| Year |
Citation |
Score |
| 2024 |
Ma C, Balaban M, Liu J, Chen S, Wilson MJ, Sun CH, Ding L, Raphael BJ. Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics. Nature Methods. PMID 39478176 DOI: 10.1038/s41592-024-02438-9 |
0.306 |
|
| 2024 |
Mullen KM, Hong J, Attiyeh MA, Hayashi A, Sakamoto H, Kohutek ZA, McIntyre CA, Zhang H, Makohon-Moore AP, Zucker A, Wood LD, Myers MA, Arnold BJ, Zaccaria S, Chou JF, ... ... Raphael BJ, et al. The Evolutionary Forest of Pancreatic Cancer. Cancer Discovery. PMID 39378050 DOI: 10.1158/2159-8290.CD-23-1541 |
0.383 |
|
| 2024 |
Sundaram L, Kumar A, Zatzman M, Salcedo A, Ravindra N, Shams S, Louie BH, Bagdatli ST, Myers MA, Sarmashghi S, Choi HY, Choi WY, Yost KE, Zhao Y, Granja JM, ... ... Raphael BJ, et al. Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers. Science (New York, N.Y.). 385: eadk9217. PMID 39236169 DOI: 10.1126/science.adk9217 |
0.408 |
|
| 2024 |
Myers MA, Arnold BJ, Bansal V, Balaban M, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome Biology. 25: 130. PMID 38773520 DOI: 10.1186/s13059-024-03267-x |
0.369 |
|
| 2024 |
Shuaibi A, Chitra U, Raphael BJ. A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer. Biorxiv : the Preprint Server For Biology. PMID 38712136 DOI: 10.1101/2024.04.24.590995 |
0.348 |
|
| 2024 |
Mai U, Chu G, Raphael BJ. Maximum Likelihood Inference of Time-scaled Cell Lineage Trees with Mixed-type Missing Data. Biorxiv : the Preprint Server For Biology. PMID 38496496 DOI: 10.1101/2024.03.05.583638 |
0.31 |
|
| 2023 |
Sashittal P, Schmidt H, Chan M, Raphael BJ. Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing. Cell Systems. 14: 1113-1121.e9. PMID 38128483 DOI: 10.1016/j.cels.2023.11.005 |
0.31 |
|
| 2023 |
Sashittal P, Zhang H, Iacobuzio-Donahue CA, Raphael BJ. ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model. Genome Biology. 24: 272. PMID 38037115 DOI: 10.1186/s13059-023-03106-5 |
0.305 |
|
| 2023 |
Schmidt H, Sashittal P, Raphael BJ. A zero-agnostic model for copy number evolution in cancer. Plos Computational Biology. 19: e1011590. PMID 37943952 DOI: 10.1371/journal.pcbi.1011590 |
0.312 |
|
| 2023 |
Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, ... ... Raphael BJ, et al. Epigenetic regulation during cancer transitions across 11 tumour types. Nature. PMID 37914932 DOI: 10.1038/s41586-023-06682-5 |
0.31 |
|
| 2023 |
Myers MA, Arnold BJ, Bansal V, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Biorxiv : the Preprint Server For Biology. PMID 37502835 DOI: 10.1101/2023.07.13.548855 |
0.382 |
|
| 2023 |
Schmidt H, Sashittal P, Raphael BJ. A zero-agnostic model for copy number evolution in cancer. Biorxiv : the Preprint Server For Biology. PMID 37090633 DOI: 10.1101/2023.04.10.536302 |
0.317 |
|
| 2023 |
Rajan S, Zaccaria S, Cannon MV, Cam M, Gross AC, Raphael BJ, Roberts RD. Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time. Cancer Research Communications. 3: 564-575. PMID 37066022 DOI: 10.1158/2767-9764.CRC-22-0348 |
0.387 |
|
| 2023 |
Sashittal P, Zhang H, Iacobuzio-Donahue CA, Raphael BJ. ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model. Biorxiv : the Preprint Server For Biology. PMID 36711528 DOI: 10.1101/2023.01.05.522408 |
0.367 |
|
| 2023 |
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, ... ... Raphael BJ, et al. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. PMID 36697832 DOI: 10.1038/s41586-022-05599-9 |
0.309 |
|
| 2022 |
