323 results on '"Nickerson, D. A."'
Search Results
52. Covalent Attachment of an Electroactive Sulfydryl Reagent in the Active Site of Cytochrome P450cam as Revealed by the Crystal Structure of the Modified Protein
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Di Gleria, K, Nickerson, D, Hill, H, Wong, L, and Fulop, V
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Colloid and Surface Chemistry ,General Chemistry ,Biochemistry ,Catalysis - Abstract
A novel electroactive sulfydryl-specific reagent, N-(2-ferrocenylethyl)maleimide (Fc-Mi), was used to attach a redox-active reporter group to cytochrome P450(cam) from Pseudomonas putida. The crystal structure of the modified enzyme was determined at 2.2 Å resolution (R(cryst) = 0.18) and compared to the structure of the wild-type enzyme complexed with its natural substrate. The results showed that two molecules of the electroactive modifier were attached to the protein. One of the ferrocenes was linked to Cys85 via the maleimide moiety and occupied the camphor-binding site in the substrate pocket. The other ferrocene was linked to Cys136 on the surface of the protein. :Significant conformational changes were observed on the distal side of the heme when camphor was replaced by ferrocene. The shift in the Soret band from 392 to 417 nm upon modification arose from the binding of a water molecule to the heme iron immediately below the ferrocene in the active site of the modified enzyme. The electrochemistry of the labeled enzyme showed clear signals originating both from the heme and from the covalently linked ferrocenes. The direct current cyclic voltammogram revealed a striking positive shift in the heme redox potential of the ferrocene-containing P450(cam) from -380 mV for the camphor-bound wild-type protein to -280 mV for the modified protein.
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- 1998
53. Mechanical Allodynia Predicts Better Outcome of Surgical Decompression for Painful Diabetic Peripheral Neuropathy.
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Chenlong Liao, Nickerson, D. Scott, Visocchi, Massimiliano, Min Yang, Pengfei Liu, Wenxiang Zhong, Han Zhou, and Wenchuan Zhang
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DIABETIC neuropathies , *ALLODYNIA , *NEURAL conduction , *PERIPHERAL nervous system , *ANXIETY , *PAIN management - Abstract
Background To determine the role of mechanical allodynia (MA) in predicting good surgical outcome for painful diabetic peripheral neuropathy (DPN). Materials and Methods Data of 192 patients with painful DPN were collected in this study, with 148 surgical patients and 44 patients in the control group. Both groups were further divided into subgroups based on the presence ofMA on admission. Clinical evaluations including the visual analog scale (VAS), the Hospital Anxiety and Depression Scale (HADS), nerve conduction velocity (NCV), and high-resolution ultrasonography (cross-sectional area, CSA) were performed preoperatively and postoperatively. Results The levels of VAS and HADS and the results of NCV and CSA were improved in the surgical group (p < 0.05). In the surgical subgroups, pain reduction, psychiatric amelioration, improvement in NCVs, and the restoration of the CSA were observed in patients with signs of MA (p < 0.05), whereas only pain reduction, psychiatric amelioration, and restoration of the CSA were noted in patients without signs of MA (p > 0.05). Furthermore, better pain reduction was achieved in patients with MA when compared with those without MA (p < 0.05). Conclusions MA is proved to be a reliable predictor of good surgical outcome for painful DPN. [ABSTRACT FROM AUTHOR]
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- 2018
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54. Illustration of Cost Saving Implications of Lower Extremity Nerve Decompression to Prevent Recurrence of Diabetic Foot Ulceration
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Rankin, Timothy M., primary, Miller, John D., additional, Gruessner, Angelika C., additional, and Nickerson, D. Scott, additional
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- 2015
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55. Recurrent de novo mutations implicate novel genes underlying simplex autism risk
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O'Roak, B. J., primary, Stessman, H. A., additional, Boyle, E. A., additional, Witherspoon, K. T., additional, Martin, B., additional, Lee, C., additional, Vives, L., additional, Baker, C., additional, Hiatt, J. B., additional, Nickerson, D. A., additional, Bernier, R., additional, Shendure, J., additional, and Eichler, E. E., additional
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- 2014
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56. Analysis of MHC class I gene expression in adult bone marrow and fetal liver of the BALB/c mouse
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Cheroutre, H., Kronenberg, M., Brorson, K., Hunt Iii, S. W., Pirooz Eghtesady, Hood, L., and Nickerson, D. A.
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Immunology ,Immunology and Allergy - Abstract
The BALB/c mouse has at least 29 class I genes encoded in the Qa, Tla, and Hmt (histocompatibility dependent on a maternally transmitted factor) regions of the MHC. The pattern of expression of these class Ib MHC genes is not well characterized, although some of their products such as the serologically detectable Qa-2 and TL Ag are expressed mainly in lymphoid and hematopoietic tissues. In this study, the expression pattern of BALB/c class I genes has been analyzed in adult bone marrow and fetal liver. cDNA libraries were synthesized from these tissues, and isolated class I cDNA clones were characterized by hybridization with oligonucleotide probes and by nucleotide sequence analysis. Of the 29 total class Ib genes, transcripts of five including Q6d, Q7d, T9c, T10c, and the 37 gene were isolated from the bone marrow cDNA library. Four of these can encode proteins; the sequence of the T10c gene demonstrates it is most likely a pseudogene. A non-overlapping set of three class Ib cDNA clones was obtained from the fetal liver, including T13c, the Thy 19.4 gene, and a previously uncharacterized class I gene provisionally designated as FL 57.2. Although the majority of H-2Dd cDNA clones that were analyzed lack introns, many of the class Ib cDNA clones contain intron sequences. This suggests that the expression of some of these genes may be regulated at the level of RNA splicing. The T13c gene encodes the thymus leukemia Ag in BALB/c mice. We have confirmed that the T13c gene is expressed in fetal liver by flow cytometric analysis of cells stained with anti-TL mAb.
