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Building a hybrid physical-statistical classifier for predicting the effect of variants related to protein-drug interactions

Build and Broaden 3.0 AND Program Evaluation

Emani P, Li B, Lou S, Xu M, Yan C.
GSID: Bcf71QpuPT8J
B Wang, C Yan, S Lou, P Emani, B Li, M Xu, X Kong… - Structure, 2019 - Elsevier

A key issue in drug design is how population variation affects drug efficacy by altering binding affinity (BA) in different individuals, an essential consideration for government regulators. Ideally, we would like to evaluate the BA perturbations of millions of...

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Wang, B., Yan, C., Lou, S., Emani, P., Li, B., Xu, M., ... & Gerstein, M. (2019). Building a hybrid physical-statistical classifier for predicting the effect of variants related to protein-drug interactions. Structure, 27(9), 1469-1481.
Wang, Bo, et al. "Building a hybrid physical-statistical classifier for predicting the effect of variants related to protein-drug interactions." Structure 27.9 (2019): 1469-1481.
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Facile preparation of oriented nanoporous silica films from solvent-free liquid-crystalline mixtures.

Chemical communications (Cambridge, England)

Mizoshita N, Tani T, Inagaki S.
PMID: 23023655
Chem Commun (Camb). 2012 Nov 11;48(87):10772-4. doi: 10.1039/c2cc36306b.

Mixtures of an amphiphilic perylene bisimide derivative and tetramethoxysilane in the absence of solvents have been found to exhibit stable columnar liquid-crystalline phases which transform into macroscopically oriented nanoporous silica films as a result of simple mechanical shearing.

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Mizoshita N, Tani T, Inagaki S. Facile preparation of oriented nanoporous silica films from solvent-free liquid-crystalline mixtures. Chem Commun (Camb). 2012;48(87):10772-4doi: 10.1039/c2cc36306b.
Mizoshita, N., Tani, T., & Inagaki, S. (2012). Facile preparation of oriented nanoporous silica films from solvent-free liquid-crystalline mixtures. Chemical communications (Cambridge, England), 48(87), 10772-4. https://doi.org/10.1039/c2cc36306b
Mizoshita, Norihiro, et al. "Facile preparation of oriented nanoporous silica films from solvent-free liquid-crystalline mixtures." Chemical communications (Cambridge, England) vol. 48,87 (2012): 10772-4. doi: https://doi.org/10.1039/c2cc36306b
Mizoshita N, Tani T, Inagaki S. Facile preparation of oriented nanoporous silica films from solvent-free liquid-crystalline mixtures. Chem Commun (Camb). 2012 Nov 11;48(87):10772-4. doi: 10.1039/c2cc36306b. PMID: 23023655.
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A Case of Metastatic Urothelial Carcinoma Treated with Pemetrexed as Third-Line Chemotherapy with Discussion and Literature Review.

Case reports in oncology

Iida K, Kawai N, Naiki T, Etani T, Ando R, Nagai T, Sugiyama Y, Naiki-Ito A, Nishio H, Okada A, Kohri K, Yasui T.
PMID: 26668577
Case Rep Oncol. 2015 Nov 01;8(3):530-5. doi: 10.1159/000442347. eCollection 2015.

Pemetrexed is an antifolate agent that is regarded as an alternative second-line chemotherapy against advanced or metastatic urothelial carcinoma (UC). However, there is limited information on pemetrexed in a third-line setting. We report a case of metastatic UC treated...