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, ... ... Raphael BJ, et al. Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications. 13: 7566. PMID 36481610 DOI: 10.1038/s41467-022-32334-9 |
0.325 |
|
| 2022 |
Park TY, Leiserson MDM, Klau GW, Raphael BJ. SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. Cell Genomics. 2. PMID 35382456 DOI: 10.1016/j.xgen.2022.100099 |
0.386 |
|
| 2021 |
Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA, Patidar R, Chen L, Wyczalkowski MA, ... ... Raphael BJ, et al. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nature Communications. 12: 5086. PMID 34429404 DOI: 10.1038/s41467-021-25177-3 |
0.394 |
|
| 2021 |
Satas G, Zaccaria S, El-Kebir M, Raphael BJ. DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Cell Systems. PMID 34416171 DOI: 10.1016/j.cels.2021.07.006 |
0.379 |
|
| 2020 |
Elyanow R, Zeira R, Land M, Raphael B. STARCH: Copy number and clone inference from spatial transcriptomics data. Physical Biology. PMID 33022659 DOI: 10.1088/1478-3975/abbe99 |
0.301 |
|
| 2020 |
Aganezov S, Raphael BJ. Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples. Genome Research. 30: 1274-1290. PMID 32887685 DOI: 10.1101/Gr.256701.119 |
0.541 |
|
| 2020 |
Aganezov S, Raphael BJ. Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples. Genome Research. 30: 1274-1290. PMID 32887685 DOI: 10.1101/gr.256701.119 |
0.457 |
|
| 2020 |
Zaccaria S, Raphael BJ. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nature Biotechnology. PMID 32879467 DOI: 10.1038/S41587-020-0661-6 |
0.485 |
|
| 2020 |
Zaccaria S, Raphael BJ. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nature Biotechnology. PMID 32879467 DOI: 10.1038/s41587-020-0661-6 |
0.389 |
|
| 2020 |
Zaccaria S, Raphael BJ. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nature Communications. 11: 4301. PMID 32879317 DOI: 10.1038/S41467-020-17967-Y |
0.467 |
|
| 2020 |
Zaccaria S, Raphael BJ. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nature Communications. 11: 4301. PMID 32879317 DOI: 10.1038/s41467-020-17967-y |
0.368 |
|
| 2020 |
Satas G, Zaccaria S, Mon G, Raphael BJ. SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses. Cell Systems. 10: 323-332.e8. PMID 32864481 DOI: 10.1016/J.Cels.2020.04.001 |
0.489 |
|
| 2020 |
Satas G, Zaccaria S, Mon G, Raphael BJ. SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses. Cell Systems. 10: 323-332.e8. PMID 32864481 DOI: 10.1016/j.cels.2020.04.001 |
0.394 |
|
| 2020 |
Myers MA, Zaccaria S, Raphael BJ. Identifying tumor clones in sparse single-cell mutation data. Bioinformatics (Oxford, England). 36: i186-i193. PMID 32657385 DOI: 10.1093/Bioinformatics/Btaa449 |
0.488 |
|
| 2020 |
Zeira R, Raphael BJ. Copy number evolution with weighted aberrations in cancer. Bioinformatics (Oxford, England). 36: i344-i352. PMID 32657354 DOI: 10.1093/Bioinformatics/Btaa470 |
0.482 |
|
| 2020 |
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, ... ... Raphael BJ, et al. Eleven grand challenges in single-cell data science. Genome Biology. 21: 31. PMID 32033589 DOI: 10.1186/S13059-020-1926-6 |
0.303 |
|
| 2020 |
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, ... ... Raphael BJ, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 578: 102-111. PMID 32025015 DOI: 10.1038/s41586-020-1965-x |
0.435 |
|
| 2020 |
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, ... ... Raphael BJ, et al. Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications. 11: 729. PMID 32024854 DOI: 10.1038/S41467-020-14367-0 |
