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Standardizing global gene expression analysis between laboratories and across platforms.

Nature methods

Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H.
PMID: 15846362
Nat Methods. 2005 May;2(5):351-6. doi: 10.1038/nmeth754. Epub 2005 Apr 21.

To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories,...

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Bammler T, Beyer RP, Bhattacharya S, et al. Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods. 2005;2(5):351-6doi: 10.1038/nmeth754.
Bammler, T., Beyer, R. P., Bhattacharya, S., Boorman, G. A., Boyles, A., Bradford, B. U., Bumgarner, R. E., Bushel, P. R., Chaturvedi, K., Choi, D., Cunningham, M. L., Deng, S., Dressman, H. K., Fannin, R. D., Farin, F. M., Freedman, J. H., Fry, R. C., Harper, A., Humble, M. C., Hurban, P., Kavanagh, T. J., Kaufmann, W. K., Kerr, K. F., Jing, L., Lapidus, J. A., Lasarev, M. R., Li, J., Li, Y. J., Lobenhofer, E. K., Lu, X., Malek, R. L., Milton, S., Nagalla, S. R., O'malley, J. P., Palmer, V. S., Pattee, P., Paules, R. S., Perou, C. M., Phillips, K., Qin, L. X., Qiu, Y., Quigley, S. D., Rodland, M., Rusyn, I., Samson, L. D., Schwartz, D. A., Shi, Y., Shin, J. L., Sieber, S. O., Slifer, S., Speer, M. C., Spencer, P. S., Sproles, D. I., Swenberg, J. A., Suk, W. A., Sullivan, R. C., Tian, R., Tennant, R. W., Todd, S. A., Tucker, C. J., Van Houten, B., Weis, B. K., Xuan, S., Zarbl, H. (2005). Standardizing global gene expression analysis between laboratories and across platforms. Nature methods, 2(5), 351-6. https://doi.org/10.1038/nmeth754
Bammler, Theodore, et al. "Standardizing global gene expression analysis between laboratories and across platforms." Nature methods vol. 2,5 (2005): 351-6. doi: https://doi.org/10.1038/nmeth754
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H. Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods. 2005 May;2(5):351-6. doi: 10.1038/nmeth754. Epub 2005 Apr 21. PMID: 15846362.
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A belt-shaped, blue luminescent, and semiconducting covalent organic framework.

Angewandte Chemie (International ed. in English)

Wan S, Guo J, Kim J, Ihee H, Jiang D.
PMID: 18830952
Angew Chem Int Ed Engl. 2008;47(46):8826-30. doi: 10.1002/anie.200803826.

No abstract available.

Cite
Wan S, Guo J, Kim J, et al. A belt-shaped, blue luminescent, and semiconducting covalent organic framework. Angew Chem Int Ed Engl. 2008;47(46):8826-30doi: 10.1002/anie.200803826.
Wan, S., Guo, J., Kim, J., Ihee, H., & Jiang, D. (2008). A belt-shaped, blue luminescent, and semiconducting covalent organic framework. Angewandte Chemie (International ed. in English), 47(46), 8826-30. https://doi.org/10.1002/anie.200803826
Wan, Shun, et al. "A belt-shaped, blue luminescent, and semiconducting covalent organic framework." Angewandte Chemie (International ed. in English) vol. 47,46 (2008): 8826-30. doi: https://doi.org/10.1002/anie.200803826
Wan S, Guo J, Kim J, Ihee H, Jiang D. A belt-shaped, blue luminescent, and semiconducting covalent organic framework. Angew Chem Int Ed Engl. 2008;47(46):8826-30. doi: 10.1002/anie.200803826. PMID: 18830952.
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A Novel Method for Continuous Determination of the Intracellular pH in Bacteria with the Internally Conjugated Fluorescent Probe 5 (and 6-)-Carboxyfluorescein Succinimidyl Ester.

Applied and environmental microbiology

Breeuwer P, Drocourt J, Rombouts FM, Abee T.
PMID: 16535209
Appl Environ Microbiol. 1996 Jan;62(1):178-83. doi: 10.1128/aem.62.1.178-183.1996.

A novel method based on the intracellular conjugation of the fluorescent probe 5 (and 6-)-carboxyfluorescein succinimidyl ester (cFSE) was developed to determine the intracellular pH of bacteria. cFSE can be taken up by bacteria in the form of its...

