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List of works by Riitta Lahesmaa

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments

scientific article

A mutant collagen XIII alters intestinal expression of immune response genes and predisposes transgenic mice to develop B-cell lymphomas

scientific article

A novel mechanism for ERK-dependent regulation of IL4 transcription during human Th2-cell differentiation

scientific article

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

scientific article

ABC-cassette transporter 1 (ABCA1) expression in epithelial cells in Chlamydia pneumoniae infection

scientific article published on 21 May 2013

AMIGO2 modulates T cell functions and its deficiency in mice ameliorates experimental autoimmune encephalomyelitis.

scientific article published on 11 January 2017

Activating transcription factor 3 is a positive regulator of human IFNG gene expression

scientific article published on 19 March 2010

An IFIH1 gene polymorphism associated with risk for autoimmunity regulates canonical antiviral defence pathways in Coxsackievirus infected human pancreatic islets

scientific article published on 21 December 2016

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

An insight into molecular mechanisms of human T helper cell differentiation

scientific article published on January 2008

An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation

scientific article published in 2012

Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling

scientific article published on 9 November 2017

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

scientific article

Autoimmune regulator induced changes in the gene expression profile of human monocyte-dendritic cell-lineage

scientific article

CD73 participates in cellular multiresistance program and protects against TRAIL-induced apoptosis

scientific article

CIP2A Constrains Th17 Differentiation by Modulating STAT3 Signaling

scientific article published on 27 February 2020

CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection

scientific article (publication date: 2016)

CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases

scientific article published on 20 June 2019

Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response

scientific article

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

scientific article published on 12 April 2018

Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12.

scientific article published in December 2005

Chlamydia pneumoniae entry into epithelial cells by clathrin-independent endocytosis

scientific article published on 21 December 2011

Chlamydia pneumoniae infection in IL-10 knock out mice: accelerated clearance but severe pulmonary inflammatory response

scientific article published on April 2008

Comparative analysis of human and mouse transcriptomes of Th17 cell priming

scientific article published on 07 March 2016

Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels

scientific article published in October 2003

Computational strategies for analyzing data in gene expression microarray experiments

scientific article

Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments

scientific article published in March 2007

Continuous hypoxic culturing of human embryonic stem cells enhances SSEA-3 and MYC levels

scientific article

Copy number variation and selection during reprogramming to pluripotency

scientific article published on March 2011

Coxsackievirus B Persistence Modifies the Proteome and the Secretome of Pancreatic Ductal Cells

scientific article published on 29 July 2019

Coxsackievirus B1 reveals strain specific differences in plasmacytoid dendritic cell mediated immunogenicity

scientific article published on 20 February 2014

DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer

scientific article

Difference in gene expression between human fetal liver and adult bone marrow mesenchymal stem cells.

scientific article published in August 2005

Differential expression of IFN regulatory factor 4 gene in human monocyte-derived dendritic cells and macrophages

scientific article

Distinct sets of developmentally regulated genes that are expressed by human oocytes and human embryonic stem cells

scientific article published on 27 November 2006

Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes

scientific article published on 15 December 2008

ERRATUM: Gene Set Enrichment Analysis Identifies LIF as a Negative Regulator of Human Th2 Cell Differentiation

scholarly article published in Scientific Reports

ESTOOLS Data@Hand: human stem cell gene expression resource.

scientific article published in September 2013

Early DNA methylation changes in children developing beta cell autoimmunity at a young age

scientific article published on 10 February 2022

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

scientific article published on 16 July 2019

Early T helper cell programming of gene expression in human

scientific article

Early signs of disease in type 1 diabetes

scientific article

Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling

article

Early target genes of IL-12 and STAT4 signaling in th cells.

scientific article

Enrichment of nucleofected primary human CD4+ T cells: a novel and efficient method for studying gene function and role in human primary T helper cell differentiation.

scientific article

Enterovirus-associated changes in blood transcriptomic profiles of children with genetic susceptibility to type 1 diabetes

scientific article published on 8 November 2017

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

scientific article

Exosomes with immune modulatory features are present in human breast milk

scientific article

Expression of human pim family genes is selectively up-regulated by cytokines promoting T helper type 1, but not T helper type 2, cell differentiation

scientific article published on 01 September 2005

Expression of leukemia inhibitory factor and its receptors is increased during differentiation of human embryonic stem cells.

