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Computation of elementary modes: a unifying framework and the new binary approach

elementary

Gagneur J, Klamt S.
GSID: X8dqarhkQCIJ
J Gagneur, S Klamt - BMC bioinformatics, 2004 - bmcbioinformatics.biomedcentral …

… We show that computing the set of elementary modes is … algorithmic methods that compute elementary modes and allows … , which computes the elementary modes as binary patterns of …

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Gagneur, J., & Klamt, S. (2004). Computation of elementary modes: a unifying framework and the new binary approach. BMC bioinformatics, 5(1), 1-21.
Gagneur, Julien, and Steffen Klamt. "Computation of elementary modes: a unifying framework and the new binary approach." BMC bioinformatics 5.1 (2004): 1-21.
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Thalassaemia haemoglobin-E disease.

Indian pediatrics

Audi PS, Malik R, Malik TK, Kamat J.
PMID: 5532072
Indian Pediatr. 1970 Nov;7(11):628-31.

No abstract available.

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Audi PS, Malik R, Malik TK, et al. Thalassaemia haemoglobin-E disease. Indian Pediatr. 1970;7(11):628-31
Audi, P. S., Malik, R., Malik, T. K., & Kamat, J. (1970). Thalassaemia haemoglobin-E disease. Indian pediatrics, 7(11), 628-31.
Audi, P S, et al. "Thalassaemia haemoglobin-E disease." Indian pediatrics vol. 7,11 (1970): 628-31.
Audi PS, Malik R, Malik TK, Kamat J. Thalassaemia haemoglobin-E disease. Indian Pediatr. 1970 Nov;7(11):628-31. PMID: 5532072.
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Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies.

Advances and applications in bioinformatics and chemistry : AABC

Poltz R, Franke R, Schweitzer K, Klamt S, Gilles ED, Naumann M.
PMID: 21918620
Adv Appl Bioinform Chem. 2009;2:125-38. doi: 10.2147/aabc.s8211. Epub 2009 Dec 03.

Genotoxic stress is induced by a broad range of DNA-damaging agents and could lead to a variety of human diseases including cancer. DNA damage is also therapeutically induced for cancer treatment with the aim to eliminate tumor cells. However,...

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Poltz R, Franke R, Schweitzer K, et al. Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. Adv Appl Bioinform Chem. 2009;2:125-38doi: 10.2147/aabc.s8211.
Poltz, R., Franke, R., Schweitzer, K., Klamt, S., Gilles, E. D., & Naumann, M. (2009). Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. Advances and applications in bioinformatics and chemistry : AABC, 2125-38. https://doi.org/10.2147/aabc.s8211
Poltz, Rainer, et al. "Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies." Advances and applications in bioinformatics and chemistry : AABC vol. 2 (2009): 125-38. doi: https://doi.org/10.2147/aabc.s8211
Poltz R, Franke R, Schweitzer K, Klamt S, Gilles ED, Naumann M. Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. Adv Appl Bioinform Chem. 2009;2:125-38. doi: 10.2147/aabc.s8211. Epub 2009 Dec 03. PMID: 21918620; PMCID: PMC3169943.
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Genetic analyses of bone morphogenetic protein 2, 4 and 7 in congenital combined pituitary hormone deficiency.

BMC endocrine disorders

Breitfeld J, Martens S, Klammt J, Schlicke M, Pfäffle R, Krause K, Weidle K, Schleinitz D, Stumvoll M, Führer D, Kovacs P, Tönjes A.
PMID: 24289245
BMC Endocr Disord. 2013 Dec 01;13:56. doi: 10.1186/1472-6823-13-56.

BACKGROUND: The complex process of development of the pituitary gland is regulated by a number of signalling molecules and transcription factors. Mutations in these factors have been identified in rare cases of congenital hypopituitarism but for most subjects with...

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Breitfeld J, Martens S, Klammt J, et al. Genetic analyses of bone morphogenetic protein 2, 4 and 7 in congenital combined pituitary hormone deficiency. BMC Endocr Disord. 2013;13:56doi: 10.1186/1472-6823-13-56.
Breitfeld, J., Martens, S., Klammt, J., Schlicke, M., Pfäffle, R., Krause, K., Weidle, K., Schleinitz, D., Stumvoll, M., Führer, D., Kovacs, P., & Tönjes, A. (2013). Genetic analyses of bone morphogenetic protein 2, 4 and 7 in congenital combined pituitary hormone deficiency. BMC endocrine disorders, 1356. https://doi.org/10.1186/1472-6823-13-56
Breitfeld, Jana, et al. "Genetic analyses of bone morphogenetic protein 2, 4 and 7 in congenital combined pituitary hormone deficiency." BMC endocrine disorders vol. 13 (2013): 56. doi: https://doi.org/10.1186/1472-6823-13-56
Breitfeld J, Martens S, Klammt J, Schlicke M, Pfäffle R, Krause K, Weidle K, Schleinitz D, Stumvoll M, Führer D, Kovacs P, Tönjes A. Genetic analyses of bone morphogenetic protein 2, 4 and 7 in congenital combined pituitary hormone deficiency. BMC Endocr Disord. 2013 Dec 01;13:56. doi: 10.1186/1472-6823-13-56. PMID: 24289245; PMCID: PMC4175098.
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COSMO-RSC: Second-Order Quasi-Chemical Theory Recovering Local Surface Correlation Effects.