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- 1991
57. Polymorphisms of the IL1-Receptor Antagonist Gene (IL1RN) Are Associated With Multiple Markers of Systemic Inflammation
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Walston, J. D., Jarvik, G. P., Carlson, C. S., Wurfel, M. M., Jenny, N. S., Nickerson, D. A., Desmarais, C., Iribarren, C., Reiner, A. P., Nord, A. S., Williams, O. D., Carty, C. L., Lange, L. A., and Rieder, M. J.
- Abstract
Circulating levels of acute phase reactant proteins such as plasma C-reactive protein (CRP) are likely influenced by multiple genes regulating the innate immune response.
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- 2008
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58. Computational multiscale modeling in the UPS physiome project: Modeling cardiac electromechanics
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Nickerson, D, Nash, M, Nielsen, P, Smith, N, and Hunter, P
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Quantitative Biology::Tissues and Organs - Abstract
We present a computational modeling and numerical simulation framework that enables the integration of multiple physics and spatiotemporal scales in models of physiological systems. This framework is the foundation of the IUPS (International Union of Physiological Sciences) Physiome Project. One novel aspect is the use of CellML, an annotated mathematical representation language, to specify model- and simulation-specific equations. Models of cardiac electromechanics at the cellular, tissue, and organ spatial scales are outlined to illustrate the development and implementation of the framework. We quantify the computational demands of performing simulations using such models and compare models of differing biophysical detail. Applications to other physiological systems are also discussed.
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- 2006
59. Acute Improvement in Intraoperative EMG Following Common Fibular Nerve Decompression in Patients with Symptomatic Diabetic Sensorimotor Peripheral Neuropathy: 1. EMG Results.
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Anderson, James C., Nickerson, D. Scott, Tracy, Brian L., Paxton, Roger J., and Yamasaki, Dwayne S.
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ELECTROMYOGRAPHY , *PERONEUS longus , *TIBIALIS anterior , *SENSORIMOTOR cortex , *NEUROPATHY - Abstract
Background and Study Aims Electromyographic (EMG) recordings of the fibularis longus (FL) and tibialis anterior (TA) muscles were performed intraoperatively during common fibular nerve (CFN) nerve decompression (ND) in patients with symptomatic diabetic sensorimotor peripheral neuropathy (DSPN) and clinical nerve compression. Materials and Methods Forty-six legs in 40 patients underwent surgical ND by external neurolysis; FL and TA muscles were monitored intraoperatively. Evoked EMGs were recorded just prior to and within 1 minute after ND. Results Thirty-eight legs (82.6%) demonstrated EMG improvement 1 minute after ND. Sixty muscles (31 FL, 29 TA) were monitored, with 44 (73.3%) improving in EMG amplitude. Mean change in EMG amplitude represented a 73.6% improvement (p < 0.0001). Changes in EMG amplitudes correlated with visual analog scale pain improvement (p = 0.03). Conclusion This is the first report of acute changes in objective EMG responses during ND of CFN in DSPN patients and demonstrates that patients with symptomatic DSPN and clinical nerve entrapment have latent but functional axons that surgical ND can improve immediately. [ABSTRACT FROM AUTHOR]
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- 2017
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60. Mutations in DYNC2H1, the cytoplasmic dynein 2, heavy chain 1 motor protein gene, cause short-rib polydactyly type I, Saldino-Noonan type.
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Badiner, N., Taylor, S.P., Forlenza, K., Lachman, R. S., Bamshad, M., Nickerson, D., Cohn, D. H., and Krakow, D.
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SHORT-rib polydactyly syndrome ,DYNEIN ,NOONAN syndrome ,CILIOPATHY ,HETEROZYGOSITY - Abstract
The short-rib polydactyly syndromes ( SRPS) are autosomal recessively inherited, genetically heterogeneous skeletal ciliopathies. SRPS phenotypes were historically categorized as types I- IV, with type I first delineated by Saldino and Noonan in 1972. Characteristic findings among all forms of SRP include short horizontal ribs, short limbs and polydactyly. The SRP type I phenotype is characterized by a very small thorax, extreme micromelia, very short, poorly mineralized long bones, and multiple organ system anomalies. To date, the molecular basis of this most severe type of SRP, also known as Saldino-Noonan syndrome, has not been determined. We identified three SRP cases that fit the original phenotypic description of SRP type I. In all three cases, exome sequence analysis revealed compound heterozygosity for mutations in DYNC2H1, which encodes the main component of the retrograde IFT A motor, cytoplasmic dynein 2 heavy chain 1. Thus SRP type I, II, III and asphyxiating thoracic dystrophy ( ATD), which also result from DYNC2H1 mutations. Herein we describe the phenotypic features, radiographic findings, and molecular basis of SRP type I. [ABSTRACT FROM AUTHOR]
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- 2017
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61. Computational Modelling of the Heart
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Smith, N, Nickerson, D, Crampin, E, and Hunter, P
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- 2004
62. A Novel Method to Describe and Share Complex Mathematical Models of Cellular Physiology
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Nickerson, D. P., primary and Buist, M. L., additional
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63. Results of whole-genome analysis from National Children's Study (NCS)
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Shendure, J., primary, Eichler, E., additional, Tabor, H., additional, Bamshad, M., additional, Nickerson, D., additional, Murray, J., additional, Specker, B., additional, Swanson, J., additional, and Faustman, E.M., additional
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- 2014
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64. Biologic Basis of Nerve Decompression Surgery for Focal Entrapments in Diabetic Peripheral Neuropathy
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Sessions, John, primary and Nickerson, D. Scott, additional
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- 2014
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65. Nerve Decompression After Diabetic Foot Ulceration May Protect Against Recurrence
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Nickerson, D. Scott, primary and Rader, Andrew J., primary
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- 2014
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66. Association of rare missense variants in the second intracellular loop of NaV1.7 sodium channels with familial autism
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Rubinstein, M, Patowary, A, Stanaway, I B, McCord, E, Nesbitt, R R, Archer, M, Scheuer, T, Nickerson, D, Raskind, W H, Wijsman, E M, Bernier, R, Catterall, W A, and Brkanac, Z
- Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder often accompanied by intellectual disability, language impairment and medical co-morbidities. The heritability of autism is high and multiple genes have been implicated as causal. However, most of these genes have been identified in de novo cases. To further the understanding of familial autism, we performed whole-exome sequencing on five families in which second- and third-degree relatives were affected. By focusing on novel and protein-altering variants, we identified a small set of candidate genes. Among these, a novel private missense C1143F variant in the second intracellular loop of the voltage-gated sodium channel NaV1.7, encoded by the SCN9A gene, was identified in one family. Through electrophysiological analysis, we show that NaV1.7C1143Fexhibits partial loss-of-function effects, resulting in slower recovery from inactivation and decreased excitability in cultured cortical neurons. Furthermore, for the same intracellular loop of NaV1.7, we found an excess of rare variants in a case–control variant-burden study. Functional analysis of one of these variants, M932L/V991L, also demonstrated reduced firing in cortical neurons. However, although this variant is rare in Caucasians, it is frequent in Latino population, suggesting that genetic background can alter its effects on phenotype. Although the involvement of the SCN1A and SCN2A genes encoding NaV1.1 and NaV1.2 channels in de novo ASD has previously been demonstrated, our study indicates the involvement of inherited SCN9A variants and partial loss-of-function of NaV1.7 channels in the etiology of rare familial ASD.