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Breeuwer P, Drocourt J, Rombouts FM, et al. A Novel Method for Continuous Determination of the Intracellular pH in Bacteria with the Internally Conjugated Fluorescent Probe 5 (and 6-)-Carboxyfluorescein Succinimidyl Ester. Appl Environ Microbiol. 1996;62(1):178-83doi: 10.1128/aem.62.1.178-183.1996.
Breeuwer, P., Drocourt, J., Rombouts, F. M., & Abee, T. (1996). A Novel Method for Continuous Determination of the Intracellular pH in Bacteria with the Internally Conjugated Fluorescent Probe 5 (and 6-)-Carboxyfluorescein Succinimidyl Ester. Applied and environmental microbiology, 62(1), 178-83. https://doi.org/10.1128/aem.62.1.178-183.1996
Breeuwer, P, et al. "A Novel Method for Continuous Determination of the Intracellular pH in Bacteria with the Internally Conjugated Fluorescent Probe 5 (and 6-)-Carboxyfluorescein Succinimidyl Ester." Applied and environmental microbiology vol. 62,1 (1996): 178-83. doi: https://doi.org/10.1128/aem.62.1.178-183.1996
Breeuwer P, Drocourt J, Rombouts FM, Abee T. A Novel Method for Continuous Determination of the Intracellular pH in Bacteria with the Internally Conjugated Fluorescent Probe 5 (and 6-)-Carboxyfluorescein Succinimidyl Ester. Appl Environ Microbiol. 1996 Jan;62(1):178-83. doi: 10.1128/aem.62.1.178-183.1996. PMID: 16535209; PMCID: PMC1388751.
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Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects.

Acta crystallographica. Section A, Foundations of crystallography

Kim J, Kim KH, Lee JH, Ihee H.
PMID: 20164650
Acta Crystallogr A. 2010 Mar;66:270-80. doi: 10.1107/S0108767309052052. Epub 2010 Feb 18.

In recent years, the time-resolved X-ray diffraction technique has been established as an excellent tool for studying reaction dynamics and protein structural transitions with the aid of 100 ps X-ray pulses generated from third-generation synchrotrons. The forthcoming advent of...

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Kim J, Kim KH, Lee JH, et al. Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects. Acta Crystallogr A. 2010;66:270-80doi: 10.1107/S0108767309052052.
Kim, J., Kim, K. H., Lee, J. H., & Ihee, H. (2010). Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects. Acta crystallographica. Section A, Foundations of crystallography, 66270-80. https://doi.org/10.1107/S0108767309052052
Kim, Jeongho, et al. "Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects." Acta crystallographica. Section A, Foundations of crystallography vol. 66 (2010): 270-80. doi: https://doi.org/10.1107/S0108767309052052
Kim J, Kim KH, Lee JH, Ihee H. Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects. Acta Crystallogr A. 2010 Mar;66:270-80. doi: 10.1107/S0108767309052052. Epub 2010 Feb 18. PMID: 20164650.
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Density functional and ab initio investigation of CF2ICF2I and CF2CF2I radicals in gas and solution phases.

The journal of physical chemistry. A

Kim J, Jun S, Kim J, Ihee H.
PMID: 19731954
J Phys Chem A. 2009 Oct 15;113(41):11059-66. doi: 10.1021/jp906756u.

Quantum chemical calculations of CF(2)ICF(2)I and (*)CF(2)CF(2)I, model systems in reaction dynamics, in the gas phase and methanol solvent are performed using the density functional theory (DFT) and multiconfigurational ab initio methods. Molecular geometries, vibrational frequencies, and vertical excitation...

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Kim J, Jun S, Kim J, et al. Density functional and ab initio investigation of CF2ICF2I and CF2CF2I radicals in gas and solution phases. J Phys Chem A. 2009;113(41):11059-66doi: 10.1021/jp906756u.
Kim, J., Jun, S., Kim, J., & Ihee, H. (2009). Density functional and ab initio investigation of CF2ICF2I and CF2CF2I radicals in gas and solution phases. The journal of physical chemistry. A, 113(41), 11059-66. https://doi.org/10.1021/jp906756u
Kim, Joonghan, et al. "Density functional and ab initio investigation of CF2ICF2I and CF2CF2I radicals in gas and solution phases." The journal of physical chemistry. A vol. 113,41 (2009): 11059-66. doi: https://doi.org/10.1021/jp906756u
Kim J, Jun S, Kim J, Ihee H. Density functional and ab initio investigation of CF2ICF2I and CF2CF2I radicals in gas and solution phases. J Phys Chem A. 2009 Oct 15;113(41):11059-66. doi: 10.1021/jp906756u. PMID: 19731954.
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International science careers survey: staying a step ahead.

