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  • Oxford University Press  (13)
  • American Physical Society (APS)  (9)
  • Nature Publishing Group (NPG)
  • 2020-2022
  • 2010-2014  (23)
  • 2000-2004
  • 2013  (23)
  • 1
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    Solitary matter waves in combined linear and nonlinear potentials: Detection, stability, and dynamics (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-09-25
    Description: Author(s): Scott Holmes, Mason A. Porter, Peter Krüger, and Panayotis G. Kevrekidis We study statically homogeneous Bose-Einstein condensates with spatially inhomogeneous interactions and outline an experimental realization of compensating linear and nonlinear potentials that can yield constant-density solutions. We illustrate how the presence of a step in the nonlinearity coeffici... [Phys. Rev. A 88, 033627] Published Tue Sep 24, 2013
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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  • 2
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    MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data (2013)
    Oxford University Press
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    Publication Date: 2013-02-13
    Description: Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms. Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis. Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html . Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Onset patterns in a simple model of localized parametric forcing (2013)
    American Physical Society (APS)
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    Publication Date: 2013-10-22
    Description: Author(s): J. Porter, I. Tinao, A. Laverón-Simavilla, and J. Rodríguez We investigate pattern selection at onset in a parametrically and inhomogeneously forced partial differential equation obtained by generalizing Mathieu's equation to include spatial interactions. No separation of scales is assumed. The proposed model is directly relevant to the case of parametricall... [Phys. Rev. E 88, 042913] Published Mon Oct 21, 2013
    Keywords: Nonlinear Dynamics and Chaos
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    De novo mutations in histone-modifying genes in congenital heart disease (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-05-15
    Description: Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. Here we compare the incidence of de novo mutations in 362 severe CHD cases and 264 controls by analysing exome sequencing of parent-offspring trios. CHD cases show a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging (premature termination, frameshift, splice site) mutations. Similar odds ratios are seen across the main classes of severe CHD. We find a marked excess of de novo mutations in genes involved in the production, removal or reading of histone 3 lysine 4 (H3K4) methylation, or ubiquitination of H2BK120, which is required for H3K4 methylation. There are also two de novo mutations in SMAD2, which regulates H3K27 methylation in the embryonic left-right organizer. The combination of both activating (H3K4 methylation) and inactivating (H3K27 methylation) chromatin marks characterizes 'poised' promoters and enhancers, which regulate expression of key developmental genes. These findings implicate de novo point mutations in several hundreds of genes that collectively contribute to approximately 10% of severe CHD.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706629/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706629/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zaidi, Samir -- Choi, Murim -- Wakimoto, Hiroko -- Ma, Lijiang -- Jiang, Jianming -- Overton, John D -- Romano-Adesman, Angela -- Bjornson, Robert D -- Breitbart, Roger E -- Brown, Kerry K -- Carriero, Nicholas J -- Cheung, Yee Him -- Deanfield, John -- DePalma, Steve -- Fakhro, Khalid A -- Glessner, Joseph -- Hakonarson, Hakon -- Italia, Michael J -- Kaltman, Jonathan R -- Kaski, Juan -- Kim, Richard -- Kline, Jennie K -- Lee, Teresa -- Leipzig, Jeremy -- Lopez, Alexander -- Mane, Shrikant M -- Mitchell, Laura E -- Newburger, Jane W -- Parfenov, Michael -- Pe'er, Itsik -- Porter, George -- Roberts, Amy E -- Sachidanandam, Ravi -- Sanders, Stephan J -- Seiden, Howard S -- State, Mathew W -- Subramanian, Sailakshmi -- Tikhonova, Irina R -- Wang, Wei -- Warburton, Dorothy -- White, Peter S -- Williams, Ismee A -- Zhao, Hongyu -- Seidman, Jonathan G -- Brueckner, Martina -- Chung, Wendy K -- Gelb, Bruce D -- Goldmuntz, Elizabeth -- Seidman, Christine E -- Lifton, Richard P -- 5U54HG006504/HG/NHGRI NIH HHS/ -- F30 HL123238/HL/NHLBI NIH HHS/ -- P30 HD018655/HD/NICHD NIH HHS/ -- T32 GM007205/GM/NIGMS NIH HHS/ -- U01 HG006546/HG/NHGRI NIH HHS/ -- U01 HL098123/HL/NHLBI NIH HHS/ -- U01 HL098147/HL/NHLBI NIH HHS/ -- U01 HL098153/HL/NHLBI NIH HHS/ -- U01 HL098162/HL/NHLBI NIH HHS/ -- U01 HL098163/HL/NHLBI NIH HHS/ -- U01-HL098123/HL/NHLBI NIH HHS/ -- U01-HL098147/HL/NHLBI NIH HHS/ -- U01-HL098153/HL/NHLBI NIH HHS/ -- U01-HL098162/HL/NHLBI NIH HHS/ -- U01-HL098163/HL/NHLBI NIH HHS/ -- U01-HL098188/HL/NHLBI NIH HHS/ -- U54 HG006504/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Jun 13;498(7453):220-3. doi: 10.1038/nature12141. Epub 2013 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23665959" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Case-Control Studies ; Child ; Chromatin/chemistry/metabolism ; DNA Mutational Analysis ; Enhancer Elements, Genetic/genetics ; Exome/genetics ; Female ; Genes, Developmental/genetics ; Heart Diseases/*congenital/*genetics/metabolism ; Histones/chemistry/*metabolism ; Humans ; Lysine/chemistry/metabolism ; Male ; Methylation ; Mutation ; Odds Ratio ; Promoter Regions, Genetic/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Noise-induced synchronization, desynchronization, and clustering in globally coupled nonidentical oscillators (2013)
