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Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.

Genome medicine

O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ.
PMID: 23537139
Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432. eCollection 2013.

BACKGROUND: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear...

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O'Rawe J, Jiang T, Sun G, et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013;5(3):28doi: 10.1186/gm432.
O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Hu, J., Bodily, P., Tian, L., Hakonarson, H., Johnson, W. E., Wei, Z., Wang, K., & Lyon, G. J. (2013). Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome medicine, 5(3), 28. https://doi.org/10.1186/gm432
O'Rawe, Jason, et al. "Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing." Genome medicine vol. 5,3 (2013): 28. doi: https://doi.org/10.1186/gm432
O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432. eCollection 2013. PMID: 23537139; PMCID: PMC3706896.
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Solvent-type-dependent polymorphism and charge transport in a long fused-ring organic semiconductor.

Nanoscale

Chen J, Shao M, Xiao K, Rondinone AJ, Loo YL, Kent PR, Sumpter BG, Li D, Keum JK, Diemer PJ, Anthony JE, Jurchescu OD, Huang J.
PMID: 24217182
Nanoscale. 2014 Jan 07;6(1):449-56. doi: 10.1039/c3nr04341j. Epub 2013 Nov 11.

Crystalline polymorphism of organic semiconductors is among the critical factors in determining the structure and properties of the resultant organic electronic devices. Herein we report for the first time a solvent-type-dependent polymorphism of a long fused-ring organic semiconductor and...

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Chen J, Shao M, Xiao K, et al. Solvent-type-dependent polymorphism and charge transport in a long fused-ring organic semiconductor. Nanoscale. 2013;6(1):449-56doi: 10.1039/c3nr04341j.
Chen, J., Shao, M., Xiao, K., Rondinone, A. J., Loo, Y. L., Kent, P. R., Sumpter, B. G., Li, D., Keum, J. K., Diemer, P. J., Anthony, J. E., Jurchescu, O. D., & Huang, J. (2014). Solvent-type-dependent polymorphism and charge transport in a long fused-ring organic semiconductor. Nanoscale, 6(1), 449-56. https://doi.org/10.1039/c3nr04341j
Chen, Jihua, et al. "Solvent-type-dependent polymorphism and charge transport in a long fused-ring organic semiconductor." Nanoscale vol. 6,1 (2014): 449-56. doi: https://doi.org/10.1039/c3nr04341j
Chen J, Shao M, Xiao K, Rondinone AJ, Loo YL, Kent PR, Sumpter BG, Li D, Keum JK, Diemer PJ, Anthony JE, Jurchescu OD, Huang J. Solvent-type-dependent polymorphism and charge transport in a long fused-ring organic semiconductor. Nanoscale. 2014 Jan 07;6(1):449-56. doi: 10.1039/c3nr04341j. Epub 2013 Nov 11. PMID: 24217182.
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SchemeLens: A Content-Aware Vector-Based Fisheye Technique for Navigating Large Systems Diagrams.

IEEE transactions on visualization and computer graphics

Cohé A, Liutkus B, Bailly G, Eagan J, Lecolinet E.
PMID: 26390464
IEEE Trans Vis Comput Graph. 2016 Jan;22(1):330-8. doi: 10.1109/TVCG.2015.2467035. Epub 2015 Aug 12.

System schematics, such as those used for electrical or hydraulic systems, can be large and complex. Fisheye techniques can help navigate such large documents by maintaining the context around a focus region, but the distortion introduced by traditional fisheye...

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Cohé A, Liutkus B, Bailly G, et al. SchemeLens: A Content-Aware Vector-Based Fisheye Technique for Navigating Large Systems Diagrams. IEEE Trans Vis Comput Graph. 2015;22(1):330-8doi: 10.1109/TVCG.2015.2467035.
Cohé, A., Liutkus, B., Bailly, G., Eagan, J., & Lecolinet, E. (2016). SchemeLens: A Content-Aware Vector-Based Fisheye Technique for Navigating Large Systems Diagrams. IEEE transactions on visualization and computer graphics, 22(1), 330-8. https://doi.org/10.1109/TVCG.2015.2467035
Cohé, Aurélie, et al. "SchemeLens: A Content-Aware Vector-Based Fisheye Technique for Navigating Large Systems Diagrams." IEEE transactions on visualization and computer graphics vol. 22,1 (2016): 330-8. doi: https://doi.org/10.1109/TVCG.2015.2467035
Cohé A, Liutkus B, Bailly G, Eagan J, Lecolinet E. SchemeLens: A Content-Aware Vector-Based Fisheye Technique for Navigating Large Systems Diagrams. IEEE Trans Vis Comput Graph. 2016 Jan;22(1):330-8. doi: 10.1109/TVCG.2015.2467035. Epub 2015 Aug 12. PMID: 26390464.
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Petascale Simulations of the Morphology and the Molecular Interface of Bulk Heterojunctions.

