List of works - Adam A Margolin

1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis

scientific article

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

scientific article published on 3 October 2017

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

scientific article published on 03 April 2020

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

scientific article

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens

scientific article

Abstract 2608: Global integration of knowledgebases for clinical interpretation of cancer variants

Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

scientific article published on 01 January 2019

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

scientific article

BREAST CANCER HISTOPATHOLOGY IMAGE ANALYSIS PIPELINE FOR TUMOR PURITY ESTIMATION.

scientific article published in April 2017

Boolean calculations made easy (for ribozymes).

scientific article published in November 2005

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data

scientific article

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

scientific article (publication date: 31 January 2017)

CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors

scientific article

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

scholarly article

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding.

scientific article published on 20 November 2007

Chemical Genomics Identifies Small-Molecule MCL1 Repressors and BCL-xL as a Predictor of MCL1 Dependency ⬇️

scientific article published on April 17, 2012

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis

scientific article published on August 2017

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

scientific article published on 06 November 2018

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

scientific article published on 18 May 2015

Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy

article

Deep learning based Nucleus Classification in pancreas histological images.

scientific article published in July 2017

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning

scientific article

Empirical Bayes analysis of quantitative proteomics experiments

scientific article

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas

scientific article

Functional kinomics identifies candidate therapeutic targets in head and neck cancer

scientific article

Functional precision medicine identifies novel druggable targets and therapeutic options in head and neck cancer.

scientific article published on 29 March 2018

Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.

scientific article published on 09 September 2009

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

scientific article published on 31 January 2018

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

scientific article

High-resolution detection and mapping of genomic DNA alterations in neuroblastoma

scientific article

Identifying the proteins to which small-molecule probes and drugs bind in cells

scholarly article

Improving breast cancer survival analysis through competition-based multidimensional modeling

scientific article

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

scientific article

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.

scientific article

Integrative Analysis on Histopathological Image for Identifying Cellular Heterogeneity

scientific article published on 01 February 2017

Localized Data Fusion for Kernel k-Means Clustering with Application to Cancer Biology ⬇️

scientific article published in January 2014

Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies

scientific article published on 12 January 2017

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

scientific article

Multiplexed immunohistochemistry image analysis using sparse coding

scientific article

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

scholarly article

PEG10 is a c-MYC target gene in cancer cells

scientific article

Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism

scientific article published on 07 May 2018

Population-level distribution and putative immunogenicity of cancer neoepitopes

scientific article published on 13 April 2018

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis.

scientific article

Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics.

scientific article

Reverse engineering cellular networks.

scientific article published on January 2006

SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks

Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting

scientific article

Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors

scientific article

Svpluscnv: analysis and visualization of complex structural variation data

scientific article published on 14 October 2020

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer

scientific article

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data

scientific article

TBIO-27. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER ADVANCING GENETIC RESEARCH IN CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECTS THROUGH LARGE SCALE INTEGRATED DATA-DRIVEN DISCOVERY AND CLOUD-BASED PLATFORMS FOR COLLABORATIVE ANALYSIS

The NIH BD2K center for big data in translational genomics

scientific article

The Stream algorithm: computationally efficient ridge-regression via Bayesian model averaging, and applications to pharmacogenomic prediction of cancer cell line sensitivity

scientific article published on January 2014

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

scientific article

Theory and limitations of genetic network inference from microarray data

scientific article

Toward better benchmarking: challenge-based methods assessment in cancer genomics

scientific article

Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia

scientific article published on 18 April 2006

Valection: design optimization for validation and verification studies

scholarly article by Christopher I Cooper published in September 2018

hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests

scientific article

List of works by Adam A Margolin

1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens

Abstract 2608: Global integration of knowledgebases for clinical interpretation of cancer variants

Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

BREAST CANCER HISTOPATHOLOGY IMAGE ANALYSIS PIPELINE FOR TUMOR PURITY ESTIMATION.

Boolean calculations made easy (for ribozymes).

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding.

Chemical Genomics Identifies Small-Molecule MCL1 Repressors and BCL-xL as a Predictor of MCL1 Dependency ⬇️

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy

Deep learning based Nucleus Classification in pancreas histological images.

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning

Empirical Bayes analysis of quantitative proteomics experiments

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas

Functional kinomics identifies candidate therapeutic targets in head and neck cancer

Functional precision medicine identifies novel druggable targets and therapeutic options in head and neck cancer.

Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

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

High-resolution detection and mapping of genomic DNA alterations in neuroblastoma

Identifying the proteins to which small-molecule probes and drugs bind in cells

Improving breast cancer survival analysis through competition-based multidimensional modeling

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.

Integrative Analysis on Histopathological Image for Identifying Cellular Heterogeneity

Localized Data Fusion for Kernel k-Means Clustering with Application to Cancer Biology ⬇️

Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

Multiplexed immunohistochemistry image analysis using sparse coding

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

PEG10 is a c-MYC target gene in cancer cells

Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism

Population-level distribution and putative immunogenicity of cancer neoepitopes

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis.

Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics.

Reverse engineering cellular networks.

SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks

Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting

Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors

Svpluscnv: analysis and visualization of complex structural variation data

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data

TBIO-27. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER ADVANCING GENETIC RESEARCH IN CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECTS THROUGH LARGE SCALE INTEGRATED DATA-DRIVEN DISCOVERY AND CLOUD-BASED PLATFORMS FOR COLLABORATIVE ANALYSIS

The NIH BD2K center for big data in translational genomics

The Stream algorithm: computationally efficient ridge-regression via Bayesian model averaging, and applications to pharmacogenomic prediction of cancer cell line sensitivity

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

Theory and limitations of genetic network inference from microarray data

Toward better benchmarking: challenge-based methods assessment in cancer genomics

Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia

Valection: design optimization for validation and verification studies

hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests