ReMixT: clone-specific genomic structure estimation in cancer

[1]  Sohrab P. Shah,et al.  deStruct: Accurate Rearrangement Detection using Breakpoint Specific Realignment , 2017, bioRxiv.

[2]  Samuel Aparicio,et al.  Scalable whole-genome single-cell library preparation without preamplification , 2017, Nature Methods.

[3]  S. C. Sahinalp,et al.  ReMixT: clone-specific genomic structure estimation in cancer , 2017, Genome Biology.

[4]  Ali Bashashati,et al.  Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer , 2016, Nature Genetics.

[5]  G. McVean,et al.  A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree , 2016, bioRxiv.

[6]  Alexandre Bouchard-Côté,et al.  Clonal genotype and population structure inference from single-cell tumor sequencing , 2016, Nature Methods.

[7]  Jian Ma,et al.  Allele-Specific Quantification of Structural Variations in Cancer Genomes , 2016, bioRxiv.

[8]  David M. Blei,et al.  Variational Inference: A Review for Statisticians , 2016, ArXiv.

[9]  Kenric Leung,et al.  The Life History of 21 Breast Cancers , 2015, Cell.

[10]  M. Nykter,et al.  The Evolutionary History of Lethal Metastatic Prostate Cancer , 2015, Nature.

[11]  Sohrab P. Shah,et al.  Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution , 2014, Nature.

[12]  Shankar Vembu,et al.  PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors , 2015, Genome Biology.

[13]  Benjamin J. Raphael,et al.  Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data , 2014, Bioinform..

[14]  Sohrab P. Shah,et al.  TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data , 2014, Genome research.

[15]  Christopher J. R. Illingworth,et al.  High-Definition Reconstruction of Clonal Composition in Cancer , 2014, Cell reports.

[16]  Christopher Yau,et al.  OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes , 2013, Bioinform..

[17]  Benjamin J. Raphael,et al.  THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data , 2013, Genome Biology.

[18]  D. Haussler,et al.  An algebraic framework to sample the rearrangement histories of a cancer metagenome with double cut and join, duplication and deletion events , 2013 .

[19]  Ryan M. Layer,et al.  LUMPY: a probabilistic framework for structural variant discovery , 2012, Genome Biology.

[20]  Benjamin J. Raphael,et al.  Reconstructing genome mixtures from partial adjacencies , 2012, BMC Bioinformatics.

[21]  Thomas Zichner,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[22]  Anne-Marie Mes-Masson,et al.  Derivation and characterization of matched cell lines from primary and recurrent serous ovarian cancer , 2012, BMC Cancer.

[23]  A. Børresen-Dale,et al.  The Life History of 21 Breast Cancers , 2012, Cell.

[24]  Benjamin J. Raphael,et al.  Reconstructing cancer genomes from paired-end sequencing data , 2012, BMC Bioinformatics.

[25]  Irmtraud M. Meyer,et al.  The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.

[26]  Y. Benjamini,et al.  Summarizing and correcting the GC content bias in high-throughput sequencing , 2012, Nucleic acids research.

[27]  C. Greenman.  Estimation of Rearrangement Phylogeny in Cancer , 2012 .

[28]  N. Carter,et al.  Estimation of rearrangement phylogeny for cancer genomes. , 2012, Genome research.

[29]  Joshua F. McMichael,et al.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.

[30]  Tatiana Popova,et al.  Supplementary Methods , 2012, Acta Neuropsychiatrica.

[31]  O. Delaneau,et al.  A linear complexity phasing method for thousands of genomes , 2011, Nature Methods.

[32]  Misko Dzamba,et al.  Detecting copy number variation with mated short reads. , 2010, Genome research.

[33]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[34]  Süleyman Cenk Sahinalp,et al.  Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes , 2009, RECOMB.

[35]  Christopher M. Bishop,et al.  Pattern Recognition and Machine Learning (Information Science and Statistics) , 2006 .

[36]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[37]  Michael I. Jordan,et al.  Factorial Hidden Markov Models , 1995, Machine Learning.

[38]  Michael I. Jordan,et al.  Exploiting Tractable Substructures in Intractable Networks , 1995, NIPS.

[39]  J. Nocedal,et al.  A Limited Memory Algorithm for Bound Constrained Optimization , 1995, SIAM J. Sci. Comput..