New biotechnology

Rindoks A, Daniłowicz E.
PMID: 18775523
N Biotechnol. 2008 Oct-Dec;25(2):125. doi: 10.1016/j.nbt.2008.08.008. Epub 2008 Aug 27.

No abstract available.

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Rindoks A, Daniłowicz E. International science careers survey: staying a step ahead. N Biotechnol. 2008;25(2):125doi: 10.1016/j.nbt.2008.08.008.
Rindoks, A., & Daniłowicz, E. (2008). International science careers survey: staying a step ahead. New biotechnology, 25(2), 125. https://doi.org/10.1016/j.nbt.2008.08.008
Rindoks, Aimee, and Daniłowicz, Emilia. "International science careers survey: staying a step ahead." New biotechnology vol. 25,2 (2008): 125. doi: https://doi.org/10.1016/j.nbt.2008.08.008
Rindoks A, Daniłowicz E. International science careers survey: staying a step ahead. N Biotechnol. 2008 Oct-Dec;25(2):125. doi: 10.1016/j.nbt.2008.08.008. Epub 2008 Aug 27. PMID: 18775523.
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Theoretical study on the reaction of Ti+ with acetone and the role of intersystem crossing.

The journal of physical chemistry. A

Kim J, Kim TK, Ihee H.
PMID: 19785445
J Phys Chem A. 2009 Oct 22;113(42):11382-9. doi: 10.1021/jp905158j.

Ti(+) is known to react with acetone (CH(3)COCH(3)) to produce TiO(+) and CH(2)CHCH(3) as products, but the detailed reaction mechanism and the most favorable reaction pathway have not yet been elucidated. Here, we investigate the doublet and quartet potential-energy...

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Kim J, Kim TK, Ihee H. Theoretical study on the reaction of Ti+ with acetone and the role of intersystem crossing. J Phys Chem A. 2009;113(42):11382-9doi: 10.1021/jp905158j.
Kim, J., Kim, T. K., & Ihee, H. (2009). Theoretical study on the reaction of Ti+ with acetone and the role of intersystem crossing. The journal of physical chemistry. A, 113(42), 11382-9. https://doi.org/10.1021/jp905158j
Kim, Joonghan, et al. "Theoretical study on the reaction of Ti+ with acetone and the role of intersystem crossing." The journal of physical chemistry. A vol. 113,42 (2009): 11382-9. doi: https://doi.org/10.1021/jp905158j
Kim J, Kim TK, Ihee H. Theoretical study on the reaction of Ti+ with acetone and the role of intersystem crossing. J Phys Chem A. 2009 Oct 22;113(42):11382-9. doi: 10.1021/jp905158j. PMID: 19785445.
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Spatiotemporal kinetics in solution studied by time-resolved X-ray liquidography (solution scattering).

Chemphyschem : a European journal of chemical physics and physical chemistry

Kim TK, Lee JH, Wulff M, Kong Q, Ihee H.
PMID: 19585639
Chemphyschem. 2009 Aug 24;10(12):1958-80. doi: 10.1002/cphc.200900154.

Information about temporally varying molecular structure during chemical processes is crucial for understanding the mechanism and function of a chemical reaction. Using ultrashort optical pulses to trigger a reaction in solution and using time-resolved X-ray diffraction (scattering) to interrogate...

