabetes. 2019 Jul 16. pii: db190287. doi: 10.2337/db19-0287. [Epub ahead of print]

PMID:
31311800
4.

An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data.

Cheng L, Ramchandran S, Vatanen T, Lietzén N, Lahesmaa R, Vehtari A, Lähdesmäki H.

Nat Commun. 2019 Apr 17;10(1):1798. doi: 10.1038/s41467-019-09785-8.

5.

Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ.

Nat Microbiol. 2019 Mar;4(3):545. doi: 10.1038/s41564-019-0393-x.

PMID:
30723264
6.

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ.

Nat Microbiol. 2019 Mar;4(3):470-479. doi: 10.1038/s41564-018-0321-5. Epub 2018 Dec 17. Erratum in: Nat Microbiol. 2019 Feb 5;:.

7.

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.

Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ.

Nature. 2018 Oct;562(7728):589-594. doi: 10.1038/s41586-018-0620-2. Epub 2018 Oct 24.

8.

Generative Models for Quantification of DNA Modifications.

Äijö T, Bonneau R, Lähdesmäki H.

Methods Mol Biol. 2018;1807:37-50. doi: 10.1007/978-1-4939-8561-6_4.

PMID:
30030802
9.

A probabilistic framework for molecular network structure inference by means of mechanistic modeling.

Timonen J, Mannerstrom H, Lahdesmaki H, Intosalmi J.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Apr 10. doi: 10.1109/TCBB.2018.2825327. [Epub ahead of print]

PMID:
29993837
10.

mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion.

Jokinen E, Heinonen M, Lähdesmäki H.

Bioinformatics. 2018 Jul 1;34(13):i274-i283. doi: 10.1093/bioinformatics/bty238.

11.

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.

Bioinformatics. 2018 Dec 1;34(23):4112-4114. doi: 10.1093/bioinformatics/bty460.

12.

Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells.

Mohammad I, Nousiainen K, Bhosale SD, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z.

PLoS Biol. 2018 May 31;16(5):e2004194. doi: 10.1371/journal.pbio.2004194. eCollection 2018 May.

13.

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

Schmidt A, Marabita F, Kiani NA, Gross CC, Johansson HJ, Éliás S, Rautio S, Eriksson M, Fernandes SJ, Silberberg G, Ullah U, Bhatia U, Lähdesmäki H, Lehtiö J, Gomez-Cabrero D, Wiendl H, Lahesmaa R, Tegnér J.

BMC Biol. 2018 May 7;16(1):47. doi: 10.1186/s12915-018-0518-3.

14.

Atopic asthma after rhinovirus-induced wheezing is associated with DNA methylation change in the SMAD3 gene promoter.

Lund RJ, Osmala M, Malonzo M, Lukkarinen M, Leino A, Salmi J, Vuorikoski S, Turunen R, Vuorinen T, Akdis C, Lähdesmäki H, Lahesmaa R, Jartti T.

Allergy. 2018 Aug;73(8):1735-1740. doi: 10.1111/all.13473. Epub 2018 May 21.

15.

Characterization and non-parametric modeling of the developing serum proteome during infancy and early childhood.

Lietzén N, Cheng L, Moulder R, Siljander H, Laajala E, Härkönen T, Peet A, Vehtari A, Tillmann V, Knip M, Lähdesmäki H, Lahesmaa R.

Sci Rep. 2018 Apr 12;8(1):5883. doi: 10.1038/s41598-018-24019-5.

16.

Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells.

Ubaid Ullah, Andrabi SBA, Tripathi SK, Dirasantha O, Kanduri K, Rautio S, Gross CC, Lehtimäki S, Bala K, Tuomisto J, Bhatia U, Chakroborty D, Elo LL, Lähdesmäki H, Wiendl H, Rasool O, Lahesmaa R.

Cell Rep. 2018 Feb 20;22(8):2094-2106. doi: 10.1016/j.celrep.2018.01.070.

17.

Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation.

Tripathi SK, Chen Z, Larjo A, Kanduri K, Nousiainen K, Äijo T, Ricaño-Ponce I, Hrdlickova B, Tuomela S, Laajala E, Salo V, Kumar V, Wijmenga C, Lähdesmäki H, Lahesmaa R.

Cell Rep. 2017 May 30;19(9):1888-1901. doi: 10.1016/j.celrep.2017.05.013.

18.

RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells.

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.

Stem Cell Reports. 2017 May 9;8(5):1442-1454. doi: 10.1016/j.stemcr.2017.04.016.

19.

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.

van Dijk AD, Lähdesmäki H, de Ridder D, Rousu J.

