List of works - Russell Schwartz

"Local rules" theory applied to polyomavirus polymorphic capsid assemblies

scientific article published in March 2000

A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure

scientific article published in 2010

A Report of the Curriculum Task Force of the ISCB Education Committee ⬇️

scholarly article

A comparative genomics approach to identifying the plasticity transcriptome.

scientific article

A consensus tree approach for reconstructing human evolutionary history and detecting population substructure

scientific article

A human genome-wide library of local phylogeny predictions for whole-genome inference problems

scientific article

A method for efficient Bayesian optimization of self-assembly systems from scattering data.

scientific article

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

scientific article published on 23 January 2013

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

scientific article published on 9 December 2010

A simplicial complex-based approach to unmixing tumor progression data

scientific article

Abstract 1934: Improved deconvolution of heterogeneous tumor data to reconstruct clonal evolution from bulk genomic samples

scientific article published in August 2015

Abstract 2182: Reconstructing evolutionary models of tumor progression from single-cell heterogeneity data

scientific article published in August 2015

Abstract 4833: Single-cell genetic analysis reveals insights into clonal development of cervical cancer and confirms TERC as an early and dominant aberration

scientific article published in August 2015

Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice

scientific article published in October 2007

Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics

scientific article

An Optimization-Based Sampling Scheme for Phylogenetic Trees

scientific article published in 2011

An optimization-based sampling scheme for phylogenetic trees

scientific article published on 27 September 2011

Applying molecular crowding models to simulations of virus capsid assembly in vitro

scientific article published on January 2014

Applying unmixing to gene expression data for tumor phylogeny inference

scientific article

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

scientific article

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

scientific article published on 23 October 2017

Bioinformatics curriculum guidelines: toward a definition of core competencies

scientific article

Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

scientific article

Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study

scientific article

Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data

scientific article

Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data

scientific article published in 2012

Comparative immunopeptidomics of humans and their pathogens

scholarly article

Computational biology and bioinformatics

scientific article published on June 2014

Computational models of molecular self-organization in cellular environments

scientific article published on January 2007

Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data

scientific article

Direct maximum parsimony phylogeny reconstruction from genotype data

scientific article

Discrete, continuous, and stochastic models of protein sorting in the Golgi apparatus

scientific article published on 25 January 2010

Efficient stochastic sampling of first-passage times with applications to self-assembly simulations

scientific article published in November 2008

Evaluating spatial constraints in cellular assembly processes using a monte carlo approach

scientific article published in January 2006

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Exploring the parameter space of complex self-assembly through virus capsid models

scientific article published on 5 October 2007

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

scientific article

Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction

scientific article published in 2006

Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

scientific article

Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure

scientific article published in January 2006

Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny

scientific article published in 2010

Generalized buneman pruning for inferring the most parsimonious multi-state phylogeny

scientific article

HER2 expression as a potential marker for response to therapy targeted to the EGFR.

scientific article published in April 2006

Haplotype parsing: methods for extracting information from human genetic variations

scientific article

Identification of novel mutations by exome sequencing in African American colorectal cancer patients

scientific article

Implementation of a Discrete Event Simulator For Biological Self-Assembly Systems

Inference of tumor phylogenies from genomic assays on heterogeneous samples

scientific article

Inference of tumor phylogenies from genomic assays on heterogeneous samples

scientific article published in 2011

Inferring models of multiscale copy number evolution for single-tumor phylogenetics

scientific article published on June 2015

Investigating scaling effects on virus capsid-like self-assembly using discrete event simulations

scientific article published in September 2007

Machine Learning Approaches for Predicting Radiation Therapy Outcomes: A Clinician's Perspective

scientific article

Medoidshift clustering applied to genomic bulk tumor data

scientific article

Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference

scientific article published on 01 July 2008

Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation

scientific article

Modeling molecular interactions to understand spatial crowding effects on heterodimer formations

scientific article published on 08 October 2007

Modeling nuclear blebs in a nucleoskeleton of independent filament networks

scientific article published on 19 August 2011

Molecular crowding shapes gene expression in synthetic cellular nanosystems

scientific article

Network-Based Inference of Cancer Progression from Microarray Data

Network-based inference of cancer progression from microarray data

scientific article

Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles

scientific article published in 2012

Novel multisample scheme for inferring phylogenetic markers from whole genome tumor profiles

scientific article

Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies

scientific article

Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model

scientific article

Pathway Complexity of Model Virus Capsid Assembly Systems

scientific article published in 2008

Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis

scientific article published on 15 July 2015

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

scientific article

Queue-based method for efficient simulation of biological self-assembly systems

scientific article published in March 2005

Reference-free inference of tumor phylogenies from single-cell sequencing data

scientific article published on 10 November 2015

Reply to 'Complexity of molecular crowding in cell-free enzymatic reaction networks'.