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Iida K, Kawai N, Naiki T, et al. A Case of Metastatic Urothelial Carcinoma Treated with Pemetrexed as Third-Line Chemotherapy with Discussion and Literature Review. Case Rep Oncol. 2015;8(3):530-5doi: 10.1159/000442347.
Iida, K., Kawai, N., Naiki, T., Etani, T., Ando, R., Nagai, T., Sugiyama, Y., Naiki-Ito, A., Nishio, H., Okada, A., Kohri, K., & Yasui, T. (2015). A Case of Metastatic Urothelial Carcinoma Treated with Pemetrexed as Third-Line Chemotherapy with Discussion and Literature Review. Case reports in oncology, 8(3), 530-5. https://doi.org/10.1159/000442347
Iida, Keitaro, et al. "A Case of Metastatic Urothelial Carcinoma Treated with Pemetrexed as Third-Line Chemotherapy with Discussion and Literature Review." Case reports in oncology vol. 8,3 (2015): 530-5. doi: https://doi.org/10.1159/000442347
Iida K, Kawai N, Naiki T, Etani T, Ando R, Nagai T, Sugiyama Y, Naiki-Ito A, Nishio H, Okada A, Kohri K, Yasui T. A Case of Metastatic Urothelial Carcinoma Treated with Pemetrexed as Third-Line Chemotherapy with Discussion and Literature Review. Case Rep Oncol. 2015 Nov 01;8(3):530-5. doi: 10.1159/000442347. eCollection 2015. PMID: 26668577; PMCID: PMC4677708.
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Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia.

Nature plants

Kubo K, Paape T, Hatakeyama M, Entani T, Takara A, Kajihara K, Tsukahara M, Shimizu-Inatsugi R, Shimizu KK, Takayama S.
PMID: 27246052
Nat Plants. 2015 Jan 08;1:14005. doi: 10.1038/nplants.2014.5.

Self-incompatibility (SI) systems in flowering plants distinguish self- and non-self pollen to prevent inbreeding. While other SI systems rely on the self-recognition between specific male- and female-determinants, the Solanaceae family has a non-self recognition system resulting in the detoxification...

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Kubo K, Paape T, Hatakeyama M, et al. Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia. Nat Plants. 2015;1:14005doi: 10.1038/nplants.2014.5.
Kubo, K., Paape, T., Hatakeyama, M., Entani, T., Takara, A., Kajihara, K., Tsukahara, M., Shimizu-Inatsugi, R., Shimizu, K. K., & Takayama, S. (2015). Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia. Nature plants, 114005. https://doi.org/10.1038/nplants.2014.5
Kubo, Ken-Ichi, et al. "Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia." Nature plants vol. 1 (2015): 14005. doi: https://doi.org/10.1038/nplants.2014.5
Kubo K, Paape T, Hatakeyama M, Entani T, Takara A, Kajihara K, Tsukahara M, Shimizu-Inatsugi R, Shimizu KK, Takayama S. Gene duplication and genetic exchange drive the evolution of S-RNase-based self-incompatibility in Petunia. Nat Plants. 2015 Jan 08;1:14005. doi: 10.1038/nplants.2014.5. PMID: 27246052.
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Engineering Compartmentalized Biomimetic Micro- and Nanocontainers.

ACS nano

Trantidou T, Friddin M, Elani Y, Brooks NJ, Law RV, Seddon JM, Ces O.
PMID: 28658575
ACS Nano. 2017 Jul 25;11(7):6549-6565. doi: 10.1021/acsnano.7b03245. Epub 2017 Jul 05.

Compartmentalization of biological content and function is a key architectural feature in biology, where membrane bound micro- and nanocompartments are used for performing a host of highly specialized and tightly regulated biological functions. The benefit of compartmentalization as a...

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Trantidou T, Friddin M, Elani Y, et al. Engineering Compartmentalized Biomimetic Micro- and Nanocontainers. ACS Nano. 2017;11(7):6549-6565doi: 10.1021/acsnano.7b03245.
Trantidou, T., Friddin, M., Elani, Y., Brooks, N. J., Law, R. V., Seddon, J. M., & Ces, O. (2017). Engineering Compartmentalized Biomimetic Micro- and Nanocontainers. ACS nano, 11(7), 6549-6565. https://doi.org/10.1021/acsnano.7b03245
Trantidou, Tatiana, et al. "Engineering Compartmentalized Biomimetic Micro- and Nanocontainers." ACS nano vol. 11,7 (2017): 6549-6565. doi: https://doi.org/10.1021/acsnano.7b03245
Trantidou T, Friddin M, Elani Y, Brooks NJ, Law RV, Seddon JM, Ces O. Engineering Compartmentalized Biomimetic Micro- and Nanocontainers. ACS Nano. 2017 Jul 25;11(7):6549-6565. doi: 10.1021/acsnano.7b03245. Epub 2017 Jul 05. PMID: 28658575.
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Ultrastructural Immunocytochemical Abnormalities of Peripheral Myelin Proteins in Hereditary Sensory-Motor Neuropathies: 12 cases.

