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MetaSanity: an integrated microbial genome evaluation and annotation pipeline

pipeline programs

Neely CJ, Graham ED, Tully BJ.
GSID: oZXu--FO4JMJ
CJ Neely, ED Graham, BJ Tully - Bioinformatics, 2020 - academic.oup.com

… MetaSanity pipeline schema. Programs and databases that are part of the MetaSanity installation are in blue boxes. Programs in the dotted orange boxes must be installed separately by the user due to licensing agreements. DB, database. (Color version...

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Neely, C. J., Graham, E. D., & Tully, B. J. (2020). MetaSanity: an integrated microbial genome evaluation and annotation pipeline. Bioinformatics, 36(15), 4341-4344.
Neely, Christopher J., Elaina D. Graham, and Benjamin J. Tully. "MetaSanity: an integrated microbial genome evaluation and annotation pipeline." Bioinformatics 36.15 (2020): 4341-4344.
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Hypoxia Inducible Factor (HIF) transcription factor family expansion, diversification, divergence and selection in eukaryotes

STEM and diversification

Graham AM, Presnell JS.
GSID: DKtD5Zkg18oJ
AM Graham, JS Presnell - PloS one, 2017 - journals.plos.org

… most likely originated in the stem lineage prior to bilaterian diversification. Four bHLH+PAS … during the whole genome duplication events in the vertebrate stem lineage (Fig 2). ARNTL …

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Graham, A. M., & Presnell, J. S. (2017). Hypoxia Inducible Factor (HIF) transcription factor family expansion, diversification, divergence and selection in eukaryotes. PloS one, 12(6), e0179545.
Graham, Allie M., and Jason S. Presnell. "Hypoxia Inducible Factor (HIF) transcription factor family expansion, diversification, divergence and selection in eukaryotes." PloS one 12.6 (2017): e0179545.
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Risks in estimating risk.

European heart journal

Graham IM, Cooney MT.
PMID: 24204012
Eur Heart J. 2014 Mar;35(9):537-9. doi: 10.1093/eurheartj/eht286. Epub 2013 Nov 07.

No abstract available.

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Graham IM, Cooney MT. Risks in estimating risk. Eur Heart J. 2013;35(9):537-9doi: 10.1093/eurheartj/eht286.
Graham, I. M., & Cooney, M. T. (2014). Risks in estimating risk. European heart journal, 35(9), 537-9. https://doi.org/10.1093/eurheartj/eht286
Graham, Ian M, and Cooney, Marie-Therese. "Risks in estimating risk." European heart journal vol. 35,9 (2014): 537-9. doi: https://doi.org/10.1093/eurheartj/eht286
Graham IM, Cooney MT. Risks in estimating risk. Eur Heart J. 2014 Mar;35(9):537-9. doi: 10.1093/eurheartj/eht286. Epub 2013 Nov 07. PMID: 24204012.
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Correction: BNIP3 Regulates AT101 [(-)-Gossypol] Induced Death in Malignant Peripheral Nerve Sheath Tumor Cells.

PloS one

Kaza N, Kohli L, Graham CD, Klocke BJ, Carroll SL, Roth KA.
PMID: 26312998
PLoS One. 2015 Aug 27;10(8):e0137153. doi: 10.1371/journal.pone.0137153. eCollection 2015.

No abstract available.

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Kaza N, Kohli L, Graham CD, et al. Correction: BNIP3 Regulates AT101 [(-)-Gossypol] Induced Death in Malignant Peripheral Nerve Sheath Tumor Cells. PLoS One. 2015;10(8):e0137153doi: 10.1371/journal.pone.0137153.
Kaza, N., Kohli, L., Graham, C. D., Klocke, B. J., Carroll, S. L., & Roth, K. A. (2015). Correction: BNIP3 Regulates AT101 [(-)-Gossypol] Induced Death in Malignant Peripheral Nerve Sheath Tumor Cells. PloS one, 10(8), e0137153. https://doi.org/10.1371/journal.pone.0137153
Kaza, Niroop, et al. "Correction: BNIP3 Regulates AT101 [(-)-Gossypol] Induced Death in Malignant Peripheral Nerve Sheath Tumor Cells." PloS one vol. 10,8 (2015): e0137153. doi: https://doi.org/10.1371/journal.pone.0137153
Kaza N, Kohli L, Graham CD, Klocke BJ, Carroll SL, Roth KA. Correction: BNIP3 Regulates AT101 [(-)-Gossypol] Induced Death in Malignant Peripheral Nerve Sheath Tumor Cells. PLoS One. 2015 Aug 27;10(8):e0137153. doi: 10.1371/journal.pone.0137153. eCollection 2015. PMID: 26312998; PMCID: PMC4552425.
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Point-of-Use Mixing of Influenza H5N1 Vaccine and MF59 Adjuvant for Pandemic Vaccination Preparedness: Antibody Responses and Safety. A Phase 1 Clinical Trial.