    American Physical Society (APS)
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    Publication Date: 2013-07-10
    Description: Author(s): Yi Ming Lai and Mason A. Porter We study ensembles of globally coupled, nonidentical phase oscillators subject to correlated noise, and we identify several important factors that cause noise and coupling to synchronize or desynchronize a system. By introducing noise in various ways, we find an estimate for the onset of synchrony o... [Phys. Rev. E 88, 012905] Published Tue Jul 09, 2013
    Keywords: Nonlinear Dynamics and Chaos
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-17
    Description: Background: Homology-based taxonomic assignment is impeded by differences between the unassigned read and reference database, forcing a rank-specific classification to the closest (and possibly incorrect) reference lineage. This assignment may be correct only to a general rank (e.g. order) and incorrect below that rank (e.g. family and genus). Algorithms like LCA avoid this by varying the predicted taxonomic rank based on matches to a set of taxonomic references. LCA and related approaches can be conservative, especially if best matches are taxonomically widespread because of events such as lateral gene transfer (LGT). Results: Our extension to LCA called SPANNER (similarity profile annotater) uses the set of best homology matches (the LCA Profile) for a given sequence and compares this profile with a set of profiles inferred from taxonomic reference organisms. SPANNER provides an assignment that is less sensitive to LGT and other confounding phenomena. In a series of trials on real and artificial datasets, SPANNER outperformed LCA-style algorithms in terms of taxonomic precision and outperformed best BLAST at certain levels of taxonomic novelty in the dataset. We identify examples where LCA made an overly conservative prediction, but SPANNER produced a more precise and correct prediction. Conclusions: By using profiles of homology matches to represent patterns of genomic similarity that arise because of vertical and lateral inheritance, SPANNER offers an effective compromise between taxonomic assignment based on best BLAST scores, and the conservative approach of LCA and similar approaches. Availability: C++ source code and binaries are freely available at http://kiwi.cs.dal.ca/Software/SPANNER . Contact: beiko@cs.dal.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Pressure and Energy Balance of Stagnating Plasmas in z-Pinch Experiments: Implications to Current Flow at Stagnation (2013)
    American Physical Society (APS)
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    Publication Date: 2013-07-17
    Description: Author(s): Y. Maron, A. Starobinets, V. I. Fisher, E. Kroupp, D. Osin, A. Fisher, C. Deeney, C. A. Coverdale, P. D. Lepell, E. P. Yu, C. Jennings, M. E. Cuneo, M. C. Herrmann, J. L. Porter, T. A. Mehlhorn, and J. P. Apruzese Detailed spectroscopic diagnostics of the stagnating plasma in two disparate z pinches allow, for the first time, the examination of the plasma properties within a 1D shock wave picture, demonstrating a good agreement with this picture. The conclusion is that for a wide range of imploding-plasma mas... [Phys. Rev. Lett. 111, 035001] Published Tue Jul 16, 2013
    Keywords: Plasma and Beam Physics
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    Valence-band structure of highly efficient p-type thermoelectric PbTe-PbS alloys (2013)
    American Physical Society (APS)
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    Publication Date: 2013-01-05
    Description: Author(s): Christopher M. Jaworski, Michele D. Nielsen, Hsin Wang, Steven N. Girard, Wei Cai, Wally D. Porter, Mercouri G. Kanatzidis, and Joseph P. Heremans Experimental evidence is given relevant to the temperature dependence of the valence band structure of PbTe and PbTe 1− x S x alloys (0.04≤ x ≤0.12), and its effect on the thermoelectric figure of merit Z T . The x =0.08 sample has Z T ∼1.55 at 773 K. The magnetic field dependence of the high-temperature Hall ... [Phys. Rev. B 87, 045203] Published Fri Jan 04, 2013
    Keywords: Semiconductors I: bulk
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Decentralized routing on spatial networks with stochastic edge weights (2013)
    American Physical Society (APS)
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    Publication Date: 2013-08-28
    Description: Author(s): Till Hoffmann, Renaud Lambiotte, and Mason A. Porter We investigate algorithms to find short paths in spatial networks with stochastic edge weights. Our formulation of the problem of finding short paths differs from traditional formulations because we specifically do not make two of the usual simplifying assumptions: (1) we allow edge weights to be st... [Phys. Rev. E 88, 022815] Published Tue Aug 27, 2013
    Keywords: Networks and Interdisciplinary Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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  • 10
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    Dark solitary waves in a class of collisionally inhomogeneous Bose-Einstein condensates (2013)
    American Physical Society (APS)
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    Publication Date: 2013-02-20
    Description: Author(s): Chang Wang, Kody J. H. Law, Panayotis G. Kevrekidis, and Mason A. Porter We study the structure, stability, and dynamics of dark solitary waves in parabolically trapped, collisionally inhomogeneous Bose-Einstein condensates (BECs) with spatially periodic variations of the scattering length. This collisional inhomogeneity yields a nonlinear lattice, which we tune from a s... [Phys. Rev. A 87, 023621] Published Tue Feb 19, 2013
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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