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Author Details

Benjamin J Raphael
Princeton University
2003
126
48
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36711528ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model.bioRxiv2023
37636316Co-evolution of <i>AR</i> gene copy number and structural complexity in endocrine therapy resistant prostate cancer.NAR Cancer2023
37553263Partial alignment of multislice spatially resolved transcriptomics data.Genome Res2023
37502835HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.bioRxiv2023
37090633A zero-agnostic model for copy number evolution in cancer.bioRxiv2023
37066022Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time.Cancer Res Commun2023
36697832Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.Nature2023
36922587Spatial epigenome-transcriptome co-profiling of mammalian tissues.Nature2023
36711750PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data.bioRxiv2023
34996889Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment.Nat Commun2022
35382456SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types.Cell Genom2022
35642016Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor.Acta Neuropathol Commun2022
36525308NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks.J Comput Biol2022
36265465Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics.Cell Syst2022
33022659STARCH: copy number and clone inference from spatial transcriptomics data.Phys Biol2021
33875650Spatially interacting phosphorylation sites and mutations in cancer.Nat Commun2021
34429404Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.Nat Commun2021
34416171DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution.Cell Syst2021
33400606NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks.J Comput Biol2021
32879467Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.Nat Biotechnol2021
32879317Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.Nat Commun2020
32033589Eleven grand challenges in single-cell data science.Genome Biol2020
31697823Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia.Blood2020
31992614netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis.Genome Res2020
32864481SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses.Cell Syst2020
32887685Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.Genome Res2020
32657385Identifying tumor clones in sparse single-cell mutation data.Bioinformatics2020
32657354Copy number evolution with weighted aberrations in cancer.Bioinformatics2020
30651371The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment.Mol Cancer Res2019
31229560CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.Cell Syst2019
29186385Identifying simultaneous rearrangements in cancer genomes.Bioinformatics2018
30217148Using controls to limit false discovery in the era of big data.BMC Bioinformatics2018
29906441Visible Machine Learning for Biomedicine.Cell2018
29950014Haplotype phasing in single-cell DNA-sequencing data.Bioinformatics2018
30423088Hierarchical HotNet: identifying hierarchies of altered subnetworks.Bioinformatics2018
29700472Inferring parsimonious migration histories for metastatic cancers.Nat Genet2018
29438696The Integrated Genomic Landscape of Thymic Epithelial Tumors.Cancer Cell2018
29658782Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.J Comput Biol2018
29625052Pathogenic Germline Variants in 10,389 Adult Cancers.Cell2018
29510987Genetic Mechanisms of Immune Evasion in Colorectal Cancer.Cancer Discov2018
29112732Identifying structural variants using linked-read sequencing data.Bioinformatics2018
28515774Complexity and algorithms for copy-number evolution problems.Algorithms Mol Biol2017
29030470Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors.Genome Res2017
28882002Tumor phylogeny inference using tree-constrained importance sampling.Bioinformatics2017
28751478Novel Gene and Network Associations Found for Acute Lymphoblastic Leukemia Using Case-Control and Family-Based Studies in Multiethnic Populations.Cancer Epidemiol Biomarkers Prev2017
28607512Network propagation: a universal amplifier of genetic associations.Nat Rev Genet2017
28522612GenomeVIP: a cloud platform for genomic variant discovery and interpretation.Genome Res2017
26813760Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer.Nat Genet2016
26536169Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.N Engl J Med2016
26645471On the Sample Complexity of Cancer Pathways Identification.J Comput Biol2016
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Collaborators

Fabio Vandin
University of Padova
Co-authored papers 15
Li Ding
McDonnell Genome Institute, Washington University School of Medicine
Co-authored papers 13
Hsin-Ta Wu
Co-authored papers 12
Michael C Wendl
Washington University in St Louis
Co-authored papers 11
Anna Ritz
Reed College
Co-authored papers 10
Michael D McLellan
McDonnell Genome Institute, Washington University in St. Louis
Co-authored papers 8
Matthew A Wyczalkowski
Washington University in St Louis
Co-authored papers 8
Ali Bashir
Google Accelerated Science Team, Google Inc
Co-authored papers 7
Amy G Robertson
Present address: Dxige Research Inc.
Co-authored papers 6
David A Wheeler
Baylor College of Medicine
Co-authored papers 6
Andrew D Cherniack
Dana-Farber Cancer Institute
Co-authored papers 6
Rehan Akbani
The University of Texas MD Anderson Cancer Center
Co-authored papers 6
Joshua F McMichael
Washington University
Co-authored papers 6
Katherine A Hoadley
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
Co-authored papers 6
Colin C Collins
University of British Columbia
Co-authored papers 6
Pavel A Pevzner
University of California
Co-authored papers 6
Feng Chen
Washington University in St Louis
Co-authored papers 5
Charles Lu
Co-authored papers 5
Cyriac Kandoth
University of California los angeles
Co-authored papers 5
Beifang Niu
Co-authored papers 5
Ken Chen
University of Texas MD Anderson Cancer Center
Co-authored papers 4
Ramaswamy Govindan
Siteman Cancer Center, Washington University School of Medicine
Co-authored papers 4
Robert J Mashl
Washington University in St. Louis
Co-authored papers 4
Kuan-Lin Huang
Icahn School of Medicine at Mount Sinai
Co-authored papers 4
Daniel C Koboldt
Institute for Genomic Medicine, Nationwide Children's Hospital
Co-authored papers 4
Nuria Lopez-Bigas
Universitat Pompeu Fabra
Co-authored papers 4
Stanislav V Volik
University of British Columbia
Co-authored papers 4
John F DiPersio
Washington University School of Medicine
Co-authored papers 4
Vineet Bafna
University of California San Diego
Co-authored papers 4
Gordon B Mills
Knight Cancer Institute, Oregon Health and Sciences University
Co-authored papers 4
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