Annals of the New York Academy of Sciences

Anani T, Sindou P, Richard L, Diot M, Vallat JM.
PMID: 29086953
Ann N Y Acad Sci. 1999 Oct;883(1):186-195. doi: 10.1111/j.1749-6632.1999.tb08581.x.

Hereditary sensorimotor neuropathies form a heterogeneous group of genetically determined diseases, of which Charcot-Marie-Tooth (CMT) disease is the most common. In order to establish relations between genotype and the expression of peripheral myelin proteins, we carried out a quantitative...

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Anani T, Sindou P, Richard L, et al. Ultrastructural Immunocytochemical Abnormalities of Peripheral Myelin Proteins in Hereditary Sensory-Motor Neuropathies: 12 cases. Ann N Y Acad Sci. 1999;883(1):186-195doi: 10.1111/j.1749-6632.1999.tb08581.x.
Anani, T., Sindou, P., Richard, L., Diot, M., & Vallat, J. M. (1999). Ultrastructural Immunocytochemical Abnormalities of Peripheral Myelin Proteins in Hereditary Sensory-Motor Neuropathies: 12 cases. Annals of the New York Academy of Sciences, 883(1), 186-195. https://doi.org/10.1111/j.1749-6632.1999.tb08581.x
Anani, Thierry, et al. "Ultrastructural Immunocytochemical Abnormalities of Peripheral Myelin Proteins in Hereditary Sensory-Motor Neuropathies: 12 cases." Annals of the New York Academy of Sciences vol. 883,1 (1999): 186-195. doi: https://doi.org/10.1111/j.1749-6632.1999.tb08581.x
Anani T, Sindou P, Richard L, Diot M, Vallat JM. Ultrastructural Immunocytochemical Abnormalities of Peripheral Myelin Proteins in Hereditary Sensory-Motor Neuropathies: 12 cases. Ann N Y Acad Sci. 1999 Oct;883(1):186-195. doi: 10.1111/j.1749-6632.1999.tb08581.x. PMID: 29086953.
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dc electric field effect on the anomalous exponent of the hopping conduction in the one-dimensional disorder model.

Physical review. E, Statistical, nonlinear, and soft matter physics

Egami T, Suzuki K, Watanabe K.
PMID: 24329230
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052123. doi: 10.1103/PhysRevE.88.052123. Epub 2013 Nov 19.

The dc electric field effect on the anomalous exponent of the hopping conduction in the disorder model is investigated. First, we explain the model and derive an analytical expression of the effective waiting time for the general case. We...

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Egami T, Suzuki K, Watanabe K. dc electric field effect on the anomalous exponent of the hopping conduction in the one-dimensional disorder model. Phys Rev E Stat Nonlin Soft Matter Phys. 2013;88(5):052123doi: 10.1103/PhysRevE.88.052123.
Egami, T., Suzuki, K., & Watanabe, K. (2013). dc electric field effect on the anomalous exponent of the hopping conduction in the one-dimensional disorder model. Physical review. E, Statistical, nonlinear, and soft matter physics, 88(5), 052123. https://doi.org/10.1103/PhysRevE.88.052123
Egami, Takeshi, et al. "dc electric field effect on the anomalous exponent of the hopping conduction in the one-dimensional disorder model." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 88,5 (2013): 052123. doi: https://doi.org/10.1103/PhysRevE.88.052123
Egami T, Suzuki K, Watanabe K. dc electric field effect on the anomalous exponent of the hopping conduction in the one-dimensional disorder model. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052123. doi: 10.1103/PhysRevE.88.052123. Epub 2013 Nov 19. PMID: 24329230.
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Clinical characteristics of pain originating from intra-articular structures of the knee joint in patients with medial knee osteoarthritis.

SpringerPlus

Ikeuchi M, Izumi M, Aso K, Sugimura N, Tani T.
PMID: 24386615
Springerplus. 2013 Nov 23;2:628. doi: 10.1186/2193-1801-2-628. eCollection 2013.

PURPOSE: Although disease progression of osteoarthritis has been well documented, pain pathophysiology is largely unknown. This study was designed with two purposes: 1) to characterize patients with knee pain predominantly originating from intra-articular structures and 2) to describe the...