0.447 |
|
| 2020 |
Elyanow R, Dumitrascu B, Engelhardt BE, Raphael BJ. netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis. Genome Research. PMID 31992614 DOI: 10.1101/Gr.251603.119 |
0.325 |
|
| 2019 |
Myers MA, Satas G, Raphael BJ. CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples. Cell Systems. PMID 31229560 DOI: 10.1016/J.Cels.2019.05.010 |
0.407 |
|
| 2019 |
Brady SW, Ma X, Bahrami A, Satas G, Wu G, Newman S, Rusch M, Putnam DK, Mulder HL, Yergeau D, Edmonson MN, Easton J, Alexandrov LB, Chen X, Mardis ER, ... ... Raphael BJ, et al. The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. Molecular Cancer Research : McR. PMID 30651371 DOI: 10.1158/1541-7786.Mcr-18-0620 |
0.406 |
|
| 2019 |
Li B, Brady SW, Ma X, Shen S, Zhang Y, Li Y, Liu Y, Wang N, Flasch D, Myers M, Mulder H, Ding L, Lu Y, Tian L, Hagiwara K, ... ... Raphael B, et al. Abstract 2872: Acquisition of drug resistance mutations during chemotherapy treatment in pediatric acute lymphoblastic leukemia Cancer Research. 79: 2872-2872. DOI: 10.1158/1538-7445.Am2019-2872 |
0.349 |
|
| 2018 |
Reyna MA, Leiserson MDM, Raphael BJ. Hierarchical HotNet: identifying hierarchies of altered subnetworks. Bioinformatics (Oxford, England). 34: i972-i980. PMID 30423088 DOI: 10.1093/Bioinformatics/Bty613 |
0.377 |
|
| 2018 |
El-Kebir M, Satas G, Raphael BJ. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics. 50: 718-726. PMID 29700472 DOI: 10.1038/S41588-018-0106-Z |
0.439 |
|
| 2018 |
Zaccaria S, El-Kebir M, Klau GW, Raphael BJ. Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29658782 DOI: 10.1089/Cmb.2017.0253 |
0.492 |
|
| 2018 |
Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, ... ... Raphael B, et al. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 173: 355-370.e14. PMID 29625052 DOI: 10.1016/J.Cell.2018.03.039 |
0.49 |
|
| 2018 |
Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, ... ... Raphael BJ, et al. Genetic mechanisms of immune evasion in colorectal cancer. Cancer Discovery. PMID 29510987 DOI: 10.1158/2159-8290.Cd-17-1327 |
0.712 |
|
| 2018 |
Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, ... ... Raphael B, et al. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell. 33: 244-258.e10. PMID 29438696 DOI: 10.1016/J.Ccell.2018.01.003 |
0.315 |
|
| 2017 |
Oesper L, Dantas S, Raphael BJ. Identifying simultaneous rearrangements in cancer genomes. Bioinformatics (Oxford, England). PMID 29186385 DOI: 10.1093/Bioinformatics/Btx745 |
0.512 |
|
| 2017 |
Elyanow R, Wu HT, Raphael BJ. Identifying structural variants using linked-read sequencing data. Bioinformatics (Oxford, England). PMID 29112732 DOI: 10.1093/Bioinformatics/Btx712 |
0.434 |
|
| 2017 |
Kuipers J, Jahn K, Raphael BJ, Beerenwinkel N. Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors. Genome Research. PMID 29030470 DOI: 10.1101/Gr.220707.117 |
0.509 |
|
| 2017 |
Satas G, Raphael BJ. Tumor phylogeny inference using tree-constrained importance sampling. Bioinformatics (Oxford, England). 33: i152-i160. PMID 28882002 DOI: 10.1093/Bioinformatics/Btx270 |
0.398 |
|
| 2017 |
Nakka P, Archer NP, Xu H, Lupo PJ, Raphael BJ, Yang JJ, Ramachandran S. Novel gene and network associations found for acute lymphoblastic leukemia using case-control and family-based studies in multi-ethnic populations. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. PMID 28751478 DOI: 10.1158/1055-9965.Epi-17-0360 |
0.388 |
|
| 2017 |
Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nature Reviews. Genetics. PMID 28607512 DOI: 10.1038/Nrg.2017.38 |
0.31 |
|
| 2017 |
Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael B, Wendl MC, et al. GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Genome Research. PMID 28522612 DOI: 10.1101/Gr.211656.116 |
0.429 |
|
| 2017 |
El-Kebir M, Raphael BJ, Shamir R, Sharan R, Zaccaria S, Zehavi M, Zeira R. Complexity and algorithms for copy-number evolution problems. Algorithms For Molecular Biology : Amb. 12: 13. PMID 28515774 DOI: 10.1186/S13015-017-0103-2 |
0.474 |
|
| 2016 |
Leiserson MD, Reyna MA, Raphael BJ. A weighted exact test for mutually exclusive mutations in cancer. Bioinformatics (Oxford, England). 32: i736-i745. PMID 27587696 DOI: 10.1093/Bioinformatics/Btw462 |
0.428 |
|
| 2016 |
Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, ... ... Raphael BJ, et al. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 30: 363. PMID 27505681 DOI: 10.1016/J.Ccell.2016.07.013 |
0.354 |
|
| 2016 |
Nakka P, Raphael BJ, Ramachandran S. Gene and Network Analysis of Common Variants Reveals Novel Associations in Multiple Complex Diseases. Genetics. PMID 27489002 DOI: 10.1534/Genetics.116.188391 |
0.367 |
|
| 2016 |
Leiserson MD, Wu HT, Vandin F, Raphael BJ. Erratum to: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer. Genome Biology. 17: 168. PMID 27485716 DOI: 10.1186/S13059-016-1034-9 |
0.354 |
|
| 2016 |
El-Kebir M, Satas G, Oesper L, Raphael BJ. Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures. Cell Systems. 3: 43-53. PMID 27467246 DOI: 10.1016/J.Cels.2016.07.004 |
0.42 |
|
| 2016 |
Leiserson MD, Vandin F, Wu HT, Raphael BJ. Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer. Nature Genetics. 48: 106-8. PMID 26813760 DOI: 10.1038/Ng.3491 |
0.423 |
|
| 2016 |
Grasso CS, Shinbrot E, Yu M, Liesersen M, Chaisson M, Chan A, Connolly C, Dai J, Du M, Fuchs C, Garraway L, Giannakis M, Harrison T, Hsu L, Huyghe J, ... ... Raphael B, et al. Abstract 136: Refining the molecular profile of colorectal tumors to expand prevention and treatment opportunities Cancer Research. 76: 136-136. DOI: 10.1158/1538-7445.Am2016-136 |
0.434 |
|
| 2015 |
Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, ... ... Raphael BJ, et al. Patterns and functional implications of rare germline variants across 12 cancer types. Nature Communications. 6: 10086. PMID 26689913 DOI: 10.1038/Ncomms10086 |
0.495 |
|
| 2015 |
Vandin F, Raphael BJ, Upfal E. On the Sample Complexity of Cancer Pathways Identification. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 26645471 DOI: 10.1089/Cmb.2015.0100 |
0.539 |
|
| 2015 |
Weinreb C, Raphael BJ. Identification of hierarchical chromatin domains. Bioinformatics (Oxford, England). PMID 26315910 DOI: 10.1093/Bioinformatics/Btv485 |
0.308 |
|
| 2015 |
Doris SM, Smith DR, Beamesderfer JN, Raphael BJ, Nathanson JA, Gerbi SA. Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics. Rna (New York, N.Y.). 21: 1719-30. PMID 26283689 DOI: 10.1261/Rna.051144.115 |
0.304 |
|
| 2015 |
Leiserson MD, Wu HT, Vandin F, Raphael BJ. CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer. Genome Biology. 16: 160. PMID 26253137 DOI: 10.1186/S13059-015-0700-7 |
0.47 |
|
| 2015 |
Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes. Nature Methods. 12: 615-621. PMID 26125594 DOI: 10.1038/Nmeth.3440 |
0.453 |
|
| 2015 |
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics (Oxford, England). 31: i62-70. PMID 26072510 DOI: 10.1093/Bioinformatics/Btv261 |
