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The LONI pipeline processing environment

pipeline programs

Toga AW.
GSID: sEZmdKggwHIJ
DE Rex, JQ Ma, AW Toga - Neuroimage, 2003 - Elsevier

… ability to link together individual executable programs, or modules, into a processing tree, or pipeline. A pipeline contains the connectivity … A pipelet is the encapsulation of a pipeline that only completes a subsection of the processing. Allowing...

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Rex, D. E., Ma, J. Q., & Toga, A. W. (2003). The LONI pipeline processing environment. Neuroimage, 19(3), 1033-1048.
Rex, David E., Jeffrey Q. Ma, and Arthur W. Toga. "The LONI pipeline processing environment." Neuroimage 19.3 (2003): 1033-1048.
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Targeting hyaluronan for the treatment of pancreatic ductal adenocarcinoma.

Acta pharmaceutica Sinica. B

Sato N, Cheng XB, Kohi S, Koga A, Hirata K.
PMID: 27006892
Acta Pharm Sin B. 2016 Mar;6(2):101-5. doi: 10.1016/j.apsb.2016.01.002. Epub 2016 Jan 21.

Progression of cancer is often associated with interactions between cancer cells and extracellular matrix (ECM) surrounding them. Increasing evidence has suggested that accumulation of hyaluronan (HA), a major component of ECM, provides a favorable microenvironment for cancer progression. Pancreatic...

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Sato N, Cheng XB, Kohi S, et al. Targeting hyaluronan for the treatment of pancreatic ductal adenocarcinoma. Acta Pharm Sin B. 2016;6(2):101-5doi: 10.1016/j.apsb.2016.01.002.
Sato, N., Cheng, X. B., Kohi, S., Koga, A., & Hirata, K. (2016). Targeting hyaluronan for the treatment of pancreatic ductal adenocarcinoma. Acta pharmaceutica Sinica. B, 6(2), 101-5. https://doi.org/10.1016/j.apsb.2016.01.002
Sato, Norihiro, et al. "Targeting hyaluronan for the treatment of pancreatic ductal adenocarcinoma." Acta pharmaceutica Sinica. B vol. 6,2 (2016): 101-5. doi: https://doi.org/10.1016/j.apsb.2016.01.002
Sato N, Cheng XB, Kohi S, Koga A, Hirata K. Targeting hyaluronan for the treatment of pancreatic ductal adenocarcinoma. Acta Pharm Sin B. 2016 Mar;6(2):101-5. doi: 10.1016/j.apsb.2016.01.002. Epub 2016 Jan 21. PMID: 27006892; PMCID: PMC4788704.
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Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient.

New microbes and new infections

Togo AH, Diop A, Dubourg G, Nguyen TT, Andrieu C, Caputo A, Couderc C, Fournier PE, Maraninchi M, Valero R, Raoult D, Million M.
PMID: 27668083
New Microbes New Infect. 2016 Aug 09;14:38-48. doi: 10.1016/j.nmni.2016.07.010. eCollection 2016 Nov.

Butyricimonas phoceensis strain AT9 (= CSUR 1981 = DSM 100664) was isolated from a stool sample from a morbidly obese French patient living in Marseille using the culturomics approach. The genome of this Gram-negative-staining, anaerobic and non-spore forming rod...

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Togo AH, Diop A, Dubourg G, et al. Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient. New Microbes New Infect. 2016;14:38-48doi: 10.1016/j.nmni.2016.07.010.
Togo, A. H., Diop, A., Dubourg, G., Nguyen, T. T., Andrieu, C., Caputo, A., Couderc, C., Fournier, P. E., Maraninchi, M., Valero, R., Raoult, D., & Million, M. (2016). Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient. New microbes and new infections, 1438-48. https://doi.org/10.1016/j.nmni.2016.07.010
Togo, A H, et al. "Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient." New microbes and new infections vol. 14 (2016): 38-48. doi: https://doi.org/10.1016/j.nmni.2016.07.010
Togo AH, Diop A, Dubourg G, Nguyen TT, Andrieu C, Caputo A, Couderc C, Fournier PE, Maraninchi M, Valero R, Raoult D, Million M. Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient. New Microbes New Infect. 2016 Aug 09;14:38-48. doi: 10.1016/j.nmni.2016.07.010. eCollection 2016 Nov. PMID: 27668083; PMCID: PMC5024336.
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'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery.