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- 2018
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67. Minimum information about a simulation experiment (MIASE).
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Waltemath, D., Adams, R., Beard, D.A., Bergmann, F.T., Bhalla, U.S., Britten, R., Chelliah, V., Cooling, M.T., Cooper, J., Crampin, E.J., Garny, A., Hoops, S., Hucka, M., Hunter, P., Klipp, E., Laibe, C., Miller, A.K., Moraru, K., Nickerson, D., Nielsen, P., Nikolski, M., Sahle, S., Sauro, H.M., Schmidt, H., Snoep, J.L., Tolle, D., Wolkenhauer, O., le Novere, N., Waltemath, D., Adams, R., Beard, D.A., Bergmann, F.T., Bhalla, U.S., Britten, R., Chelliah, V., Cooling, M.T., Cooper, J., Crampin, E.J., Garny, A., Hoops, S., Hucka, M., Hunter, P., Klipp, E., Laibe, C., Miller, A.K., Moraru, K., Nickerson, D., Nielsen, P., Nikolski, M., Sahle, S., Sauro, H.M., Schmidt, H., Snoep, J.L., Tolle, D., Wolkenhauer, O., and le Novere, N.
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- 2011
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68. Minimum Information About a Simulation Experiment (MIASE)
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Bourne, PE, Waltemath, D, Adams, R, Beard, DA, Bergmann, FT, Bhalla, US, Britten, R, Chelliah, V, Cooling, MT, Cooper, J, Crampin, EJ, Garny, A, Hoops, S, Hucka, M, Hunter, P, Klipp, E, Laibe, C, Miller, AK, Moraru, I, Nickerson, D, Nielsen, P, Nikolski, M, Sahle, S, Sauro, HM, Schmidt, H, Snoep, JL, Tolle, D, Wolkenhauer, O, Le Novere, N, Bourne, PE, Waltemath, D, Adams, R, Beard, DA, Bergmann, FT, Bhalla, US, Britten, R, Chelliah, V, Cooling, MT, Cooper, J, Crampin, EJ, Garny, A, Hoops, S, Hucka, M, Hunter, P, Klipp, E, Laibe, C, Miller, AK, Moraru, I, Nickerson, D, Nielsen, P, Nikolski, M, Sahle, S, Sauro, HM, Schmidt, H, Snoep, JL, Tolle, D, Wolkenhauer, O, and Le Novere, N
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- 2011
69. Characterization of Statin Dose Response in Electronic Medical Records
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Wei, W-Q, primary, Feng, Q, additional, Jiang, L, additional, Waitara, M S, additional, Iwuchukwu, O F, additional, Roden, D M, additional, Jiang, M, additional, Xu, H, additional, Krauss, R M, additional, Rotter, J I, additional, Nickerson, D A, additional, Davis, R L, additional, Berg, R L, additional, Peissig, P L, additional, McCarty, C A, additional, Wilke, R A, additional, and Denny, J C, additional
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- 2013
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70. Reconsidering Nerve Decompression: An Overlooked Opportunity to Limit Diabetic Foot Ulcer Recurrence and Amputation
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Nickerson, D. Scott, primary
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- 2013
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71. Can Peripheral Nerve Treatment Have An Impact On Balance And Gait?
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Nickerson, D. Scott
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- 2016
72. Variation in the TLR10/TLR1/TLR6 locus is the major genetic determinant of interindividual difference in TLR1/2-mediated responses
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Mikacenic, C, primary, Reiner, A P, additional, Holden, T D, additional, Nickerson, D A, additional, and Wurfel, M M, additional
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- 2012
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73. scAAV-mediated gene transfer of interleukin-1-receptor antagonist to synovium and articular cartilage in large mammalian joints
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Watson, R S, primary, Broome, T A, additional, Levings, P P, additional, Rice, B L, additional, Kay, J D, additional, Smith, A D, additional, Gouze, E, additional, Gouze, J-N, additional, Dacanay, E A, additional, Hauswirth, W W, additional, Nickerson, D M, additional, Dark, M J, additional, Colahan, P T, additional, and Ghivizzani, S C, additional
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- 2012
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74. Comparison of the Gibbs and Suga formulations of cardiac energetics: the demise of “isoefficiency”
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Han, J.-C., primary, Taberner, A. J., additional, Tran, K., additional, Goo, S., additional, Nickerson, D. P., additional, Nash, M. P., additional, Nielsen, P. M. F., additional, Crampin, E. J., additional, and Loiselle, D. S., additional
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- 2012
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75. Relating components of pressure-volume area in Suga's formulation of cardiac energetics to components of the stress-time integral
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Han, J.-C., primary, Taberner, A. J., additional, Tran, K., additional, Nickerson, D. P., additional, Nash, M. P., additional, Nielsen, P. M. F., additional, Crampin, E. J., additional, and Loiselle, D. S., additional
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- 2012
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76. Novel rare variants in congenital cardiac arrhythmia genes are frequent in drug-induced torsades de pointes
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Ramirez, A H, primary, Shaffer, C M, additional, Delaney, J T, additional, Sexton, D P, additional, Levy, S E, additional, Rieder, M J, additional, Nickerson, D A, additional, George, A L, additional, and Roden, D M, additional
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- 2012
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77. Intra-Abdominal Hypertension and Abdominal Compartment Syndrome after Abdominal Wall Reconstruction: Quaternary Syndromes?