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Ikeuchi M, Izumi M, Aso K, et al. Clinical characteristics of pain originating from intra-articular structures of the knee joint in patients with medial knee osteoarthritis. Springerplus. 2013;2:628doi: 10.1186/2193-1801-2-628.
Ikeuchi, M., Izumi, M., Aso, K., Sugimura, N., & Tani, T. (2013). Clinical characteristics of pain originating from intra-articular structures of the knee joint in patients with medial knee osteoarthritis. SpringerPlus, 2628. https://doi.org/10.1186/2193-1801-2-628
Ikeuchi, Masahiko, et al. "Clinical characteristics of pain originating from intra-articular structures of the knee joint in patients with medial knee osteoarthritis." SpringerPlus vol. 2 (2013): 628. doi: https://doi.org/10.1186/2193-1801-2-628
Ikeuchi M, Izumi M, Aso K, Sugimura N, Tani T. Clinical characteristics of pain originating from intra-articular structures of the knee joint in patients with medial knee osteoarthritis. Springerplus. 2013 Nov 23;2:628. doi: 10.1186/2193-1801-2-628. eCollection 2013. PMID: 24386615; PMCID: PMC3877413.
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Identifying the true origin of sustained monomorphic ventricular tachycardia associated with dilated-phase hypertrophic cardiomyopathy: A case of successful catheter ablation.

Journal of arrhythmia

Kawakami H, Nagai T, Fujii A, Uetani T, Nishimura K, Inoue K, Suzuki J, Satomi K, Okura T, Higaki J, Ogimoto A.
PMID: 26702325
J Arrhythm. 2015 Dec;31(6):406-9. doi: 10.1016/j.joa.2015.06.003. Epub 2015 Jul 14.

This case report describes sustained monomorphic ventricular tachycardia (VT) caused by a large epicardial scar, related to dilated-phase hypertrophic cardiomyopathy mimicking VT originating from the apical septum. VT resolved with epicardial catheter ablation. The exit of the VT circuit...

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Kawakami H, Nagai T, Fujii A, et al. Identifying the true origin of sustained monomorphic ventricular tachycardia associated with dilated-phase hypertrophic cardiomyopathy: A case of successful catheter ablation. J Arrhythm. 2015;31(6):406-9doi: 10.1016/j.joa.2015.06.003.
Kawakami, H., Nagai, T., Fujii, A., Uetani, T., Nishimura, K., Inoue, K., Suzuki, J., Satomi, K., Okura, T., Higaki, J., & Ogimoto, A. (2015). Identifying the true origin of sustained monomorphic ventricular tachycardia associated with dilated-phase hypertrophic cardiomyopathy: A case of successful catheter ablation. Journal of arrhythmia, 31(6), 406-9. https://doi.org/10.1016/j.joa.2015.06.003
Kawakami, Hiroshi, et al. "Identifying the true origin of sustained monomorphic ventricular tachycardia associated with dilated-phase hypertrophic cardiomyopathy: A case of successful catheter ablation." Journal of arrhythmia vol. 31,6 (2015): 406-9. doi: https://doi.org/10.1016/j.joa.2015.06.003
Kawakami H, Nagai T, Fujii A, Uetani T, Nishimura K, Inoue K, Suzuki J, Satomi K, Okura T, Higaki J, Ogimoto A. Identifying the true origin of sustained monomorphic ventricular tachycardia associated with dilated-phase hypertrophic cardiomyopathy: A case of successful catheter ablation. J Arrhythm. 2015 Dec;31(6):406-9. doi: 10.1016/j.joa.2015.06.003. Epub 2015 Jul 14. PMID: 26702325; PMCID: PMC4672081.
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Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model.

Physical review. E, Statistical, nonlinear, and soft matter physics

Wu B, Iwashita T, Egami T.
PMID: 26651691
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Nov;92(5):052303. doi: 10.1103/PhysRevE.92.052303. Epub 2015 Nov 04.

Liquids are condensed matter in which atoms are strongly correlated in position and momentum. The atomic pair density function (PDF) is used often in describing such correlation. However, elucidation of many properties requires higher degrees of correlation than the...