0.41 |
|
| 2015 |
Leiserson MD, Gramazio CC, Hu J, Wu HT, Laidlaw DH, Raphael BJ. MAGI: visualization and collaborative annotation of genomic aberrations. Nature Methods. 12: 483-4. PMID 26020500 DOI: 10.1038/Nmeth.3412 |
0.335 |
|
| 2015 |
Vandin F, Papoutsaki A, Raphael BJ, Upfal E. Accurate computation of survival statistics in genome-wide studies. Plos Computational Biology. 11: e1004071. PMID 25950620 DOI: 10.1371/Journal.Pcbi.1004071 |
0.481 |
|
| 2015 |
Parks MM, Lawrence CE, Raphael BJ. Detecting non-allelic homologous recombination from high-throughput sequencing data. Genome Biology. 16: 72. PMID 25886137 DOI: 10.1186/S13059-015-0633-1 |
0.434 |
|
| 2015 |
Raphael BJ, Vandin F. Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 510-27. PMID 25785493 DOI: 10.1089/Cmb.2014.0161 |
0.446 |
|
| 2015 |
Leiserson MD, Vandin F, Wu HT, Dobson JR, Eldridge JV, Thomas JL, Papoutsaki A, Kim Y, Niu B, McLellan M, Lawrence MS, Gonzalez-Perez A, Tamborero D, Cheng Y, Ryslik GA, ... ... Raphael BJ, et al. Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nature Genetics. 47: 106-14. PMID 25501392 DOI: 10.1038/Ng.3168 |
0.493 |
|
| 2015 |
Wu H, Leiserson MDM, Vandin F, Raphael BJ. Abstract 1936: CoMEt: A statistical approach to identify combinations of mutually exclusive alterations in cancer Cancer Research. 75: 1936-1936. DOI: 10.1158/1538-7445.Am2015-1936 |
0.518 |
|
| 2015 |
Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes Nature Methods. 12: 615-621. DOI: 10.1038/nmeth.3440 |
0.337 |
|
| 2015 |
Vandin F, Raphael BJ, Upfal E. On the sample complexity of cancer pathways identification Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 326-337. DOI: 10.1007/978-3-319-16706-0_33 |
0.393 |
|
| 2014 |
Weinreb C, Oesper L, Raphael BJ. Open adjacencies and k-breaks: detecting simultaneous rearrangements in cancer genomes. Bmc Genomics. 15: S4. PMID 25572114 DOI: 10.1186/1471-2164-15-S6-S4 |
0.481 |
|
| 2014 |
Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ. Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics (Oxford, England). 30: 3458-66. PMID 25355789 DOI: 10.1093/Bioinformatics/Btu714 |
0.413 |
|
| 2014 |
Oesper L, Satas G, Raphael BJ. Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. Bioinformatics (Oxford, England). 30: 3532-40. PMID 25297070 DOI: 10.1093/Bioinformatics/Btu651 |
0.455 |
|
| 2014 |
Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, ... ... Raphael BJ, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 158: 929-44. PMID 25109877 DOI: 10.1016/J.Cell.2014.06.049 |
0.71 |
|
| 2014 |
Ding L, Wendl MC, McMichael JF, Raphael BJ. Expanding the computational toolbox for mining cancer genomes. Nature Reviews. Genetics. 15: 556-70. PMID 25001846 DOI: 10.1038/Nrg3767 |
0.555 |
|
| 2014 |
Hajirasouliha I, Mahmoody A, Raphael BJ. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinformatics (Oxford, England). 30: i78-86. PMID 24932008 DOI: 10.1093/Bioinformatics/Btu284 |
0.406 |
|
| 2014 |
Wu HT, Hajirasouliha I, Raphael BJ. Detecting independent and recurrent copy number aberrations using interval graphs. Bioinformatics (Oxford, England). 30: i195-203. PMID 24931984 DOI: 10.1093/Bioinformatics/Btu276 |
0.425 |
|
| 2014 |
Brodsky AS, Fischer A, Miller DH, Vang S, MacLaughlan S, Wu HT, Yu J, Steinhoff M, Collins C, Smith PJ, Raphael BJ, Brard L. Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease. Plos One. 9: e94476. PMID 24732363 DOI: 10.1371/Journal.Pone.0094476 |
0.383 |
|