Open forum infectious diseases

Mulligan MJ, Bernstein DI, Frey S, Winokur P, Rouphael N, Dickey M, Edupuganti S, Spearman P, Anderson E, Graham I, Noah DL, Mangal B, Kim S, Hill H, Whitaker J, Emery W, Beck A, Stephens K, Hartwell B, Ogilvie M, Rimann N, Osinski E, Destefano E, Gajadhar T, Strudwick A, Pierce K, Lai L, Yue L, Wang D, Ying C, Cline A, Foltz T, Wagner N, Dull G, Pacatte T, Taggart B, Johnson V, Haller L, Looney C, Li S, May M, Myers B, May R, Parker L, Cochran N, Bowen D, Bell M, Scoggins J, Burns A, Stablein C, Wolff M, Jolles B, Leung B, Lambert L, Shorer S, Buchanan W, Murray S, Chang S, Gorman R.
PMID: 25734170
Open Forum Infect Dis. 2014 Nov 18;1(3):ofu102. doi: 10.1093/ofid/ofu102. eCollection 2014 Dec.

BACKGROUND: Avian influenza A/H5N1 has threatened human health for nearly 2 decades. Avian influenza A vaccine without adjuvant is poorly immunogenic. A flexible rapid tactic for mass vaccination will be needed if a pandemic occurs.METHODS: A multicenter, randomized, blinded...

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Mulligan MJ, Bernstein DI, Frey S, et al. Point-of-Use Mixing of Influenza H5N1 Vaccine and MF59 Adjuvant for Pandemic Vaccination Preparedness: Antibody Responses and Safety. A Phase 1 Clinical Trial. Open Forum Infect Dis. 2014;1(3):ofu102doi: 10.1093/ofid/ofu102.
Mulligan, M. J., Bernstein, D. I., Frey, S., Winokur, P., Rouphael, N., Dickey, M., Edupuganti, S., Spearman, P., Anderson, E., Graham, I., Noah, D. L., Mangal, B., Kim, S., Hill, H., Whitaker, J., Emery, W., Beck, A., Stephens, K., Hartwell, B., Ogilvie, M., Rimann, N., Osinski, E., Destefano, E., Gajadhar, T., Strudwick, A., Pierce, K., Lai, L., Yue, L., Wang, D., Ying, C., Cline, A., Foltz, T., Wagner, N., Dull, G., Pacatte, T., Taggart, B., Johnson, V., Haller, L., Looney, C., Li, S., May, M., Myers, B., May, R., Parker, L., Cochran, N., Bowen, D., Bell, M., Scoggins, J., Burns, A., Stablein, C., Wolff, M., Jolles, B., Leung, B., Lambert, L., Shorer, S., Buchanan, W., Murray, S., Chang, S., & Gorman, R. (2014). Point-of-Use Mixing of Influenza H5N1 Vaccine and MF59 Adjuvant for Pandemic Vaccination Preparedness: Antibody Responses and Safety. A Phase 1 Clinical Trial. Open forum infectious diseases, 1(3), ofu102. https://doi.org/10.1093/ofid/ofu102
Mulligan, Mark J, et al. "Point-of-Use Mixing of Influenza H5N1 Vaccine and MF59 Adjuvant for Pandemic Vaccination Preparedness: Antibody Responses and Safety. A Phase 1 Clinical Trial." Open forum infectious diseases vol. 1,3 (2014): ofu102. doi: https://doi.org/10.1093/ofid/ofu102
Mulligan MJ, Bernstein DI, Frey S, Winokur P, Rouphael N, Dickey M, Edupuganti S, Spearman P, Anderson E, Graham I, Noah DL, Mangal B, Kim S, Hill H, Whitaker J, Emery W, Beck A, Stephens K, Hartwell B, Ogilvie M, Rimann N, Osinski E, Destefano E, Gajadhar T, Strudwick A, Pierce K, Lai L, Yue L, Wang D, Ying C, Cline A, Foltz T, Wagner N, Dull G, Pacatte T, Taggart B, Johnson V, Haller L, Looney C, Li S, May M, Myers B, May R, Parker L, Cochran N, Bowen D, Bell M, Scoggins J, Burns A, Stablein C, Wolff M, Jolles B, Leung B, Lambert L, Shorer S, Buchanan W, Murray S, Chang S, Gorman R. Point-of-Use Mixing of Influenza H5N1 Vaccine and MF59 Adjuvant for Pandemic Vaccination Preparedness: Antibody Responses and Safety. A Phase 1 Clinical Trial. Open Forum Infect Dis. 2014 Nov 18;1(3):ofu102. doi: 10.1093/ofid/ofu102. eCollection 2014 Dec. PMID: 25734170; PMCID: PMC4324215.
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Improvement in the estimation of cardiovascular risk by carotid intima-medial thickness: A report from the Dublin Cardiohealth station study.

