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Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): an integrated case-control analysis pipeline

pipeline programs

Pappas DJ, Hollenbach JA.
GSID: 217w4hCv3BUJ
DJ Pappas, W Marin, JA Hollenbach, SJ Mack - Human immunology, 2016 - Elsevier

… pipeline designed for the standardized analysis of highly-polymorphic genetic data, specifically for the HLA and KIR genetic systems. Most modern genetic analysis programs … BIGDAWG obviates the error-prone reformatting needed to traffic data between multiple programs, and …

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Pappas, D. J., Marin, W., Hollenbach, J. A., & Mack, S. J. (2016). Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): an integrated case-control analysis pipeline. Human immunology, 77(3), 283-287.
Pappas, Derek J., et al. "Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): an integrated case-control analysis pipeline." Human immunology 77.3 (2016): 283-287.
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Roof Instability: What Reportable Noninjury Roof Falls in Underground Coal Mines Can Tell Us.

Professional safety

Bajpayee TS, Pappas DM, Ellenberger JL.
PMID: 26435556
Prof Saf. 2014 Mar;59(3):57-62.

No abstract available.

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Bajpayee TS, Pappas DM, Ellenberger JL. Roof Instability: What Reportable Noninjury Roof Falls in Underground Coal Mines Can Tell Us. Prof Saf. 2014;59(3):57-62
Bajpayee, T. S., Pappas, D. M., & Ellenberger, J. L. (2014). Roof Instability: What Reportable Noninjury Roof Falls in Underground Coal Mines Can Tell Us. Professional safety, 59(3), 57-62.
Bajpayee, T S, et al. "Roof Instability: What Reportable Noninjury Roof Falls in Underground Coal Mines Can Tell Us." Professional safety vol. 59,3 (2014): 57-62.
Bajpayee TS, Pappas DM, Ellenberger JL. Roof Instability: What Reportable Noninjury Roof Falls in Underground Coal Mines Can Tell Us. Prof Saf. 2014 Mar;59(3):57-62. PMID: 26435556; PMCID: PMC4591184.
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Determination of uronic acids in isolated hemicelluloses from kenaf using diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and the curve-fitting deconvolution method.

Applied spectroscopy

Batsoulis AN, Nacos MK, Pappas CS, Tarantilis PA, Mavromoustakos T, Polissiou MG.
PMID: 17140480
Appl Spectrosc. 2004 Feb;58(2):199-202. doi: 10.1366/000370204322842931.

Hemicellulose samples were isolated from kenaf (Hibiscus cannabinus L.). Hemicellulosic fractions usually contain a variable percentage of uronic acids. The uronic acid content (expressed in polygalacturonic acid) of the isolated hemicelluloses was determined by diffuse reflectance infrared Fourier transform...

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Batsoulis AN, Nacos MK, Pappas CS, et al. Determination of uronic acids in isolated hemicelluloses from kenaf using diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and the curve-fitting deconvolution method. Appl Spectrosc. 2004;58(2):199-202doi: 10.1366/000370204322842931.
Batsoulis, A. N., Nacos, M. K., Pappas, C. S., Tarantilis, P. A., Mavromoustakos, T., & Polissiou, M. G. (2004). Determination of uronic acids in isolated hemicelluloses from kenaf using diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and the curve-fitting deconvolution method. Applied spectroscopy, 58(2), 199-202. https://doi.org/10.1366/000370204322842931
Batsoulis, A N, et al. "Determination of uronic acids in isolated hemicelluloses from kenaf using diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and the curve-fitting deconvolution method." Applied spectroscopy vol. 58,2 (2004): 199-202. doi: https://doi.org/10.1366/000370204322842931
Batsoulis AN, Nacos MK, Pappas CS, Tarantilis PA, Mavromoustakos T, Polissiou MG. Determination of uronic acids in isolated hemicelluloses from kenaf using diffuse reflectance infrared fourier transform spectroscopy (DRIFTS) and the curve-fitting deconvolution method. Appl Spectrosc. 2004 Feb;58(2):199-202. doi: 10.1366/000370204322842931. PMID: 17140480.
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Age and ethnic variations in sebaceous lipids.

Dermato-endocrinology

Pappas A, Fantasia J, Chen T.
PMID: 24194973
Dermatoendocrinol. 2013 Apr 01;5(2):319-24. doi: 10.4161/derm.25366.