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Kirkpatrick, A. W., Nickerson, D., Roberts, D. J., Rosen, M. J., McBeth, P. B., Petro, C. C., Berrevoet, Frederik, Sugrue, M., Xiao, Jimmy, and Ball, C. G.
- Abstract
Background and Aims: Reconstruction with reconstitution of the container function of the abdominal compartment is increasingly being performed in patients with massive ventral hernia previously deemed inoperable. This situation places patients at great risk of severe intra-abdominal hypertension and abdominal compartment syndrome if organ failure ensues. Intra-abdominal hypertension and especially abdominal compartment syndrome may be devastating systemic complications with systematic and progressive organ failure and death. We thus reviewed the pathophysiology and reported clinical experiences with abnormalities of intra-abdominal pressure in the context of abdominal wall reconstruction.Material and Methods: Bibliographic databases (1950–2015), websites, textbooks, and the bibliographies of previously recovered articles for reports or data relating to intra-abdominal pressure, intra-abdominal hypertension, and the abdominal compartment syndrome in relation to ventral, incisional, or abdominal hernia repair or abdominal wall reconstruction.Results: Surgeons should thus consider and carefully measure intra-abdominal pressure and its resultant effects on respiratory parameters and function during abdominal wall reconstruction. The intra-abdominal pressure post-operatively will be a result of the new intra-peritoneal volume and the abdominal wall compliance. Strategies surgeons may utilize to ameliorate intra-abdominal pressure rise after abdominal wall reconstruction including temporizing paralysis of the musculature either temporarily or semi-permanently, pre-operative progressive pneumoperitoneum, permanently removing visceral contents, or surgically releasing the musculature to increase the abdominal container volume. In patients without complicating shock and inflammation, and in whom the abdominal wall anatomy has been so functionally adapted to maximize compliance, intra-abdominal hypertension may be transient and tolerable.Conclusions: Intra-abdominal hypertension/abdominal compartment syndrome in the specific setting of abdominal wall reconstruction without other complication may be considered as a quaternary situation considering the classification nomenclature of the Abdominal Compartment Society. Greater awareness of intra-abdominal pressure in abdominal wall reconstruction is required and ongoing study of these concerns is required.
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- 2017
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78. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
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Chhibber, A, French, C E, Yee, S W, Gamazon, E R, Theusch, E, Qin, X, Webb, A, Papp, A C, Wang, A, Simmons, C Q, Konkashbaev, A, Chaudhry, A S, Mitchel, K, Stryke, D, Ferrin, T E, Weiss, S T, Kroetz, D L, Sadee, W, Nickerson, D A, Krauss, R M, George, A L, Schuetz, E G, Medina, M W, Cox, N J, Scherer, S E, Giacomini, K M, and Brenner, S E
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Variation in the expression level and activity of genes involved in drug disposition and action (‘pharmacogenes’) can affect drug response and toxicity, especially when in tissues of pharmacological importance. Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-sequencing (RNA-seq) to determine the expression levels and alternative splicing of 389 Pharmacogenomics Research Network pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines, which are used widely in pharmacogenomics studies. Analysis of RNA-seq data from 139 different individuals across the 5 tissues (20–45 individuals per tissue type) revealed substantial variation in both expression levels and splicing across samples and tissue types. Comparison with GTEx data yielded a consistent picture. This in-depth exploration also revealed 183 splicing events in pharmacogenes that were previously not annotated. Overall, this study serves as a rich resource for the research community to inform biomarker and drug discovery and use.
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- 2017
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79. A homozygous missense mutation in <italic>SLC25A16</italic> associated with autosomal recessive isolated fingernail dysplasia in a Pakistani family.
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Khan, S., Ansar, M., Khan, A. K., Shah, K., Muhammad, N., Shahzad, S., Nickerson, D. A., Bamshad, M. J., Santos‐Cortez, R. L. P., Leal, S. M., and Ahmad, W.
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FINGERNAILS ,DYSPLASIA ,GENETIC disorders ,ERYTHEMA ,FAMILIAL diseases ,DIAGNOSIS ,DISEASES - Abstract
The article discusses a study on a Pakistani family with individuals affected of segregating fingernail dysplasia in an autosomal recessive manner. It mentions affected family members displayed a severe form of onychodystrophy with mild erythema and swelling of the proximal and lateral nail folds. it also mentions differences in phenotype severity among affected individuals suggest the possible role of factors such as heterogeneity in genetic background, modifier genes or environmental factors.
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- 2018
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80. C-C5-05: Genetic Risk Factors: Idiopathic Thrombocytopenic Purpura following the First Dose of Measles-Mumps-Rubella Vaccination in Children
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Hemmes, M., primary, Davis, R., additional, Buttolph, T., additional, Qiang, Y., additional, Nickerson, D., additional, Johnsen, J., additional, and Carlson, C., additional
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- 2011
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81. A non-redundant role for induced regulatory T cells in mucosal tolerance.