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Kim TK, Lee JH, Wulff M, et al. Spatiotemporal kinetics in solution studied by time-resolved X-ray liquidography (solution scattering). Chemphyschem. 2009;10(12):1958-80doi: 10.1002/cphc.200900154.
Kim, T. K., Lee, J. H., Wulff, M., Kong, Q., & Ihee, H. (2009). Spatiotemporal kinetics in solution studied by time-resolved X-ray liquidography (solution scattering). Chemphyschem : a European journal of chemical physics and physical chemistry, 10(12), 1958-80. https://doi.org/10.1002/cphc.200900154
Kim, Tae Kyu, et al. "Spatiotemporal kinetics in solution studied by time-resolved X-ray liquidography (solution scattering)." Chemphyschem : a European journal of chemical physics and physical chemistry vol. 10,12 (2009): 1958-80. doi: https://doi.org/10.1002/cphc.200900154
Kim TK, Lee JH, Wulff M, Kong Q, Ihee H. Spatiotemporal kinetics in solution studied by time-resolved X-ray liquidography (solution scattering). Chemphyschem. 2009 Aug 24;10(12):1958-80. doi: 10.1002/cphc.200900154. PMID: 19585639.
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QEEG Measures in Huntington's Disease: A Pilot Study.

PLoS currents

Hunter A, Bordelon Y, Cook I, Leuchter A.
PMID: 21037796
PLoS Curr. 2010 Oct 25;2:RRN1192. doi: 10.1371/currents.RRN1192.

Structural brain changes as measured with Magnetic Resonance Imaging (MRI) are associated with progression of Huntington's Disease (HD), a trinucleotide repeat neurodegenerative disorder. Neurophysiological measures may offer additional biomarkers of the onset and progression of brain disease. We used...

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Hunter A, Bordelon Y, Cook I, et al. QEEG Measures in Huntington's Disease: A Pilot Study. PLoS Curr. 2010;2:RRN1192doi: 10.1371/currents.RRN1192.
Hunter, A., Bordelon, Y., Cook, I., & Leuchter, A. (2010). QEEG Measures in Huntington's Disease: A Pilot Study. PLoS currents, 2RRN1192. https://doi.org/10.1371/currents.RRN1192
Hunter, Aimee, et al. "QEEG Measures in Huntington's Disease: A Pilot Study." PLoS currents vol. 2 (2010): RRN1192. doi: https://doi.org/10.1371/currents.RRN1192
Hunter A, Bordelon Y, Cook I, Leuchter A. QEEG Measures in Huntington's Disease: A Pilot Study. PLoS Curr. 2010 Oct 25;2:RRN1192. doi: 10.1371/currents.RRN1192. PMID: 21037796; PMCID: PMC2964156.
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'Pincer' pyridine dicarbene complexes of nickel and their derivatives. Unusual ring opening of a coordinated imidazol-2-ylidene.

Dalton transactions (Cambridge, England : 2003)

Pugh D, Boyle A, Danopoulos AA.
PMID: 18274690
Dalton Trans. 2008 Feb 28;(8):1087-94. doi: 10.1039/b715769j. Epub 2008 Jan 09.

The reaction of NiBr2(DME), DME = 1,2-dimethoxyethane, with the pincer pyridine dicarbene ligands (C-N-C) ( 2) and (C-NMe-C) ( 2Me), (C-N-C = 2,6-bis-[(DiPP)imidazol-2-ylidene]pyridine, C-NMe-C = 2,6-bis-[(DiPP)imidazol-2-ylidene]-3,5-dimethylpyridine, DiPP = 2,6-diisopropylphenyl) gave the square planar complexes [Ni(C-N(Me)-C)Br]Br, 3.( Br)- and 3Me.(...

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Pugh D, Boyle A, Danopoulos AA. 'Pincer' pyridine dicarbene complexes of nickel and their derivatives. Unusual ring opening of a coordinated imidazol-2-ylidene. Dalton Trans. 2008;(8):1087-94doi: 10.1039/b715769j.
Pugh, D., Boyle, A., & Danopoulos, A. A. (2008). 'Pincer' pyridine dicarbene complexes of nickel and their derivatives. Unusual ring opening of a coordinated imidazol-2-ylidene. Dalton transactions (Cambridge, England : 2003), (8), 1087-94. https://doi.org/10.1039/b715769j
Pugh, David, et al. "'Pincer' pyridine dicarbene complexes of nickel and their derivatives. Unusual ring opening of a coordinated imidazol-2-ylidene." Dalton transactions (Cambridge, England : 2003) vol. ,8 (2008): 1087-94. doi: https://doi.org/10.1039/b715769j
Pugh D, Boyle A, Danopoulos AA. 'Pincer' pyridine dicarbene complexes of nickel and their derivatives. Unusual ring opening of a coordinated imidazol-2-ylidene. Dalton Trans. 2008 Feb 28;(8):1087-94. doi: 10.1039/b715769j. Epub 2008 Jan 09. PMID: 18274690.
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Three-dimensional nanopillar-array photovoltaics on low-cost and flexible substrates.

