Results 61 to 70 of about 120,987 (294)

SAFS: A Deep Feature Selection Approach for Precision Medicine

, 2017
In this paper, we propose a new deep feature selection method based on deep architecture. Our method uses stacked auto-encoders for feature representation in higher-level abstraction.
Levy, Phillip, Li, Xiangrui, Nezhad, Milad Zafar, Yang, Kai, Zhu, Dongxiao   +4 more
core   +1 more source

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Rice Galaxy: An open resource for plant science [PDF]

, 2019
Background: Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery ...
Alexandrov, Nickolai, Beaume, Nicolas, Dereeper, Alexis, Dizon, Joshua, Droc, Gaëtan, Haga, Jason, Juanillas, Venice, Kretzschmar, Tobias, Lang, Jillian M., Larmande, Pierre, Leach, Jan E., Mansueto, Locedie, Mauleon, Ramil P., Mendoza, John Robert, Perdon, Jon Peter, Plale, Beth, Ratharanjan, Kunalan, Ruiz, Manuel, Thomson, Michael J., Triplett, Lindsay, Zhou, Gabriel   +20 more
core   +1 more source

DNA methylation and expression of MAPRE3 affect overall survival of early‐stage non‐small cell lung cancer patients

Molecular Oncology, EarlyView.
Both cg12821679MAPRE3 methylation and MAPRE3 expression are significantly associated with overall survival (OS) of non‐small cell lung cancer. Meanwhile, MAPRE3 expression significantly modified the effect of smoking cessation on OS. Smoking cessation benefits OS merely for patients with high MAPRE3 expression.
Chao Chen, Jiancheng Cheng, Ruili Hou, Xiaoyuan Zheng, Li Su, Maria Moksnes Bjaanæs, Anna Karlsson, Maria Planck, Johan Staaf, Åslaug Helland, Manel Esteller, David C. Christiani, Feng Chen, Xiaofei Cao, Ruyang Zhang   +14 more
wiley   +1 more source

Integrative taxonomy refutes a species hypothesis: The asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae)

Ecology and Evolution, 2019
Molecular tools are commonly directed at refining taxonomies and the species that constitute their fundamental units. This has been especially insightful for groups for which species hypotheses are ambiguous and have largely been based on morphological ...
Michael K. Young, Rebecca J. Smith, Kristine L. Pilgrim, Matthew P. Fairchild, Michael K. Schwartz   +4 more
doaj   +1 more source

Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda) [PDF]

, 2015
Background: Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1-6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies.
García-Gil, Maria Rosario, Lin, Yao-Cheng, Ranade, Sonali Sachin, Van de Peer, Yves   +3 more
core   +2 more sources

Large‐scale bidirectional arrayed genetic screens identify OXR1 and EMC4 as modifiers of αSynuclein aggregation

FEBS Open Bio, EarlyView.
Activation of the mitochondrial protein OXR1 increases pSyn129 αSynuclein aggregation by lowering ATP levels and altering mitochondrial membrane potential, particularly in response to MSA‐derived fibrils. In contrast, ablation of the ER protein EMC4 enhances autophagic flux and lysosomal clearance, broadly reducing α‐synuclein aggregates.
Sandesh Neupane, Lea Nikolić, Lorenzo Maraio, Thomas Goiran, Nathan Karpilovsky, Stefano Sellitto, Vangelis Bouris, Jiang‐An Yin, Ronald Melki, Edward A Fon, Adriano Aguzzi, Elena De Cecco   +11 more
wiley   +1 more source

ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines [PDF]

PeerJ, 2020
Background With the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardized metadata curation approaches have become increasingly ...
Angelo D. Armijos Carrion, Damien D. Hinsinger, Joeri S. Strijk   +2 more
doaj   +2 more sources

Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions [PDF]

, 2019
Several genomic prediction models combining genotype × environment (G×E) interactions have recently been developed and used for genomic selection (GS) in plant breeding programs. G×E interactions reduce selection accuracy and limit genetic gains in plant
Francisco, Felipe O., Fritsche-Neto, Roberto, Gonçalves, Paulo De Souza, Le Guen, Vincent, Scaloppi Junior, Erivaldo José, Souza, Anete Pereira, Souza, Livia Moura   +6 more
core   +2 more sources

Identifying gene expression signatures for risk stratification of postoperative adjuvant chemotherapy in colorectal cancer

FEBS Open Bio, EarlyView.
A novel signature integrating genome‐wide analysis with clinical factors predicts recurrence in stage II colorectal cancer and enables a new risk stratification to guide postoperative adjuvant chemotherapy. Clinical risk stratification for postoperative recurrence in patients with pathological stage II (pStage II) colorectal cancer (CRC) is essential ...
Mayuko Otomo, Keisuke Okuno, Shuichi Watanabe, Sakiko Oba, Hiroyasu Kagawa, Masanori Tokunaga, Daisuke Ban, Yusuke Kinugasa   +7 more
wiley   +1 more source