scientific article

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

scientific article published on 28 October 2014

Flotillin-1 (Reggie-2) Contributes to Chlamydia pneumoniae Growth and Is Associated with Bacterial Inclusion ⬇️

scientific article published on January 3, 2012

From a gene-centric to whole-proteome view of differentiation of T helper cell subsets

scientific article published on 07 October 2013

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

scientific article published on 11 May 2015

GIMAP Proteins in T-Lymphocytes ⬇️

scientific article published on August 31, 2010

Gene Set Enrichment Analysis Identifies LIF as a Negative Regulator of Human Th2 Cell Differentiation ⬇️

scientific article published on June 18, 2012

Gene expression profiling during differentiation of human monocytes to macrophages or dendritic cells

scientific article published on 26 June 2007

Gene expression profiling of immune-competent human cells exposed to engineered zinc oxide or titanium dioxide nanoparticles

scientific article

Gene expression signatures characterizing the development of lymphocyte response during experimental Chlamydia pneumoniae infection.

scientific article published on 04 February 2009

Gene expression signatures of seven individual human embryonic stem cell lines

scientific article

Genetic and epigenetic stability of human pluripotent stem cells.

scientific article published on 11 September 2012

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

scientific article published in May 2017

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation

Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood ⬇️

scientific article published on November 5, 2012

Genome-wide identification of novel genes involved in early Th1 and Th2 cell differentiation

scientific article published on 01 March 2007

Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming

scientific article

Genomic views of STAT function in CD4+ T helper cell differentiation

scientific article

Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization

scientific article

Global phospholipidomics analysis reveals selective pulmonary peroxidation profiles upon inhalation of single-walled carbon nanotubes

journal article published in 2011

Gut-adipose tissue axis in hepatic fat accumulation in humans.

scientific article

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells

scientific article

Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels

scientific article published on 01 November 2002

High-efficiency gene transfer to primary T lymphocytes by recombinant adenovirus vectors ⬇️

scientific article published on February 1, 2002

High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity

article

High-throughput karyotyping of human pluripotent stem cells.

scientific article published on 11 July 2012

Hyper-phosphorylation of Sequestosome-1 Distinguishes Resistance to Cisplatin in Patient Derived High Grade Serous Ovarian Cancer Cells.

scientific article

IFN-alpha and IL-12 activate IFN regulatory factor 1 (IRF-1), IRF-4, and IRF-8 gene expression in human NK and T cells

scientific article published on 01 November 2003

IL-12 up-regulates T-bet independently of IFN-gamma in human CD4+ T cells

scientific article published on 01 November 2005

Identification of Sphingomyelinase on the Surface of Chlamydia pneumoniae: Possible Role in the Entry into Its Host Cells

scientific article published on 13 March 2014

Identification of early gene expression changes during human Th17 cell differentiation

scientific article published on 27 April 2012

Identification of genes involved in the initiation of human Th1 or Th2 cell commitment

scientific article

Identification of global regulators of T-helper cell lineage specification

scientific article

Identification of novel IL-4/Stat6-regulated genes in T lymphocytes.

scientific article

Identification of novel Stat6 regulated proteins in IL-4-treated mouse lymphocytes

scientific article published in February 2009

Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes

scientific article published on 01 November 2003

Immunological biomarkers for the development and progression of type 1 diabetes

scientific article published on 12 September 2018

Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays

scientific article published in January 2006

In vitro allergen-induced mRNA expression of signaling lymphocytic activation molecule by PBMC of patients with allergic rhinitis is increased during specific pollen immunotherapy

scientific article (publication date: December 2003)

Innate immune activity is detected prior to seroconversion in children with HLA-conferred type 1 diabetes susceptibility

scientific article published on 18 February 2014

Integrating probe-level expression changes across generations of Affymetrix arrays

scientific article

Integration of signals from the B-cell antigen receptor and the IL-4 receptor leads to a cooperative shift in the cellular response axis

scientific article

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

scientific article published on 13 December 2014

Interleukin-4 Inhibits Caspase-3 by Regulating Several Proteins in the Fas Pathway during Initial Stages of Human T Helper 2 Cell Differentiation

article

Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases

scientific article published on 18 July 2013

Kinetics and STAT4- or STAT6-mediated regulation of genes involved in lymphocyte polarization to Th1 and Th2 cells.