New microbes and new infections

Togo AH, Khelaifia S, Bittar F, Maraninchi M, Raoult D, Million M.
PMID: 27358742
New Microbes New Infect. 2016 Jun 02;13:15-6. doi: 10.1016/j.nmni.2016.05.015. eCollection 2016 Sep.

We report the principal characteristics of 'Eisenbergiella massiliensis' sp. nov. strain AT11 (CSURP = P2120, DSM = 101499) that was isolated from a stool sample collected after bariatric surgery of a 56-year-old obese French woman.

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Togo AH, Khelaifia S, Bittar F, et al. 'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery. New Microbes New Infect. 2016;13:15-6doi: 10.1016/j.nmni.2016.05.015.
Togo, A. H., Khelaifia, S., Bittar, F., Maraninchi, M., Raoult, D., & Million, M. (2016). 'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery. New microbes and new infections, 1315-6. https://doi.org/10.1016/j.nmni.2016.05.015
Togo, A H, et al. "'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery." New microbes and new infections vol. 13 (2016): 15-6. doi: https://doi.org/10.1016/j.nmni.2016.05.015
Togo AH, Khelaifia S, Bittar F, Maraninchi M, Raoult D, Million M. 'Eisenbergiella massiliensis', a new species isolated from human stool collected after bariatric surgery. New Microbes New Infect. 2016 Jun 02;13:15-6. doi: 10.1016/j.nmni.2016.05.015. eCollection 2016 Sep. PMID: 27358742; PMCID: PMC4917486.
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Fusion of .

Zoological letters

Inoue Y, Kumagai M, Zhang X, Saga T, Wang D, Koga A, Takeda H.
PMID: 29484202
Zoological Lett. 2018 Feb 21;4:6. doi: 10.1186/s40851-018-0089-8. eCollection 2018.

BACKGROUND: Endogenous viral elements play important roles in eukaryotic evolution by giving rise to genetic novelties. Herpesviruses are a large family of DNA viruses, most of which do not have the ability to endogenize into host genomes. Recently, we...

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Inoue Y, Kumagai M, Zhang X, et al. Fusion of . Zoological Lett. 2018;4:6doi: 10.1186/s40851-018-0089-8.
Inoue, Y., Kumagai, M., Zhang, X., Saga, T., Wang, D., Koga, A., & Takeda, H. (2018). Fusion of . Zoological letters, 46. https://doi.org/10.1186/s40851-018-0089-8
Inoue, Yusuke, et al. "Fusion of ." Zoological letters vol. 4 (2018): 6. doi: https://doi.org/10.1186/s40851-018-0089-8
Inoue Y, Kumagai M, Zhang X, Saga T, Wang D, Koga A, Takeda H. Fusion of . Zoological Lett. 2018 Feb 21;4:6. doi: 10.1186/s40851-018-0089-8. eCollection 2018. PMID: 29484202; PMCID: PMC5822658.
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Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints.

Journal of scientific computing

Lin T, Guyader CL, Dinov I, Thompson P, Toga A, Vese L.
PMID: 24273381
J Sci Comput. 2012 Mar;50(3). doi: 10.1007/s10915-011-9563-6.

This paper proposes a numerical algorithm for image registration using energy minimization and nonlinear elasticity regularization. Application to the registration of gene expression data to a neuroanatomical mouse atlas in two dimensions is shown. We apply a nonlinear elasticity...

