List of works - Ilya Shmulevich

A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy

scientific article published in January 2007

A data integration framework for prediction of transcription factor targets

scientific article

A multilevel pan-cancer map links gene mutations to cancer hallmarks

scientific article

Activities and sensitivities in boolean network models.

scientific article published on 22 July 2004

Adaptable data management for systems biology investigations

scientific article

Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling

scientific article

An inhibition-based stochastic countable-time decision model

scientific article published in May 2002

Analysis of angiogenesis usingin vitroexperiments and stochastic growth models

article

Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma

scientific article

Augmentation of response to chemotherapy by microRNA-506 through regulation of RAD51 in serous ovarian cancers

scientific article

Automated quantification of lymph node size and number in surgical specimens of stage II colorectal cancer

scientific article published in January 2005

Basin entropy in Boolean network ensembles

scientific article published on 9 April 2007

Binary analysis and optimization-based normalization of gene expression data

scientific article

Biocellion: accelerating computer simulation of multicellular biological system models

scientific article

Biochemical and statistical network models for systems biology

scientific article published on 3 August 2007

Biological Information as Set-Based Complexity

scientific article published on 25 February 2010

Breakdown probabilities of recursive stack filters

Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images

scientific article

CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer

scientific article

Cell death as a trigger for morphogenesis

scientific article published on 22 March 2018

Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma

scientific article

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data

scientific article

Combining dependent P-values with an empirical adaptation of Brown's method

scientific article

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

article

Correction of Misclassifications Using a Proximity-Based Estimation Method

Correction of misclassifications in primary local image recognition using a nonlinear graph-based estimation technique

Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.

scientific article published on 2 April 2008

Critical dynamics in genetic regulatory networks: examples from four kingdoms

scientific article

Critical networks exhibit maximal information diversity in structure-dynamics relationships

scientific article published on 4 February 2008

Data extraction from composite oligonucleotide microarrays

scientific article

Deterministic and stochastic models of genetic regulatory networks

scientific article published on January 2009

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

scientific article published on March 2004

Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer

scientific article

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

scientific article

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

scientific article published in April 2018

Eukaryotic cells are dynamically ordered or critical but not chaotic

scientific article

Extraction of the number of peroxisomes in yeast cells by automated image analysis

scientific article

Fewer permutations, more accurate P-values

scientific article published on June 2009

Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

scientific article published on 8 March 2009

Gene expression dynamics in the macrophage exhibit criticality

scholarly article

Gene perturbation and intervention in probabilistic Boolean networks

scientific article

Gene-pair expression signatures reveal lineage control

scientific article

Genome-wide analysis of effectors of peroxisome biogenesis

scientific article

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites ⬇️

scientific article published on July 27, 2010

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

scientific article published in April 2018

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression

scientific article

Growing genetic regulatory networks from seed genes

scientific article published on 10 February 2004

Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas

scientific article

Identification of combination gene sets for glioma classification.

scientific article

Identification of copy number variants in whole-genome data using Reference Coverage Profiles

scientific article

Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARalpha).

scientific article

Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-level Homology ⬇️

scientific article published on August 27, 2012

Inference of Boolean networks using sensitivity regularization

scientific article published on January 2008

Inference of Genetic Regulatory Networks Via Best-Fit Extensions

Inference of Genetic Regulatory Networks via Best-Fit Extensions

Information-theoretic analysis of the dynamics of an executable biological model

scientific article

Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion

scientific article

Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma

scientific article

Key nodes of a microRNA network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer ⬇️

scientific article

Large-scale molecular characterization and analysis of gastric cancer

scientific article published on August 2014

Literature-based discovery of new candidates for drug repurposing

scientific article published on 25 April 2016

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

scientific article

MIIP haploinsufficiency induces chromosomal instability and promotes tumour progression in colorectal cancer

scientific article published on 14 October 2016

MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer

scientific article

Misclassification correction in primary local recognition of component images of multichannel remote sensing data

Model selection in genomics

scientific article

Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression

scientific article published in September 2005

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

scientific article

Multiscale representation of genomic signals

scientific article

Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center

scientific article

NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells

scientific article published on 23 March 2009

Noise in a Small Genetic Circuit that Undergoes Bifurcation

scientific article

On the Limitations of Biological Knowledge ⬇️

scientific article published on November 1, 2012

Oncogenic Signaling Pathways in The Cancer Genome Atlas

scientific article published in April 2018

Pathogenic Germline Variants in 10,389 Adult Cancers

scientific article published in April 2018

Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays

scientific article published in May 2006

Pathway analysis of informative genes from microarray data reveals that metabolism and signal transduction genes distinguish different subtypes of lymphomas

scientific article

Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions

scientific article published on 05 March 2014

ProbCD: enrichment analysis accounting for categorization uncertainty

scientific article (publication date: 12 October 2007)

