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List of works by Olga Troyanskaya

"Getting started in...": a series not to miss

scientific article

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

scientific article

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape

scientific article published on 23 January 2019

A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: Guidelines from the Kidney Precision Medicine Project

scientific article published on 16 November 2020

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

scientific article

A genomewide functional network for the laboratory mouse

scientific article

A global genetic interaction network maps a wiring diagram of cellular function

scientific article

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.

scientific article published on 14 May 2018

A new system for comparative functional genomics of Saccharomyces yeasts

scientific article

A scalable method for integration and functional analysis of multiple microarray datasets

scientific article published on 27 September 2006

Accurate detection of aneuploidies in array CGH and gene expression microarray data

scientific article

Accurate evaluation and analysis of functional genomics data and methods ⬇️

scientific article published on January 23, 2012

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development

scientific article published on 25 September 2019

Accurate quantification of functional analogy among close homologs

scientific article

An effective statistical evaluation of ChIPseq dataset similarity

scientific article published on 19 January 2012

An integrative tissue-network approach to identify and test human disease genes

article

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry

scientific article

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields

scientific article published on 03 December 2008

Assessing the functional structure of genomic data

scientific article

Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries

scientific article published on 01 June 2019

BAYESIAN DATA INTEGRATION: A FUNCTIONAL PERSPECTIVE

BAYESIAN DATA INTEGRATION: A FUNCTIONAL PERSPECTIVE

Bayesian data integration: a functional perspective

scientific article

Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery

scientific article published on 10 July 2017

Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

scientific article

Chapter 2: Data-Driven View of Disease Biology ⬇️

scientific article published on December 27, 2012

Comparative gene expression between two yeast species

scientific article

Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data

scientific article

Computational identification of cellular networks and pathways

scientific article published on 14 May 2007

Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis

scientific article

Context-sensitive data integration and prediction of biological networks

scientific article

Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae

scientific article

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast

scientific article

Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity

scientific article published on 7 July 2017

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.

scientific article published on 16 July 2018

Defining cell-type specificity at the transcriptional level in human disease

scientific article published on 15 August 2013

Detailing regulatory networks through large scale data integration

scientific article

Directing experimental biology: a case study in mitochondrial biogenesis

scientific article

Discovering biological networks from diverse functional genomic data

scientific article

Discovery of biological networks from diverse functional genomic data

scientific article

Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies

scientific article published on 04 September 2020

Diversity of gene expression in adenocarcinoma of the lung

scientific article (publication date: 20 November 2001)

Enabling Precision Medicine through Integrative Network Models

scientific article published on 09 July 2018

Endothelial cell diversity revealed by global expression profiling

scientific article

Exploring the functional landscape of gene expression: directed search of large microarray compendia

scientific article

Exploring the human genome with functional maps

scientific article published on 26 February 2009

FNTM: a server for predicting functional networks of tissues in mouse

scientific article published on 4 May 2015

Finding function: evaluation methods for functional genomic data

scientific article

Functional analysis of gene duplications in Saccharomyces cerevisiae

scientific article published on 6 December 2006

Functional genomics complements quantitative genetics in identifying disease-gene associations

scientific article

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes

scientific article

GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.

scientific article published in July 2018

GIANT API: an application programming interface for functional genomics

scientific article published on 20 April 2016

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool

scientific article published on 10 October 2006

Gene expression patterns in ovarian carcinomas

scientific article

Genome-wide characterization of genetic and functional dysregulation in autism spectrum disorder

scholarly article published 9 June 2016

Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder

scientific article

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid

scientific article published on 27 November 2020

Genomic analyses implicate noncoding de novo variants in congenital heart disease

scientific article published on 29 June 2020

Global analysis of gene function in yeast by quantitative phenotypic profiling

scientific article

Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans

scientific article

Global quantitative modeling of chromatin factor interactions

scientific article

Graphle: Interactive exploration of large, dense graphs

scientific article (publication date: 14 December 2009)

Hierarchical multi-label prediction of gene function

scientific article published on 12 January 2006

IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment

scientific article

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.

scientific article published on 12 May 2015

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

scientific article

ISCB/SPRINGER series in computational biology.

scientific article

Implications of Big Data for cell biology

scientific article

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

scientific article

Integrated analysis of microarray results

scientific article

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

scientific article published on 31 December 2010

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling

scientific article published on 9 September 2011

Integrative systems biology for data-driven knowledge discovery ⬇️

scientific article published on September 1, 2010

Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases

scientific article

Interpretation of an individual functional genomics experiment guided by massive public data

scientific article published on 26 November 2018

Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells

scientific article

Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development

scientific article published on 21 August 2020

Low-variance RNAs identify Parkinson's disease molecular signature in blood

scientific article published on 18 March 2015

Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.