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Lin T, Guyader CL, Dinov I, et al. Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints. J Sci Comput. 2012;50(3)doi: 10.1007/s10915-011-9563-6.
Lin, T., Guyader, C. L., Dinov, I., Thompson, P., Toga, A., & Vese, L. (2012). Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints. Journal of scientific computing, 50(3), . https://doi.org/10.1007/s10915-011-9563-6
Lin, Tungyou, et al. "Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints." Journal of scientific computing vol. 50,3 (2012). doi: https://doi.org/10.1007/s10915-011-9563-6
Lin T, Guyader CL, Dinov I, Thompson P, Toga A, Vese L. Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints. J Sci Comput. 2012 Mar;50(3). doi: 10.1007/s10915-011-9563-6. PMID: 24273381; PMCID: PMC3838306.
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Case Report: Severe acute respiratory distress by tracheal obstruction due to a congenital thyroid teratoma.

F1000Research

Colleti Junior J, Tannuri U, Monti Lora F, Armelin Benites EC, Koga W, Honda Imamura J, Rute Moutinho P, Brunow de Carvalho W.
PMID: 26664704
F1000Res. 2015 Jun 22;4:159. doi: 10.12688/f1000research.6589.2. eCollection 2015.

Congenital teratoma is a rare condition and is a germ cell tumor composed of elements from one or more of the embryonic germ layers and contain tissues usually foreign to the anatomic site of origin. We report a case...

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Colleti Junior J, Tannuri U, Monti Lora F, et al. Case Report: Severe acute respiratory distress by tracheal obstruction due to a congenital thyroid teratoma. F1000Res. 2015;4:159doi: 10.12688/f1000research.6589.2.
Colleti Junior, J., Tannuri, U., Monti Lora, F., Armelin Benites, E. C., Koga, W., Honda Imamura, J., Rute Moutinho, P., & Brunow de Carvalho, W. (2015). Case Report: Severe acute respiratory distress by tracheal obstruction due to a congenital thyroid teratoma. F1000Research, 4159. https://doi.org/10.12688/f1000research.6589.2
Colleti Junior, Jose, et al. "Case Report: Severe acute respiratory distress by tracheal obstruction due to a congenital thyroid teratoma." F1000Research vol. 4 (2015): 159. doi: https://doi.org/10.12688/f1000research.6589.2
Colleti Junior J, Tannuri U, Monti Lora F, Armelin Benites EC, Koga W, Honda Imamura J, Rute Moutinho P, Brunow de Carvalho W. Case Report: Severe acute respiratory distress by tracheal obstruction due to a congenital thyroid teratoma. F1000Res. 2015 Jun 22;4:159. doi: 10.12688/f1000research.6589.2. eCollection 2015. PMID: 26664704; PMCID: PMC4654446.
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Lobular carcinoma of the breast with gastrointestinal metastasis.

Proceedings (Baylor University. Medical Center)

Jones C, Tong AW, Mir M, Coyle Y.
PMID: 25552798
Proc (Bayl Univ Med Cent). 2015 Jan;28(1):50-3. doi: 10.1080/08998280.2015.11929185.

We present the case of a 74-year-old woman with metastatic lobular carcinoma with an occult breast primary presenting as a suspected ampullary tumor due to its ampullary metastasis. The patient's clinical presentation is of interest in two aspects. First,...

