ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data
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Chittibabu Guda | Javeed Iqbal | C. Guda | J. Iqbal | N. N. Vellichirammal | You Li | T. Heavican | You Li | Tayla B. Heavican | Neetha N. Vellichirammal
[1] D. Tietze. Bird Species , 2018, Fascinating Life Sciences.
[2] Sarah C. Ayling,et al. The Ensembl gene annotation system , 2016, Database J. Biol. Databases Curation.
[3] J. McPherson,et al. Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.
[4] A. Moorman. New and emerging prognostic and predictive genetic biomarkers in B-cell precursor acute lymphoblastic leukemia , 2016, Haematologica.
[5] Hui Li,et al. Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data , 2016, Scientific Reports.
[6] Yanjun Qi,et al. Recurrent chimeric fusion RNAs in non-cancer tissues and cells , 2016, Nucleic acids research.
[7] Adrian V. Lee,et al. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data , 2015, Nucleic acids research.
[8] Mengmeng Zhang,et al. Disabled homolog 2 is required for migration and invasion of prostate cancer cells , 2015, Frontiers of Medicine.
[9] Cathy H. Wu,et al. Abstract 4859: Development of a cancer transcriptome analysis toolkit: identification of gene fusions in chronic lymphocytic leukemia , 2015 .
[10] B. Johansson,et al. The emerging complexity of gene fusions in cancer , 2015, Nature Reviews Cancer.
[11] Can Alkan,et al. Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells , 2015, Nature Communications.
[12] A. Oshlack,et al. JAFFA: High sensitivity transcriptome-focused fusion gene detection , 2015, bioRxiv.
[13] Hui Li,et al. Chimeric RNAs generated by intergenic splicing in normal and cancer cells , 2014, Genes, chromosomes & cancer.
[14] O. Kallioniemi,et al. FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data , 2014, bioRxiv.
[15] Nicolas Stransky,et al. The landscape of kinase fusions in cancer , 2014, Nature Communications.
[16] J. Akers,et al. RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas , 2014, Genome research.
[17] Benjamin J. Raphael,et al. Expanding the computational toolbox for mining cancer genomes , 2014, Nature Reviews Genetics.
[18] S. Karmakar,et al. The SMRT coregulator enhances growth of estrogen receptor-α-positive breast cancer cells by promotion of cell cycle progression and inhibition of apoptosis. , 2014, Endocrinology.
[19] Melissa J. Landrum,et al. RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..
[20] Wei Zhang,et al. Fusion genes in solid tumors: an emerging target for cancer diagnosis and treatment , 2013, Chinese journal of cancer.
[21] Hong-Tao Xu,et al. Aberrant hypermethylation and reduced expression of disabled-2 promote the development of lung cancers. , 2013, International journal of oncology.
[22] Rui Henrique,et al. Novel 5' fusion partners of ETV1 and ETV4 in prostate cancer. , 2013, Neoplasia.
[23] Marco Beccuti,et al. State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? , 2013, BMC Bioinformatics.
[24] M. Nykter,et al. The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. , 2013, The Journal of clinical investigation.
[25] Alan Bridge,et al. New and continuing developments at PROSITE , 2012, Nucleic Acids Res..
[26] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[27] Jun Wang,et al. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data , 2013, Genome Biology.
[28] M. Ragan,et al. Next-generation phylogenomics , 2013, Biology Direct.
[29] Alberto Magi,et al. Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript , 2012, Bioinform..
[30] Mithat Gönen,et al. Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials , 2012, Haematologica.
[31] B. Faircloth,et al. Primer3—new capabilities and interfaces , 2012, Nucleic acids research.
[32] Jian Ye,et al. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction , 2012, BMC Bioinformatics.
[33] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[34] H. Kantarjian,et al. Improved survival in chronic myeloid leukemia since the introduction of imatinib therapy: a single-institution historical experience. , 2011, Blood.
[35] Dmitri Loguinov,et al. Probabilistic near-duplicate detection using simhash , 2011, CIKM '11.
[36] Fang Fang,et al. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution , 2011, Bioinform..
[37] A. Børresen-Dale,et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing , 2011, Genome Biology.
[38] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[39] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[40] P. Edwards. Fusion genes and chromosome translocations in the common epithelial cancers , 2009, The Journal of pathology.