| 2014 |
Raphael BJ, Dobson JR, Oesper L, Vandin F. Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. Genome Medicine. 6: 5. PMID 24479672 DOI: 10.1186/Gm524 |
0.494 |
|
| 2014 |
Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, ... ... Raphael BJ, et al. Integrated analysis of germline and somatic variants in ovarian cancer. Nature Communications. 5: 3156. PMID 24448499 DOI: 10.1038/Ncomms4156 |
0.479 |
|
| 2013 |
Leiserson MD, Eldridge JV, Ramachandran S, Raphael BJ. Network analysis of GWAS data. Current Opinion in Genetics & Development. 23: 602-10. PMID 24287332 DOI: 10.1016/J.Gde.2013.09.003 |
0.36 |
|
| 2013 |
Raphael BJ. Making connections: using networks to stratify human tumors. Nature Methods. 10: 1077-8. PMID 24173383 DOI: 10.1038/Nmeth.2704 |
0.381 |
|
| 2013 |
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MD, Miller CA, Welch JS, Walter MJ, Wendl MC, ... ... Raphael BJ, et al. Mutational landscape and significance across 12 major cancer types. Nature. 502: 333-9. PMID 24132290 DOI: 10.1038/Nature12634 |
0.488 |
|
| 2013 |
Oesper L, Mahmoody A, Raphael BJ. THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biology. 14: R80. PMID 23895164 DOI: 10.1186/Gb-2013-14-7-R80 |
0.485 |
|
| 2013 |
Leiserson MD, Blokh D, Sharan R, Raphael BJ. Simultaneous identification of multiple driver pathways in cancer. Plos Computational Biology. 9: e1003054. PMID 23717195 DOI: 10.1371/Journal.Pcbi.1003054 |
0.473 |
|
| 2013 |
Ho AS, Kannan K, Roy DM, Morris LG, Ganly I, Katabi N, Ramaswami D, Walsh LA, Eng S, Huse JT, Zhang J, Dolgalev I, Huberman K, Heguy A, Viale A, ... ... Raphael BJ, et al. The mutational landscape of adenoid cystic carcinoma. Nature Genetics. 45: 791-8. PMID 23685749 DOI: 10.1038/Ng.2643 |
0.448 |
|
| 2013 |
Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson G, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, et al. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia New England Journal of Medicine. 368: 2059-2074. PMID 23634996 DOI: 10.1056/Nejmoa1301689 |
0.36 |
|
| 2013 |
Ding L, Raphael BJ, Chen F, Wendl MC. Advances for studying clonal evolution in cancer. Cancer Letters. 340: 212-9. PMID 23353056 DOI: 10.1016/J.Canlet.2012.12.028 |
0.484 |
|
| 2013 |
Vandin F, Papoutsaki A, Raphael BJ, Upfal E. Genome-wide survival analysis of somatic mutations in cancer Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 285-286. DOI: 10.1007/978-3-642-37195-0_26 |
0.398 |
|
| 2013 |
Oesper L, Mahmoody A, Raphael BJ. Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 171-172. DOI: 10.1007/978-3-642-37195-0_14 |
0.381 |
|
| 2012 |
Raphael BJ. Chapter 6: Structural variation and medical genomics. Plos Computational Biology. 8: e1002821. PMID 23300412 DOI: 10.1371/Journal.Pcbi.1002821 |
0.44 |
|
| 2012 |
Mahmoody A, Kahn CL, Raphael BJ. Reconstructing genome mixtures from partial adjacencies. Bmc Bioinformatics. 13: S9. PMID 23282028 DOI: 10.1186/1471-2105-13-S19-S9 |
0.493 |
|
| 2012 |
Vandin F, Upfal E, Raphael BJ. Finding driver pathways in cancer: models and algorithms. Algorithms For Molecular Biology : Amb. 7: 23. PMID 22954134 DOI: 10.1186/1748-7188-7-23 |
0.501 |
|
| 2012 |
Grasso CS, Wu YM, Robinson DR, Cao X, Dhanasekaran SM, Khan AP, Quist MJ, Jing X, Lonigro RJ, Brenner JC, Asangani IA, Ateeq B, Chun SY, Siddiqui J, Sam L, ... ... Raphael BJ, et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature. 487: 239-43. PMID 22722839 DOI: 10.1038/Nature11125 |
0.42 |
|
| 2012 |
