Lista de obras -

A data integration framework for prediction of transcription factor targets

artículo científico publicado en 2009

A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data

artículo científico publicado en 2009

A linear model for transcription factor binding affinity prediction in protein binding microarrays

artículo científico publicado en 2011

A protein-protein interaction guided method for competitive transcription factor binding improves target predictions

artículo científico publicado en 2009

A subpopulation model to analyze heterogeneous cell differentiation dynamics

artículo científico publicado en 2016

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

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

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2018

Comparative analysis of human and mouse transcriptomes of Th17 cell priming

artículo científico publicado en 2016

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

artículo científico publicado en 2013

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

artículo científico publicado en 2016

Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis

artículo científico

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

artículo científico publicado en 2014

Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis

artículo científico publicado en 2004

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

artículo científico publicado en 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

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

artículo científico publicado en 2016

Estimation and inversion of the effects of cell population asynchrony in gene expression time-series

article

Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data

artículo científico publicado en 2013

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

artículo científico publicado en 2014

Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music

artículo científico publicado en 2013

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

artículo científico publicado en 2010

Genomic Signal Processing

scholarly article by Ulisses Braga Neto et al published 4 January 2011 in EURASIP Journal on Advances in Signal Processing

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

artículo científico publicado en 2018

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

artículo científico publicado en 2013

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

artículo científico publicado en 2012

Identification of early gene expression changes during human Th17 cell differentiation.

artículo científico publicado en 2012

Identification of global regulators of T-helper cell lineage specification

artículo científico publicado en 2015

In silico microdissection of microarray data from heterogeneous cell populations

artículo científico publicado en 2005

Inference of Boolean networks using sensitivity regularization

artículo científico

Inference of Genetic Regulatory Networks via Best-Fit Extensions

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

artículo científico publicado en 2014

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

artículo científico

Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

artículo científico publicado en 2009

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX.

artículo científico publicado en 2013

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

artículo científico publicado en 2014

Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction

On Learning Gene Regulatory Networks Under the Boolean Network Model

Probabilistic analysis of gene expression measurements from heterogeneous tissues

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

scientific article published on 01 March 2019

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

artículo científico publicado en 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

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

artículo científico publicado en 2017

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

artículo científico publicado en 2012

Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network

artículo científico publicado en 2010

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

artículo científico publicado en 2006

Robust Fisher's Test for Periodicity Detection in Noisy Biological Time Series

Robust detection of periodic time series measured from biological systems

artículo científico publicado en 2005

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data

artículo científico publicado en 2007

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements

artículo científico publicado en 2013

Standard of hygiene and immune adaptation in newborn infants

article

Structure learning for Bayesian networks as models of biological networks

artículo científico publicado en 2013

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

artículo científico publicado en 2016

Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding.

artículo científico publicado en 2009

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

scholarly article published by Päivi Pöhö in 2016

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

artículo científico publicado en 2015

The effect of listening to music on human transcriptome

artículo científico publicado en 2015

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

artículo científico publicado en 2015

The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population

artículo científico publicado en 2013

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

artículo científico publicado en 2018

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

artículo científico publicado en 2015

The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers

artículo científico publicado en 2011

The role of certain Post classes in Boolean network models of genetic networks

artículo científico publicado en 2003

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

artículo científico publicado en 2015

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

artículo científico publicado en 2016

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

artículo científico publicado en 2018

Lista de obras de

A data integration framework for prediction of transcription factor targets

A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data

A linear model for transcription factor binding affinity prediction in protein binding microarrays

A protein-protein interaction guided method for competitive transcription factor binding improves target predictions

A subpopulation model to analyze heterogeneous cell differentiation dynamics

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

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

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

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

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

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

Comparative analysis of human and mouse transcriptomes of Th17 cell priming

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

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

Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis

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

Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis

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

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

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

Estimation and inversion of the effects of cell population asynchrony in gene expression time-series

Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data

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

Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music

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

Genomic Signal Processing

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

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

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

Identification of early gene expression changes during human Th17 cell differentiation.

Identification of global regulators of T-helper cell lineage specification

In silico microdissection of microarray data from heterogeneous cell populations

Inference of Boolean networks using sensitivity regularization

Inference of Genetic Regulatory Networks via Best-Fit Extensions

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

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

Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

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

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

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

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

Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX.

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

Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction

On Learning Gene Regulatory Networks Under the Boolean Network Model

Probabilistic analysis of gene expression measurements from heterogeneous tissues

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

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

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

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

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

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

Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

Robust Fisher's Test for Periodicity Detection in Noisy Biological Time Series

Robust detection of periodic time series measured from biological systems

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data

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

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

Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements

Standard of hygiene and immune adaptation in newborn infants

Structure learning for Bayesian networks as models of biological networks

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

Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding.

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

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

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

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

The effect of listening to music on human transcriptome

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

The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population

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

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

The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers

The role of certain Post classes in Boolean network models of genetic networks

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

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

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