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Jones C, Tong AW, Mir M, et al. Lobular carcinoma of the breast with gastrointestinal metastasis. Proc (Bayl Univ Med Cent). 2015;28(1):50-3doi: 10.1080/08998280.2015.11929185.
Jones, C., Tong, A. W., Mir, M., & Coyle, Y. (2015). Lobular carcinoma of the breast with gastrointestinal metastasis. Proceedings (Baylor University. Medical Center), 28(1), 50-3. https://doi.org/10.1080/08998280.2015.11929185
Jones, Catherine, et al. "Lobular carcinoma of the breast with gastrointestinal metastasis." Proceedings (Baylor University. Medical Center) vol. 28,1 (2015): 50-3. doi: https://doi.org/10.1080/08998280.2015.11929185
Jones C, Tong AW, Mir M, Coyle Y. Lobular carcinoma of the breast with gastrointestinal metastasis. Proc (Bayl Univ Med Cent). 2015 Jan;28(1):50-3. doi: 10.1080/08998280.2015.11929185. PMID: 25552798; PMCID: PMC4264710.
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DEVELOPMENT OF THE "RICH CLUB" IN BRAIN CONNECTIVITY NETWORKS FROM 438 ADOLESCENTS & ADULTS AGED 12 TO 30.

Proceedings. IEEE International Symposium on Biomedical Imaging

Dennis EL, Jahanshad N, Toga AW, McMahon KL, de Zubicaray GI, Hickie I, Wright MJ, Thompson PM.
PMID: 24827471
Proc IEEE Int Symp Biomed Imaging. 2013;624-627. doi: 10.1109/ISBI.2013.6556552.

The 'rich club' coefficient describes a phenomenon where a network's hubs (high-degree nodes) are on average more intensely interconnected than lower-degree nodes. Networks with rich clubs often have an efficient, higher-order organization, but we do not yet know how...

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Dennis EL, Jahanshad N, Toga AW, et al. DEVELOPMENT OF THE "RICH CLUB" IN BRAIN CONNECTIVITY NETWORKS FROM 438 ADOLESCENTS & ADULTS AGED 12 TO 30. Proc IEEE Int Symp Biomed Imaging. 2013;624-627doi: 10.1109/ISBI.2013.6556552.
Dennis, E. L., Jahanshad, N., Toga, A. W., McMahon, K. L., de Zubicaray, G. I., Hickie, I., Wright, M. J., & Thompson, P. M. (2013). DEVELOPMENT OF THE "RICH CLUB" IN BRAIN CONNECTIVITY NETWORKS FROM 438 ADOLESCENTS & ADULTS AGED 12 TO 30. Proceedings. IEEE International Symposium on Biomedical Imaging, 624-627. https://doi.org/10.1109/ISBI.2013.6556552
Dennis, Emily L, et al. "DEVELOPMENT OF THE "RICH CLUB" IN BRAIN CONNECTIVITY NETWORKS FROM 438 ADOLESCENTS & ADULTS AGED 12 TO 30." Proceedings. IEEE International Symposium on Biomedical Imaging vol. (2013): 624-627. doi: https://doi.org/10.1109/ISBI.2013.6556552
Dennis EL, Jahanshad N, Toga AW, McMahon KL, de Zubicaray GI, Hickie I, Wright MJ, Thompson PM. DEVELOPMENT OF THE "RICH CLUB" IN BRAIN CONNECTIVITY NETWORKS FROM 438 ADOLESCENTS & ADULTS AGED 12 TO 30. Proc IEEE Int Symp Biomed Imaging. 2013;624-627. doi: 10.1109/ISBI.2013.6556552. PMID: 24827471; PMCID: PMC4017916.
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Superconductivity without inversion symmetry: MnSi versus CePt3Si.

Physical review letters

Frigeri PA, Agterberg DF, Koga A, Sigrist M.
PMID: 15089500
Phys Rev Lett. 2004 Mar 05;92(9):097001. doi: 10.1103/PhysRevLett.92.097001. Epub 2004 Mar 03.

Superconductivity in materials without spatial inversion symmetry is studied. We show that in contrast to common belief, spin-triplet pairing is not entirely excluded in such systems. Moreover, paramagnetic limiting is analyzed for both spin-singlet and -triplet pairing. The lack...