The journal of physical chemistry. A

Klamt A.
PMID: 26963690
J Phys Chem A. 2016 Mar 31;120(12):2049-56. doi: 10.1021/acs.jpca.6b00757. Epub 2016 Mar 18.

The conductor-like screening model for realistic solvation (COSMO-RS) was introduced 20 years ago and meanwhile has become an important tool for the prediction of fluid phase equilibrium properties. Starting from quantum chemical information about the surface polarity of solutes...

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Klamt A. COSMO-RSC: Second-Order Quasi-Chemical Theory Recovering Local Surface Correlation Effects. J Phys Chem A. 2016;120(12):2049-56doi: 10.1021/acs.jpca.6b00757.
Klamt, A. (2016). COSMO-RSC: Second-Order Quasi-Chemical Theory Recovering Local Surface Correlation Effects. The journal of physical chemistry. A, 120(12), 2049-56. https://doi.org/10.1021/acs.jpca.6b00757
Klamt, A. "COSMO-RSC: Second-Order Quasi-Chemical Theory Recovering Local Surface Correlation Effects." The journal of physical chemistry. A vol. 120,12 (2016): 2049-56. doi: https://doi.org/10.1021/acs.jpca.6b00757
Klamt A. COSMO-RSC: Second-Order Quasi-Chemical Theory Recovering Local Surface Correlation Effects. J Phys Chem A. 2016 Mar 31;120(12):2049-56. doi: 10.1021/acs.jpca.6b00757. Epub 2016 Mar 18. PMID: 26963690.
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First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale.

The journal of physical chemistry. A

Klamt A, Eckert F, Diedenhofen M, Beck ME.
PMID: 26313337
J Phys Chem A. 2003 Nov 06;107(44):9380-6. doi: 10.1021/jp034688o.

The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a statistical thermodynamics treatment for more realistic solvation (RS) simulations, has been used for the direct prediction of pKa constants of a large variety...

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Klamt A, Eckert F, Diedenhofen M, et al. First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale. J Phys Chem A. 2003;107(44):9380-6doi: 10.1021/jp034688o.
Klamt, A., Eckert, F., Diedenhofen, M., & Beck, M. E. (2003). First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale. The journal of physical chemistry. A, 107(44), 9380-6. https://doi.org/10.1021/jp034688o
Klamt, Andreas, et al. "First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale." The journal of physical chemistry. A vol. 107,44 (2003): 9380-6. doi: https://doi.org/10.1021/jp034688o
Klamt A, Eckert F, Diedenhofen M, Beck ME. First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale. J Phys Chem A. 2003 Nov 06;107(44):9380-6. doi: 10.1021/jp034688o. PMID: 26313337.
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Cryoglobulinemic membranoproliferative glomerulonephritis associated with mucosa-associated lymphoid tissue lymphoma treated with rituximab.

Clinical nephrology. Case studies

Ha AY, Noronha N, Gleason P, Winkler JN, Butera JN, Henriksen KJ, Hu SL.
PMID: 29043134
Clin Nephrol Case Stud. 2016 Jan 19;4:1-4. doi: 10.5414/CNCS108740. eCollection 2016.

Cryoglobulinemia and mucosa-associated lymphoid tissue (MALT) lymphoma are diseases characterized by B-cell dysregulation and overproduction of antibodies. Vasculitis and cutaneous manifestations are common, but renal involvement is rare. A 65-year-old woman with type 1 cryoglobulinemia and MALT lymphomas of...

