Strange India All Strange Things About India and world


  • Tang, J. et al. The genomic landscapes of individual melanocytes from human skin. Nature 586, 600–605 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fowler, J. C. et al. Selection of oncogenic mutant clones in normal human skin varies with body site. Cancer Discov. 11, 340–361 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Reed, R. In New Concepts in Surgical Pathology of the Skin 89–90 (Wiley, 1976).

  • Wang, K. C., Helms, J. A. & Chang, H. Y. Regeneration, repair and remembering identity: the three Rs of Hox gene expression. Trends Cell Biol. 19, 268–275 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Curtin, J. A. et al. Distinct sets of genetic alterations in melanoma. N. Engl. J. Med. 353, 2135–2147 (2005).

    CAS 
    PubMed 

    Google Scholar 

  • Hayward, N. K. et al. Whole-genome landscapes of major melanoma subtypes. Nature 545, 175–180 (2017).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Petrelli, F. et al. Prognostic survival associated with left-sided vs right-sided colon cancer: a systematic review and meta-analysis. JAMA Oncol. 3, 211–219 (2017).

    PubMed 

    Google Scholar 

  • Rabbie, R., Ferguson, P., Molina-Aguilar, C., Adams, D. J. & Robles-Espinoza, C. D. Melanoma subtypes: genomic profiles, prognostic molecular markers and therapeutic possibilities. J. Pathol. 247, 539–551 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Belote, R. L. et al. Human melanocyte development and melanoma dedifferentiation at single-cell resolution. Nat. Cell Biol. 23, 1035–1047 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • Moon, H. et al. Melanocyte stem cell activation and translocation initiate cutaneous melanoma in response to UV exposure. Cell Stem Cell 21, 665–678.e666 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Kohler, C. et al. Mouse cutaneous melanoma induced by mutant Braf arises from expansion and dedifferentiation of mature pigmented melanocytes. Cell Stem Cell 21, 679–693.e676 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Newell, F. et al. Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity. Nat. Commun. 11, 5259 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yeh, I. et al. Targeted genomic profiling of acral melanoma. J. Natl Cancer Inst. 111, 1068–1077 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liang, W. S. et al. Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma. Genome Res. 27, 524–532 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Klemen, N. D. et al. Survival after checkpoint inhibitors for metastatic acral, mucosal and uveal melanoma. J. Immunother. Cancer 8, e000341 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Shoushtari, A. N. et al. The efficacy of anti-PD-1 agents in acral and mucosal melanoma. Cancer 122, 3354–3362 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012).

    PubMed 

    Google Scholar 

  • Zehir, A. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 23, 703–713 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Luo, L. Y. & Hahn, W. C. Oncogenic signaling adaptor proteins. J. Genet. Genomics 42, 521–529 (2015).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Bentires-Alj, M. et al. A role for the scaffolding adapter GAB2 in breast cancer. Nat. Med. 12, 114–121 (2006).

    CAS 
    PubMed 

    Google Scholar 

  • Cheung, H. W. et al. Amplification of CRKL induces transformation and epidermal growth factor receptor inhibitor resistance in human non-small cell lung cancers. Cancer Discov. 1, 608–625 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hemmeryckx, B. et al. Crkl enhances leukemogenesis in BCR/ABL P190 transgenic mice. Cancer Res. 61, 1398–1405 (2001).

    CAS 
    PubMed 

    Google Scholar 

  • Chernoff, K. A. et al. GAB2 amplifications refine molecular classification of melanoma. Clin. Cancer Res. 15, 4288–4291 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Horst, B. et al. Gab2-mediated signaling promotes melanoma metastasis. Am. J. Pathol. 174, 1524–1533 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Eshiba, S. et al. Stem cell spreading dynamics intrinsically differentiate acral melanomas from nevi. Cell Rep. 36, 109492 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • Nakamura, T., Gehrke, A. R., Lemberg, J., Szymaszek, J. & Shubin, N. H. Digits and fin rays share common developmental histories. Nature 537, 225–228 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shubin, N. H., Daeschler, E. B. & Jenkins, F. A. Jr The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature 440, 764–771 (2006).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Xu, B., Feng, X. & Burdine, R. D. Categorical data analysis in experimental biology. Dev. Biol. 348, 3–11 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Philippidou, P. & Dasen, J. S. Hox genes: choreographers in neural development, architects of circuit organization. Neuron 80, 12–34 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • Petit, F., Sears, K. E. & Ahituv, N. Limb development: a paradigm of gene regulation. Nat. Rev. Genet. 18, 245–258 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • Sheth, R. et al. Distal limb patterning requires modulation of cis-regulatory activities by HOX13. Cell Rep. 17, 2913–2926 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, S. et al. Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP–seq peaks. Nucleic Acids Res. 47, W206–W211 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chablais, F. & Jazwinska, A. IGF signaling between blastema and wound epidermis is required for fin regeneration. Development 137, 871–879 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • Dhupkar, P., Zhao, H., Mujoo, K., An, Z. & Zhang, N. Crk II silencing down-regulates IGF-IR and inhibits migration and invasion of prostate cancer cells. Biochem. Biophys. Rep. 8, 382–388 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhang, J. et al. CRKL mediates p110β-dependent PI3K signaling in PTEN-deficient cancer cells. Cell Rep. 20, 549–557 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tanna, C. E., Goss, L. B., Ludwig, C. G. & Chen, P. W. Arf GAPs as regulators of the actin cytoskeleton—an update. Int. J. Mol. Sci. 20, 442 (2019).