ACS nano

Carrillo JM, Seibers Z, Kumar R, Matheson MA, Ankner JF, Goswami M, Bhaskaran-Nair K, Shelton WA, Sumpter BG, Kilbey SM.
PMID: 27299676
ACS Nano. 2016 Jul 26;10(7):7008-22. doi: 10.1021/acsnano.6b03009. Epub 2016 Jun 20.

Understanding how additives interact and segregate within bulk heterojunction (BHJ) thin films is critical for exercising control over structure at multiple length scales and delivering improvements in photovoltaic performance. The morphological evolution of poly(3-hexylthiophene) (P3HT) and phenyl-C61-butyric acid methyl...

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Carrillo JM, Seibers Z, Kumar R, et al. Petascale Simulations of the Morphology and the Molecular Interface of Bulk Heterojunctions. ACS Nano. 2016;10(7):7008-22doi: 10.1021/acsnano.6b03009.
Carrillo, J. M., Seibers, Z., Kumar, R., Matheson, M. A., Ankner, J. F., Goswami, M., Bhaskaran-Nair, K., Shelton, W. A., Sumpter, B. G., & Kilbey, S. M. (2016). Petascale Simulations of the Morphology and the Molecular Interface of Bulk Heterojunctions. ACS nano, 10(7), 7008-22. https://doi.org/10.1021/acsnano.6b03009
Carrillo, Jan-Michael Y, et al. "Petascale Simulations of the Morphology and the Molecular Interface of Bulk Heterojunctions." ACS nano vol. 10,7 (2016): 7008-22. doi: https://doi.org/10.1021/acsnano.6b03009
Carrillo JM, Seibers Z, Kumar R, Matheson MA, Ankner JF, Goswami M, Bhaskaran-Nair K, Shelton WA, Sumpter BG, Kilbey SM. Petascale Simulations of the Morphology and the Molecular Interface of Bulk Heterojunctions. ACS Nano. 2016 Jul 26;10(7):7008-22. doi: 10.1021/acsnano.6b03009. Epub 2016 Jun 20. PMID: 27299676.
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Accurate measurement of the residual birefringence in VECSEL: Towards understanding of the polarization behavior under spin-polarized pumping.

Optics express

Frougier J, Baili G, Sagnes I, Dolfi D, George JM, Alouini M.
PMID: 25968994
Opt Express. 2015 Apr 20;23(8):9573-88. doi: 10.1364/OE.23.009573.

In this paper we report birefringence measurements of an optically pumped (100)-oriented InGaAs/GaAsP multiple quantum well (MQWs) Vertical External Cavity Surface Emitting Laser (VECSEL) in oscillating conditions. The proposed technique relies on the measurement in the microwave domain of...

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Frougier J, Baili G, Sagnes I, et al. Accurate measurement of the residual birefringence in VECSEL: Towards understanding of the polarization behavior under spin-polarized pumping. Opt Express. 2015;23(8):9573-88doi: 10.1364/OE.23.009573.
Frougier, J., Baili, G., Sagnes, I., Dolfi, D., George, J. M., & Alouini, M. (2015). Accurate measurement of the residual birefringence in VECSEL: Towards understanding of the polarization behavior under spin-polarized pumping. Optics express, 23(8), 9573-88. https://doi.org/10.1364/OE.23.009573
Frougier, Julien, et al. "Accurate measurement of the residual birefringence in VECSEL: Towards understanding of the polarization behavior under spin-polarized pumping." Optics express vol. 23,8 (2015): 9573-88. doi: https://doi.org/10.1364/OE.23.009573
Frougier J, Baili G, Sagnes I, Dolfi D, George JM, Alouini M. Accurate measurement of the residual birefringence in VECSEL: Towards understanding of the polarization behavior under spin-polarized pumping. Opt Express. 2015 Apr 20;23(8):9573-88. doi: 10.1364/OE.23.009573. PMID: 25968994.
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A computational workflow for designing silicon donor qubits.