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Ha AY, Noronha N, Gleason P, et al. Cryoglobulinemic membranoproliferative glomerulonephritis associated with mucosa-associated lymphoid tissue lymphoma treated with rituximab. Clin Nephrol Case Stud. 2016;4:1-4doi: 10.5414/CNCS108740.
Ha, A. Y., Noronha, N., Gleason, P., Winkler, J. N., Butera, J. N., Henriksen, K. J., & Hu, S. L. (2016). Cryoglobulinemic membranoproliferative glomerulonephritis associated with mucosa-associated lymphoid tissue lymphoma treated with rituximab. Clinical nephrology. Case studies, 41-4. https://doi.org/10.5414/CNCS108740
Ha, Austin Y, et al. "Cryoglobulinemic membranoproliferative glomerulonephritis associated with mucosa-associated lymphoid tissue lymphoma treated with rituximab." Clinical nephrology. Case studies vol. 4 (2016): 1-4. doi: https://doi.org/10.5414/CNCS108740
Ha AY, Noronha N, Gleason P, Winkler JN, Butera JN, Henriksen KJ, Hu SL. Cryoglobulinemic membranoproliferative glomerulonephritis associated with mucosa-associated lymphoid tissue lymphoma treated with rituximab. Clin Nephrol Case Stud. 2016 Jan 19;4:1-4. doi: 10.5414/CNCS108740. eCollection 2016. PMID: 29043134; PMCID: PMC5437996.
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Interpretation of experimental hydrogen-bond enthalpies and entropies from COSMO polarisation charge densities.

Physical chemistry chemical physics : PCCP

Klamt A, Reinisch J, Eckert F, Graton J, Le Questel JY.
PMID: 23552689
Phys Chem Chem Phys. 2013 May 21;15(19):7147-54. doi: 10.1039/c3cp44611e.

In this work, experimental hydrogen-bond (HB) enthalpies measured in previous works for a wide range of acceptor molecules in dilute mixtures of 4-fluorophenol in non-polar solvents are quantified from COSMO polarisation charge densities σ of HB acceptors (HBA). As...

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Klamt A, Reinisch J, Eckert F, et al. Interpretation of experimental hydrogen-bond enthalpies and entropies from COSMO polarisation charge densities. Phys Chem Chem Phys. 2013;15(19):7147-54doi: 10.1039/c3cp44611e.
Klamt, A., Reinisch, J., Eckert, F., Graton, J., & Le Questel, J. Y. (2013). Interpretation of experimental hydrogen-bond enthalpies and entropies from COSMO polarisation charge densities. Physical chemistry chemical physics : PCCP, 15(19), 7147-54. https://doi.org/10.1039/c3cp44611e
Klamt, Andreas, et al. "Interpretation of experimental hydrogen-bond enthalpies and entropies from COSMO polarisation charge densities." Physical chemistry chemical physics : PCCP vol. 15,19 (2013): 7147-54. doi: https://doi.org/10.1039/c3cp44611e
Klamt A, Reinisch J, Eckert F, Graton J, Le Questel JY. Interpretation of experimental hydrogen-bond enthalpies and entropies from COSMO polarisation charge densities. Phys Chem Chem Phys. 2013 May 21;15(19):7147-54. doi: 10.1039/c3cp44611e. PMID: 23552689.
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Role of endoscopic ultrasonography in intramural bronchogenic cysts: case reports and review of the literature.

Endoscopic ultrasound

Klamt A, Di Loreto A, Valle RD, Lukashok HP, Robles-Medranda C.
PMID: 24949355
Endosc Ultrasound. 2012 Oct;1(3):162-4. doi: 10.7178/eus.03.008.

The differentiation between a solid and cystic lesion is not always easy. EUS has provided a minimally invasive approach to the diagnosis of benign mediastinal cysts. Our report describes two cases of intramural bronchogenic cysts and reviews the role...

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Klamt A, Di Loreto A, Valle RD, et al. Role of endoscopic ultrasonography in intramural bronchogenic cysts: case reports and review of the literature. Endosc Ultrasound. 2012;1(3):162-4doi: 10.7178/eus.03.008.
Klamt, A., Di Loreto, A., Valle, R. D., Lukashok, H. P., & Robles-Medranda, C. (2012). Role of endoscopic ultrasonography in intramural bronchogenic cysts: case reports and review of the literature. Endoscopic ultrasound, 1(3), 162-4. https://doi.org/10.7178/eus.03.008
Klamt, Alexandre, et al. "Role of endoscopic ultrasonography in intramural bronchogenic cysts: case reports and review of the literature." Endoscopic ultrasound vol. 1,3 (2012): 162-4. doi: https://doi.org/10.7178/eus.03.008
Klamt A, Di Loreto A, Valle RD, Lukashok HP, Robles-Medranda C. Role of endoscopic ultrasonography in intramural bronchogenic cysts: case reports and review of the literature. Endosc Ultrasound. 2012 Oct;1(3):162-4. doi: 10.7178/eus.03.008. PMID: 24949355; PMCID: PMC4062226.
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Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS.

Journal of chemical theory and computation

Renz M, Kess M, Diedenhofen M, Klamt A, Kaupp M.
PMID: 26605584
J Chem Theory Comput. 2012 Nov 13;8(11):4189-203. doi: 10.1021/ct300545x. Epub 2012 Sep 14.