scientific article published in June 2014

Response of an Actin Filament Network Model Under Cyclic Stretching Through a Coarse Grained Monte Carlo Approach

scientific article published on 16 June 2010

Response of an actin filament network model under cyclic stretching through a coarse grained Monte Carlo approach

scientific article

Robust unmixing of tumor states in array comparative genomic hybridization data

scientific article

Robustness of inference of haplotype block structure

scientific article published in January 2003

Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees

scientific article published in 2006

Simulated de novo assembly of golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion

scientific article published on 9 May 2008

Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics

scientific article published on 7 October 2005

Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity yet conserved genomic imbalances and gain of MYC during progression.

scientific article

Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis.

scientific article

Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green's function reaction dynamics

scientific article published on 12 September 2008

Stochastic steady state gain in a gene expression process with mRNA degradation control

scientific article

Structurally governed cell mechanotransduction through multiscale modeling

scientific article

Surveying capsid assembly pathways through simulation-based data fitting

scientific article

The development and application of bioinformatics core competencies to improve bioinformatics training and education

scientific article published in February 2018

Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments

scientific article (publication date: 2012)

Tumor Phylogenetics in the NGS Era: Strategies, Challenges, and Future Prospects

scientific article published in 2013

Unified regression model of binding equilibria in crowded environments

scientific article published on 20 September 2011

Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life

scientific article published in May 2001

List of works by Russell Schwartz

"Local rules" theory applied to polyomavirus polymorphic capsid assemblies

A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure

A Report of the Curriculum Task Force of the ISCB Education Committee ⬇️

A comparative genomics approach to identifying the plasticity transcriptome.

A consensus tree approach for reconstructing human evolutionary history and detecting population substructure

A human genome-wide library of local phylogeny predictions for whole-genome inference problems

A method for efficient Bayesian optimization of self-assembly systems from scattering data.

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

A simplicial complex-based approach to unmixing tumor progression data

Abstract 1934: Improved deconvolution of heterogeneous tumor data to reconstruct clonal evolution from bulk genomic samples

Abstract 2182: Reconstructing evolutionary models of tumor progression from single-cell heterogeneity data

Abstract 4833: Single-cell genetic analysis reveals insights into clonal development of cervical cancer and confirms TERC as an early and dominant aberration

Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice

Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics

An Optimization-Based Sampling Scheme for Phylogenetic Trees

An optimization-based sampling scheme for phylogenetic trees

Applying molecular crowding models to simulations of virus capsid assembly in vitro

Applying unmixing to gene expression data for tumor phylogeny inference

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

Bioinformatics curriculum guidelines: toward a definition of core competencies

Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study

Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data

Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data

Comparative immunopeptidomics of humans and their pathogens

Computational biology and bioinformatics

Computational models of molecular self-organization in cellular environments

Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data

Direct maximum parsimony phylogeny reconstruction from genotype data

Discrete, continuous, and stochastic models of protein sorting in the Golgi apparatus

Efficient stochastic sampling of first-passage times with applications to self-assembly simulations

Evaluating spatial constraints in cellular assembly processes using a monte carlo approach

Evolution of genes and genomes on the Drosophila phylogeny

Exploring the parameter space of complex self-assembly through virus capsid models

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction

Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure

Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny

Generalized buneman pruning for inferring the most parsimonious multi-state phylogeny

HER2 expression as a potential marker for response to therapy targeted to the EGFR.

Haplotype parsing: methods for extracting information from human genetic variations

Identification of novel mutations by exome sequencing in African American colorectal cancer patients

Implementation of a Discrete Event Simulator For Biological Self-Assembly Systems

Inference of tumor phylogenies from genomic assays on heterogeneous samples

Inference of tumor phylogenies from genomic assays on heterogeneous samples

Inferring models of multiscale copy number evolution for single-tumor phylogenetics

Investigating scaling effects on virus capsid-like self-assembly using discrete event simulations

Machine Learning Approaches for Predicting Radiation Therapy Outcomes: A Clinician's Perspective

Medoidshift clustering applied to genomic bulk tumor data

Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference

Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation

Modeling molecular interactions to understand spatial crowding effects on heterodimer formations

Modeling nuclear blebs in a nucleoskeleton of independent filament networks

Molecular crowding shapes gene expression in synthetic cellular nanosystems

Network-Based Inference of Cancer Progression from Microarray Data

Network-based inference of cancer progression from microarray data

Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles

Novel multisample scheme for inferring phylogenetic markers from whole genome tumor profiles

Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies

Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model

Pathway Complexity of Model Virus Capsid Assembly Systems

Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

Queue-based method for efficient simulation of biological self-assembly systems

Reference-free inference of tumor phylogenies from single-cell sequencing data

Reply to 'Complexity of molecular crowding in cell-free enzymatic reaction networks'.

Response of an Actin Filament Network Model Under Cyclic Stretching Through a Coarse Grained Monte Carlo Approach

Response of an actin filament network model under cyclic stretching through a coarse grained Monte Carlo approach

Robust unmixing of tumor states in array comparative genomic hybridization data

Robustness of inference of haplotype block structure

Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees

Simulated de novo assembly of golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion

Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics

Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity yet conserved genomic imbalances and gain of MYC during progression.

Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis.

Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green's function reaction dynamics