BMC Bioinformatics. 2016 Dec 13;17(Suppl 16):437. doi: 10.1186/s12859-016-1305-1. No abstract available.

20.

TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells.

Tsagaratou A, González-Avalos E, Rautio S, Scott-Browne JP, Togher S, Pastor WA, Rothenberg EV, Chavez L, Lähdesmäki H, Rao A.

Nat Immunol. 2017 Jan;18(1):45-53. doi: 10.1038/ni.3630. Epub 2016 Nov 21.

21.

A subpopulation model to analyze heterogeneous cell differentiation dynamics.

Chan YH, Intosalmi J, Rautio S, Lähdesmäki H.

Bioinformatics. 2016 Nov 1;32(21):3306-3313. Epub 2016 Jul 10.

PMID:
27402901
22.

Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells.

Rahkonen N, Stubb A, Malonzo M, Edelman S, Emani MR, Närvä E, Lähdesmäki H, Ruohola-Baker H, Lahesmaa R, Lund R.

Stem Cell Res. 2016 Nov;17(3):498-503. doi: 10.1016/j.scr.2016.09.025. Epub 2016 Sep 24.

23.

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

Äijö T, Yue X, Rao A, Lähdesmäki H.

Bioinformatics. 2016 Sep 1;32(17):i511-i519. doi: 10.1093/bioinformatics/btw468.

24.

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

Intosalmi J, Nousiainen K, Ahlfors H, Lähdesmäki H.

Bioinformatics. 2016 Jun 15;32(12):i288-i296. doi: 10.1093/bioinformatics/btw274.

25.

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Cell. 2016 Jun 2;165(6):1551. doi: 10.1016/j.cell.2016.05.056. No abstract available.

26.

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Cell. 2016 May 5;165(4):842-53. doi: 10.1016/j.cell.2016.04.007. Epub 2016 Apr 28. Erratum in: Cell. 2016 Jun 2;165(6):1551.

27.

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.

Äijö T, Huang Y, Mannerström H, Chavez L, Tsagaratou A, Rao A, Lähdesmäki H.

Genome Biol. 2016 Mar 14;17:49. doi: 10.1186/s13059-016-0911-6.

28.

Comparative analysis of human and mouse transcriptomes of Th17 cell priming.

Tuomela S, Rautio S, Ahlfors H, Öling V, Salo V, Ullah U, Chen Z, Hämälistö S, Tripathi SK, Äijö T, Rasool O, Soueidan H, Wessels L, Stockinger B, Lähdesmäki H, Lahesmaa R.

Oncotarget. 2016 Mar 22;7(12):13416-28. doi: 10.18632/oncotarget.7963.

29.

Epigenetic Silencing of the Key Antioxidant Enzyme Catalase in Karyotypically Abnormal Human Pluripotent Stem Cells.

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.

Sci Rep. 2016 Feb 25;6:22190. doi: 10.1038/srep22190.

30.

Control of Foxp3 stability through modulation of TET activity.

Yue X, Trifari S, Äijö T, Tsagaratou A, Pastor WA, Zepeda-Martínez JA, Lio CW, Li X, Huang Y, Vijayanand P, Lähdesmäki H, Rao A.

J Exp Med. 2016 Mar 7;213(3):377-97. doi: 10.1084/jem.20151438. Epub 2016 Feb 22.

31.

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae.

Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D.

PLoS One. 2016 Feb 22;11(2):e0148320. doi: 10.1371/journal.pone.0148320. eCollection 2016.

32.

MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis.

Rautio S, Lähdesmäki H.

BMC Bioinformatics. 2015 Dec 24;16:413. doi: 10.1186/s12859-015-0834-3.

33.

Identification of global regulators of T-helper cell lineage specification.

Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R.

Genome Med. 2015 Nov 20;7:122. doi: 10.1186/s13073-015-0237-0.

34.

Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data.

Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H.

BMC Syst Biol. 2015 Nov 17;9:81. doi: 10.1186/s12918-015-0223-6.

35.

Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex.

Balasubramani A, Larjo A, Bassein JA, Chang X, Hastie RB, Togher SM, Lähdesmäki H, Rao A.

Nat Commun. 2015 Jun 22;6:7307. doi: 10.1038/ncomms8307.

36.

Using multi-step proposal distribution for improved MCMC convergence in Bayesian network structure learning.

Larjo A, Lähdesmäki H.

EURASIP J Bioinform Syst Biol. 2015 Jun 20;2015:6. doi: 10.1186/s13637-015-0024-7. eCollection 2015 Dec.

37.