Preventive medicine reports

Cooney M, Cooney MT, Maher V, Khan B, Leong T, Graham I.
PMID: 26844144
Prev Med Rep. 2015 Aug 13;2:725-9. doi: 10.1016/j.pmedr.2015.08.004. eCollection 2015.

BACKGROUND: The 5th Joint Task Force European guidelines on cardiovascular disease (CVD) prevention recommend the measurement of carotid intima-media thickness (CIMT) in asymptomatic individuals at moderate risk (Class IIa). We aimed to evaluate the ability of CIMT to further...

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Cooney M, Cooney MT, Maher V, et al. Improvement in the estimation of cardiovascular risk by carotid intima-medial thickness: A report from the Dublin Cardiohealth station study. Prev Med Rep. 2015;2:725-9doi: 10.1016/j.pmedr.2015.08.004.
Cooney, M., Cooney, M. T., Maher, V., Khan, B., Leong, T., & Graham, I. (2015). Improvement in the estimation of cardiovascular risk by carotid intima-medial thickness: A report from the Dublin Cardiohealth station study. Preventive medicine reports, 2725-9. https://doi.org/10.1016/j.pmedr.2015.08.004
Cooney, Maeve, et al. "Improvement in the estimation of cardiovascular risk by carotid intima-medial thickness: A report from the Dublin Cardiohealth station study." Preventive medicine reports vol. 2 (2015): 725-9. doi: https://doi.org/10.1016/j.pmedr.2015.08.004
Cooney M, Cooney MT, Maher V, Khan B, Leong T, Graham I. Improvement in the estimation of cardiovascular risk by carotid intima-medial thickness: A report from the Dublin Cardiohealth station study. Prev Med Rep. 2015 Aug 13;2:725-9. doi: 10.1016/j.pmedr.2015.08.004. eCollection 2015. PMID: 26844144; PMCID: PMC4721475.
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A physiological comparison of three techniques for reviving sockeye salmon exposed to a severe capture stressor during upriver migration.

Conservation physiology

Raby GD, Wilson SM, Patterson DA, Hinch SG, Clark TD, Farrell AP, Cooke SJ.
PMID: 27293700
Conserv Physiol. 2015 Apr 21;3(1):cov015. doi: 10.1093/conphys/cov015. eCollection 2015.

Capture of fish in commercial and recreational fisheries causes disruption to their physiological homeostasis and can result in delayed mortality for fish that are released. For fish that are severely impaired, it may be desirable to attempt revival prior...

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Raby GD, Wilson SM, Patterson DA, et al. A physiological comparison of three techniques for reviving sockeye salmon exposed to a severe capture stressor during upriver migration. Conserv Physiol. 2015;3(1):cov015doi: 10.1093/conphys/cov015.
Raby, G. D., Wilson, S. M., Patterson, D. A., Hinch, S. G., Clark, T. D., Farrell, A. P., & Cooke, S. J. (2015). A physiological comparison of three techniques for reviving sockeye salmon exposed to a severe capture stressor during upriver migration. Conservation physiology, 3(1), cov015. https://doi.org/10.1093/conphys/cov015
Raby, Graham D, et al. "A physiological comparison of three techniques for reviving sockeye salmon exposed to a severe capture stressor during upriver migration." Conservation physiology vol. 3,1 (2015): cov015. doi: https://doi.org/10.1093/conphys/cov015
Raby GD, Wilson SM, Patterson DA, Hinch SG, Clark TD, Farrell AP, Cooke SJ. A physiological comparison of three techniques for reviving sockeye salmon exposed to a severe capture stressor during upriver migration. Conserv Physiol. 2015 Apr 21;3(1):cov015. doi: 10.1093/conphys/cov015. eCollection 2015. PMID: 27293700; PMCID: PMC4778444.
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A Preliminary Exploration of Former Smokers Enrolled in an Internet Smoking Cessation Program.

