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| Publication Date | Article Title | Author(s) |
| 2-Sep-2020 | Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. | Zaccaria, Simone; Raphael, Benjamin J |
| 5-Feb-2020 | Analyses of non-coding somatic drivers in 2,658 cancer whole genomes | Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A; Shapira, Ofer; et al |
| 19-Jun-2019 | CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples. | Myers, Matthew A; Satas, Gryte; Raphael, Benjamin J |
| Jan-2017 | Complexity and algorithms for copy-number evolution problems. | El-Kebir, Mohammed; Raphael, Benjamin J; Shamir, Ron; Sharan, Roded; Zaccaria, Simone; et al |
| Jul-2020 | Copy number evolution with weighted aberrations in cancer. | Zeira, Ron; Raphael, Benjamin J |
| 7-Feb-2020 | Eleven grand challenges in single-cell data science. | Lähnemann, David; Köster, Johannes; Szczurek, Ewa; McCarthy, Davis J; Hicks, Stephanie C; et al |
| Oct-2016 | Gene and Network Analysis of Common Variants Reveals Novel Associations in Multiple Complex Diseases. | Nakka, Priyanka; Raphael, Benjamin J; Ramachandran, Sohini |
| Jul-2018 | Haplotype phasing in single-cell DNA-sequencing data. | Satas, Gryte; Raphael, Benjamin J |
| Sep-2018 | Hierarchical HotNet: identifying hierarchies of altered subnetworks. | Reyna, Matthew A; Leiserson, Mark DM; Raphael, Benjamin J |
| Jan-2018 | Identifying simultaneous rearrangements in cancer genomes. | Oesper, Layla; Dantas, Simone; Raphael, Benjamin J |
| Jan-2018 | Identifying structural variants using linked-read sequencing data. | Elyanow, Rebecca; Wu, Hsin-Ta; Raphael, Benjamin J |
| Jul-2020 | Identifying tumor clones in sparse single-cell mutation data. | Myers, Matthew A; Zaccaria, Simone; Raphael, Benjamin J |
| 2022 | A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements | Simonaitis, Pijus; Raphael, Benjamin J |
| Feb-2020 | netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis. | Elyanow, Rebecca; Dumitrascu, Bianca; Engelhardt, Barbara E; Raphael, Benjamin J |
| Oct-2017 | Novel Gene and Network Associations Found for Acute Lymphoblastic Leukemia Using Case-Control and Family-Based Studies in Multiethnic Populations. | Nakka, Priyanka; Archer, Natalie P; Xu, Heng; Lupo, Philip J; Raphael, Benjamin J; et al |
| 5-Feb-2020 | Pathway and network analysis of more than 2500 whole cancer genomes | Reyna, Matthew A; Haan, David; Paczkowska, Marta; Verbeke, Lieven P C; Vazquez, Miguel; et al |
| 1-Jan-2019 | Random walks on hypergraphs with edge-dependent vertex weights | Chitra, U; Raphael, Benjamin J |
| 4-Sep-2020 | Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples. | Aganezov, Sergey; Raphael, Benjamin J |
| Apr-2020 | SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses. | Satas, Gryte; Zaccaria, Simone; Mon, Geoffrey; Raphael, Benjamin J |
| 1-Jan-2020 | Single-cell tumor phylogeny inference with copy-number constrained mutation losses | Satas, G; Zaccaria, S; Mon, G; Raphael, Benjamin J |
