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List of works by Paul Spellman

A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes

article

A central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma.

scientific article

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

scientific article

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

scientific article published on 18 June 2021

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

scientific article

A guide to microarray experiments-an open letter to the scientific journals

scientific article published in The Lancet

A humanized leucine zipper-TRAIL hybrid induces apoptosis of tumors both in vitro and in vivo

scientific article

A new treasure in the breast cancer gene hunt

scientific article published on 01 April 2011

A robust prognostic signature for hormone-positive node-negative breast cancer

scientific article published on 11 October 2013

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

scientific article

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods

scientific article published on 04 February 2009

A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047.

scientific article

ARTIK-52 induces replication-dependent DNA damage and p53 activation exclusively in cells of prostate and breast cancer origin.

scientific article published on 22 December 2015

ATM suppresses SATB1-induced malignant progression in breast epithelial cells

scientific article

Amplification of 11q13 in ovarian carcinoma

scientific article published on 01 June 2008

An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer

scientific article published on 15 February 2022

An open letter on microarray data from the MGED Society

scientific article published on November 2004

Analysis of molecular inversion probe performance for allele copy number determination

scientific article

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

scientific article

BT-02FUNCTIONALLY-DEFINED THERAPEUTIC TARGETS IN DIFFUSE INTRINSIC PONTINE GLIOMA.

scientific article published on 21 April 2015

Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition

scientific article published on January 2009

Bayesian inference of signaling network topology in a cancer cell line

scientific article

CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING.

scientific article

COMPARISON OF SPARSE CODING AND KERNEL METHODS FOR HISTOPATHOLOGICAL CLASSIFICATION OF GLIOBASTOMA MULTIFORME.

scientific article

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge

scientific article published on 12 May 2021

Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching

scientific article published on 01 January 2013

Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer.

scientific article published in April 2019

Circulating-tumor DNA as an early detection and diagnostic tool

scientific article

Classification of Histology Sections via Multispectral Convolutional Sparse Coding

scientific article

Classification of Tumor Histology via Morphometric Context

scientific article published on June 2013

Cluster analysis and display of genome-wide expression patterns

scientific article

Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts

scientific article published on 12 January 2009

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

article

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

scientific article published on 4 November 2015

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

scientific article

Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling.

scientific article published on 19 December 2016

Correction: Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer

scientific article published on 11 October 2017

Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib

scientific article

Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer

scientific article published on 16 July 2015

Deep Functional and Molecular Characterization of a High-Risk Undifferentiated Pleomorphic Sarcoma

scientific article published on 04 May 2020

Design and implementation of microarray gene expression markup language (MAGE-ML)

scientific article

Detecting cancer by monitoring circulating tumor DNA

scientific article published on 01 May 2014

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer

scientific article published in Nature Communications

EXPERIMENTAL THERAPEUTICS AND PHARMACOLOGY

article

Epigenetic loss of heterogeneity from low to high grade localized prostate tumours

scientific article published on 15 December 2021

Erratum to: Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer

scientific article published on 9 February 2017

Erratum to: Modeling precision treatment of breast cancer

scientific article published on 12 May 2015

Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease

scientific article published on 28 August 2015

Exon-level microarray analyses identify alternative splicing programs in breast cancer

scientific article

FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer

scientific article published on 06 October 2016

Final words: cell age and cell cycle are unlinked

scientific article published in June 2004

FuGE: Functional Genomics Experiment Object Model

scientific article published on January 2006

Functionally defined therapeutic targets in diffuse intrinsic pontine glioma

scientific article (publication date: June 2015)

Functionally defined therapeutic targets in diffuse intrinsic pontine glioma.

scientific article

GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer

scientific article published on April 2013

Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer

scientific article published on July 2016

GenomeGraphs: integrated genomic data visualization with R

scientific article

Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells?

scientific article

Genomic and transcriptional events associated with poor clinical responses to conventional therapies.

scientific article published on 17 June 2005

Genomic expression programs in the response of yeast cells to environmental changes

scientific article (publication date: December 2000)

Global optimization of somatic variant identification in cancer genomes with a global community challenge

scientific article

HER-2 gene amplification in human breast cancer without concurrent HER-2 over-expression

scientific article published on 15 August 2013

High Grade Gliomas and DIPG

scholarly article

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

scientific article

High-throughput method for analyzing methylation of CpGs in targeted genomic regions

scientific article

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets

Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR

scientific article published on 15 June 2016

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

scientific article published on 11 November 2021

Inferring causal molecular networks: empirical assessment through a community-based effort

scientific article

Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma

scientific article (publication date: 2012)

