Author details

Full Name

Yuri Nikolsky

Affiliation

ORCID

Career Start Year

1994

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
28849560	Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.	Methods in Molecular Biology	2017
28849565	Analysis of cis-Regulatory Elements in Gene Co-expression Networks in Cancer.	Methods in Molecular Biology	2017
27774999	Nucleotide diversity analysis highlights functionally important genomic regions.	Scientific Reports	2016
27436340	Toward high-resolution population genomics using archaeological samples.	DNA Res	2016
26747447	The mysterious orphans of Mycoplasmataceae.	Biology Direct	2016
26865217	Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry.	Scientific Reports	2016
27848968	In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development.	Nature Communications	2016
27824868	Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer.	PLoS One	2016
27671678	Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes.	Cancer Res	2016
26107615	Development of a Drug-Response Modeling Framework to Identify Cell Line Derived Translational Biomarkers That Can Predict Treatment Outcome to Erlotinib or Sorafenib.	PLoS One	2015
26000039	Reconstitution of the ERG Gene Expression Network Reveals New Biomarkers and Therapeutic Targets in ERG Positive Prostate Tumors.	Journal of Cancer	2015
26109056	Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.	Genome Biol	2015
25150839	The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.	Nat Biotechnol	2014
24937458	JARID1B is a luminal lineage-driving oncogene in breast cancer.	Cancer Cell	2014
24510058	A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.	Nat Commun	2014
23593264	Drug target prediction and repositioning using an integrated network-based approach.	PLoS One	2013
23770079	Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics.	Cell Stem Cell	2013
21861759	A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes on transition to squamous epithelium.		2012
22583392	Prediction of organ toxicity endpoints by QSAR modeling based on precise chemical-histopathology annotations.		2012
22448124	Putative multifunctional signature of lung metastases in dedifferentiated chondrosarcoma.	Sarcoma	2012
22709571	Genomic characterization of explant tumorgraft models derived from fresh patient tumor tissue.	Journal of Translational Medicine	2012
23176192	Knowledge-based analysis of proteomics data.	BMC Bioinformatics	2012
21098291	Altered antisense-to-sense transcript ratios in breast cancer.	Proc Natl Acad Sci U S A	2012
21838869	A systems biology strategy for predicting similarities and differences of drug effects: evidence for drug-specific modulation of inflammation in atherosclerosis.	BMC Systems Biology	2011
21398405	Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.	Cancer Res	2011
21163964	The genetic landscape of the childhood cancer medulloblastoma.	Science	2011
21254873	Quantitative knowledge-based analysis in compound safety assessment.		2011
21533021	Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.	PLoS Genet	2011
21633165	The JAK2/STAT3 signaling pathway is required for growth of CD44âºCD24â» stem cell-like breast cancer cells in human tumors.	J Clin Invest	2011
20064235	Effect of training-sample size and classification difficulty on the accuracy of genomic predictors.	Breast Cancer Res	2010
20824474	Systems biology approaches to the study of cardiovascular drugs.	Methods in Molecular Biology	2010
21364822	Interactions between an inflammatory response to infection and protein trafficking pathways favor correction of defective protein trafficking in Cystic Fibrosis.		2010
20676074	The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.	Nat Biotechnol	2010
20676069	Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes.	Pharmacogenomics J	2010
20676066	Genomic indicators in the blood predict drug-induced liver injury.	Pharmacogenomics J	2010
20676064	Consistency of predictive signature genes and classifiers generated using different microarray platforms.	Pharmacogenomics J	2010
20377895	Integrated network analysis of transcriptomic and proteomic data in psoriasis.	BMC Systems Biology	2010
20158879	Bimodal gene expression patterns in breast cancer.	BMC Genomics	2010
19597786	Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platform.	Methods in Molecular Biology	2009
19309513	Identifying disease-specific genes based on their topological significance in protein networks.	BMC Systems Biology	2009
19426536	Network analysis of human glaucomatous optic nerve head astrocytes.	BMC Med Genomics	2009
19776212	Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals.	Toxicol Sci	2009
19760825	Protein networks and pathway analysis. Preface.	Methods in Molecular Biology	2009
19597794	MetaMiner (CF): a disease-oriented bioinformatics analysis environment.	Methods in Molecular Biology	2009
18990241	The transcriptomic signature of fasting murine liver.	BMC Genomics	2008
19014478	A comprehensive functional analysis of tissue specificity of human gene expression.	BMC Biology	2008
19010930	Genome-wide functional synergy between amplified and mutated genes in human breast cancer.	Cancer Res	2008
20020920	Characteristics of genomic signatures derived using univariate methods and mechanistically anchored functional descriptors for predicting drug- and xenobiotic-induced nephrotoxicity.	Toxicology Mechanisms and Methods	2008
18455123	Regulation of in situ to invasive breast carcinoma transition.	Cancer Cell	2008
18772397	Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.	Science	2008