Results 61 to 70 of about 743,811 (309)

Biological Machine Learning Combined with Campylobacter Population Genomics Reveals Virulence Gene Allelic Variants Cause Disease

Microorganisms, 2020
Highly dimensional data generated from bacterial whole-genome sequencing is providing an unprecedented scale of information that requires an appropriate statistical analysis framework to infer biological function from populations of genomes.
DJ Darwin R. Bandoy, Bart C. Weimer
doaj   +1 more source

Circular RNA expression landscapes in myelodysplastic neoplasms: Associations with mutational signatures and disease progression

Molecular Oncology, EarlyView.
In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge, Morten Tulstrup, Gabriele Todisco, Pedro Moura, Christophe Côme, Jakob Werner Hansen, Jakob Schmidt Jespersen, Balthasar Schlotmann, Maria Creignou, Mette Dahl, Claudia Schöllkopf, Klas Raaschou‐Jensen, Krister Wennerberg, Bo Porse, Joachim Weischenfeldt, Eva Hellström‐Lindberg, Lasse Sommer Kristensen, Kirsten Grønbæk   +17 more
wiley   +1 more source

The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes

, 2005
Overbeek R, Begley T, Butler RM, et al. The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes. Nucleic Acids Research.
Hanson, Andrew, Olson, Robert, McHardy, Alice C., Goesmann, Alexander ; https://orcid.org/, Osterman, Andrei, Stevens, Rick, Butler, Ralph M, Ruckert, Christian, Pusch, Gordon D, Butler, Ralph M., Disz, Terry, de Crecy-Lagard, Valerie, Frank, Ed D, Fonstein, Michael, Gerdes, Svetlana, Larsen, Niels, Portnoy, Vasiliy, Frank, Ed D., Goesmann, Alexander, Crécy-Lagard, Valérie de, Choudhuri, Jomuna V., McHardy, Alice C, Thiele, Ines, Olsen, Gary, Overbeek, Ross, Meyer, Folker, Ye, Yuzhen, Begley, Tadhg, Pusch, Gordon D., Choudhuri, Jomuna V, Chuang, Han-Yu, Krause, Lutz, Kubal, Michael, Iwata-Reuyl, Dirk, Rodionov, Dmitry A, Cohoon, Matthew, Edwards, Robert, Diaz, Naryttza N., Rodionov, Dmitry A., Neuweger, Heiko, Linke, Burkhard, Zagnitko, Olga, Vassieva, Olga, Glass, Elizabeth M., Diaz, Naryttza, Rückert, Christian ; https://orcid.org/, Glass, Elizabeth M, Jensen, Roy, Jamshidi, Neema, Steiner, Jason, Vonstein, Veronika   +50 more
core   +1 more source

Personal genomes in progress: from the Human Genome Project to the Personal Genome Project

Dialogues in Clinical Neuroscience, 2010
The cost of a diploid human genome sequence has dropped from about $70M to $2000 since 2007--even as the standards for redundancy have increased from 7x to 40x in order to improve call rates. Coupled with the low return on investment for common single-nucleotide polylmorphisms, this has caused a significant rise in interest in correlating genome ...
Lunshof, J., Bobe, J., Aach, J., Angrist, M., Thakuria, J., Vorhaus, D., Hoehe, M., Church, G.   +7 more
openaire   +5 more sources

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

Novel approach for deriving genome wide SNP analysis data from archived blood spots [PDF]

, 2012
BACKGROUND: The ability to transport and store DNA at room temperature in low volumes has the advantage of optimising cost, time and storage space.
Walling, Grant A, Fowler Katie E, Fowler, K., Fowler, Katie E., Griffin, Darren K, Griffin, D., Reitter, Chris P, Reitter Chris P, Griffin Darren K, Griffin, Darren K., Reitter, C., Walling, G., Walling Grant A   +12 more
core   +1 more source

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

eLife, 2014
Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mtDNA are ...
Young Seok Ju, Ludmil B Alexandrov, Moritz Gerstung, Inigo Martincorena, Serena Nik-Zainal, Manasa Ramakrishna, Helen R Davies, Elli Papaemmanuil, Gunes Gundem, Adam Shlien, Niccolo Bolli, Sam Behjati, Patrick S Tarpey, Jyoti Nangalia, Charles E Massie, Adam P Butler, Jon W Teague, George S Vassiliou, Anthony R Green, Ming-Qing Du, Ashwin Unnikrishnan, John E Pimanda, Bin Tean Teh, Nikhil Munshi, Mel Greaves, Paresh Vyas, Adel K El-Naggar, Tom Santarius, V Peter Collins, Richard Grundy, Jack A Taylor, D Neil Hayes, David Malkin, ICGC Breast Cancer Group, ICGC Chronic Myeloid Disorders Group, ICGC Prostate Cancer Group, Christopher S Foster, Anne Y Warren, Hayley C Whitaker, Daniel Brewer, Rosalind Eeles, Colin Cooper, David Neal, Tapio Visakorpi, William B Isaacs, G Steven Bova, Adrienne M Flanagan, P Andrew Futreal, Andy G Lynch, Patrick F Chinnery, Ultan McDermott, Michael R Stratton, Peter J Campbell   +52 more
doaj   +1 more source

Narcolepsy type I-associated DNA methylation and gene expression changes in the human leukocyte antigen region

Scientific Reports, 2023
Narcolepsy type 1 (NT1) is caused by a loss of hypothalamic orexin-producing cells, and autoreactive CD4+ and CD8+ T cells have been suggested to play a role in the autoimmune mechanism.
Kugui Yoshida-Tanaka, Mihoko Shimada, Yoshiko Honda, Akihiro Fujimoto, Katsushi Tokunaga, Makoto Honda, Taku Miyagawa   +6 more
doaj   +1 more source

Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer

Molecular Oncology, EarlyView.
Tumors contain diverse cellular states whose behavior is shaped by context‐dependent gene coordination. By comparing gene–gene relationships across biological contexts, we identify adaptive transcriptional modules that reorganize into distinct vulnerability axes.
Brian Nelson, Lyanne Delgado‐Coka, Natalia Marchenko, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer, Alisa Yurovsky, Trey Ideker, Gábor Balázsi, Thomas MacCarthy, Scott Powers   +9 more
wiley   +1 more source

Pre‐analytical optimization of cell‐free DNA and extracellular vesicle‐derived DNA for mutation detection in liquid biopsies

Molecular Oncology, EarlyView.
Pre‐analytical handling critically determines liquid biopsy performance. This study defines practical best‐practice conditions for cell‐free DNA (cfDNA) and extracellular vesicle–derived DNA (evDNA), showing how processing time, storage conditions, tube type, and plasma input volume affect DNA integrity and mutation detection.
Jonas Dohmen, Lucrezia De Santis, Bret M. Stephens, Vincent Bernard, Jörg C. Kalff, Lara Braun, Phillipp Leyendecker, Johannes Röttgen, Daniel Weissinger, Anirban Maitra, Paola A. Guerrero, Alexander Semaan   +11 more
wiley   +1 more source