Nanotechnology

Humble TS, Ericson MN, Jakowski J, Huang J, Britton C, Curtis FG, Dumitrescu EF, Mohiyaddin FA, Sumpter BG.
PMID: 27641513
Nanotechnology. 2016 Oct 21;27(42):424002. doi: 10.1088/0957-4484/27/42/424002. Epub 2016 Sep 19.

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational...

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Humble TS, Ericson MN, Jakowski J, et al. A computational workflow for designing silicon donor qubits. Nanotechnology. 2016;27(42):424002doi: 10.1088/0957-4484/27/42/424002.
Humble, T. S., Ericson, M. N., Jakowski, J., Huang, J., Britton, C., Curtis, F. G., Dumitrescu, E. F., Mohiyaddin, F. A., & Sumpter, B. G. (2016). A computational workflow for designing silicon donor qubits. Nanotechnology, 27(42), 424002. https://doi.org/10.1088/0957-4484/27/42/424002
Humble, Travis S, et al. "A computational workflow for designing silicon donor qubits." Nanotechnology vol. 27,42 (2016): 424002. doi: https://doi.org/10.1088/0957-4484/27/42/424002
Humble TS, Ericson MN, Jakowski J, Huang J, Britton C, Curtis FG, Dumitrescu EF, Mohiyaddin FA, Sumpter BG. A computational workflow for designing silicon donor qubits. Nanotechnology. 2016 Oct 21;27(42):424002. doi: 10.1088/0957-4484/27/42/424002. Epub 2016 Sep 19. PMID: 27641513.
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Low-Frequency Interlayer Raman Modes to Probe Interface of Twisted Bilayer MoS2.

Nano letters

Huang S, Liang L, Ling X, Puretzky AA, Geohegan DB, Sumpter BG, Kong J, Meunier V, Dresselhaus MS.
PMID: 26797083
Nano Lett. 2016 Feb 10;16(2):1435-44. doi: 10.1021/acs.nanolett.5b05015. Epub 2016 Jan 26.

van der Waals homo- and heterostructures assembled by stamping monolayers together present optoelectronic properties suitable for diverse applications. Understanding the details of the interlayer stacking and resulting coupling is crucial for tuning these properties. We investigated the low-frequency interlayer...

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Huang S, Liang L, Ling X, et al. Low-Frequency Interlayer Raman Modes to Probe Interface of Twisted Bilayer MoS2. Nano Lett. 2016;16(2):1435-44doi: 10.1021/acs.nanolett.5b05015.
Huang, S., Liang, L., Ling, X., Puretzky, A. A., Geohegan, D. B., Sumpter, B. G., Kong, J., Meunier, V., & Dresselhaus, M. S. (2016). Low-Frequency Interlayer Raman Modes to Probe Interface of Twisted Bilayer MoS2. Nano letters, 16(2), 1435-44. https://doi.org/10.1021/acs.nanolett.5b05015
Huang, Shengxi, et al. "Low-Frequency Interlayer Raman Modes to Probe Interface of Twisted Bilayer MoS2." Nano letters vol. 16,2 (2016): 1435-44. doi: https://doi.org/10.1021/acs.nanolett.5b05015
Huang S, Liang L, Ling X, Puretzky AA, Geohegan DB, Sumpter BG, Kong J, Meunier V, Dresselhaus MS. Low-Frequency Interlayer Raman Modes to Probe Interface of Twisted Bilayer MoS2. Nano Lett. 2016 Feb 10;16(2):1435-44. doi: 10.1021/acs.nanolett.5b05015. Epub 2016 Jan 26. PMID: 26797083.
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Nanostructure enhanced ionic transport in fullerene reinforced solid polymer electrolytes.

Physical chemistry chemical physics : PCCP

Sun CN, Zawodzinski TA, Tenhaeff WE, Ren F, Keum JK, Bi S, Li D, Ahn SK, Hong K, Rondinone AJ, Carrillo JM, Do C, Sumpter BG, Chen J.
PMID: 25733054
Phys Chem Chem Phys. 2015 Mar 28;17(12):8266-75. doi: 10.1039/c4cp05583g.

Solid polymer electrolytes, such as polyethylene oxide (PEO) based systems, have the potential to replace liquid electrolytes in secondary lithium batteries with flexible, safe, and mechanically robust designs. Previously reported PEO nanocomposite electrolytes routinely use metal oxide nanoparticles that...