JMIR research protocols

Cha S, Cohn AM, Elmasry H, Graham AL.
PMID: 27302500
JMIR Res Protoc. 2016 Jun 14;5(2):e119. doi: 10.2196/resprot.5542.

BACKGROUND: Internet interventions may have an important role to play in helping self-quitters maintain an initial period of abstinence. Little is known about the characteristics and utilization patterns of former smokers who use Internet cessation programs.OBJECTIVE: The overarching aim...

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Cha S, Cohn AM, Elmasry H, et al. A Preliminary Exploration of Former Smokers Enrolled in an Internet Smoking Cessation Program. JMIR Res Protoc. 2016;5(2):e119doi: 10.2196/resprot.5542.
Cha, S., Cohn, A. M., Elmasry, H., & Graham, A. L. (2016). A Preliminary Exploration of Former Smokers Enrolled in an Internet Smoking Cessation Program. JMIR research protocols, 5(2), e119. https://doi.org/10.2196/resprot.5542
Cha, Sarah, et al. "A Preliminary Exploration of Former Smokers Enrolled in an Internet Smoking Cessation Program." JMIR research protocols vol. 5,2 (2016): e119. doi: https://doi.org/10.2196/resprot.5542
Cha S, Cohn AM, Elmasry H, Graham AL. A Preliminary Exploration of Former Smokers Enrolled in an Internet Smoking Cessation Program. JMIR Res Protoc. 2016 Jun 14;5(2):e119. doi: 10.2196/resprot.5542. PMID: 27302500; PMCID: PMC4925934.
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Physician tobacco screening and advice to quit among U.S. adolescents - National Survey on Drug Use and Health, 2013.

Tobacco induced diseases

Collins L, Smiley SL, Moore RA, Graham AL, Villanti AC.
PMID: 28077940
Tob Induc Dis. 2017 Jan 10;15:2. doi: 10.1186/s12971-016-0107-6. eCollection 2017.

BACKGROUND: Initiating tobacco use in adolescence increases the risk of nicotine dependence and continued smoking. Physician screening for tobacco use increases the odds of physicians intervening with patients who smoke; However, without appropriate follow-through by the physician, screening for...

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Collins L, Smiley SL, Moore RA, et al. Physician tobacco screening and advice to quit among U.S. adolescents - National Survey on Drug Use and Health, 2013. Tob Induc Dis. 2017;15:2doi: 10.1186/s12971-016-0107-6.
Collins, L., Smiley, S. L., Moore, R. A., Graham, A. L., & Villanti, A. C. (2017). Physician tobacco screening and advice to quit among U.S. adolescents - National Survey on Drug Use and Health, 2013. Tobacco induced diseases, 152. https://doi.org/10.1186/s12971-016-0107-6
Collins, Lauren, et al. "Physician tobacco screening and advice to quit among U.S. adolescents - National Survey on Drug Use and Health, 2013." Tobacco induced diseases vol. 15 (2017): 2. doi: https://doi.org/10.1186/s12971-016-0107-6
Collins L, Smiley SL, Moore RA, Graham AL, Villanti AC. Physician tobacco screening and advice to quit among U.S. adolescents - National Survey on Drug Use and Health, 2013. Tob Induc Dis. 2017 Jan 10;15:2. doi: 10.1186/s12971-016-0107-6. eCollection 2017. PMID: 28077940; PMCID: PMC5223531.
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Harnessing speckle for a sub-femtometre resolved broadband wavemeter and laser stabilization.

Nature communications

Metzger NK, Spesyvtsev R, Bruce GD, Miller B, Maker GT, Malcolm G, Mazilu M, Dholakia K.
PMID: 28580938
Nat Commun. 2017 Jun 05;8:15610. doi: 10.1038/ncomms15610.

The accurate determination and control of the wavelength of light is fundamental to many fields of science. Speckle patterns resulting from the interference of multiple reflections in disordered media are well-known to scramble the information content of light by...