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

scientific article published on 25 March 2009

Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer ⬇️

scientific article published on July 24, 2013

Integrated analysis of germline and somatic variants in ovarian cancer.

scientific article

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1

scientific article

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology

scientific article

International network of cancer genome projects

scientific article

Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association ⬇️

scientific article published on 04 December 2012

Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines

scientific article published on 26 October 2020

Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma

scientific article

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection

scientific article published on 10 January 2018

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

scientific article

Methods and challenges in timing chromosomal abnormalities within cancer samples

scientific article published on 23 September 2013

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

Modeling precision treatment of breast cancer

scientific article published on January 2013

Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells.

scientific article

Morphometic analysis of TCGA glioblastoma multiforme ⬇️

scientific article published on December 20, 2011

Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies

scientific article published on 19 October 2021

Multireference Level Set for the Characterization of Nuclear Morphology in Glioblastoma Multiforme ⬇️

scientific article published on September 10, 2012

Multiregion exome sequencing of ovarian immature teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components

scientific article published on 07 January 2020

Neutral tumor evolution?

scientific article

Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation

scientific article

Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities

scientific article

Overcoming endocrine resistance due to reduced PTEN levels in estrogen receptor-positive breast cancer by co-targeting mammalian target of rapamycin, protein kinase B, or mitogen-activated protein kinase kinase.

scientific article

P1-06-22: Identification of Biomarkers in Breast Cancer for Prediction of Response to PARP Inhibitor Olaparib

article by A Daemen et al published 15 December 2011 in Cancer Research

Parent-specific copy number in paired tumor-normal studies using circular binary segmentation

scientific article

Patient-specific factors influence somatic variation patterns in von Hippel-Lindau disease renal tumours

scientific article published on 13 May 2016

Phospholipid Scramblase 1, an interferon-regulated gene located at 3q23, is regulated by SnoN/SkiL in ovarian cancer cells ⬇️

scientific article published on April 26, 2013

Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination.

scientific article

Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies

scientific article published on 25 April 2022

Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types

Prediction of epigenetically regulated genes in breast cancer cell lines

scientific article

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma

scientific article

Reply: whole-culture synchronization - effective tools for cell cycle studies

scientific article

Sparse combinatorial inference with an application in cancer biology

scientific article

Src and STAT3 inhibitors synergize to promote tumor inhibition in renal cell carcinoma

scientific article published on 26 November 2015

Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology

scientific article published on January 2013

Stacked Predictive Sparse Decomposition for Classification of Histology Sections ⬇️

scientific article published on 23 December 2014

Standards for microarray data

scientific article

Standards for microarray data: an open letter

scientific article

Submission of microarray data to public repositories

scientific article

Subtype and pathway specific responses to anticancer compounds in breast cancer

scientific article published on 14 October 2011

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy

scientific article published on 03 April 2011

Systematic variation in gene expression patterns in human cancer cell lines

scientific article (publication date: March 2000)

TRAIL-Based High Throughput Screening Reveals a Link between TRAIL-Mediated Apoptosis and Glutathione Reductase, a Key Component of Oxidative Stress Response

scientific article

Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing

scientific article published in January 2012

Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity

scientific article published on 25 March 2019

Temporal dissection of tumorigenesis in primary cancers

scientific article

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

scientific article published in April 2018

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

The Integrated Genomic Landscape of Thymic Epithelial Tumors

scientific article published in February 2018

The Somatic Genomic Landscape of Glioblastoma

article

The Stanford Microarray Database

scientific article

The evolutionary history of 2,658 cancers

The evolutionary history of 2,658 cancers

scientific article published on 06 February 2020

The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression.

scientific article published on June 2007

The somatic genomic landscape of glioblastoma

scientific article

The underlying principles of scientific publication.

scientific article published in November 2002

Timing chromosomal abnormalities using mutation data.

scientific article published on 19 September 2011

Top-down standards will not serve systems biology

scientific article published in Nature

Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI ⬇️

scientific article published on March 18, 2011

Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes.

scientific article

Transient commensal clonal interactions can drive tumor metastasis

scientific article published on 16 November 2020

Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

scientific article

Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis ⬇️

scientific article published on March 11, 2011

Xenografts faithfully recapitulate breast cancer-specific gene expression patterns of parent primary breast tumors

scientific article published on 02 September 2012

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