The landscape of copy number variations in Finnish families with autism spectrum disorders.

Kanduri C, Kantojärvi K, Salo PM, Vanhala R, Buck G, Blancher C, Lähdesmäki H, Järvelä I.

Autism Res. 2016 Jan;9(1):9-16. doi: 10.1002/aur.1502. Epub 2015 Jun 6.

PMID:
26052927
38.

GIMAP GTPase family genes: potential modifiers in autoimmune diabetes, asthma, and allergy.

Heinonen MT, Laine AP, Söderhäll C, Gruzieva O, Rautio S, Melén E, Pershagen G, Lähdesmäki HJ, Knip M, Ilonen J, Henttinen TA, Kere J, Lahesmaa R; Finnish Pediatric Diabetes Registry.

J Immunol. 2015 Jun 15;194(12):5885-94. doi: 10.4049/jimmunol.1500016. Epub 2015 May 11.

39.

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

Kähärä J, Lähdesmäki H.

Bioinformatics. 2015 Sep 1;31(17):2852-9. doi: 10.1093/bioinformatics/btv294. Epub 2015 May 7.

PMID:
25957350
40.

The effect of music performance on the transcriptome of professional musicians.

Kanduri C, Kuusi T, Ahvenainen M, Philips AK, Lähdesmäki H, Järvelä I.

Sci Rep. 2015 Mar 25;5:9506. doi: 10.1038/srep09506.

41.

The effect of listening to music on human transcriptome.

Kanduri C, Raijas P, Ahvenainen M, Philips AK, Ukkola-Vuoti L, Lähdesmäki H, Järvelä I.

PeerJ. 2015 Mar 12;3:e830. doi: 10.7717/peerj.830. eCollection 2015.

42.

The transcription factor NFAT promotes exhaustion of activated CD8⁺ T cells.

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.

Immunity. 2015 Feb 17;42(2):265-278. doi: 10.1016/j.immuni.2015.01.006. Epub 2015 Feb 10.

43.

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 5.

44.

Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells.

Laurila K, Autio R, Kong L, Närvä E, Hussein S, Otonkoski T, Lahesmaa R, Lähdesmäki H.

BioData Min. 2014 Dec 13;7(1):32. doi: 10.1186/s13040-014-0032-2. eCollection 2014.

45.

Serum proteomes distinguish children developing type 1 diabetes in a cohort with HLA-conferred susceptibility.

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.

Diabetes. 2015 Jun;64(6):2265-78. doi: 10.2337/db14-0983. Epub 2015 Jan 23.

46.

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity.

Hrdlickova B, Kumar V, Kanduri K, Zhernakova DV, Tripathi S, Karjalainen J, Lund RJ, Li Y, Ullah U, Modderman R, Abdulahad W, Lähdesmäki H, Franke L, Lahesmaa R, Wijmenga C, Withoff S.

Genome Med. 2014 Oct 28;6(10):88. doi: 10.1186/s13073-014-0088-0. eCollection 2014.

47.

Tubulin- and actin-associating GIMAP4 is required for IFN-γ secretion during Th cell differentiation.

Heinonen MT, Kanduri K, Lähdesmäki HJ, Lahesmaa R, Henttinen TA.

Immunol Cell Biol. 2015 Feb;93(2):158-66. doi: 10.1038/icb.2014.86. Epub 2014 Oct 7.

48.

Standard of hygiene and immune adaptation in newborn infants.

Kallionpää H, Laajala E, Öling V, Härkönen T, Tillmann V, Dorshakova NV, Ilonen J, Lähdesmäki H, Knip M, Lahesmaa R; DIABIMMUNE Study Group.

Clin Immunol. 2014 Nov;155(1):136-47. doi: 10.1016/j.clim.2014.09.009. Epub 2014 Sep 22.

49.

Systematic annotation of celiac disease loci refines pathological pathways and suggests a genetic explanation for increased interferon-gamma levels.

Kumar V, Gutierrez-Achury J, Kanduri K, Almeida R, Hrdlickova B, Zhernakova DV, Westra HJ, 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.

Hum Mol Genet. 2015 Jan 15;24(2):397-409. doi: 10.1093/hmg/ddu453. Epub 2014 Sep 4.

PMID:
25190711
50.

Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation.

Tsagaratou A, Äijö T, Lio CW, Yue X, Huang Y, Jacobsen SE, Lähdesmäki H, Rao A.

Proc Natl Acad Sci U S A. 2014 Aug 12;111(32):E3306-15. doi: 10.1073/pnas.1412327111. Epub 2014 Jul 28.

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