Oesper L, Ritz A, Aerni SJ, Drebin R, Raphael BJ. Reconstructing cancer genomes from paired-end sequencing data. Bmc Bioinformatics. 13: S10. PMID 22537039 DOI: 10.1186/1471-2105-13-S6-S10 |
0.514 |
|
| 2012 |
Sindi SS, Onal S, Peng LC, Wu HT, Raphael BJ. An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biology. 13: R22. PMID 22452995 DOI: 10.1186/Gb-2012-13-3-R22 |
0.373 |
|
| 2012 |
Cáceres A, Sindi SS, Raphael BJ, Cáceres M, González JR. Identification of polymorphic inversions from genotypes. Bmc Bioinformatics. 13: 28. PMID 22321652 DOI: 10.1186/1471-2105-13-28 |
0.329 |
|
| 2012 |
Vandin F, Clay P, Upfal E, Raphael BJ. Discovery of mutated subnetworks associated with clinical data in cancer. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 55-66. PMID 22174262 |
0.371 |
|
| 2012 |
Vandin F, Upfal E, Raphael BJ. De novo discovery of mutated driver pathways in cancer. Genome Research. 22: 375-85. PMID 21653252 DOI: 10.1101/Gr.120477.111 |
0.503 |
|
| 2012 |
Vandin F, Upfal E, Raphael BJ. Algorithms and genome sequencing: Identifying driver pathways in cancer Computer. 45: 39-46. DOI: 10.1109/Mc.2012.71 |
0.507 |
|
| 2012 |
Vandin F, Upfal E, Raphael BJ. Workshop: Algorithms for discovery of mutated pathways in cancer 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182678 |
0.361 |
|
| 2011 |
Stuckey A, Fischer A, Miller DH, Hillenmeyer S, Kim KK, Ritz A, Singh RK, Raphael BJ, Brard L, Brodsky AS. Integrated genomics of ovarian xenograft tumor progression and chemotherapy response. Bmc Cancer. 11: 308. PMID 21781307 DOI: 10.1186/1471-2407-11-308 |
0.445 |
|
| 2011 |
Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG. Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proceedings of the National Academy of Sciences of the United States of America. 108: 11093-8. PMID 21685335 DOI: 10.1073/Pnas.1101135108 |
0.36 |
|
| 2011 |
Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ. Detection of recurrent rearrangement breakpoints from copy number data. Bmc Bioinformatics. 12: 114. PMID 21510904 DOI: 10.1186/1471-2105-12-114 |
0.438 |
|
| 2011 |
Vandin F, Upfal E, Raphael BJ. Algorithms for detecting significantly mutated pathways in cancer. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 507-22. PMID 21385051 DOI: 10.1089/Cmb.2010.0265 |
0.494 |
|
| 2010 |
O'Brien TM, Ritz AM, Raphael BJ, Laidlaw DH. Gremlin: an interactive visualization model for analyzing genomic rearrangements. Ieee Transactions On Visualization and Computer Graphics. 16: 918-26. PMID 20975128 DOI: 10.1109/Tvcg.2010.163 |
0.392 |
|
| 2010 |
Kahn CL, Hristov BH, Raphael BJ. Parsimony and likelihood reconstruction of human segmental duplications. Bioinformatics (Oxford, England). 26: i446-52. PMID 20823306 DOI: 10.1093/Bioinformatics/Btq368 |
0.359 |
|
| 2010 |
Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, ... ... Raphael BJ, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987 |
0.507 |
|
| 2010 |
Ritz A, Bashir A, Raphael BJ. Structural variation analysis with strobe reads. Bioinformatics (Oxford, England). 26: 1291-8. PMID 20378554 DOI: 10.7490/F1000Research.340.1 |
0.38 |
|
| 2010 |
Sindi SS, Raphael BJ. Identification and frequency estimation of inversion polymorphisms from haplotype data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 517-31. PMID 20377461 DOI: 10.1089/Cmb.2009.0185 |
0.321 |
|
| 2010 |
Bashir A, Lu Q, Carson D, Raphael BJ, Liu YT, Bafna V. Optimizing PCR assays for DNA-based cancer diagnostics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 369-81. PMID 20377451 DOI: 10.1089/Cmb.2009.0203 |