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Wu B, Iwashita T, Egami T. Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model. Phys Rev E Stat Nonlin Soft Matter Phys. 2015;92(5):052303doi: 10.1103/PhysRevE.92.052303.
Wu, B., Iwashita, T., & Egami, T. (2015). Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model. Physical review. E, Statistical, nonlinear, and soft matter physics, 92(5), 052303. https://doi.org/10.1103/PhysRevE.92.052303
Wu, Bin, et al. "Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 92,5 (2015): 052303. doi: https://doi.org/10.1103/PhysRevE.92.052303
Wu B, Iwashita T, Egami T. Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model. Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Nov;92(5):052303. doi: 10.1103/PhysRevE.92.052303. Epub 2015 Nov 04. PMID: 26651691.
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Thickness control of 3-dimensional mesoporous silica ultrathin films by wet-etching.

Nanoscale

Kobayashi M, Susuki K, Otani T, Enomoto S, Otsuji H, Kuroda Y, Wada H, Shimojima A, Homma T, Kuroda K.
PMID: 28590482
Nanoscale. 2017 Jun 22;9(24):8321-8329. doi: 10.1039/c7nr01560g.

The thickness of 3-dimensional (3D) mesoporous silica ultrathin films was controlled at a single-nanometer scale by wet-etching. A drop casting method with an aqueous etchant of ammonium fluoride was effective in etching the surfaces of films in the direction...

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Kobayashi M, Susuki K, Otani T, et al. Thickness control of 3-dimensional mesoporous silica ultrathin films by wet-etching. Nanoscale. 2017;9(24):8321-8329doi: 10.1039/c7nr01560g.
Kobayashi, M., Susuki, K., Otani, T., Enomoto, S., Otsuji, H., Kuroda, Y., Wada, H., Shimojima, A., Homma, T., & Kuroda, K. (2017). Thickness control of 3-dimensional mesoporous silica ultrathin films by wet-etching. Nanoscale, 9(24), 8321-8329. https://doi.org/10.1039/c7nr01560g
Kobayashi, Maho, et al. "Thickness control of 3-dimensional mesoporous silica ultrathin films by wet-etching." Nanoscale vol. 9,24 (2017): 8321-8329. doi: https://doi.org/10.1039/c7nr01560g
Kobayashi M, Susuki K, Otani T, Enomoto S, Otsuji H, Kuroda Y, Wada H, Shimojima A, Homma T, Kuroda K. Thickness control of 3-dimensional mesoporous silica ultrathin films by wet-etching. Nanoscale. 2017 Jun 22;9(24):8321-8329. doi: 10.1039/c7nr01560g. PMID: 28590482.
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Crossover from Localized to Cascade Relaxations in Metallic Glasses.

Physical review letters

Fan Y, Iwashita T, Egami T.
PMID: 26252694
Phys Rev Lett. 2015 Jul 24;115(4):045501. doi: 10.1103/PhysRevLett.115.045501. Epub 2015 Jul 21.

Thermally activated deformation is investigated in two metallic glass systems with different cooling histories. By probing the atomic displacements and stress changes on the potential energy landscape, two deformation modes, a localized process and cascade process, have observed. The...

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Fan Y, Iwashita T, Egami T. Crossover from Localized to Cascade Relaxations in Metallic Glasses. Phys Rev Lett. 2015;115(4):045501doi: 10.1103/PhysRevLett.115.045501.
Fan, Y., Iwashita, T., & Egami, T. (2015). Crossover from Localized to Cascade Relaxations in Metallic Glasses. Physical review letters, 115(4), 045501. https://doi.org/10.1103/PhysRevLett.115.045501
Fan, Yue, et al. "Crossover from Localized to Cascade Relaxations in Metallic Glasses." Physical review letters vol. 115,4 (2015): 045501. doi: https://doi.org/10.1103/PhysRevLett.115.045501
Fan Y, Iwashita T, Egami T. Crossover from Localized to Cascade Relaxations in Metallic Glasses. Phys Rev Lett. 2015 Jul 24;115(4):045501. doi: 10.1103/PhysRevLett.115.045501. Epub 2015 Jul 21. PMID: 26252694.
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Showing 1 to 12 of 635 entries