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Sun CN, Zawodzinski TA, Tenhaeff WE, et al. Nanostructure enhanced ionic transport in fullerene reinforced solid polymer electrolytes. Phys Chem Chem Phys. 2015;17(12):8266-75doi: 10.1039/c4cp05583g.
Sun, C. N., Zawodzinski, T. A., Tenhaeff, W. E., Ren, F., Keum, J. K., Bi, S., Li, D., Ahn, S. K., Hong, K., Rondinone, A. J., Carrillo, J. M., Do, C., Sumpter, B. G., & Chen, J. (2015). Nanostructure enhanced ionic transport in fullerene reinforced solid polymer electrolytes. Physical chemistry chemical physics : PCCP, 17(12), 8266-75. https://doi.org/10.1039/c4cp05583g
Sun, Che-Nan, et al. "Nanostructure enhanced ionic transport in fullerene reinforced solid polymer electrolytes." Physical chemistry chemical physics : PCCP vol. 17,12 (2015): 8266-75. doi: https://doi.org/10.1039/c4cp05583g
Sun CN, Zawodzinski TA, Tenhaeff WE, Ren F, Keum JK, Bi S, Li D, Ahn SK, Hong K, Rondinone AJ, Carrillo JM, Do C, Sumpter BG, Chen J. Nanostructure enhanced ionic transport in fullerene reinforced solid polymer electrolytes. Phys Chem Chem Phys. 2015 Mar 28;17(12):8266-75. doi: 10.1039/c4cp05583g. PMID: 25733054.
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The Mechanism of Lung Volume Change during Mechanical Ventilation.

American journal of respiratory and critical care medicine

Carney DE, Bredenberg CE, Schiller HJ, Picone AL, McCann UG, Gatto LA, Bailey G, Fillinger M, Nieman GF.
PMID: 10556143
Am J Respir Crit Care Med. 1999 Nov 01;160(5):1697-1702.

To understand ventilator-induced lung injury (VILI) during positive pressure ventilation, mechanisms of normal alveolar mechanics must first be established. Isotropic "balloonlike" alveolar volume (VA) change has been viewed as the prevailing mechanism of normal lung volume (VL) changes. We...

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Carney DE, Bredenberg CE, Schiller HJ, et al. The Mechanism of Lung Volume Change during Mechanical Ventilation. Am J Respir Crit Care Med. 1999;160(5):1697-1702
Carney, D. E., Bredenberg, C. E., Schiller, H. J., Picone, A. L., McCann, U. G., Gatto, L. A., Bailey, G., Fillinger, M., & Nieman, G. F. (1999). The Mechanism of Lung Volume Change during Mechanical Ventilation. American journal of respiratory and critical care medicine, 160(5), 1697-1702.
Carney, et al. "The Mechanism of Lung Volume Change during Mechanical Ventilation." American journal of respiratory and critical care medicine vol. 160,5 (1999): 1697-1702.
Carney DE, Bredenberg CE, Schiller HJ, Picone AL, McCann UG, Gatto LA, Bailey G, Fillinger M, Nieman GF. The Mechanism of Lung Volume Change during Mechanical Ventilation. Am J Respir Crit Care Med. 1999 Nov 01;160(5):1697-1702. PMID: 10556143.
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Direct synthesis of 4-arylpiperidines via palladium/copper(I)-cocatalyzed Negishi coupling of a 4-piperidylzinc iodide with aromatic halides and triflates.

The Journal of organic chemistry

Corley EG, Conrad K, Murry JA, Savarin C, Holko J, Boice G.
PMID: 15255748
J Org Chem. 2004 Jul 23;69(15):5120-3. doi: 10.1021/jo049647i.

A general procedure for the synthesis of 4-arylpiperidines via the coupling of 4-(N-BOC-piperidyl)zinc iodide with aryl halides and triflates is presented. The reaction requires cocatalysis with both Cl(2)Pd(dppf) and a copper(I) species. An improved, safer procedure for the activation...

