Calling somatic SNVs and indels with Mutect2 D Benjamin, T Sato, K Cibulskis, G Getz, C Stewart, L Lichtenstein
BioRxiv, 861054, 2019
409 2019 Mitochondrial DNA variation across 56,434 individuals in gnomAD KM Laricchia, NJ Lake, NA Watts, M Shand, A Haessly, L Gauthier, ...
Genome research 32 (3), 569-582, 2022
61 2022 Friedel oscillations as a probe of fermionic quasiparticles EG Dalla Torre, D Benjamin, Y He, D Dentelski, E Demler
Physical Review B 93 (20), 205117, 2016
47 2016 Single-Band Model of Resonant Inelastic X-Ray Scattering by Quasiparticles in High- Cuprate Superconductors D Benjamin, I Klich, E Demler
Physical review letters 112 (24), 247002, 2014
47 2014 Quantification of somatic mutation flow across individual cell division events by lineage sequencing Y Brody, RJ Kimmerling, YE Maruvka, D Benjamin, JJ Elacqua, ...
Genome research 28 (12), 1901-1918, 2018
30 2018 Variational polaron method for Bose-Bose mixtures D Benjamin, E Demler
Physical Review A 89 (3), 033615, 2014
30 2014 Exploring quasiparticles in high-Tc cuprates through photoemission, tunneling, and x-ray scattering experiments EG Dalla Torre, Y He, D Benjamin, E Demler
New Journal of Physics 17 (2), 022001, 2015
23 2015 Microscopic theory of resonant soft-X-ray scattering in materials with charge order: The example of charge stripes in high-temperature cuprate superconductors D Benjamin, D Abanin, P Abbamonte, E Demler
Physical review letters 110 (13), 137002, 2013
19 2013 GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data M Babadi, JM Fu, SK Lee, AN Smirnov, LD Gauthier, M Walker, ...
Nature genetics 55 (9), 1589-1597, 2023
17 2023 Calling somatic snvs and indels with mutect2. BioRxiv. 2019: 861054 D Benjamin, T Sato, K Cibulskis, G Getz, C Stewart, L Lichtenstein
View Article, 0
17 GATK-gCNV: a rare copy number variant discovery algorithm and its application to exome sequencing in the UK biobank M Babadi, JM Fu, SK Lee, AN Smirnov, LD Gauthier, M Walker, ...
bioRxiv, 2022.08. 25.504851, 2022
8 2022 GATK CNV: copy-number variation discovery from coverage data M Babadi, DI Benjamin, SK Lee, A Smirnov, A Chevalier, L Lichtenstein, ...
Cancer Research 77 (13_Supplement), 3580-3580, 2017
8 2017 Probing competing and intertwined orders with resonant inelastic x-ray scattering in the hole-doped cuprates D Benjamin, I Klich, E Demler
Physical Review B 92 (3), 035151, 2015
8 2015 Calling somatic SNVs and indels with Mutect2. 2019; bioRxiv doi: 02 December 2019, preprint: not peer reviewedhttps D Benjamin, T Sato, K Cibulskis, G Getz, C Stewart, L Lichtenstein
doi. org/10.1101/861054, 0
6 Calling Somatic SNVs and Indels with Mutect2. bioRxiv, 861054 (2019) D Benjamin, T Sato, K Cibulskis, G Getz, C Stewart, L Lichtenstein
Acknowledgments: We thank all members of the Jan Vijg’s laboratory for …, 0
5 A validated lineage-derived somatic truth data set enables benchmarking in cancer genome analysis M Shand, J Soto, L Lichtenstein, D Benjamin, Y Farjoun, Y Brody, ...
Communications Biology 3 (1), 744, 2020
4 2020 Pair HMM probabilistic realignment in HaplotypeCaller and Mutect D Benjamin
Broad Institute. Available online: https://github. com/broadinstitute/gatk …, 2018
3 2018 GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data A Chevalier, L Lichtenstein, A Smirnov, SK Lee, M Babidi, DI Benjamin, ...
Cancer Research 77 (13_Supplement), 3581-3581, 2017
3 2017 Superconducting pairing in resonant inelastic x-ray scattering Y Shi, D Benjamin, E Demler, I Klich
Physical Review B 94 (9), 094516, 2016
3 2016 GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data (Aug, 10.1038/s41588-023-01449-0, 2023) M Babadi, JM Fu, SK Lee, AN Smirnov, LD Gauthier, M Walker, ...
NATURE GENETICS, 2024
2024