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Items: 1 to 20 of 72

1.

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.

2.

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.

PMID:
27869820
3.

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
4.

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.

5.

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.

PMID:
27587669
6.

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.

7.

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.

PMID:
27259157
8.

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.

PMID:
27133167
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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
20.

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.

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