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List of works by Benjamin J. Raphael

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data

scientific article

A geometric approach for classification and comparison of structural variants

scientific article published on June 2009

A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation

scientific article published on 14 July 2009

A novel method for multiple alignment of sequences with repeated and shuffled elements

scientific article published on November 2004

A path to translation: How 3D patient tumor avatars enable next generation precision oncology

scientific article published on 12 December 2022

A sequence-based survey of the complex structural organization of tumor genomes

scientific article

A weighted exact test for mutually exclusive mutations in cancer

scientific article

Abstract 801: Surprisingly conserved copy numbers from cell to cell within structurally complex tumors challenge the unstable genome hypothesis

scientific article published in 2022

Accurate computation of survival statistics in genome-wide studies

scientific article published on 7 May 2015

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

scientific article published on 02 September 2020

Advances for studying clonal evolution in cancer ⬇️

scientific article published on January 23, 2013

Algorithms for detecting significantly mutated pathways in cancer

scientific article published in March 2011

Alignment and Integration of Spatial Transcriptomics Data

scientific article published on 16 March 2021

Alignment and integration of spatial transcriptomics data

scientific article published in 2022

An integrative probabilistic model for identification of structural variation in sequencing data ⬇️

scientific article published on January 1, 2012

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Analysis of segmental duplications via duplication distance

scientific article published in August 2008

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples

scientific article published on 19 June 2019

Characterization of structural variants with single molecule and hybrid sequencing approaches

scientific article

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

scientific article published on 02 September 2020

CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer

scientific article

Complexity and algorithms for copy-number evolution problems

scientific article

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

scientific article published on 4 November 2015

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

scientific article

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

article

Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia

scientific article published on 21 July 2008

Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor

scientific article published on 31 May 2022

Copy number evolution with weighted aberrations in cancer

scientific article published on 01 July 2020

Copy-Number Evolution Problems: Complexity and Algorithms

Data from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Data from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Data from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

De novo discovery of mutated driver pathways in cancer

scientific article published on 7 June 2011

DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution

scientific article published on 27 February 2021

DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution

scientific article published on 20 October 2021

Decoding the fine-scale structure of a breast cancer genome and transcriptome

scientific article

Detecting independent and recurrent copy number aberrations using interval graphs

scientific article

Detection of recurrent rearrangement breakpoints from copy number data

scientific article

Discovery of mutated subnetworks associated with clinical data in cancer

scientific article published on January 1, 2012

Discovery of phosphorylation motif mixtures in phosphoproteomics data

scientific article

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

Erratum to: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer

scientific article published on 2 August 2016

Expanding the computational toolbox for mining cancer genomes

scientific article

Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease.

scientific article

Finding driver pathways in cancer: models and algorithms

scientific article published on 6 September 2012

Genetic mechanisms of immune evasion in colorectal cancer

scientific article published on 6 March 2018

GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

scientific article

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

scientific article

Gremlin: an interactive visualization model for analyzing genomic rearrangements

scientific article published in November 2010

HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

scientific article published on 15 July 2023

Haplotype phasing in single-cell DNA-sequencing data.

scientific article published in July 2018

Hierarchical HotNet: identifying hierarchies of altered subnetworks

scholarly article by Matthew A Reyna published in September 2018

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

scientific article published on 30 January 2014

Identifying repeat domains in large genomes

scientific article published on 31 January 2006

Identifying simultaneous rearrangements in cancer genomes.

scientific article published on 27 November 2017

Identifying structural variants using linked-read sequencing data

scientific article published on 3 November 2017

Identifying tumor clones in sparse single-cell mutation data

scientific article published on 01 July 2020

Inferring parsimonious migration histories for metastatic cancers

scientific article published on 26 April 2018

Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures

scientific article published on July 2016

Integrated analysis of germline and somatic variants in ovarian cancer.

scientific article

Integrated genomics of ovarian xenograft tumor progression and chemotherapy response

scientific article

Integrating genetic dependencies and genomic alterations across pathways and cancer types

scientific article published on 14 July 2020

International network of cancer genome projects

scientific article

MAGI: visualization and collaborative annotation of genomic aberrations

scientific article published on 01 June 2015

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

scientific article

Mutational landscape and significance across 12 major cancer types

scientific article

NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks

scientific article published in December 2022

NetMix2: Unifying network propagation and altered subnetworks

scientific article published on 2 February 2022

Network analysis of GWAS data

scientific article

Network propagation: a universal amplifier of genetic associations

scientific article published on 12 June 2017

On the Sample Complexity of Cancer Pathways Identification.

scientific article published on 8 December 2015

PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data

scientific article published on 8 January 2023

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

scientific article

Parsimony and likelihood reconstruction of human segmental duplications ⬇️

scientific article published on September 15, 2010

Partial alignment of multislice spatially resolved transcriptomics data

scientific article published in July 2023

Pathogenic Germline Variants in 10,389 Adult Cancers

scientific article published in April 2018

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Pathway and network analysis of more than 2,500 whole cancer genomes

Pathway and network analysis of more than 2500 whole cancer genomes

scientific article published on 05 February 2020

Patterns and functional implications of rare germline variants across 12 cancer types

scientific article

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

scientific article published on 16 April 2018

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data

scientific article

Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells

scientific article

Quantitative time-resolved phosphoproteomic analysis of mast cell signaling

scientific article

Reconstructing cancer genomes from paired-end sequencing data

scientific article

Reconstructing genome mixtures from partial adjacencies ⬇️

scientific article published on December 19, 2012

Reconstructing tumor amplisomes

scientific article published on August 2004

Reconstructing tumor genome architectures

scientific article published in October 2003

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

scientific article

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

scientific article published on 04 September 2020

Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer

scientific article published in January 2016

SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses

scientific article published on 01 April 2020

STARCH: Copy number and clone inference from spatial transcriptomics data

scientific article published on 06 October 2020

STARCH: Copy number and clone inference from spatial transcriptomics data

scientific article published on 13 July 2020

Simultaneous Identification of Multiple Driver Pathways in Cancer ⬇️

scientific article published on May 23, 2013

Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data

scientific article

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

scientific article

Spatial epigenome–transcriptome co-profiling of mammalian tissues

scholarly article

Spatially Interacting Phosphorylation Sites and Mutations in Cancer

scientific article published on 15 February 2021

Spatially interacting phosphorylation sites and mutations in cancer

scientific article published on 19 April 2021

Structural variation analysis with strobe reads

scientific article published on 08 April 2010

Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published in April 2023

Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 31 August 2021

SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types

scientific article published in 2022

Supplementary Figure S1 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S1 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S1 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Figure S1 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S2 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S2 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S2 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S2 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Figure S3 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S3 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S3 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S3 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Figure S4 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S4 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S4 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Figure S4 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S5 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S5 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S5 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Figure S5 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S6 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S6 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S6 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S6 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Figure S7 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S7 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S7 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S7 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Figure S8 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Figure S8 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Figure S8 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Figure S8 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Table S1 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Table S1 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Table S1 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Table S1 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

Supplementary Table S2 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

scientific article published on 12 April 2023

Supplementary Table S2 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

Supplementary Table S2 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Supplementary Table S2 from Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

scientific article published on 4 April 2023

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

scientific article

The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

scientific article published on 16 January 2019

The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data

scientific article

The mutational landscape of adenoid cystic carcinoma

scientific article published on 19 May 2013

Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia

scientific article published on 01 January 2020

Tumor phylogeny inference using tree-constrained importance sampling

scientific article published in July 2017

Visible Machine Learning for Biomedicine

scientific article published on 01 June 2018

netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis

scientific article published on 28 January 2020

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