0.425 |
|
| 2010 |
Kahn CL, Mozes S, Raphael BJ. Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. Algorithms For Molecular Biology : Amb. 5: 11. PMID 20047668 DOI: 10.1186/1748-7188-5-11 |
0.408 |
|
| 2009 |
Nguyen V, Cao L, Lin JT, Hung N, Ritz A, Yu K, Jianu R, Ulin SP, Raphael BJ, Laidlaw DH, Brossay L, Salomon AR. A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation. Molecular & Cellular Proteomics : McP. 8: 2418-31. PMID 19605366 DOI: 10.1074/Mcp.M800307-Mcp200 |
0.308 |
|
| 2009 |
Sindi S, Helman E, Bashir A, Raphael BJ. A geometric approach for classification and comparison of structural variants. Bioinformatics (Oxford, England). 25: i222-30. PMID 19477992 DOI: 10.1093/Bioinformatics/Btp208 |
0.394 |
|
| 2009 |
Messmer BT, Raphael BJ, Aerni SJ, Widhopf GF, Rassenti LZ, Gribben JG, Kay NE, Kipps TJ. Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia. Leukemia Research. 33: 368-76. PMID 18640719 DOI: 10.1016/J.Leukres.2008.05.022 |
0.359 |
|
| 2009 |
Bashir A, Lu Q, Carson D, Raphael B, Liu YT, Bafna V. Optimizing PCR assays for DNA based cancer diagnostics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 220-235. DOI: 10.1007/978-3-642-02008-7_17 |
0.32 |
|
| 2008 |
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. Plos Computational Biology. 4: e1000051. PMID 18404202 DOI: 10.1371/Journal.Pcbi.1000051 |
0.492 |
|
| 2008 |
Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, et al. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biology. 9: R59. PMID 18364049 DOI: 10.1186/Gb-2008-9-3-R59 |
0.462 |
|
| 2007 |
Bashir A, Liu YT, Raphael BJ, Carson D, Bafna V. Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics (Oxford, England). 23: 2807-15. PMID 17766270 DOI: 10.1093/Bioinformatics/Btm390 |
0.389 |
|
| 2007 |
Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, ... ... Raphael BJ, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biology. 5: e16. PMID 17355171 DOI: 10.1371/Journal.Pbio.0050016 |
0.317 |
|
| 2006 |
Chaisson MJ, Raphael BJ, Pevzner PA. Microinversions in mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America. 103: 19824-9. PMID 17189424 DOI: 10.1073/Pnas.0603984103 |
0.341 |
|
| 2006 |
Jones NC, Zhi D, Raphael BJ. AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Research. 34: W613-6. PMID 16845083 DOI: 10.1093/Nar/Gkl288 |
0.308 |
|
| 2006 |
Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, et al. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Research. 16: 394-404. PMID 16461635 DOI: 10.1101/Gr.4247306 |
0.495 |
|
| 2005 |
Messmer BT, Raphael BJ, Aerni SJ, Widhopf GF, Rassenti LZ, Toy TL, Kipps TJ. A Bioinformatic Approach to CLL IGHV Sequence Analysis Identifies Extensive Ig Sequence Archetypes among BothMutated and Unmutated Sequences. Blood. 106: 176-176. DOI: 10.1182/Blood.V106.11.176.176 |
0.392 |
|
| 2004 |
Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Research. 14: 2336-46. PMID 15520295 DOI: 10.1101/Gr.2657504 |
0.324 |
|
| 2004 |
Raphael BJ, Pevzner PA. Reconstructing tumor amplisomes. Bioinformatics (Oxford, England). 20: i265-73. PMID 15262808 DOI: 10.1093/bioinformatics/bth931 |
0.31 |
|
| 2003 |
Raphael BJ, Volik S, Collins C, Pevzner PA. Reconstructing tumor genome architectures. Bioinformatics (Oxford, England). 19: ii162-71. PMID 14534186 DOI: 10.1093/bioinformatics/btg1074 |
0.334 |
|
| Show low-probability matches. |