Topological methods for genomics: Present and future directions

Goodwin, 2016, Coming of age: ten years of next-generation sequencing technologies, Nat Rev Genet, 17, 333, 10.1038/nrg.2016.49 Metzker, 2010, Sequencing technologies – the next generation, Nat Rev Genet, 11, 31, 10.1038/nrg2626 Buermans, 2014, Next generation sequencing technology: advances and applications, Biochim Biophys Acta, 1842, 1932, 10.1016/j.bbadis.2014.06.015 Carlsson, 2009, Topology and data, Bull Am Math Soc, 46, 255, 10.1090/S0273-0979-09-01249-X Carlsson, 2014, Topological pattern recognition for point cloud data, Acta Numer, 23, 289, 10.1017/S0962492914000051 Ghrist, 2014 Edelsbrunner, 2010 Chan, 2013, Topology of viral evolution, Proc Natl Acad Sci U S A, 110, 18566, 10.1073/pnas.1313480110 Camara, 2016, Topological data analysis generates high-resolution, genome-wide maps of human recombination, Cell Syst, 3, 83, 10.1016/j.cels.2016.05.008 Nicolau, 2011, Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival, Proc Natl Acad Sci U S A, 108, 7265, 10.1073/pnas.1102826108 Arsuaga, 2015, Identification of copy number aberrations in breast cancer subtypes using persistence topology, Microarrays, 4, 339, 10.3390/microarrays4030339 Li, 2015, Identification of type 2 diabetes subgroups through topological analysis of patient similarity, Sci Transl Med, 7, 311ra174, 10.1126/scitranslmed.aaa9364 Hinks, 2016, Multidimensional endotyping in patients with severe asthma reveals inflammatory heterogeneity in matrix metalloproteinases and chitinase 3-like protein 1, J Allergy Clin Immunol, 138, 61, 10.1016/j.jaci.2015.11.020 Cahoy, 2008, A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function, J Neurosci, 28, 264, 10.1523/JNEUROSCI.4178-07.2008 BICT'15 Proceedings of the 9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS) 2015. Pages 177-180. arXiv preprint arXiv:1511.01426 Perea, 2015, SW1PerS: sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data, BMC Bioinforma, 16, 257, 10.1186/s12859-015-0645-6 Dequeant, 2008, Comparison of pattern detection methods in microarray time series of the segmentation clock, PLoS One, 3, e2856, 10.1371/journal.pone.0002856 Nolte, 2010, The tangled tale of phase space, Physics Today, 63, 33, 10.1063/1.3397041 Gawad, 2016, Single-cell genome sequencing: current state of the science, Nat Rev Genet, 17, 175, 10.1038/nrg.2015.16 Macaulay, 2014, Single cell genomics: advances and future perspectives, PLoS Genet, 10, e1004126, 10.1371/journal.pgen.1004126 Clark, 2016, Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity, Genome Biol, 17, 72, 10.1186/s13059-016-0944-x Lefschetz, 2015 Mendelson, 1990 Hatcher, 2002, 606 Zomorodian, 2005, Computing persistent homology, Discrete Comput Geom, 33, 249, 10.1007/s00454-004-1146-y Edelsbrunner, 2002, Topological persistence and simplification, Discrete Comput Geometry, 28, 511, 10.1007/s00454-002-2885-2 Ghrist, 2008, Barcodes: the persistent topology of data, Bull Am Math Soc, 45, 61, 10.1090/S0273-0979-07-01191-3 Emmett, 2014, Characterizing scales of genetic recombination and antibiotic resistance in pathogenic bacteria using topological data analysis, 540 Camara, 2016, Inference of ancestral recombination graphs through topological data analysis, PLoS Comput Biol, 12, e1005071, 10.1371/journal.pcbi.1005071 International Conference on Machine Learning (ICML), 2014. Workshop on Topological Methods in Machine Learning. arXiv preprint arXiv:1406.4582. Hunter, 2015, Meiotic recombination: the essence of heredity, Cold Spring Harb Perspect Biol, 7 McDonald, 2016, Reassortment in segmented RNA viruses: mechanisms and outcomes, Nat Rev Microbiol, 14, 448, 10.1038/nrmicro.2016.46 Ochman, 2000, Lateral gene transfer and the nature of bacterial innovation, Nature, 405, 299, 10.1038/35012500 Gao, 2013, Human infection with a novel avian-origin influenza A (H7N9) virus, N Engl J Med, 368, 1888, 10.1056/NEJMoa1304459 Weinberger, 2014, The complexity of some topological inference problems, Found Comput Math, 14, 1277, 10.1007/s10208-013-9152-1 Singh, 2007, Topological methods for the analysis of high dimensional data sets and 3D object recognition, 91 Chin, 2011, Cancer genomics: from discovery science to personalized medicine, Nat Med, 17, 297, 10.1038/nm.2323 van de Vijver, 2002, A gene-expression signature as a predictor of survival in breast cancer, N Engl J Med, 347, 1999, 10.1056/NEJMoa021967 Torres, 2016, Tracking resilience to infections by mapping disease space, PLoS Biol, 14, e1002436, 10.1371/journal.pbio.1002436 Blumberg, 2014, Robust statistics, hypothesis testing, and confidence intervals for persistent homology on metric measure spaces, Found Comput Math, 14, 745, 10.1007/s10208-014-9201-4 Chazal, 2015, Convergence rates for persistence diagram estimation in topological data analysis, J Mach Learn Res, 16, 3603 Balakrishnan, 2013 Carlsson, 2009, Zigzag persistent homology and real-valued functions, 247 Carlsson, 2010, Zigzag persistence, Found Comput Math, 10, 367, 10.1007/s10208-010-9066-0 Carlsson, 2009, The theory of multidimensional persistence, Discrete Comput Geom, 42, 71, 10.1007/s00454-009-9176-0 Bendich, 2016, Scaffoldings and spines: organizing high-dimensional data using cover trees, local principal component analysis, and persistent homology, arXiv preprint arXiv:1602.06245 Abecasis, 2012, An integrated map of genetic variation from 1,092 human genomes, Nature, 491, 56, 10.1038/nature11632 Cancer Genome Atlas N, 2012, Comprehensive molecular portraits of human breast tumours, Nature, 490, 61, 10.1038/nature11412