Results 101 to 110 of about 596,095 (346)

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations [PDF]

, 2011
Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools.
Dale, Ryan K., Pedersen, Brent S., Quinlan, Aaron R.   +2 more
core   +1 more source

Loci specific epigenetic drug sensitivity. [PDF]

, 2020
Therapeutic targeting of epigenetic modulators offers a novel approach to the treatment of multiple diseases. The cellular consequences of chemical compounds that target epigenetic regulators (epi-drugs) are complex.
Pilko, Anna, Wollman, Roy, Zhang, Thanutra   +2 more
core   +1 more source

cDNA-RNA subtractive hybridization reveals increased expression of mycocerosic acid synthase in intracellular Mycobacterium bovis BCG. [PDF]

, 2001
Identifying genes that are differentially expressed by Mycobacterium bovis BCG after phagocytosis by macrophages will facilitate the understanding of the molecular mechanisms of host cell-intracellular pathogen interactions. To identify such genes a cDNA-
Centre Gunnels Wood, Irene M. Monahan, Joseph A. Mangan, Martin J. Everett, Ming-shi Li, Philip D. Butcher, Simon J. Waddell, Steve L. Martin   +7 more
core   +3 more sources

Respiratory complex I‐mediated NAD+ regeneration regulates cancer cell proliferation through the transcriptional and translational control of p21Cip1 expression by SIRT3 and SIRT7

Molecular Oncology, EarlyView.
NAD+ regeneration by mitochondrial complex I NADH dehydrogenase is important for cancer cell proliferation. Specifically, NAD+ is necessary for the activities of NAD+‐dependent deacetylases SIRT3 and SIRT7, which suppress the expression of p21Cip1 cyclin‐dependent kinase inhibitor, an antiproliferative molecule, at the translational and transcriptional
Masato Higurashi, Kazunori Mori, Hidetsugu Nakagawa, Momoko Uchida, Fumihiro Ishikawa, Motoko Shibanuma   +5 more
wiley   +1 more source

New library construction method for single-cell genomes. [PDF]

PLoS ONE, 2017
A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions.
Larry Xi, Alexander Belyaev, Sandra Spurgeon, Xiaohui Wang, Haibiao Gong, Robert Aboukhalil, Richard Fekete   +6 more
doaj   +1 more source

FindeR: Accelerating FM-Index-based Exact Pattern Matching in Genomic Sequences through ReRAM technology [PDF]

arXiv, 2019
Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for genome analysis. Because of errors from sequencing machines and genetic variations, approximate pattern matching (
arxiv  

The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation [PDF]

, 2008
We isolated and characterized a Brassica C genome-specific CACTA element, which was designated Bot1 (Brassica oleracea transposon 1). After analysing phylogenetic relationships, copy numbers and sequence similarity of Bot1 and Bot1 analogues in B ...
AGI, Arabidopsis Genome Initiative, Alix, Alix, Alix, Bandelt, Bateman, Bennetzen, Brunner, Casacuberta, Cui, Darling, DeMarco, Deragon, Edgar, Eichler, Fedoroff, Feschotte, Gaeta, Gish, Grandbastien, Hawkins, He, Heslop-Harrison, IHGSC, Inaba, Inagaki, Itoh, Jacobs, Jiang, Johnston, Kapitonov, Kapitonov, Kawasaki, Kazazian, Kubis, Kubis, Kuhn, Kurtz, Le, Leflon, Lenoir, Lysak, Maddison, Meyers, Miura, Morgante, Morgante, Nacken, Nicolas, Ozeki, O’Neill, Pereira, Peterson, Posada, Rocarro, Rodríguez, Schwarzacher, Shiba, Snowden, Snowdon, Sonnhammer, Strachan, Suzuki, Swofford, Talbert, Town, Turcotte, U, Vicient, Walbot, Wang, Wendel, Wicker, Wicker, Yang, Yang, Yu, Zabala, Zabala, Zhang, Zhang   +80 more
core   +1 more source

Analysis of comprehensive genomic profiling of solid tumors with a novel assay for broad analysis in clinical diagnostics

Molecular Oncology, EarlyView.
In molecular cancer diagnostics, comprehensive genomic profiling (CGP) is going to replace the small NGS panels since it provides all clinically relevant somatic variants as well as genomic biomarkers with clinical value. Here, we compared two CGP assays and demonstrate that the choice for diagnostic implementation will depend on the specific ...
Guy Froyen, Pieter‐Jan Volders, Ellen Geerdens, Severine Berden, Joni Van der Meulen, Aaron De Cock, Stefanie Vermeire, Jacques Van Huysse, Marie de Barsy, Gabriela Beniuga, Wendy W. J. de Leng, Anne M. L. Jansen, Imke Demers, Zeliha Ozgur, Hendrikus Jan Dubbink, Ernst‐Jan M. Speel, Wilfred F. J. van IJcken, Brigitte Maes   +17 more
wiley   +1 more source

Digital karyotyping reveals probable target genes at 7q21.3 locus in hepatocellular carcinoma

BMC Medical Genomics, 2011
Background Hepatocellular carcinoma (HCC) is a worldwide malignant liver tumor with high incidence in China. Subchromosomal amplifications and deletions accounted for major genomic alterations occurred in HCC.
Wang Shengyue, Kong Yalin, Shen Yan, Chen Yangyi, Yan Huadong, Liang Jianping, Zhang Hongyi, Dong Hui, Zhao Guoping, Jin Weirong   +9 more
doaj   +1 more source

Response to neoadjuvant chemotherapy in early breast cancers is associated with epithelial–mesenchymal transition and tumor‐infiltrating lymphocytes

Molecular Oncology, EarlyView.
Epithelial–mesenchymal transition (EMT) and tumor‐infiltrating lymphocytes (TILs) are associated with early breast cancer response to neoadjuvant chemotherapy (NAC). This study evaluated EMT and TIL shifts, with immunofluorescence and RNA sequencing, at diagnosis and in residual tumors as potential biomarkers associated with treatment response.
Françoise Derouane, Jérôme Ambroise, Cédric van Marcke, Mieke Van Bockstal, Martine Berlière, Christine Galant, Hélène Dano, Médina Lougué, Elena Benidovskaya, Guy Jerusalem, Vincent Bours, Claire Josse, Jérôme Thiry, Aurélie Daumerie, Caroline Bouzin, Cyril Corbet, François P. Duhoux   +16 more
wiley   +1 more source