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Metzger NK, Spesyvtsev R, Bruce GD, et al. Harnessing speckle for a sub-femtometre resolved broadband wavemeter and laser stabilization. Nat Commun. 2017;8:15610doi: 10.1038/ncomms15610.
Metzger, N. K., Spesyvtsev, R., Bruce, G. D., Miller, B., Maker, G. T., Malcolm, G., Mazilu, M., & Dholakia, K. (2017). Harnessing speckle for a sub-femtometre resolved broadband wavemeter and laser stabilization. Nature communications, 815610. https://doi.org/10.1038/ncomms15610
Metzger, Nikolaus Klaus, et al. "Harnessing speckle for a sub-femtometre resolved broadband wavemeter and laser stabilization." Nature communications vol. 8 (2017): 15610. doi: https://doi.org/10.1038/ncomms15610
Metzger NK, Spesyvtsev R, Bruce GD, Miller B, Maker GT, Malcolm G, Mazilu M, Dholakia K. Harnessing speckle for a sub-femtometre resolved broadband wavemeter and laser stabilization. Nat Commun. 2017 Jun 05;8:15610. doi: 10.1038/ncomms15610. PMID: 28580938; PMCID: PMC5465361.
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Lagrangian 3D tracking of fluorescent microscopic objects in motion.

The Review of scientific instruments

Darnige T, Figueroa-Morales N, Bohec P, Lindner A, Clément E, Fenesi B, Graham JD.
PMID: 28571422
Rev Sci Instrum. 2017 May;88(5):055106. doi: 10.1063/1.4982820.

We describe the development of a tracking device, mounted on an epi-fluorescent inverted microscope, suited to obtain time resolved 3D Lagrangian tracks of fluorescent passive or active micro-objects in microfluidic devices. The system is based on real-time image processing,...

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Darnige T, Figueroa-Morales N, Bohec P, et al. Lagrangian 3D tracking of fluorescent microscopic objects in motion. Rev Sci Instrum. 2017;88(5):055106doi: 10.1063/1.4982820.
Darnige, T., Figueroa-Morales, N., Bohec, P., Lindner, A., Clément, E., Fenesi, B., & Graham, J. D. (2017). Lagrangian 3D tracking of fluorescent microscopic objects in motion. The Review of scientific instruments, 88(5), 055106. https://doi.org/10.1063/1.4982820
Darnige, T, et al. "Lagrangian 3D tracking of fluorescent microscopic objects in motion." The Review of scientific instruments vol. 88,5 (2017): 055106. doi: https://doi.org/10.1063/1.4982820
Darnige T, Figueroa-Morales N, Bohec P, Lindner A, Clément E, Fenesi B, Graham JD. Lagrangian 3D tracking of fluorescent microscopic objects in motion. Rev Sci Instrum. 2017 May;88(5):055106. doi: 10.1063/1.4982820. PMID: 28571422.
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Bioremediation efficacy-comparison of nutrient removal from an anaerobic digest waste-based medium by an algal consortium before and after cryopreservation.

Journal of applied phycology

Silkina A, Nelson GD, Bayliss CE, Pooley CL, Day JG.
PMID: 28572708
J Appl Phycol. 2017;29(3):1331-1341. doi: 10.1007/s10811-017-1066-x. Epub 2017 Feb 05.

An algal consortium was isolated from an integrated steelmaking site at TATA Steel Strip Products Ltd. in Port Talbot, UK, and its bioremediation capacity tested. Excellent "bioremediation" was observed when the mixed culture was "applied" to diluted effluent from...

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Silkina A, Nelson GD, Bayliss CE, et al. Bioremediation efficacy-comparison of nutrient removal from an anaerobic digest waste-based medium by an algal consortium before and after cryopreservation. J Appl Phycol. 2017;29(3):1331-1341doi: 10.1007/s10811-017-1066-x.
Silkina, A., Nelson, G. D., Bayliss, C. E., Pooley, C. L., & Day, J. G. (2017). Bioremediation efficacy-comparison of nutrient removal from an anaerobic digest waste-based medium by an algal consortium before and after cryopreservation. Journal of applied phycology, 29(3), 1331-1341. https://doi.org/10.1007/s10811-017-1066-x
Silkina, Alla, et al. "Bioremediation efficacy-comparison of nutrient removal from an anaerobic digest waste-based medium by an algal consortium before and after cryopreservation." Journal of applied phycology vol. 29,3 (2017): 1331-1341. doi: https://doi.org/10.1007/s10811-017-1066-x
Silkina A, Nelson GD, Bayliss CE, Pooley CL, Day JG. Bioremediation efficacy-comparison of nutrient removal from an anaerobic digest waste-based medium by an algal consortium before and after cryopreservation. J Appl Phycol. 2017;29(3):1331-1341. doi: 10.1007/s10811-017-1066-x. Epub 2017 Feb 05. PMID: 28572708; PMCID: PMC5429893.
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Showing 1 to 12 of 880 entries