scientific article

L1TD1 - a prognostic marker for colon cancer

scientific article published on 23 July 2019

Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors

journal article published in 2018

Mapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo

scientific article

Mass Spectrometry-Based Serum Proteomics for Biomarker Discovery and Validation

scientific article published in January 2017

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

scientific article published on 24 September 2016

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

scientific article

NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation

scientific article published on 02 April 2019

NanoMiner - integrative human transcriptomics data resource for nanoparticle research

scientific article

New separation-free assay technique for SNPs using two-photon excitation fluorometry.

scientific article

Notch signaling regulates the differentiation of neural crest from human pluripotent stem cells

scientific article published on 25 February 2014

PARP-14, a member of the B aggressive lymphoma family, transduces survival signals in primary B cells.

scientific article published on 15 January 2009

PRELI is a mitochondrial regulator of human primary T-helper cell apoptosis, STAT6, and Th2-cell differentiation

scientific article

PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use.

scientific article

Postpartum-activation of multiple sclerosis is associated with down-regulation of tolerogenic HLA-G

scientific article published on 11 June 2007

Pre-processing of Orbitrap higher energy collisional dissociation tandem mass spectra to reduce erroneous iTRAQ ratios

scientific article published on 01 September 2012

Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies

scientific article published on 16 July 2009

Proteome characterization of human T helper 1 and 2 cells

scientific article published on 01 January 2004

Proteome profiling of interleukin-12 treated human T helper cells

scientific article published in August 2005

Proteomic and transcriptomic characterization of interferon-?-induced human primary T helper cells

scientific article published on 01 February 2005

Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation

scientific article

Pulmonary sarcoidosis is associated with exosomal vitamin D-binding protein and inflammatory molecules

scientific article

Quality classification of tandem mass spectrometry data

scientific article

Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization

scientific article published on 26 December 2018

Quantitative proteomics analysis of signalosome dynamics in primary T cells identifies the surface receptor CD6 as a Lat adaptor-independent TCR signaling hub

scientific journal article

Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation

scientific article

Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation

scientific article

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

scientific article published on May 2017

RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation

scientific article

Reactive oxygen species deficiency induces autoimmunity with type 1 interferon signature.

scientific article

Reproducibility-optimized test statistic for ranking genes in microarray studies

scientific article published in July 2008

SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation

scientific article

Serum Proteomic Profiling to Identify Biomarkers of Premature Carotid Atherosclerosis.

scientific article

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

scientific article published on 23 January 2015

Standard of hygiene and immune adaptation in newborn infants

article

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

scientific article published on 4 September 2014

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process

scientific article

T-cell activation induces selective changes of cellular lipidome

scientific article

Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells

scientific journal article

Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma

scientific article published on August 2006

The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency

scientific article published on 19 February 2015

The Transcription Factor MAZR/PATZ1 Regulates the Development of FOXP3+ Regulatory T Cells

scientific article published on 01 December 2019

The progress and potential of proteomic biomarkers for type 1 diabetes in children

scientific article published on 20 December 2016

The regulation and role of c-FLIP in human Th cell differentiation

scientific article

The role of Interleukin-32 in Autoimmunity

scientific article published on 17 December 2020

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

scientific article published on 7 May 2018

Timing of infant feeding in relation to childhood asthma and allergic diseases

scientific article published on 22 November 2012

Total C4B deficiency due to gene deletion and gene conversion in a patient with severe infections

scientific article

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

scientific article published in February 2018

Transcriptional and epigenetic regulation of T-helper lineage specification

scientific article

Transcriptional response of human dendritic cells to Borrelia garinii--defective CD38 and CCR7 expression detected.

scientific article published on 17 April 2007

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

scientific article published on 7 October 2014

Unique gene expression signature by human embryonic stem cells cultured under serum-free conditions correlates with their enhanced and prolonged growth in an undifferentiated stage

scientific article published on 11 August 2005

Up-regulation of host cell genes during interferon-gamma-induced persistent Chlamydia pneumoniae infection in HL cells

scientific article published on 13 December 2006

snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions

scientific article published on 01 December 2018

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