scientific article published on 28 October 2014

Machine learning, the kidney, and genotype-phenotype analysis

scientific article published on 01 April 2020

Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells

scientific article

Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons

scientific article published on 20 August 2019

Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans

scientific article published on 06 July 2016

Minor Isozymes Tailor Yeast Metabolism to Carbon Availability

Missing value estimation methods for DNA microarrays

scientific article (publication date: June 2001)

Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies

scientific article published on 13 December 2006

Modeling transcriptional regulation of model species with deep learning

scientific article published on 22 April 2021

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

scientific article

Nested effects models for high-dimensional phenotyping screens

scientific article published in July 2007

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries

scientific article published on 25 February 2019

New genetic signals for lung function highlight pathways and pleiotropy, and chronic obstructive pulmonary disease associations across multiple ancestries

scholarly article published 12 June 2018

Nonparametric methods for identifying differentially expressed genes in microarray data

scientific article

Nucleosome-coupled expression differences in closely-related species

scientific article

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

scientific article published on 12 September 2013

Organoid single cell profiling identifies a transcriptional signature of glomerular disease

scientific article published on 10 January 2019

PILGRM: an interactive data-driven discovery platform for expert biologists ⬇️

scientific article published on June 7, 2011

Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis

scientific article

Predicting cellular growth from gene expression signatures

scientific article

Predicting effects of noncoding variants with deep learning-based sequence model

scientific article published on 24 August 2015

Predicting gene function in a hierarchical context with an ensemble of classifiers

scientific article published on 27 June 2008

Presenilin 1 phosphorylation regulates amyloid-β degradation by microglia

scientific article published on 13 August 2020

Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states

scientific article published on 4 February 2016

Putting microarrays in a context: integrated analysis of diverse biological data

scientific article

Putting the 'bio' into bioinformatics

scientific article

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

scientific article

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares

scientific article published on 01 July 2020

SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures

scientific article published in November 2022

SARS-CoV-2 Transmission among Marine Recruits during Quarantine

scientific article published on 11 November 2020

SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease

scientific article published on 07 October 2020

SARS-CoV-2 receptor networks in diabetic kidney disease, BK-Virus nephropathy and COVID-19 associated acute kidney injury

scientific article published on 13 May 2020

SEEDLING DEVELOPMENT IN SPECIES OF CHAMAESYCE (EUPHORBIACEAE) WITH ERECT GROWTH HABITS

article published in 1998

Scalable, Dynamic Analysis and Visualization for Genomic Datasets

scholarly article published 2007

Selected proceedings of the First Summit on Translational Bioinformatics 2008.

scientific article

Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis

scientific article published on 24 June 2020

Selene: a PyTorch-based deep learning library for sequence data

scientific article published on 28 March 2019

Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity

scientific article

Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab

scholarly article by Shakila Jabeen et al published 2018 in OncoImmunology

Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components

scientific article

Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker

scientific article published on 26 March 2020

Single nucleus multi-omics regulatory landscape of the murine pituitary

scientific article published on 11 May 2021

Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney

scientific article published on 30 August 2018

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

scientific article published on 12 June 2020

Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations

scientific article published on 01 February 2020

Systematic planning of genome-scale experiments in poorly studied species

scientific article

Systemic and cell type-specific gene expression patterns in scleroderma skin

scientific article

Systems-level dynamic analyses of fate change in murine embryonic stem cells

scientific article

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

scientific article published on 12 January 2015

The Sleipnir library for computational functional genomics

scientific article

The genetic landscape of a cell

scientific article

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction

scientific article published on 26 June 2009

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms

scientific article

Tissue-specific functional networks for prioritizing phenotype and disease genes

scientific article

Tools and applications for large-scale display walls

scientific article

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression

article

Understanding multicellular function and disease with human tissue-specific networks

scientific article published on 27 April 2015

Variation in gene expression patterns in follicular lymphoma and the response to rituximab

scientific article

Variation in gene expression patterns in human gastric cancers

scientific article published on 17 April 2003

Viewing the Larger Context of Genomic Data through Horizontal Integration

Visualization methods for statistical analysis of microarray clusters

scientific article

Visualization-based discovery and analysis of genomic aberrations in microarray data

scientific article

Voices in methods development

scientific article published on 01 October 2019

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

scientific article published on 27 May 2019

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