[41] Ka F To,et al. Putative tumour-suppressor gene DAB2 is frequently down regulated by promoter hypermethylation in nasopharyngeal carcinoma , 2010, BMC Cancer.
[42] S. Luo,et al. Chimeric transcript discovery by paired-end transcriptome sequencing , 2009, Proceedings of the National Academy of Sciences.
[43] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[44] Herve Avet-Loiseau,et al. Loss of the SMRT/NCoR2 corepressor correlates with JAG2 overexpression in multiple myeloma. , 2009, Cancer research.
[45] Hanna Eskelinen,et al. Inhibition of MAPK-signaling pathway promotes the interaction of the corepressor SMRT with the human androgen receptor and mediates repression of prostate cancer cell growth in the presence of antiandrogens. , 2009, Journal of molecular endocrinology.
[46] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[47] Lee T. Sam,et al. Transcriptome Sequencing to Detect Gene Fusions in Cancer , 2009, Nature.
[48] Christophe Lemetre,et al. An introduction to artificial neural networks in bioinformatics - application to complex microarray and mass spectrometry datasets in cancer studies , 2008, Briefings Bioinform..
[49] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[50] B. Johansson,et al. The impact of translocations and gene fusions on cancer causation , 2007, Nature Reviews Cancer.
[51] Tatiana Tatusova,et al. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..
[52] Ingo Roeder,et al. Dynamic modeling of imatinib-treated chronic myeloid leukemia: functional insights and clinical implications , 2006, Nature Medicine.
[53] Ioannis Panagopoulos,et al. Fusion of ETV6 with an intronic sequence of the BAZ2A gene in a paediatric pre‐B acute lymphoblastic leukaemia with a cryptic chromosome 12 rearrangement , 2006, British journal of haematology.
[54] Daniel J. Blankenberg,et al. Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.
[55] C. Nowell. The minute chromosome (Ph1) in chronic granulocytic leukemia , 1962, Blut: Zeitschrift für die Gesamte Blutforschung.
[56] C. Peterson,et al. The SANT domain: a unique histone-tail-binding module? , 2004, Nature Reviews Molecular Cell Biology.
[57] C. Müller,et al. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. , 2003, Molecular cell.
[58] L. Espinosa,et al. IκBα and p65 Regulate the Cytoplasmic Shuttling of Nuclear Corepressors: Cross-talk between Notch and NFκB Pathways , 2003 .
[59] L. Espinosa,et al. IkappaBalpha and p65 regulate the cytoplasmic shuttling of nuclear corepressors: cross-talk between Notch and NFkappaB pathways. , 2003, Molecular biology of the cell.
[60] B. Calabretta,et al. Post-transcriptional mechanisms in BCR/ABL leukemogenesis: role of shuttling RNA-binding proteins , 2002, Oncogene.
[61] Moses Charikar,et al. Similarity estimation techniques from rounding algorithms , 2002, STOC '02.
[62] Mathew W. Wright,et al. The HUGO Gene Nomenclature Committee (HGNC) , 2001, Human Genetics.
[63] R. Aebersold,et al. CD28 stimulation regulates its association with N‐ethylmaleimide‐sensitive fusion protein and other proteins involved in vesicle sorting , 2001, Proteomics.
[64] S. Bohlander. Fusion genes in leukemia: an emerging network , 2001, Cytogenetic and Genome Research.
[65] M T Bejarano,et al. NK cell triggering by the human costimulatory molecules CD80 and CD86. , 1999, Journal of immunology.
[66] M. Carroll,et al. CGP 57148, a tyrosine kinase inhibitor, inhibits the growth of cells expressing BCR-ABL, TEL-ABL, and TEL-PDGFR fusion proteins. , 1997, Blood.
[67] Robert M. Zink,et al. Bird species diversity , 1996, Nature.
[68] S. Karlin,et al. Over- and under-representation of short oligonucleotides in DNA sequences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[69] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[70] J. Rowley. A New Consistent Chromosomal Abnormality in Chronic Myelogenous Leukaemia identified by Quinacrine Fluorescence and Giemsa Staining , 1973, Nature.
[71] P. Nowell. The minute chromosome (Phl) in chronic granulocytic leukemia. , 1962, Blut.
[72] Can Alkan,et al. Activating mutations of STAT5B and STAT3 in lymphomas derived from gamma delta-T or NK cells , 2022 .