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Haribhai, D, primary, Williams, J, additional, Jia, S, additional, Nickerson, D, additional, Treslley-Schmitt, E, additional, Yassai, M, additional, Li, S, additional, Zheng, Y, additional, Simpson, P, additional, Gorski, J, additional, Salzman, N, additional, Hessner, M, additional, Chatila, T, additional, and Williams, C, additional
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- 2011
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82. Massively parallel sequencing and rare disease
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Ng, S. B., primary, Nickerson, D. A., additional, Bamshad, M. J., additional, and Shendure, J., additional
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- 2010
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83. Early stage diabetic Charcot Foot syndrome may respond to nerve decompression
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Nickerson, D. Scott, primary, Alzheimer, Daniel, additional, and Dellon, A. Lee, additional
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- 2009
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84. Differential Effects of Ramipril on Ambulatory Blood Pressure in African Americans and Caucasians
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MORAN, A, primary, SIMON, J, additional, SHIBOSKI, S, additional, PICKERING, T, additional, WATERS, D, additional, ROTTER, J, additional, LYON, C, additional, NICKERSON, D, additional, YANG, H, additional, and SAAD, M, additional
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- 2007
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85. Modeling Cardiac Electrical Activity at the Cell and Tissue Levels
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AUSTIN, T. M, primary, HOOKS, D. A, additional, HUNTER, P. J, additional, NICKERSON, D. P, additional, PULLAN, A. J, additional, SANDS, G. B, additional, SMAILL, B. H, additional, and TREW, M. L, additional
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- 2006
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86. Diverting Ostomy in Adult Patients with Perineal Burns
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Nickerson, D, primary, Gomez, M, additional, Beveridge, M, additional, Cartotto, R, additional, and Fish, J S., additional
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- 2006
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87. Multiscale modelling of cardiac mechanics
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Nickerson, D., primary, Stevens, C., additional, Nash, M., additional, and Hunter, P., additional
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- 2006
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88. The Noble cardiac ventricular electrophysiology models in CellML
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NICKERSON, D, primary and HUNTER, P, additional
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- 2006
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89. A mathematical model of ovine skeletal muscle
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Davidson, J., primary, Cheng, L., additional, Nickerson, D., additional, Shorten, P., additional, Soboleva, T., additional, Clarke, R., additional, and Pullan, A., additional
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- 2006
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90. Use of Pharmacogenetics and Clinical Factors To Predict the Maintenance Dose of Warfarin.
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Gage, B. F., primary, Eby, C. S., primary, Johnson, J. A., primary, Rieder, M. J., primary, Ridker, P. M., primary, Rettie, A. E., primary, Aquilante, C., primary, Milligan, P. E., primary, Marsh, S., primary, Voora, D., primary, Langaee, T., primary, Veenstra, D. L., primary, Birman-Deych, E., primary, Glynn, R., primary, Nickerson, D. A., primary, and McLeod, H. L., primary
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- 2005
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91. Using CellML in Computational Models of Multiscale Physiology
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Nickerson, D., primary and Hunter, P., additional
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- 2005
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92. Addendum to counting by weighing and the seed testing problem
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NICKERSON, D M, primary
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- 2003
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93. The Functional Consequences of Polymorphisms in the Human PON1 Gene.
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Ridley, Anne, Frampton, Jon, Mackness, Bharti, Mackness, Mike, Aviram, Michael, Paragh, György, Furlong, C.E., Richter, R.J, Li, W.-F., Brophy, V.H., Carlson, C., Rieder, M., Nickerson, D., Costa, L.G., Ranchalis, J., Lusis, A.J., Shih, D.M., Tward, A., and Jarvik, G.P.
- Abstract
Early research on population distributions of plasma PON1 paraoxonase activity indicated a polymorphic distribution with high, intermediate and low metabolizers. Cloning and characterization of the cDNA encoding human PON1 and follow-on experiments demonstrated that the molecular basis of the activity polymorphism (PM) was a Q192R PM with PON1R192 specifying high paraoxonase activity. Further research demonstrated that the PON1192 polymorphism had little effect on the catalytic efficiencies of hydrolysis of phenylacetate and diazoxon (DZO), but did affect the efficiencies of hydrolysis of chlorpyrifos oxon (CPO), soman and sarin, with PON1R192 having a higher efficiency of CPO hydrolysis and PON1Q192 having higher rates of hydrolysis of soman and sarin. Plots of rates of DZO hydrolysis (at a salt concentration that differentially inhibited PON1R192) vs. paraoxon hydrolysis clearly separated the three PON1192 phenotypes (QQ, QR, RR) and also showed a wide range of activity among individuals with the same PON1192 genotype. The term PON1 status was introduced to include both PON1192 functional genotype and plasma PON1 level,both important in determining risk for either exposure to specific organophosphorus compounds (OPs) or disease. Characterization of 5 promoter-region polymorphisms by several groups indicated that an Sp1 binding site was responsible for significant(~30%) variation in plasma PON1 levels. Re-sequencing of the PON1 genes of 47 individuals (24 African-American/23 European) revealed an additional 180 polymorphisms in 27 kb of the PON1 genomic DNA including 8 more 5' regulatory region PMs, 1 coding region polymorphism (W194X), 162 additional intronic PMs and 9 additional 3' UTR PMs. The generation of PON1 null mice and "PON1 humanized mice" expressing either tgHuPON1R192 or tgHuPON1Q192 at the same levels on the PON1−/− background allowed for a functional analysis of the Q192R PM under physiological conditions. Toxicology experiments with the PON1 humanized mice and the PON1 null mice injected with purified human PON1192 alloforms clearly demonstrated that the catalytic efficiency of substrate hydrolysis is important in determining whether PON1 is able to protect against a given OP exposure. HuPON1R192 protects well against CPO and DZO exposure, but HuPON1Q192 does not protect well against CPO exposure and neither protects against PO exposure. Studies on PON1 status and carotid artery disease show that low PON1 levels are a risk factor. The effects of PON1192 alloforms on rates of hydrolysis of quorum sensing factors are not yet known. Taken together, these data along with those of the leading researchers in the PON1 field indicate that it is important to measure PON1 levels/activities in any epidemiological study. SNP analysis alone is inadequate for epidemiological studies, due to the wide variability of PON1 levels within the three PON1192 genotypes Q/Q, Q/R R/R). Even the most comprehensive PON1 SNP analyses are unable to accurately predict PON1 levels. PON1 activity or level accurately predicts CHD risk, while genotype does not [ABSTRACT FROM AUTHOR]
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- 2008
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94. A Computational Model of Cardiac Electromechanics.
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Nickerson, D., Niederer, S., Stevens, C., Nash, M., and Hunter, P.
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- 2006
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95. Toward a Curated CellML Model Repository.
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Nickerson, D., Stevens, C., Halstead, M., Hunter, P., and Nielsen, P.