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks

scientific article published in February 2002

Probabilistic analysis of gene expression measurements from heterogeneous tissues

scientific article

Probabilistic inference of transcription factor binding from multiple data sources

scientific article

Quantification of in vitro cell invasion through image analysis

scientific article

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

scientific article published on April 2006

Robust estimation of protein expression ratios with lysate microarray technology.

scientific article

Robust quantification of in vitro angiogenesis through image analysis

scientific article published in April 2005

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

scientific article

Simcluster: clustering enumeration gene expression data on the simplex space

scientific article

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle

scientific article

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

scientific article

Steady-state analysis of genetic regulatory networks modelled by probabilistic boolean networks

scientific article

Structure learning for Bayesian networks as models of biological networks

scientific article published in January 2013

Systems biology driven software design for the research enterprise

scientific article

Taming data

scientific article

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

The Cancer Genome Atlas Pan-Cancer analysis project

scientific article

The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research

scientific article published on November 2017

The Somatic Genomic Landscape of Glioblastoma

article

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

scientific article

The somatic genomic landscape of glioblastoma

scientific article

Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues

scientific article

Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma

scientific article published on February 2013

Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma

scientific article

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics

scientific article

Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies

scientific article

Using Incomplete Trios to Boost Confidence in Family Based Association Studies

scientific article published on 18 March 2016

Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation

scientific article

List of works by Ilya Shmulevich

A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy

A data integration framework for prediction of transcription factor targets

A multilevel pan-cancer map links gene mutations to cancer hallmarks

Activities and sensitivities in boolean network models.

Adaptable data management for systems biology investigations

Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling

An inhibition-based stochastic countable-time decision model

Analysis of angiogenesis usingin vitroexperiments and stochastic growth models

Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma

Augmentation of response to chemotherapy by microRNA-506 through regulation of RAD51 in serous ovarian cancers

Automated quantification of lymph node size and number in surgical specimens of stage II colorectal cancer

Basin entropy in Boolean network ensembles

Binary analysis and optimization-based normalization of gene expression data

Biocellion: accelerating computer simulation of multicellular biological system models

Biochemical and statistical network models for systems biology

Biological Information as Set-Based Complexity

Breakdown probabilities of recursive stack filters

Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images

CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer

Cell death as a trigger for morphogenesis

Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data

Combining dependent P-values with an empirical adaptation of Brown's method

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Comprehensive Characterization of Cancer Driver Genes and Mutations

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Correction of Misclassifications Using a Proximity-Based Estimation Method

Correction of misclassifications in primary local image recognition using a nonlinear graph-based estimation technique

Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.

Critical dynamics in genetic regulatory networks: examples from four kingdoms

Critical networks exhibit maximal information diversity in structure-dynamics relationships

Data extraction from composite oligonucleotide microarrays

Deterministic and stochastic models of genetic 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

Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer

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

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Eukaryotic cells are dynamically ordered or critical but not chaotic

Extraction of the number of peroxisomes in yeast cells by automated image analysis

Fewer permutations, more accurate P-values

Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

Gene expression dynamics in the macrophage exhibit criticality

Gene perturbation and intervention in probabilistic Boolean networks

Gene-pair expression signatures reveal lineage control

Genome-wide analysis of effectors of peroxisome biogenesis

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites ⬇️

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression

Growing genetic regulatory networks from seed genes

Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas

Identification of combination gene sets for glioma classification.

Identification of copy number variants in whole-genome data using Reference Coverage Profiles

Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARalpha).

Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-level Homology ⬇️

Inference of Boolean networks using sensitivity regularization

Inference of Genetic Regulatory Networks Via Best-Fit Extensions

Inference of Genetic Regulatory Networks via Best-Fit Extensions

Information-theoretic analysis of the dynamics of an executable biological model

Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion

Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma

Key nodes of a microRNA network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer ⬇️

Large-scale molecular characterization and analysis of gastric cancer

Literature-based discovery of new candidates for drug repurposing

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

MIIP haploinsufficiency induces chromosomal instability and promotes tumour progression in colorectal cancer

MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer

Misclassification correction in primary local recognition of component images of multichannel remote sensing data

Model selection in genomics

Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

Multiscale representation of genomic signals

Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center

NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells

Noise in a Small Genetic Circuit that Undergoes Bifurcation

On the Limitations of Biological Knowledge ⬇️

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Pathogenic Germline Variants in 10,389 Adult Cancers

Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays