Tumor phylogenetics

Peng, Wayne

doi:10.1038/ng.2240

Nat Genet

2012

DOI: 10.1038/ng.2240

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Tumor phylogenetics

Wayne Peng¹

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2015

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Cited by 2 publications

(6 citation statements)

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“…The above results are qualitatively consistent with the experimental observations in the superconducting state [2]. We also note that very recent ARPES experiment on the insulating samples has also revealed that the energy gap is anisotropic, i.e., it reaches the maxima value at the Brillouin zone boundary and is minimum at the diagonal direction [5]. This experimental result can also be ex- plained qualitatively based on our model.…”

supporting

confidence: 92%

“…Therefore, the above nodal gap should exist both in the superconducting state and the normal state. Our results for the nodal gap are qualitatively consistent with the experiments [1][2][3][4][5][6][7]. The momentum dependence of the energy gap along the Fermi surface is studied in Fig.…”

supporting

confidence: 89%

“…For hole doped samples, the hot spots are close to the antinodal points. Thus the anisotropic gap in non-superconducting materials [5] is understandable. We have also checked numerically (not shown here) that similar anisotropic behavior can be reproduced with the model including both the ID-SDW order and the ddensity-wave order (or the AF order).…”

mentioning

confidence: 99%

“…The energy gap is one of the most important properties in the studies of the high-T c superconductors. Recently, measurements of the energy gaps by angle-resolved photoemission spectroscopy (ARPES) in lightly doped high-T c materials revealed the existence of the non-zero energy gap along the diagonal directions of the Brillouin zone (also referred to the "nodal gap") [1][2][3][4][5][6]. The earliest indication of fully gapped single-particle excitation was reported in Ref.…”

mentioning

confidence: 99%

“…It has been observed in several families of cuprates [1][2][3][4][5][6][7]. Moreover, it has been reported that the nodal gap exists in the antiferromagnetic (AF) state [5,6], the spin glass region [3], as well as the superconducting and normal states for deeply underdoped region [1,2,4,7]. This result is surprising and contrasts the usual understanding of the d-wave superconducting pairing or the conventional pseudogap behavior, both should generate energy nodes along diagonal lines of the Brillouin zone.…”

mentioning

confidence: 99%

See 4 more Smart Citations

“Nodal Gap” Induced by the Incommensurate Diagonal Spin Density Modulation in Underdoped High-TcSuperconductors

Zhou

Zhu

2015

Advances in Condensed Matter Physics

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Recently it was revealed that the whole Fermi surface is fully gapped for several families of underdoped cuprates. The existence of the finite energy gap along the d-wave nodal lines ("nodal gap") contrasts the common understanding of the d-wave pairing symmetry, which challenges the present theories for the high-Tc superconductors. Here we propose that the incommensurate diagonal spin-density-wave order can account for the above experimental observation. The Fermi surface and the local density of states are also studied. Our results are in good agreement with many important experiments in high-Tc superconductors.

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supporting

confidence: 92%

supporting

confidence: 89%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

“Nodal Gap” Induced by the Incommensurate Diagonal Spin Density Modulation in Underdoped High-TcSuperconductors

Zhou

Zhu

2015

Advances in Condensed Matter Physics

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Reference-free inference of tumor phylogenies from single-cell sequencing data

Subramanian

Schwartz

2015

BMC Genomics

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BackgroundEffective management and treatment of cancer continues to be complicated by the rapid evolution and resulting heterogeneity of tumors. Phylogenetic study of cell populations in single tumors provides a way to delineate intra-tumoral heterogeneity and identify robust features of evolutionary processes. The introduction of single-cell sequencing has shown great promise for advancing single-tumor phylogenetics; however, the volume and high noise in these data present challenges for inference, especially with regard to chromosome abnormalities that typically dominate tumor evolution. Here, we investigate a strategy to use such data to track differences in tumor cell genomic content during progression.ResultsWe propose a reference-free approach to mining single-cell genome sequence reads to allow predictive classification of tumors into heterogeneous cell types and reconstruct models of their evolution. The approach extracts k-mer counts from single-cell tumor genomic DNA sequences, and uses differences in normalized k-mer frequencies as a proxy for overall evolutionary distance between distinct cells. The approach computationally simplifies deriving phylogenetic markers, which normally relies on first aligning sequence reads to a reference genome and then processing the data to extract meaningful progression markers for constructing phylogenetic trees. The approach also provides a way to bypass some of the challenges that massive genome rearrangement typical of tumor genomes presents for reference-based methods. We illustrate the method on a publicly available breast tumor single-cell sequencing dataset.ConclusionsWe have demonstrated a computational approach for learning tumor progression from single cell sequencing data using k-mer counts. k-mer features classify tumor cells by stage of progression with high accuracy. Phylogenies built from these k-mer spectrum distance matrices yield splits that are statistically significant when tested for their ability to partition cells at different stages of cancer.

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Tumor phylogenetics

Cited by 2 publications

References 1 publication

“Nodal Gap” Induced by the Incommensurate Diagonal Spin Density Modulation in Underdoped High-TcSuperconductors

“Nodal Gap” Induced by the Incommensurate Diagonal Spin Density Modulation in Underdoped High-TcSuperconductors

Reference-free inference of tumor phylogenies from single-cell sequencing data

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