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- 2006
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96. Evaluation of the SCORTEN as a Prognostic Score for Toxic Epidermal Necrolysis Syndrome
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Nickerson, D., primary, Dickson, B., additional, Gomez, M., additional, and Cartotto, R., additional
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- 2002
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97. Burn Unit Evaluation of the Bispectral Index (BIS)
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Nickerson, D., primary and Fish, J. S., additional
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- 2002
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98. Increased opsonic capacity of serum in chronic heroin addiction.
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Nickerson, D. Scott, Williams Jr., Ralph C., Boxmeyer, Margaret, Quie, Paul G., Nickerson, D S, Williams, R C Jr, Boxmeyer, M, and Quie, P G
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OPSONINS & opsonic index ,SERUM ,DRUG abuse ,HEROIN ,PHAGOCYTOSIS ,IMMUNOGLOBULINS ,IMMUNOGLOBULIN analysis ,ESCHERICHIA coli ,GAMMA globulins ,IMMUNOELECTROPHORESIS ,LEUCOCYTES ,SEPSIS ,SERRATIA ,STAPHYLOCOCCUS ,SUBSTANCE abuse - Abstract
Studies of phagocytosis promoting capacity and immunoglobulin levels were conducted in a group of 25 long-term heroin addicts. Sera were collected from addicts at Lexington, Ky.; Synanon House, San Francisco; and Albuquerque, N. M. Striking increments in heat-stable opsonins for Escherichia coli and Serratia marcescens were found in many addicts' sera as compared with normal control sera. Marked elevations of gamma M (up to 660 mg/100 ml) were found in many sera. accompanied by 19S antibacterial opsonins as demonstrated by separations in sucrose density gradients. Antigamma-globulin factors were present in 36% of the addicts studied. There was no impairment in ingestion or killing of test bacteria by polymorphonuclear leukocytes obtained from subjects on substitution narcotic therapy. [ABSTRACT FROM AUTHOR]
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- 1970
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99. Human genome meeting 2016
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Srivastava, A., Wang, Y., Huang, R., Skinner, C., Thompson, T., Pollard, L., Wood, T., Luo, F., Stevenson, R., Polimanti, R., Gelernter, J., Lin, X., Lim, I., Wu, Y., Teh, A., Chen, L., Aris, I., Soh, S., Tint, M., MacIsaac, J., Yap, F., Kwek, K., Saw, S., Kobor, M., Meaney, M., Godfrey, K., Chong, Y., Holbrook, J., Lee, Y., Gluckman, P., Karnani, N., Kapoor, A., Lee, D., Chakravarti, A., Maercker, C., Graf, F., Boutros, M., Stamoulis, G., Santoni, F., Makrythanasis, P., Letourneau, A., Guipponi, M., Panousis, N., Garieri, M., Ribaux, P., Falconnet, E., Borel, C., Antonarakis, S., Kumar, S., Curran, J., Blangero, J., Chatterjee, S., Kapoor, A., Akiyama, J., Auer, D., Berrios, C., Pennacchio, L., Chakravarti, A., Donti, T., Cappuccio, G., Miller, M., Atwal, P., Kennedy, A., Cardon, A., Bacino, C., Emrick, L., Hertecant, J., Baumer, F., Porter, B., Bainbridge, M., Bonnen, P., Graham, B., Sutton, R., Sun, Q., Elsea, S., Hu, Z., Wang, P., Zhu, Y., Zhao, J., Xiong, M., Bennett, David, Hidalgo-Miranda, A., Romero-Cordoba, S., Rodriguez-Cuevas, S., Rebollar-Vega, R., Tagliabue, E., Iorio, M., D’Ippolito, E., Baroni, S., Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A., Andersson, R., Itoh, M., Lassmann, T., Hayashizaki, Y., Carninci, P., Forrest, A., Semple, C., Rosenthal, E., Shirts, B., Amendola, L., Gallego, C., Horike-Pyne, M., Burt, A., Robertson, P., Beyers, P., Nefcy, C., Veenstra, D., Hisama, F., Bennett, R., Dorschner, M., Nickerson, D., Smith, J., Patterson, K., Crosslin, D., Nassir, R., Zubair, N., Harrison, T., Peters, U., Jarvik, G., Menghi, F., Inaki, K., Woo, X., Kumar, P., Grzeda, K., Malhotra, A., Kim, H., Ucar, D., Shreckengast, P., Karuturi, K., Keck, J., Chuang, J., Liu, E., Ji, B., Tyler, A., Ananda, G., Carter, G., Nikbakht, H., Montagne, M., Zeinieh, M., Harutyunyan, A., Mcconechy, M., Jabado, N., Lavigne, P., Majewski, J., Goldstein, J., Overman, M., Varadhachary, G., Shroff, R., Wolff, R., Javle, M., Futreal, A., Fogelman, D., Bravo, L., Fajardo, W., Gomez, H., Castaneda, C., Rolfo, C., Pinto, J., Akdemir, K., Chin, L., Futreal, A., Patterson, S., Statz, C., Mockus, S., Nikolaev, S., Bonilla, X., Parmentier, L., King, B., Bezrukov, F., Kaya, G., Zoete, V., Seplyarskiy, V., Sharpe, H., McKee, T., Letourneau, A., Ribaux, P., Popadin, K., Basset-Seguin, N., Chaabene, R., Santoni, F., Andrianova, M., Guipponi, M., Garieri, M., Verdan, C., Grosdemange, K., Sumara, O., Eilers, M., Aifantis, I., Michielin, O., de