This study was conducted to compare lipid components of sebum from persons from three ethnic backgrounds-Caucasian, African American and Northern Asian. Men and women with no acne in two age groups (18‒25 y and 35‒45 y) were recruited. Skin...

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Pappas A, Fantasia J, Chen T. Age and ethnic variations in sebaceous lipids. Dermatoendocrinol. 2013;5(2):319-24doi: 10.4161/derm.25366.
Pappas, A., Fantasia, J., & Chen, T. (2013). Age and ethnic variations in sebaceous lipids. Dermato-endocrinology, 5(2), 319-24. https://doi.org/10.4161/derm.25366
Pappas, Apostolos, et al. "Age and ethnic variations in sebaceous lipids." Dermato-endocrinology vol. 5,2 (2013): 319-24. doi: https://doi.org/10.4161/derm.25366
Pappas A, Fantasia J, Chen T. Age and ethnic variations in sebaceous lipids. Dermatoendocrinol. 2013 Apr 01;5(2):319-24. doi: 10.4161/derm.25366. PMID: 24194973; PMCID: PMC3772921.
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Observation of reentrant integer quantum Hall states in the lowest Landau level.

Physical review letters

Liu Y, Pappas CG, Shayegan M, Pfeiffer LN, West KW, Baldwin KW.
PMID: 22861882
Phys Rev Lett. 2012 Jul 20;109(3):036801. doi: 10.1103/PhysRevLett.109.036801. Epub 2012 Jul 17.

Measurements on very low disorder two-dimensional electrons confined to relatively wide GaAs quantum well samples with tunable density reveal a close competition between the electron liquid and solid phases near the Landau level filling factor ν=1. As the density...

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Liu Y, Pappas CG, Shayegan M, et al. Observation of reentrant integer quantum Hall states in the lowest Landau level. Phys Rev Lett. 2012;109(3):036801doi: 10.1103/PhysRevLett.109.036801.
Liu, Y., Pappas, C. G., Shayegan, M., Pfeiffer, L. N., West, K. W., & Baldwin, K. W. (2012). Observation of reentrant integer quantum Hall states in the lowest Landau level. Physical review letters, 109(3), 036801. https://doi.org/10.1103/PhysRevLett.109.036801
Liu, Yang, et al. "Observation of reentrant integer quantum Hall states in the lowest Landau level." Physical review letters vol. 109,3 (2012): 036801. doi: https://doi.org/10.1103/PhysRevLett.109.036801
Liu Y, Pappas CG, Shayegan M, Pfeiffer LN, West KW, Baldwin KW. Observation of reentrant integer quantum Hall states in the lowest Landau level. Phys Rev Lett. 2012 Jul 20;109(3):036801. doi: 10.1103/PhysRevLett.109.036801. Epub 2012 Jul 17. PMID: 22861882.
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The Nuclearity of the Active Site for Methane to Methanol Conversion in Cu-Mordenite: A Quantitative Assessment.

Journal of the American Chemical Society

Pappas DK, Martini A, Dyballa M, Kvande K, Teketel S, Lomachenko KA, Baran R, Glatzel P, Arstad B, Berlier G, Lamberti C, Bordiga S, Olsbye U, Svelle S, Beato P, Borfecchia E.
PMID: 30346154
J Am Chem Soc. 2018 Nov 14;140(45):15270-15278. doi: 10.1021/jacs.8b08071. Epub 2018 Nov 02.

The direct conversion of methane to methanol (MTM) is a reaction that has the potential to disrupt a great part of the synthesis gas-derived chemical industry. However, despite many decades of research, active enough catalysts and suitable processes for...