A recently proposed quantum-chemical protocol for the description of the character of organic mixed-valence (MV) compounds, close from both sides to the localized/delocalized borderline, is evaluated and extended for a series of dinitroaryl radical anions 1-6. A combination of...

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Renz M, Kess M, Diedenhofen M, et al. Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS. J Chem Theory Comput. 2012;8(11):4189-203doi: 10.1021/ct300545x.
Renz, M., Kess, M., Diedenhofen, M., Klamt, A., & Kaupp, M. (2012). Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS. Journal of chemical theory and computation, 8(11), 4189-203. https://doi.org/10.1021/ct300545x
Renz, Manuel, et al. "Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS." Journal of chemical theory and computation vol. 8,11 (2012): 4189-203. doi: https://doi.org/10.1021/ct300545x
Renz M, Kess M, Diedenhofen M, Klamt A, Kaupp M. Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS. J Chem Theory Comput. 2012 Nov 13;8(11):4189-203. doi: 10.1021/ct300545x. Epub 2012 Sep 14. PMID: 26605584.
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A comparison between the two general sets of linear free energy descriptors of Abraham and Klamt.

Journal of chemical information and computer sciences

Zissimos AM, Abraham MH, Klamt A, Eckert F, Wood J.
PMID: 12444728
J Chem Inf Comput Sci. 2002 Nov-Dec;42(6):1320-31. doi: 10.1021/ci025530o.

Two sets of molecular descriptors, the five experimental Abraham, and the five COSMOments of Klamt's COSMO-RS, have been compared for a data set of 470 compounds. Both sets are considered as almost complete sets of LFER. The two sets...

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Zissimos AM, Abraham MH, Klamt A, et al. A comparison between the two general sets of linear free energy descriptors of Abraham and Klamt. J Chem Inf Comput Sci. 2002;42(6):1320-31doi: 10.1021/ci025530o.
Zissimos, A. M., Abraham, M. H., Klamt, A., Eckert, F., & Wood, J. (2002). A comparison between the two general sets of linear free energy descriptors of Abraham and Klamt. Journal of chemical information and computer sciences, 42(6), 1320-31. https://doi.org/10.1021/ci025530o
Zissimos, Andreas M, et al. "A comparison between the two general sets of linear free energy descriptors of Abraham and Klamt." Journal of chemical information and computer sciences vol. 42,6 (2002): 1320-31. doi: https://doi.org/10.1021/ci025530o
Zissimos AM, Abraham MH, Klamt A, Eckert F, Wood J. A comparison between the two general sets of linear free energy descriptors of Abraham and Klamt. J Chem Inf Comput Sci. 2002 Nov-Dec;42(6):1320-31. doi: 10.1021/ci025530o. PMID: 12444728.
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Ontogeny of alpha-amylase gene expression in sea bass larvae (Lates calcarifer).

Marine biotechnology (New York, N.Y.)

Ma P, Sivaloganathan B, Reddy PK, Chan WK, Lam TJ.
PMID: 14961339
Mar Biotechnol (NY). 2001 Sep;3(5):463-9. doi: 10.1007/s10126-001-0018-1.

The enzymatic activities of alpha-amylase and its corresponding messenger RNA levels in developing sea bass (Lates calcarifer) larvae were studied from hatching until 27 days post hatching (dph). An increasing activity of amylase enzyme was measured until 5 dph,...

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Ma P, Sivaloganathan B, Reddy PK, et al. Ontogeny of alpha-amylase gene expression in sea bass larvae (Lates calcarifer). Mar Biotechnol (NY). 2001;3(5):463-9doi: 10.1007/s10126-001-0018-1.
Ma, P., Sivaloganathan, B., Reddy, P. K., Chan, W. K., & Lam, T. J. (2001). Ontogeny of alpha-amylase gene expression in sea bass larvae (Lates calcarifer). Marine biotechnology (New York, N.Y.), 3(5), 463-9. https://doi.org/10.1007/s10126-001-0018-1
Ma, P, et al. "Ontogeny of alpha-amylase gene expression in sea bass larvae (Lates calcarifer)." Marine biotechnology (New York, N.Y.) vol. 3,5 (2001): 463-9. doi: https://doi.org/10.1007/s10126-001-0018-1
Ma P, Sivaloganathan B, Reddy PK, Chan WK, Lam TJ. Ontogeny of alpha-amylase gene expression in sea bass larvae (Lates calcarifer). Mar Biotechnol (NY). 2001 Sep;3(5):463-9. doi: 10.1007/s10126-001-0018-1. PMID: 14961339.
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Showing 1 to 12 of 204 entries