Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
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Hiroki Ohta | Azusa Tanaka | Akihiro Fujimoto | Yasuhiro Ishitsuka | Jun-ichirou Yasunaga | Masao Matsuoka | M. Matsuoka | A. Fujimoto | J. Yasunaga | A. Tanaka | Yasuhiro Ishitsuka | Hiroki Ohta | Akihiro Fujimoto | Jun-ichirou Yasunaga | Azusa Tanaka
[1] Charles R. M. Bangham,et al. CADM1/TSLC1 Identifies HTLV-1-Infected Cells and Determines Their Susceptibility to CTL-Mediated Lysis , 2016, PLoS pathogens.
[2] Shiqi Tu,et al. An introduction to computational tools for differential binding analysis with ChIP-seq data , 2017, Quantitative Biology.
[3] Denne Reed,et al. Fossils from Mille-Logya, Afar, Ethiopia, elucidate the link between Pliocene environmental changes and Homo origins , 2020, Nature Communications.
[4] Renata Walewska,et al. Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks , 2016, Nature Communications.
[5] M. Ramalho-Santos,et al. Open chromatin in pluripotency and reprogramming , 2010, Nature Reviews Molecular Cell Biology.
[6] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[7] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[8] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[9] Daniel Müllner,et al. Modern hierarchical, agglomerative clustering algorithms , 2011, ArXiv.
[10] Manolis Kellis,et al. ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.
[11] Chuan He,et al. Fate by RNA methylation: m6A steers stem cell pluripotency , 2015, Genome Biology.
[12] P. Vyas,et al. Coexistence of LMPP-like and GMP-like leukemia stem cells in acute myeloid leukemia. , 2011, Cancer cell.
[13] M. Shimoyama,et al. Diagnostic criteria and classification of clinical subtypes of adult T‐cell leukaemia‐lymphoma , 1991, British journal of haematology.
[14] Warren D. Sharp,et al. Comment on “The earliest modern humans outside Africa” , 2018, Science.
[15] David J. C. MacKay,et al. Information Theory, Inference, and Learning Algorithms , 2004, IEEE Transactions on Information Theory.
[16] Christoph Bock,et al. Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL , 2020, Nature Communications.
[17] Howard Y. Chang,et al. Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.
[18] Rafael A. Irizarry,et al. quantro: a data-driven approach to guide the choice of an appropriate normalization method , 2015, Genome Biology.
[19] Manuel Llinás,et al. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond , 2016, PLoS pathogens.
[20] Kuan-Teh Jeang,et al. Human T-cell leukaemia virus type 1 (HTLV-1) infectivity and cellular transformation , 2007, Nature Reviews Cancer.
[21] Rory Stark. Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer , 2012, RECOMB.
[22] Michael W. Pfaffl,et al. Normalization Strategies for Microrna Profiling Experiments: a 'normal' Way to a Hidden Layer of Complexity? , 2010 .
[23] Howard Y. Chang,et al. Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors. , 2017, Cancer cell.
[24] Mauro A. A. Castro,et al. The chromatin accessibility landscape of primary human cancers , 2018, Science.
[25] David R. Powell,et al. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis , 2020, Genome Biology.
[26] Alicia N. Schep,et al. Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility , 2016, Cell.
[27] P Rudge,et al. In vivo cellular tropism of human T-cell leukemia virus type 1 , 1990, Journal of virology.
[28] J. Stamatoyannopoulos,et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns , 2011, Nature Genetics.
[29] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[30] Patrick Lombard,et al. CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities , 2014, Nucleic Acids Res..
[31] Sandy L. Klemm,et al. Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.
[32] Howard Y. Chang,et al. Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution , 2016, Nature Genetics.
[33] Francine E. Garrett-Bakelman,et al. CD99 is a therapeutic target on disease stem cells in myeloid malignancies , 2017, Science Translational Medicine.
[34] Nathan C. Sheffield,et al. The accessible chromatin landscape of the human genome , 2012, Nature.
[35] A Okayama,et al. Clinical significance of CADM1/TSLC1/IgSF4 expression in adult T-cell leukemia/lymphoma , 2012, Leukemia.
[36] Howard Y. Chang,et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.