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Pappas DK, Martini A, Dyballa M, et al. The Nuclearity of the Active Site for Methane to Methanol Conversion in Cu-Mordenite: A Quantitative Assessment. J Am Chem Soc. 2018;140(45):15270-15278doi: 10.1021/jacs.8b08071.
Pappas, D. K., Martini, A., Dyballa, M., Kvande, K., Teketel, S., Lomachenko, K. A., Baran, R., Glatzel, P., Arstad, B., Berlier, G., Lamberti, C., Bordiga, S., Olsbye, U., Svelle, S., Beato, P., & Borfecchia, E. (2018). The Nuclearity of the Active Site for Methane to Methanol Conversion in Cu-Mordenite: A Quantitative Assessment. Journal of the American Chemical Society, 140(45), 15270-15278. https://doi.org/10.1021/jacs.8b08071
Pappas, Dimitrios K, et al. "The Nuclearity of the Active Site for Methane to Methanol Conversion in Cu-Mordenite: A Quantitative Assessment." Journal of the American Chemical Society vol. 140,45 (2018): 15270-15278. doi: https://doi.org/10.1021/jacs.8b08071
Pappas DK, Martini A, Dyballa M, Kvande K, Teketel S, Lomachenko KA, Baran R, Glatzel P, Arstad B, Berlier G, Lamberti C, Bordiga S, Olsbye U, Svelle S, Beato P, Borfecchia E. The Nuclearity of the Active Site for Methane to Methanol Conversion in Cu-Mordenite: A Quantitative Assessment. J Am Chem Soc. 2018 Nov 14;140(45):15270-15278. doi: 10.1021/jacs.8b08071. Epub 2018 Nov 02. PMID: 30346154.
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Deactivation of Zeolite Catalyst H-ZSM-5 during Conversion of Methanol to Gasoline: Operando Time- and Space-Resolved X-ray Diffraction.

The journal of physical chemistry letters

Rojo-Gama D, Mentel L, Kalantzopoulos GN, Pappas DK, Dovgaliuk I, Olsbye U, Lillerud KP, Beato P, Lundegaard LF, Wragg DS, Svelle S.
PMID: 29494162
J Phys Chem Lett. 2018 Mar 15;9(6):1324-1328. doi: 10.1021/acs.jpclett.8b00094. Epub 2018 Mar 05.

The deactivation of zeolite catalyst H-ZSM-5 by coking during the conversion of methanol to hydrocarbons was monitored by high-energy space- and time-resolved operando X-ray diffraction (XRD) . Space resolution was achieved by continuous scanning along the axial length of...

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Rojo-Gama D, Mentel L, Kalantzopoulos GN, et al. Deactivation of Zeolite Catalyst H-ZSM-5 during Conversion of Methanol to Gasoline: Operando Time- and Space-Resolved X-ray Diffraction. J Phys Chem Lett. 2018;9(6):1324-1328doi: 10.1021/acs.jpclett.8b00094.
Rojo-Gama, D., Mentel, L., Kalantzopoulos, G. N., Pappas, D. K., Dovgaliuk, I., Olsbye, U., Lillerud, K. P., Beato, P., Lundegaard, L. F., Wragg, D. S., & Svelle, S. (2018). Deactivation of Zeolite Catalyst H-ZSM-5 during Conversion of Methanol to Gasoline: Operando Time- and Space-Resolved X-ray Diffraction. The journal of physical chemistry letters, 9(6), 1324-1328. https://doi.org/10.1021/acs.jpclett.8b00094
Rojo-Gama, Daniel, et al. "Deactivation of Zeolite Catalyst H-ZSM-5 during Conversion of Methanol to Gasoline: Operando Time- and Space-Resolved X-ray Diffraction." The journal of physical chemistry letters vol. 9,6 (2018): 1324-1328. doi: https://doi.org/10.1021/acs.jpclett.8b00094
Rojo-Gama D, Mentel L, Kalantzopoulos GN, Pappas DK, Dovgaliuk I, Olsbye U, Lillerud KP, Beato P, Lundegaard LF, Wragg DS, Svelle S. Deactivation of Zeolite Catalyst H-ZSM-5 during Conversion of Methanol to Gasoline: Operando Time- and Space-Resolved X-ray Diffraction. J Phys Chem Lett. 2018 Mar 15;9(6):1324-1328. doi: 10.1021/acs.jpclett.8b00094. Epub 2018 Mar 05. PMID: 29494162.
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Avian Stress-Related Transcriptome and Selenotranscriptome: Role during Exposure to Heavy Metals and Heat Stress.

Antioxidants (Basel, Switzerland)

Seremelis I, Danezis GP, Pappas AC, Zoidis E, Fegeros K.
PMID: 31295914
Antioxidants (Basel). 2019 Jul 10;8(7). doi: 10.3390/antiox8070216.

Selenium, through incorporation into selenoproteins, is one of the key elements of the antioxidant system. Over the past few years there has been increased interest in exploring those molecular mechanisms in chicken, responsible for the development of this protection...