Sauvage, F., Antonarakis, S., Likhitrattanapisal, S., Lincoln, S., Kurian, A., Desmond, A., Yang, S., Kobayashi, Y., Ford, J., Ellisen, L., Peters, T., Alvarez, K., Hollingsworth, E., Lopez-Terrada, D., Hastie, A., Dzakula, Z., Pang, A., Lam, E., Anantharaman, T., Saghbini, M., Cao, H., Gonzaga-Jauregui, C., Ma, L., King, A., Rosenzweig, E., Krishnan, U., Reid, J., Overton, J., Dewey, F., Chung, W., Small, K., DeLuca, A., Cremers, F., Lewis, R., Puech, V., Bakall, B., Silva-Garcia, R., Rohrschneider, K., Leys, M., Shaya, F., Stone, E., Sobreira, N., Schiettecatte, F., Ling, H., Pugh, E., Witmer, D., Hetrick, K., Zhang, P., Doheny, K., Valle, D., Hamosh, A., Jhangiani, S., Akdemir, Z., Bainbridge, M., Charng, W., Wiszniewski, W., Gambin, T., Karaca, E., Bayram, Y., Eldomery, M., Posey, J., Doddapaneni, H., Hu, J., Sutton, V., Muzny, D., Boerwinkle, E., Valle, D., Lupski, J., Gibbs, R., Shekar, S., Salerno, W., English, A., Mangubat, A., Bruestle, J., Thorogood, A., Knoppers, B., Takahashi, H., Nitta, K., Kozhuharova, A., Suzuki, A., Sharma, H., Cotella, D., Santoro, C., Zucchelli, S., Gustincich, S., Carninci, P., Mulvihill, J., Baynam, G., Gahl, W., Groft, S., Kosaki, K., Lasko, P., Melegh, B., Taruscio, D., Ghosh, R., Plon, S., Scherer, S., Qin, X., Sanghvi, R., Walker, K., Chiang, T., Muzny, D., Wang, L., Black, J., Boerwinkle, E., Weinshilboum, R., Gibbs, R., Karpinets, T., Calderone, T., Wani, K., Yu, X., Creasy, C., Haymaker, C., Forget, M., Nanda, V., Roszik, J., Wargo, J., Haydu, L., Song, X., Lazar, A., Gershenwald, J., Davies, M., Bernatchez, C., Zhang, J., Futreal, A., Woodman, S., Chesler, E., Reynolds, T., Bubier, J., Phillips, C., Langston, M., Baker, E., Xiong, M., Ma, L., Lin, N., Amos, C., Lin, N., Wang, P., Zhu, Y., Zhao, J., Calhoun, V., Xiong, M., Dobretsberger, O., Egger, M., Leimgruber, F., Sadedin, S., Oshlack, A., Antonio, V., Ono, N., Ahmed, Z., Bolisetty, M., Zeeshan, S., Anguiano, E., Ucar, D., Sarkar, A., Nandineni, M., Zeng, C., Shao, J., Cao, H., Hastie, A., Pang, A., Lam, E., Liang, T., Pham, K., Saghbini, M., Dzakula, Z., Chee-Wei, Y., Dongsheng, L., Lai-Ping, W., Lian, D., Hee, R., Yunus, Y., Aghakhanian, F., Mokhtar, S., Lok-Yung, C., Bhak, J., Phipps, M., Shuhua, X., Yik-Ying, T., Kumar, V., Boon-Peng, H., Campbell, I., Young, M., James, P., Rain, M., Mohammad, G., Kukreti, R., Pasha, Q., Akilzhanova, A., Guelly, C., Abilova, Z., Rakhimova, S., Akhmetova, A., Kairov, U., Trajanoski, S., Zhumadilov, Z., Bekbossynova, M., Schumacher, C., Sandhu, S., Harkins, T., Makarov, V., Doddapaneni, H., Glenn, R., Momin, Z., Dilrukshi, B., Chao, H., Meng, Q., Gudenkauf, B., Kshitij, R., Jayaseelan, J., Nessner, C., Lee, S., Blankenberg, K., Lewis, L., Hu, J., Han, Y., Dinh, H., Jireh, S., Walker, K., Boerwinkle, E., Muzny, D., Gibbs, R., Hu, J., Walker, K., Buhay, C., Liu, X., Wang, Q., Sanghvi, R., Doddapaneni, H., Ding, Y., Veeraraghavan, N., Yang, Y., Boerwinkle, E., Beaudet, A., Eng, C., Muzny, D., Gibbs, R., Worley, K., Liu, Y., Hughes, D., Murali, S., Harris, R., English, A., Qin, X., Hampton, O., Larsen, P., Beck, C., Han, Y., Wang, M., Doddapaneni, H., Kovar, C., Salerno, W., Yoder, A., Richards, S., Rogers, J., Lupski, J., Muzny, D., Gibbs, R., Meng, Q., Bainbridge, M., Wang, M., Doddapaneni, H., Han, Y., Muzny, D., Gibbs, R., Harris, R., Raveenedran, M., Xue, C., Dahdouli, M., Cox, L., Fan, G., Ferguson, B., Hovarth, J., Johnson, Z., Kanthaswamy, S., Kubisch, M., Platt, M., Smith, D., Vallender, E., Wiseman, R., Liu, X., Below, J., Muzny, D., Gibbs, R., Yu, F., Rogers, J., Lin, J., Zhang, Y., Ouyang, Z., Moore, A., Wang, Z., Hofmann, J., Purdue, M., Stolzenberg-Solomon, R., Weinstein, S., Albanes, D., Liu, C., Cheng, W., Lin, T., Lan, Q., Rothman, N., Berndt, S., Chen, E., Bahrami, H., Khoshzaban, A., Keshal, S., Bahrami, H., Khoshzaban, A., Keshal, S., Alharbi, K., Zhalbinova, M., Akilzhanova, A., Rakhimova, S., Bekbosynova, M., Myrzakhmetova, S., Matar, M., Mili, N., Molinari, R., Ma, Y., Guerrier, S., Elhawary, N., Tayeb, M., Bogari, N., Qotb, N., McClymont, S., Hook, P., Goff, L., McCallion, A., Kong, Y., Charette, J., Hicks, W., Naggert, J., Zhao, L., Nishina, P., Edrees, B., Athar, M., Al-Allaf, F., Taher, M., Khan, W., Bouazzaoui, A., Harbi, N., Safar, R., Al-Edressi, H., Anazi, A., Altayeb, N., Ahmed, M., Alansary, K., Abduljaleel, Z., Kratz, A., Beguin, P., Poulain, S., Kaneko, M., Takahiko, C., Matsunaga, A., Kato, S., Suzuki, A., Bertin, N., Lassmann, T., Vigot, R., Carninci, P., Plessy, C., Launey, T., Graur, D., Lee, D., Kapoor, A., Chakravarti, A., Friis-Nielsen, J., Izarzugaza, J., Brunak, S., Chakraborty, A., Basak, J., Mukhopadhyay, A., Soibam, B., Das, D., Biswas, N., Das, S., Sarkar, S., Maitra, A., Panda, C., Majumder, P., Morsy, H., Gaballah, A., Samir, M., Shamseya, M., Mahrous, H., Ghazal, A., Arafat, W., Hashish, M., Gruber, J., Jaeger, N., Snyder, M., Patel, K., Bowman, S., Davis, T., Kraushaar, D., Emerman, A., Russello, S., Henig, N., Hendrickson, C., Zhang, K., Rodriguez-Dorantes, M., Cruz-Hernandez, C., Garcia-Tobilla, C., Solorzano-Rosales, S., Jäger, N., Chen, J., Haile, R., Hitchins, M., Brooks, J., Snyder, M., Jiménez-Morales, S., Ramírez, M., Nuñez, J., Bekker, V., Leal, Y., Jiménez, E., Medina, A., Hidalgo, A., Mejía, J., Halytskiy, V., Naggert, J., Collin, G., DeMauro, K., Hanusek, R., Nishina, P., Belhassa, K., Belhassan, K., Bouguenouch, L., Samri, I., Sayel, H., moufid, FZ., El Bouchikhi, I., Trhanint, S., Hamdaoui, H., Elotmani, I., Khtiri, I., Kettani, O., Quibibo, L., Ahagoud, M., Abbassi, M., Ouldim, K., Marusin, A., Kornetov, A., Swarovskaya, M., Vagaiceva, K., Stepanov, V., De La Paz, E., Sy, R., Nevado, J., Reganit, P., Santos, L., Magno, J., Punzalan, F., Ona, D., Llanes, E., Santos-Cortes, R., Tiongco, R., Aherrera, J., Abrahan, L., Pagauitan-Alan, P., Morelli, K., Domire, J., Pyne, N., Harper, S., Burgess, R., Zhalbinova, M., Akilzhanova, A., Rakhimova, S., Bekbosynova, M., Myrzakhmetova, S., Gari, M., Dallol, A., Alsehli, H., Gari, A., Gari, M., Abuzenadah, A., Thomas, M., Sukhai, M., Garg, S., Misyura, M., Zhang, T., Schuh, A., Stockley, T., Kamel-Reid, S., Sherry, S., Xiao, C., Slotta, D., Rodarmer, K., Feolo, M., Kimelman, M., Godynskiy, G., O’Sullivan, C., Yaschenko, E., Xiao, C., Yaschenko, E., Sherry, S., Rangel-Escareño, C., Rueda-Zarate, H., Tayubi, I., Mohammed, R., Ahmed, I., Ahmed, T., Seth, S., Amin, S., Song, X., Mao, X., Sun, H., Verhaak, R., Futreal, A., Zhang, J., Whiite, S., Chiang, T., English, A., Farek, J., Kahn, Z., Salerno, W., Veeraraghavan, N., Boerwinkle, E., Gibbs, R., Kasukawa, T., Lizio, M., Harshbarger, J., Hisashi, S., Severin, J., Imad, A., Sahin, S., Freeman, T., Baillie, K., Sandelin, A., Carninci, P., Forrest, A., Kawaji, H., Salerno, W., English, A., Shekar, S., Mangubat, A., Bruestle, J., Boerwinkle, E., Gibbs, R., Salem, A., Ali, M., Ibrahim, A., Ibrahim, M., Barrera, H., Garza, L., Torres, J., Barajas, V., Ulloa-Aguirre, A., Kershenobich, D., Mortaji, Shahroj, Guizar, Pedro, Loera, Eliezer, Moreno, Karen, De León, Adriana, Monsiváis, Daniela, Gómez, Jackeline, Cardiel, Raquel, Fernandez-Lopez, J., Bonifaz-Peña, V., Rangel-Escareño, C., Hidalgo-Miranda, A., Contreras, A., Polfus, L., Wang, X., Philip, V., Carter, G., Abuzenadah, A., Gari, M., Turki, R., Dallol, A., Uyar, A., Kaygun, A., Zaman, S., Marquez, E., George, J., Ucar, D., Hendrickson, C., Emerman, A., Kraushaar, D., Bowman, S., Henig, N., Davis, T., Russello, S., Patel, K., Starr, D., Baird, M., Kirkpatrick, B., Sheets, K., Nitsche, R., Prieto-Lafuente, L., Landrum, M., Lee, J., Rubinstein, W., Maglott, D., Thavanati, P., de Dios, A., Hernandez, R., Aldrate, M., Mejia, M., Kanala, K., Abduljaleel, Z., Khan, W., Al-Allaf, F., Athar, M., Taher, M., Shahzad, N., Bouazzaoui, A., Huber, E., Dan, A., Al-Allaf, F., Herr, W., Sprotte, G., Köstler, J., Hiergeist, A., Gessner, A., Andreesen, R., Holler, E., Al-Allaf, F., Alashwal, A., Abduljaleel, Z., Taher, M., Bouazzaoui, A., Abalkhail, H., Al-Allaf, A., Bamardadh, R., Athar, M., Filiptsova, O., Kobets, M., Kobets, Y., Burlaka, I., Timoshyna, I., Filiptsova, O., Kobets, M., Kobets, Y., Burlaka, I., Timoshyna, I., Filiptsova, O., Kobets, M., Kobets, Y., Burlaka, I., Timoshyna, I., Al-allaf, F., Mohiuddin, M., Zainularifeen, A., Mohammed, A., Abalkhail, H., Owaidah, T., and Bouazzaoui, A.
- Abstract
O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3rd7mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLRgene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar
- Published
- 2016
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100. An account of a lake sediment geochemical survey conducted over certain volcanic belts within the Slave structural province of the Northwest Territories during 1972
- Author
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Nickerson, D, primary
- Published
- 1973
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