Search Results - "de Koning, A"

Repetitive elements may comprise over two-thirds of the human genome by de Koning, A P Jason, Gu, Wanjun, Castoe, Todd A, Batzer, Mark A, Pollock, David D

“…Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of…”
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CHROMOSPHERE TO 1 au SIMULATION OF THE 2011 MARCH 7th EVENT: A COMPREHENSIVE STUDY OF CORONAL MASS EJECTION PROPAGATION by Jin, M., Manchester, W. B., Holst, B. van der, Sokolov, I., Tóth, G., Vourlidas, A., Koning, C. A. de, Gombosi, T. I.

“…ABSTRACT We perform and analyze the results of a global magnetohydrodynamic simulation of the fast coronal mass ejection (CME) that occurred on 2011 March 7…”
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Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake by Castoe, Todd A, Poole, Alexander W, de Koning, A P Jason, Jones, Kenneth L, Tomback, Diana F, Oyler-McCance, Sara J, Fike, Jennifer A, Lance, Stacey L, Streicher, Jeffrey W, Smith, Eric N, Pollock, David D

“…Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and…”
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Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence by CASTOE, TODD A, POOLE, ALEXANDER W, GU, WANJUN, JASONdeKONING, A.P, DAZA, JUAN M, SMITH, ERIC N, POLLOCK, DAVID D

“…Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions…”
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Evidence for an ancient adaptive episode of convergent molecular evolution by Castoe, Todd A, de Koning, A.P. Jason, Kim, Hyun-Min, Gu, Wanjun, Noonan, Brice P, Naylor, Gavin, Jiang, Zhi J, Parkinson, Christopher L, Pollock, David D

“…Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions…”
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Wright-Fisher exact solver (WFES): scalable analysis of population genetic models without simulation or diffusion theory by Krukov, Ivan, de Sanctis, Bianca, de Koning, A P Jason

“…The simplifying assumptions that are used widely in theoretical population genetics may not always be appropriate for empirical population genetics. General…”
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The interface of protein structure, protein biophysics, and molecular evolution by Liberles, David A., Teichmann, Sarah A., Bahar, Ivet, Bastolla, Ugo, Bloom, Jesse, Bornberg‐Bauer, Erich, Colwell, Lucy J., de Koning, A. P. Jason, Dokholyan, Nikolay V., Echave, Julian, Elofsson, Arne, Gerloff, Dietlind L., Goldstein, Richard A., Grahnen, Johan A., Holder, Mark T., Lakner, Clemens, Lartillot, Nicholas, Lovell, Simon C., Naylor, Gavin, Perica, Tina, Pollock, David D., Pupko, Tal, Regan, Lynne, Roger, Andrew, Rubinstein, Nimrod, Shakhnovich, Eugene, Sjölander, Kimmen, Sunyaev, Shamil, Teufel, Ashley I., Thorne, Jeffrey L., Thornton, Joseph W., Weinreich, Daniel M., Whelan, Simon

“…The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic…”
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De novo and inherited loss-of-function variants of ATP2B2 are associated with rapidly progressive hearing impairment by Smits, Jeroen J., Oostrik, Jaap, Beynon, Andy J., Kant, Sarina G., de Koning Gans, Pia A. M., Rotteveel, Liselotte J. C., Klein Wassink-Ruiter, Jolien S., Free, Rolien H., Maas, Saskia M., van de Kamp, Jiddeke, Merkus, Paul, Koole, Wouter, Feenstra, Ilse, Admiraal, Ronald J. C., Lanting, Cornelis P., Schraders, Margit, Yntema, Helger G., Pennings, Ronald J. E., Kremer, Hannie

“…ATP2B2 encodes the PMCA2 Ca 2+ pump that plays an important role in maintaining ion homeostasis in hair cells among others by extrusion of Ca 2+ from the…”
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Allele Age Under Non-Classical Assumptions is Clarified by an Exact Computational Markov Chain Approach by De Sanctis, Bianca, Krukov, Ivan, de Koning, A. P. Jason

“…Determination of the age of an allele based on its population frequency is a well-studied problem in population genetics, for which a variety of approximations…”
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EzMap: a simple pipeline for reproducible analysis of the human virome by Czeczko, Patrick, Greenway, Steven C, de Koning, A P Jason

“…In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in…”
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Effects of Fis on Escherichia coli gene expression during different growth stages by Bradley, Meranda D, Beach, Michael B, de Koning, A. P. Jason, Pratt, Timothy S, Osuna, Robert

“…1 Department of Biological Science, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA 2 Department of Biology, Chemistry, and Physics,…”
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Parenting Interacts With Plasticity Genes in Predicting Behavioral Outcomes in Preschoolers by Letourneau, Nicole L., de Koning, A. P. Jason, Sekhon, Bikram, Ntanda, Henry N., Kobor, Michael, Deane, Andrea J., Morin, Alexander M., Dewey, Deborah, Campbell, Tavis S., Giesbrecht, Gerald F.

“…Background Public health and pediatric nurses typically focus on supporting parenting to reduce the likelihood of children’s behavioral problems. Studies have…”
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Expression of risk genes linked to vitamin D receptor super-enhancer regions and their association with phenotype severity in multiple sclerosis by Orton, Sarah M, Sangha, Amarpreet, Gupta, Mehul, Martens, Kristina, Metz, Luanne M, de Koning, A P J, Pfeffer, Gerald

“…Multiple sclerosis (MS) is a chronic debilitating neurological condition with a wide range of phenotype variability. A complex interplay of genetic and…”
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Associations Among Parental Caregiving Quality, Cannabinoid Receptor 1 Expression-Based Polygenic Scores, and Infant-Parent Attachment: Evidence for Differential Genetic Susceptibility? by Potter-Dickey, Amelia, Letourneau, Nicole, Silveira, Patricia P., Ntanda, Henry, Giesbrecht, Gerald F., Hart, Martha, Dewell, Sarah, de Koning, A. P. Jason

“…Attachment is a biological evolutionary system contributing to infant survival. When primary caregivers/parents are sensitive and responsive to their infants’…”
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Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome by Perry, Blair W, Card, Daren C, McGlothlin, Joel W, Pasquesi, Giulia I M, Adams, Richard H, Schield, Drew R, Hales, Nicole R, Corbin, Andrew B, Demuth, Jeffery P, Hoffmann, Federico G, Vandewege, Michael W, Schott, Ryan K, Bhattacharyya, Nihar, Chang, Belinda S W, Casewell, Nicholas R, Whiteley, Gareth, Reyes-Velasco, Jacobo, Mackessy, Stephen P, Gamble, Tony, Storey, Kenneth B, Biggar, Kyle K, Passow, Courtney N, Kuo, Chih-Horng, McGaugh, Suzanne E, Bronikowski, Anne M, de Koning, A P Jason, Edwards, Scott V, Pfrender, Michael E, Minx, Patrick, Brodie, 3rd, Edmund D, Brodie, Jr, Edmund D, Warren, Wesley C, Castoe, Todd A

“…Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here,…”
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CCL22 is a biomarker of cartilage injury and plays a functional role in chondrocyte apoptosis by Ren, G., Whittaker, J.L., Leonard, C., De Rantere, D., Pang, D.S.J., Salo, P., Fritzler, M., Kapoor, M., de Koning, A.P.J., Jaremko, J.L., Emery, C.A., Krawetz, R.J.

“…Osteoarthritis (OA) is one of the leading causes of disability worldwide. Previous history of knee injury is a significant risk factor for OA. It has been…”
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Defining social innovation for post-secondary educational institutions: a concept analysis by Benzies, K. M, Nicholas, D. B, Hayden, K. A, Barnas, T, de Koning, A, Bharwani, A, Armstrong, J, Day, J

“…Education, research, and contribution to society through innovation are the three missions of post-secondary educational institutions. There is a gap in…”
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Human Intestinal PEPT1 Transporter Expression and Localization in Preterm and Term Infants by Mooij, Miriam G, de Koning, Barbara E A, Lindenbergh-Kortleve, Dicky J, Simons-Oosterhuis, Ytje, van Groen, Bianca D, Tibboel, Dick, Samsom, Janneke N, de Wildt, Saskia N

“…The intestinal influx oligopeptide transporter peptide transporter 1 (PEPT1) (SLC15A1) is best known for nutrient-derived di- and tripeptide transport. Its…”
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Anthropometrics and fat mass, but not fat-free mass, are compromised in infants requiring parenteral nutrition after neonatal intestinal surgery by Vlug, Lotte E, Neelis, Esther G, Wells, Jonathan CK, Fewtrell, Mary S, Kastelijn, Wendy LM, Olieman, Joanne F, Vermeulen, Marijn J, Roelants, Jorine A, Rizopoulos, Dimitris, Wijnen, René MH, Rings, Edmond HHM, de Koning, Barbara AE, Hulst, Jessie M

“…Children with intestinal failure (IF) receiving long-term parenteral nutrition (PN) have altered body composition (BC), but data on BC changes from start of PN…”
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The emerging role of mega-urban regions in the sustainability of global production-consumption systems by Doran, E., Golden, J., Matus, K., Lebel, L., Timmer, V., van ‘t Zelfde, M., de Koning, A.

“…Mega-urban regions (MURs) are important consumers or traders of resources from, or producers of wastes destined for, the global hinterlands. These roles,…”
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