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Seremelis I, Danezis GP, Pappas AC, et al. Avian Stress-Related Transcriptome and Selenotranscriptome: Role during Exposure to Heavy Metals and Heat Stress. Antioxidants (Basel). 2019;8(7)doi: 10.3390/antiox8070216.
Seremelis, I., Danezis, G. P., Pappas, A. C., Zoidis, E., & Fegeros, K. (2019). Avian Stress-Related Transcriptome and Selenotranscriptome: Role during Exposure to Heavy Metals and Heat Stress. Antioxidants (Basel, Switzerland), 8(7), . https://doi.org/10.3390/antiox8070216
Seremelis, Isidoros, et al. "Avian Stress-Related Transcriptome and Selenotranscriptome: Role during Exposure to Heavy Metals and Heat Stress." Antioxidants (Basel, Switzerland) vol. 8,7 (2019). doi: https://doi.org/10.3390/antiox8070216
Seremelis I, Danezis GP, Pappas AC, Zoidis E, Fegeros K. Avian Stress-Related Transcriptome and Selenotranscriptome: Role during Exposure to Heavy Metals and Heat Stress. Antioxidants (Basel). 2019 Jul 10;8(7). doi: 10.3390/antiox8070216. PMID: 31295914; PMCID: PMC6680911.
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TNFi Cycling Versus Changing Mechanism of Action in TNFi-Experienced Patients: Result of the Corrona CERTAIN Comparative Effectiveness Study.

ACR open rheumatology

Curtis JR, Kremer JM, Reed G, John AK, Pappas DA.
PMID: 34741435
ACR Open Rheumatol. 2022 Jan;4(1):65-73. doi: 10.1002/acr2.11337. Epub 2021 Nov 05.

OBJECTIVE: Comparative effectiveness research can inform treatment decisions regarding the choice of biologics for rheumatoid arthritis (RA). The objective of this study is to compare the efficacy of tumor necrosis factor inhibitors (TNFis) and non-TNFis (nTNFis) in real-world patients...

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Curtis JR, Kremer JM, Reed G, et al. TNFi Cycling Versus Changing Mechanism of Action in TNFi-Experienced Patients: Result of the Corrona CERTAIN Comparative Effectiveness Study. ACR Open Rheumatol. 2021;4(1):65-73doi: 10.1002/acr2.11337.
Curtis, J. R., Kremer, J. M., Reed, G., John, A. K., & Pappas, D. A. (2022). TNFi Cycling Versus Changing Mechanism of Action in TNFi-Experienced Patients: Result of the Corrona CERTAIN Comparative Effectiveness Study. ACR open rheumatology, 4(1), 65-73. https://doi.org/10.1002/acr2.11337
Curtis, Jeffrey R, et al. "TNFi Cycling Versus Changing Mechanism of Action in TNFi-Experienced Patients: Result of the Corrona CERTAIN Comparative Effectiveness Study." ACR open rheumatology vol. 4,1 (2022): 65-73. doi: https://doi.org/10.1002/acr2.11337
Curtis JR, Kremer JM, Reed G, John AK, Pappas DA. TNFi Cycling Versus Changing Mechanism of Action in TNFi-Experienced Patients: Result of the Corrona CERTAIN Comparative Effectiveness Study. ACR Open Rheumatol. 2022 Jan;4(1):65-73. doi: 10.1002/acr2.11337. Epub 2021 Nov 05. PMID: 34741435.
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Rapid screening on aflatoxins' presence in .

Journal of food science and technology

Valasi L, Georgiadou M, Tarantilis PA, Yanniotis S, Pappas CS.
PMID: 33505080
J Food Sci Technol. 2021 Jan;58(1):356-365. doi: 10.1007/s13197-020-04549-5. Epub 2020 Jun 06.

Aflatoxin

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Valasi L, Georgiadou M, Tarantilis PA, et al. Rapid screening on aflatoxins' presence in . J Food Sci Technol. 2020;58(1):356-365doi: 10.1007/s13197-020-04549-5.
Valasi, L., Georgiadou, M., Tarantilis, P. A., Yanniotis, S., & Pappas, C. S. (2021). Rapid screening on aflatoxins' presence in . Journal of food science and technology, 58(1), 356-365. https://doi.org/10.1007/s13197-020-04549-5
Valasi, Lydia, et al. "Rapid screening on aflatoxins' presence in ." Journal of food science and technology vol. 58,1 (2021): 356-365. doi: https://doi.org/10.1007/s13197-020-04549-5
Valasi L, Georgiadou M, Tarantilis PA, Yanniotis S, Pappas CS. Rapid screening on aflatoxins' presence in . J Food Sci Technol. 2021 Jan;58(1):356-365. doi: 10.1007/s13197-020-04549-5. Epub 2020 Jun 06. PMID: 33505080; PMCID: PMC7813946.
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Durability of Response to Tocilizumab Therapy in Rheumatoid Arthritis: Data from the US-Based Corrona Rheumatoid Arthritis Registry.