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Corley EG, Conrad K, Murry JA, et al. Direct synthesis of 4-arylpiperidines via palladium/copper(I)-cocatalyzed Negishi coupling of a 4-piperidylzinc iodide with aromatic halides and triflates. J Org Chem. 2004;69(15):5120-3doi: 10.1021/jo049647i.
Corley, E. G., Conrad, K., Murry, J. A., Savarin, C., Holko, J., & Boice, G. (2004). Direct synthesis of 4-arylpiperidines via palladium/copper(I)-cocatalyzed Negishi coupling of a 4-piperidylzinc iodide with aromatic halides and triflates. The Journal of organic chemistry, 69(15), 5120-3. https://doi.org/10.1021/jo049647i
Corley, Edward G, et al. "Direct synthesis of 4-arylpiperidines via palladium/copper(I)-cocatalyzed Negishi coupling of a 4-piperidylzinc iodide with aromatic halides and triflates." The Journal of organic chemistry vol. 69,15 (2004): 5120-3. doi: https://doi.org/10.1021/jo049647i
Corley EG, Conrad K, Murry JA, Savarin C, Holko J, Boice G. Direct synthesis of 4-arylpiperidines via palladium/copper(I)-cocatalyzed Negishi coupling of a 4-piperidylzinc iodide with aromatic halides and triflates. J Org Chem. 2004 Jul 23;69(15):5120-3. doi: 10.1021/jo049647i. PMID: 15255748.
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Unique chemical reactivity of a graphene nanoribbon's zigzag edge.

The Journal of chemical physics

Jiang DE, Sumpter BG, Dai S.
PMID: 17430050
J Chem Phys. 2007 Apr 07;126(13):134701. doi: 10.1063/1.2715558.

The zigzag edge of a graphene nanoribbon possesses a unique electronic state that is near the Fermi level and localized at the edge carbon atoms. The authors investigate the chemical reactivity of these zigzag edge sites by examining their...

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Jiang DE, Sumpter BG, Dai S. Unique chemical reactivity of a graphene nanoribbon's zigzag edge. J Chem Phys. 2007;126(13):134701doi: 10.1063/1.2715558.
Jiang, D. E., Sumpter, B. G., & Dai, S. (2007). Unique chemical reactivity of a graphene nanoribbon's zigzag edge. The Journal of chemical physics, 126(13), 134701. https://doi.org/10.1063/1.2715558
Jiang, De-en, et al. "Unique chemical reactivity of a graphene nanoribbon's zigzag edge." The Journal of chemical physics vol. 126,13 (2007): 134701. doi: https://doi.org/10.1063/1.2715558
Jiang DE, Sumpter BG, Dai S. Unique chemical reactivity of a graphene nanoribbon's zigzag edge. J Chem Phys. 2007 Apr 07;126(13):134701. doi: 10.1063/1.2715558. PMID: 17430050.
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Effects of growth hormone administration on skeletal muscle glutamine metabolism in severely traumatized patients: preliminary report.

Clinical nutrition (Edinburgh, Scotland)

Biolo G, Iscra F, Toigo G, Ciocchi B, Situlin R, Gullo A, Guarnieri G.
PMID: 16844576
Clin Nutr. 1997 Apr;16(2):89-91. doi: 10.1016/s0261-5614(97)80029-5.

We have investigated the effects of 24 h human recombinant growth hormone (hGH) administration on leg muscle glutamine exchange and protein kinetics in severely traumatized patients. Muscle amino acid exchange and protein balance were evaluated using the leg arteriovenous...

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Biolo G, Iscra F, Toigo G, et al. Effects of growth hormone administration on skeletal muscle glutamine metabolism in severely traumatized patients: preliminary report. Clin Nutr. 1997;16(2):89-91doi: 10.1016/s0261-5614(97)80029-5.
Biolo, G., Iscra, F., Toigo, G., Ciocchi, B., Situlin, R., Gullo, A., & Guarnieri, G. (1997). Effects of growth hormone administration on skeletal muscle glutamine metabolism in severely traumatized patients: preliminary report. Clinical nutrition (Edinburgh, Scotland), 16(2), 89-91. https://doi.org/10.1016/s0261-5614(97)80029-5
Biolo, G, et al. "Effects of growth hormone administration on skeletal muscle glutamine metabolism in severely traumatized patients: preliminary report." Clinical nutrition (Edinburgh, Scotland) vol. 16,2 (1997): 89-91. doi: https://doi.org/10.1016/s0261-5614(97)80029-5
Biolo G, Iscra F, Toigo G, Ciocchi B, Situlin R, Gullo A, Guarnieri G. Effects of growth hormone administration on skeletal muscle glutamine metabolism in severely traumatized patients: preliminary report. Clin Nutr. 1997 Apr;16(2):89-91. doi: 10.1016/s0261-5614(97)80029-5. PMID: 16844576.
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Showing 1 to 12 of 321 entries