Nature materials

Fan Z, Razavi H, Do JW, Moriwaki A, Ergen O, Chueh YL, Leu PW, Ho JC, Takahashi T, Reichertz LA, Neale S, Yu K, Wu M, Ager JW, Javey A.
PMID: 19578336
Nat Mater. 2009 Aug;8(8):648-53. doi: 10.1038/nmat2493. Epub 2009 Jul 05.

Solar energy represents one of the most abundant and yet least harvested sources of renewable energy. In recent years, tremendous progress has been made in developing photovoltaics that can be potentially mass deployed. Of particular interest to cost-effective solar...

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Fan Z, Razavi H, Do JW, et al. Three-dimensional nanopillar-array photovoltaics on low-cost and flexible substrates. Nat Mater. 2009;8(8):648-53doi: 10.1038/nmat2493.
Fan, Z., Razavi, H., Do, J. W., Moriwaki, A., Ergen, O., Chueh, Y. L., Leu, P. W., Ho, J. C., Takahashi, T., Reichertz, L. A., Neale, S., Yu, K., Wu, M., Ager, J. W., & Javey, A. (2009). Three-dimensional nanopillar-array photovoltaics on low-cost and flexible substrates. Nature materials, 8(8), 648-53. https://doi.org/10.1038/nmat2493
Fan, Zhiyong, et al. "Three-dimensional nanopillar-array photovoltaics on low-cost and flexible substrates." Nature materials vol. 8,8 (2009): 648-53. doi: https://doi.org/10.1038/nmat2493
Fan Z, Razavi H, Do JW, Moriwaki A, Ergen O, Chueh YL, Leu PW, Ho JC, Takahashi T, Reichertz LA, Neale S, Yu K, Wu M, Ager JW, Javey A. Three-dimensional nanopillar-array photovoltaics on low-cost and flexible substrates. Nat Mater. 2009 Aug;8(8):648-53. doi: 10.1038/nmat2493. Epub 2009 Jul 05. PMID: 19578336.
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5,7-Dimeth-oxy-2-(4-methoxy-phen-yl)-4H-1-benzopyran-4-one methanol solvate monohydrate.

Acta crystallographica. Section E, Structure reports online

Aree T, Sabphon C, Sawasdee P.
PMID: 21578297
Acta Crystallogr Sect E Struct Rep Online. 2009 Oct 10;65:o2693. doi: 10.1107/S1600536809040513.

In the title compound (alternatively called 4',5,7-trimethoxy-flavone methanol solvate hydrate), C(18)H(16)O(5)·CH(3)OH·H(2)O, the flavone mol-ecule is almost planar, the inter-planar angle between the planes of the benzopyran-4-one group and the attached benzene ring being 4.69 (9)°. In the crystal, the...

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Aree T, Sabphon C, Sawasdee P. 5,7-Dimeth-oxy-2-(4-methoxy-phen-yl)-4H-1-benzopyran-4-one methanol solvate monohydrate. Acta Crystallogr Sect E Struct Rep Online. 2009;65:o2693doi: 10.1107/S1600536809040513.
Aree, T., Sabphon, C., & Sawasdee, P. (2009). 5,7-Dimeth-oxy-2-(4-methoxy-phen-yl)-4H-1-benzopyran-4-one methanol solvate monohydrate. Acta crystallographica. Section E, Structure reports online, 65o2693. https://doi.org/10.1107/S1600536809040513
Aree, Thammarat, et al. "5,7-Dimeth-oxy-2-(4-methoxy-phen-yl)-4H-1-benzopyran-4-one methanol solvate monohydrate." Acta crystallographica. Section E, Structure reports online vol. 65 (2009): o2693. doi: https://doi.org/10.1107/S1600536809040513
Aree T, Sabphon C, Sawasdee P. 5,7-Dimeth-oxy-2-(4-methoxy-phen-yl)-4H-1-benzopyran-4-one methanol solvate monohydrate. Acta Crystallogr Sect E Struct Rep Online. 2009 Oct 10;65:o2693. doi: 10.1107/S1600536809040513. PMID: 21578297; PMCID: PMC2971445.
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