Rheumatology and therapy

Pappas DA, Blachley T, Best JH, Zlotnick S, Reiss WG, Emeanuru K, Kremer JM.
PMID: 33630272
Rheumatol Ther. 2021 Mar;8(1):467-481. doi: 10.1007/s40744-021-00285-0. Epub 2021 Feb 25.

INTRODUCTION: Understanding the durability of response to treatment and factors associated with failure to maintain response in a real-world setting can inform treatment decisions for patients with rheumatoid arthritis (RA). The aim of this study was to analyze durability...

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Pappas DA, Blachley T, Best JH, et al. Durability of Response to Tocilizumab Therapy in Rheumatoid Arthritis: Data from the US-Based Corrona Rheumatoid Arthritis Registry. Rheumatol Ther. 2021;8(1):467-481doi: 10.1007/s40744-021-00285-0.
Pappas, D. A., Blachley, T., Best, J. H., Zlotnick, S., Reiss, W. G., Emeanuru, K., & Kremer, J. M. (2021). Durability of Response to Tocilizumab Therapy in Rheumatoid Arthritis: Data from the US-Based Corrona Rheumatoid Arthritis Registry. Rheumatology and therapy, 8(1), 467-481. https://doi.org/10.1007/s40744-021-00285-0
Pappas, Dimitrios A, et al. "Durability of Response to Tocilizumab Therapy in Rheumatoid Arthritis: Data from the US-Based Corrona Rheumatoid Arthritis Registry." Rheumatology and therapy vol. 8,1 (2021): 467-481. doi: https://doi.org/10.1007/s40744-021-00285-0
Pappas DA, Blachley T, Best JH, Zlotnick S, Reiss WG, Emeanuru K, Kremer JM. Durability of Response to Tocilizumab Therapy in Rheumatoid Arthritis: Data from the US-Based Corrona Rheumatoid Arthritis Registry. Rheumatol Ther. 2021 Mar;8(1):467-481. doi: 10.1007/s40744-021-00285-0. Epub 2021 Feb 25. PMID: 33630272; PMCID: PMC7991054.
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Factors associated with increased suicidality risk following referral for isotretinoin commencement.

Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists

Lappas AS, Edwards Suarez L, Tzanetakou V, Morton S, Schofield C, Christodoulou NG.
PMID: 34266294
Australas Psychiatry. 2021 Jul 15;10398562211029955. doi: 10.1177/10398562211029955. Epub 2021 Jul 15.

OBJECTIVE: To establish whether there is a significant change in suicidality risk following psychiatric assessment for commencement of isotretinoin and identify factors that underpin any potential risk change.METHOD: Retrospective cohort study. Suicidality risk was defined as a combination of...

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Lappas AS, Edwards Suarez L, Tzanetakou V, et al. Factors associated with increased suicidality risk following referral for isotretinoin commencement. Australas Psychiatry. 2021;10398562211029955doi: 10.1177/10398562211029955.
Lappas, A. S., Edwards Suarez, L., Tzanetakou, V., Morton, S., Schofield, C., & Christodoulou, N. G. (2021). Factors associated with increased suicidality risk following referral for isotretinoin commencement. Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists, 10398562211029955. https://doi.org/10.1177/10398562211029955
Lappas, Andreas S, et al. "Factors associated with increased suicidality risk following referral for isotretinoin commencement." Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists vol. (2021): 10398562211029955. doi: https://doi.org/10.1177/10398562211029955
Lappas AS, Edwards Suarez L, Tzanetakou V, Morton S, Schofield C, Christodoulou NG. Factors associated with increased suicidality risk following referral for isotretinoin commencement. Australas Psychiatry. 2021 Jul 15;10398562211029955. doi: 10.1177/10398562211029955. Epub 2021 Jul 15. PMID: 34266294.
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Showing 1 to 12 of 204 entries