    PubMed Central 

    Google Scholar 

  • Fritsch, R. et al. RAS and RHO families of GTPases directly regulate distinct phosphoinositide 3-kinase isoforms. Cell 153, 1050–1063 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ye, L., Robertson, M. A., Mastracci, T. L. & Anderson, R. M. An insulin signaling feedback loop regulates pancreas progenitor cell differentiation during islet development and regeneration. Dev. Biol. 409, 354–369 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Zhang, Y. M. et al. Distant insulin signaling regulates vertebrate pigmentation through the sheddase Bace2. Dev. Cell 45, 580–594.e587 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Baggiolini, A. et al. Developmental chromatin programs determine oncogenic competence in melanoma. Science 373, eabc1048 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • Farshidfar, F. et al. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nat Commun 13, 898 (2022). https://doi.org/10.1038/s41467-022-28566-4

  • Kim, K. et al. Clinicopathologic characteristics of early gastric cancer according to specific intragastric location. BMC Gastroenterol. 19, 24 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Razumilava, N. & Gores, G. J. Cholangiocarcinoma. Lancet 383, 2168–2179 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Tang, Q. et al. Anatomic mapping of molecular subtypes in diffuse glioma. BMC Neurol. 17, 183 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • White, R. M. et al. Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell 2, 183–189 (2008).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • White, R. M. et al. DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature 471, 518–522 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kaufman, C. K. et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science 351, aad2197 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Genomic classification of cutaneous melanoma. Cell 161, 1681–1696 (2015).

    Google Scholar 

  • Dankort, D. et al. BrafV600E cooperates with Pten loss to induce metastatic melanoma. Nat. Genet. 41, 544–552 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shen, R. & Seshan, V. E. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 44, e131 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, B. & Dewey, C. N. RSEM- accurate transcript quantification from RNA-seq data with or without a reference genome. BMC. Bioinformatics 12, 1471–2105 (2011).

    Google Scholar 

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Korotkevich, G., Sukhov, V. & Sergushichev, A. Fast gene set enrichment analysis. Preprint at https://doi.org/10.1101/060012 (2019).

  • Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260–D266 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • Grossman, R. L. et al. Toward a shared vision for cancer genomic data. N. Engl. J. Med. 375, 1109–1112 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Hoadley, K. A. et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 158, 929–944 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive and integrated genomic characterization of adult soft tissue sarcomas. Cell 171, 950–965.e928 (2017).

    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive and integrative genomic characterization of hepatocellular carcinoma. Cell 169, 1327–1341.e1323 (2017).

    PubMed Central 

    Google Scholar 

  • Robertson, A. G. et al. Comprehensive molecular characterization of muscle-invasive bladder cancer. Cell 171, 540–556.e525 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fishbein, L. et al. Comprehensive molecular characterization of pheochromocytoma and paraganglioma. Cancer Cell 31, 181–193 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature 511, 543–550 (2014).

    ADS 
    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513, 202–209 (2014).

    ADS 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507, 315–322 (2014).

    ADS 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).

    ADS 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).

    ADS 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519–525 (2012).

    ADS 
    PubMed Central 

    Google Scholar 

  • Ciriello, G. et al. Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163, 506–519 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. The molecular taxonomy of primary prostate cancer. Cell 163, 1011–1025 (2015).

    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008).

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517, 576–582 (2015).

    ADS 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. Nature 497, 67–73 (2013).

    ADS 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499, 43–49 (2013).

    ADS 
    PubMed Central 

    Google Scholar 

  • Davis, C. F. et al. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell 26, 319–330 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368, 2059–2074 (2013).

    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).

    PubMed Central 

    Google Scholar 

  • Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462–477 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • The Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159, 676–690 (2014).

    Google Scholar 

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhang, Y. et al. Model-based analysis of ChIP–seq (MACS). Genome Biol. 9, R137 (2008).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • Kall, L., Canterbury, J. D., Weston, J., Noble, W. S. & MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923–925 (2007).

    PubMed 

    Google Scholar 

  • The, M., MacCoss, M. J., Noble, W. S. & Kall, L. Fast and accurate protein false discovery rates on large-scale proteomics data sets with Percolator 3.0. J. Am. Soc. Mass. Spectrom. 27, 1719–1727 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sparks, A. B. et al. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCy, Crk, and Grb2. Proc. Natl Acad. Sci. USA 93, 1540–1544 (1996).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Birge, R. B., Kalodimos, C., Inagaki, F. & Tanaka, S. Crk and CrkL adaptor proteins: networks for physiological and pathological signaling. Cell Commun. Signal. 7, 13 (2009).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Tothova, Z. et al. Multiplex CRISPR/Cas9-based genome editing in human hematopoietic stem cells models clonal hematopoiesis and myeloid neoplasia. Cell Stem Cell 21, 547–555.e548 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lindsay, H. et al. CrispRVariants charts the mutation spectrum of genome engineering experiments. Nat. Biotechnol. 34, 701–702 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • DeLuca, D. S. et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28, 1530–1532 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hu, Y. et al. An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinf. 12, 1471–2105 (2011).

    Google Scholar 

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e3529 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jolliffe, I. T. Principal Component Analysis and Factor Analysis (Springer, 1986).

  • McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://doi.org/10.48550/arXiv.1802.03426 (2018).

  • Baron, M. et al. The stress-like cancer cell state is a consistent component of tumorigenesis. Cell Syst. 11, 536–546.e537 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hunter, M. V., Moncada, R., Weiss, J. M., Yanai, I. & White, R. M. Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. Nat. Commun. 12, 6278 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Freese, N. H., Norris, D. C. & Loraine, A. E. Integrated genome browser: visual analytics platform for genomics. Bioinformatics 32, 2089–2095 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 



  • Source link

    Leave a Reply

    Your email address will not be published.