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Frigeri PA, Agterberg DF, Koga A, et al. Superconductivity without inversion symmetry: MnSi versus CePt3Si. Phys Rev Lett. 2004;92(9):097001doi: 10.1103/PhysRevLett.92.097001.
Frigeri, P. A., Agterberg, D. F., Koga, A., & Sigrist, M. (2004). Superconductivity without inversion symmetry: MnSi versus CePt3Si. Physical review letters, 92(9), 097001. https://doi.org/10.1103/PhysRevLett.92.097001
Frigeri, P A, et al. "Superconductivity without inversion symmetry: MnSi versus CePt3Si." Physical review letters vol. 92,9 (2004): 097001. doi: https://doi.org/10.1103/PhysRevLett.92.097001
Frigeri PA, Agterberg DF, Koga A, Sigrist M. Superconductivity without inversion symmetry: MnSi versus CePt3Si. Phys Rev Lett. 2004 Mar 05;92(9):097001. doi: 10.1103/PhysRevLett.92.097001. Epub 2004 Mar 03. PMID: 15089500.
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Gene transfer and cloning of flanking chromosomal regions using the medaka fish Tol2 transposable element.

Marine biotechnology (New York, N.Y.)

Koga A, Hori H, Sakaizumi M.
PMID: 14961283
Mar Biotechnol (NY). 2002 Jan;4(1):6-11. doi: 10.1007/s10126-001-0086-2.

For the ultimate purpose of developing genetic tools using the medaka fish Tol2 transposable element, we examined whether it can transfer a marker gene into the fish genome and also be applied for cloning of chromosomal regions adjacent to...

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Koga A, Hori H, Sakaizumi M. Gene transfer and cloning of flanking chromosomal regions using the medaka fish Tol2 transposable element. Mar Biotechnol (NY). 2002;4(1):6-11doi: 10.1007/s10126-001-0086-2.
Koga, A., Hori, H., & Sakaizumi, M. (2002). Gene transfer and cloning of flanking chromosomal regions using the medaka fish Tol2 transposable element. Marine biotechnology (New York, N.Y.), 4(1), 6-11. https://doi.org/10.1007/s10126-001-0086-2
Koga, Akihiko, et al. "Gene transfer and cloning of flanking chromosomal regions using the medaka fish Tol2 transposable element." Marine biotechnology (New York, N.Y.) vol. 4,1 (2002): 6-11. doi: https://doi.org/10.1007/s10126-001-0086-2
Koga A, Hori H, Sakaizumi M. Gene transfer and cloning of flanking chromosomal regions using the medaka fish Tol2 transposable element. Mar Biotechnol (NY). 2002 Jan;4(1):6-11. doi: 10.1007/s10126-001-0086-2. PMID: 14961283.
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iTools: a framework for classification, categorization and integration of computational biology resources.

PloS one

Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW.
PMID: 18509477
PLoS One. 2008 May 28;3(5):e2265. doi: 10.1371/journal.pone.0002265.

The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion...

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Dinov ID, Rubin D, Lorensen W, et al. iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One. 2008;3(5):e2265doi: 10.1371/journal.pone.0002265.
Dinov, I. D., Rubin, D., Lorensen, W., Dugan, J., Ma, J., Murphy, S., Kirschner, B., Bug, W., Sherman, M., Floratos, A., Kennedy, D., Jagadish, H. V., Schmidt, J., Athey, B., Califano, A., Musen, M., Altman, R., Kikinis, R., Kohane, I., Delp, S., Parker, D. S., & Toga, A. W. (2008). iTools: a framework for classification, categorization and integration of computational biology resources. PloS one, 3(5), e2265. https://doi.org/10.1371/journal.pone.0002265
Dinov, Ivo D, et al. "iTools: a framework for classification, categorization and integration of computational biology resources." PloS one vol. 3,5 (2008): e2265. doi: https://doi.org/10.1371/journal.pone.0002265
Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW. iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One. 2008 May 28;3(5):e2265. doi: 10.1371/journal.pone.0002265. PMID: 18509477; PMCID: PMC2386255.
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Showing 1 to 12 of 368 entries