Inferring Clonal Composition from Multiple Sections of a Breast Cancer
暂无分享,去创建一个
Junfeng Wang | William Stafford Noble | Daniela Witten | Habil Zare | Alex Hu | C. Anthony Blau | Kris Weber | Josh Smith | Debbie Nickerson | ChaoZhong Song | D. Witten | C. A. Blau | Alex Hu | Habil Zare | ChaoZhong Song | K. Weber | D. Nickerson | Josh Smith | Junfeng Wang | C. Blau
[1] M. Stephens,et al. Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis , 2010, PLoS genetics.
[2] R. E. Jones,et al. Nonlinear finite elements , 1978 .
[3] Ali Bashashati,et al. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling , 2013, The Journal of pathology.
[4] Joshua F. McMichael,et al. The Origin and Evolution of Mutations in Acute Myeloid Leukemia , 2012, Cell.
[5] Bo Chen,et al. Automatic estimation the number of clusters in hierarchical data clustering , 2010, Proceedings of 2010 IEEE/ASME International Conference on Mechatronic and Embedded Systems and Applications.
[6] Pasi Fränti,et al. Knee Point Detection in BIC for Detecting the Number of Clusters , 2008, ACIVS.
[7] A. Bouchard-Côté,et al. PyClone: statistical inference of clonal population structure in cancer , 2014, Nature Methods.
[8] A. Børresen-Dale,et al. Mutational Processes Molding the Genomes of 21 Breast Cancers , 2012, Cell.
[9] John E. Dennis,et al. Numerical methods for unconstrained optimization and nonlinear equations , 1983, Prentice Hall series in computational mathematics.
[10] M. Gerstung,et al. Reliable detection of subclonal single-nucleotide variants in tumour cell populations , 2012, Nature Communications.
[11] R. Tibshirani,et al. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. , 2009, Biostatistics.
[12] Jinlong Wu. Binomial Matrix Factorization for Discrete Collaborative Filtering , 2009, 2009 Ninth IEEE International Conference on Data Mining.
[13] Joshua F. McMichael,et al. Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft , 2010, Nature.
[14] David E. Irwin,et al. Finding a "Kneedle" in a Haystack: Detecting Knee Points in System Behavior , 2011, 2011 31st International Conference on Distributed Computing Systems Workshops.
[15] Lucas P. Watkins,et al. Detection of intensity change points in time-resolved single-molecule measurements. , 2005, The journal of physical chemistry. B.
[16] Shankar Vembu,et al. Inferring clonal evolution of tumors from single nucleotide somatic mutations , 2012, BMC Bioinformatics.
[17] P. Campbell,et al. Single-cell mutational profiling and clonal phylogeny in cancer , 2013, Genome research.
[18] R. Fletcher. Practical Methods of Optimization , 1988 .
[19] Benjamin J. Raphael,et al. THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data , 2013, Genome Biology.
[20] H. Swerdlow,et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.
[21] F. Markowetz,et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.
[22] Huanming Yang,et al. Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm , 2012, Cell.
[23] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[24] Serafim Batzoglou,et al. Genome evolution during progression to breast cancer , 2013, Genome research.
[25] J. Troge,et al. Tumour evolution inferred by single-cell sequencing , 2011, Nature.
[26] Jonathan M Irish,et al. Single Cell Profiling of Potentiated Phospho-Protein Networks in Cancer Cells , 2004, Cell.
[27] T. M. Williams,et al. Practical Methods of Optimization. Vol. 1: Unconstrained Optimization , 1980 .
[28] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[29] Adrian E. Raftery,et al. Model-Based Clustering, Discriminant Analysis, and Density Estimation , 2002 .
[30] T. M. Williams. Practical Methods of Optimization. Vol. 2 — Constrained Optimization , 1982 .
[31] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer , 2011, Nature Biotechnology.
[32] Pasi Fränti,et al. Knee Point Detection on Bayesian Information Criterion , 2008, 2008 20th IEEE International Conference on Tools with Artificial Intelligence.
[33] Raphael Gottardo,et al. flowClust: a Bioconductor package for automated gating of flow cytometry data , 2009, BMC Bioinformatics.
[34] Kevin P. Murphy,et al. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors , 2010, Bioinform..
[35] M. Nowak,et al. Distant Metastasis Occurs Late during the Genetic Evolution of Pancreatic Cancer , 2010, Nature.
[36] Michael I. Jordan,et al. Tree-Structured Stick Breaking for Hierarchical Data , 2010, NIPS.
[37] R. Shibata. Statistical aspects of model selection , 1989 .
[38] S. Wold. Cross-Validatory Estimation of the Number of Components in Factor and Principal Components Models , 1978 .
[39] T. Speed,et al. Model selection and prediction: Normal regression , 1993 .
[40] Nathan Srebro,et al. Fast maximum margin matrix factorization for collaborative prediction , 2005, ICML.
[41] D. Rubin,et al. Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .
[42] Daniel A. Powers,et al. Statistical Methods for Categorical Data Analysis , 1999 .
[43] Joshua F. McMichael,et al. Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.
[44] Huanming Yang,et al. Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor , 2012, Cell.
[45] Amit Dhingra,et al. Rapid and accurate pyrosequencing of angiosperm plastid genomes , 2006, BMC Plant Biology.
[46] P. Wriggers. Nonlinear Finite Element Methods , 2008 .
[47] Marco A. Marra,et al. Cancer genome-sequencing study design , 2013, Nature Reviews Genetics.
[48] Ken Chen,et al. Clonal architecture of secondary acute myeloid leukemia. , 2012, The New England journal of medicine.
[49] Ryan D. Morin,et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution , 2009, Nature.
[50] Radford M. Neal. Pattern Recognition and Machine Learning , 2007, Technometrics.
[51] P. A. Futreal,et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.
[52] Hongyu Zhao,et al. SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data , 2013, PloS one.
[53] Lani F. Wu,et al. Molecular Systems Biology 6; Article number 369; doi:10.1038/msb.2010.22 Citation: Molecular Systems Biology 6:369 , 2022 .
[54] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[55] Irmtraud M. Meyer,et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.
[56] Ya-Xiang Yuan,et al. Optimization Theory and Methods: Nonlinear Programming , 2010 .
[57] A. McKenna,et al. Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.
[58] Patrick O. Perry,et al. Bi-cross-validation of the SVD and the nonnegative matrix factorization , 2009, 0908.2062.
[59] Ken Chen,et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..
[60] G. Schwarz. Estimating the Dimension of a Model , 1978 .
[61] Y. Kluger,et al. TrAp: a tree approach for fingerprinting subclonal tumor composition , 2013, Nucleic acids research.
[62] J. Troge,et al. Inferring tumor progression from genomic heterogeneity. , 2010, Genome research.
[63] Jacob A. Tennessen,et al. Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes , 2012, Science.
[64] Jenny Taylor,et al. Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. , 2012, Blood.