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Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data

pipeline programs

Baheti S, Kanwar R.
GSID: NfVSroXD87IJ
S Baheti, R Kanwar… - BMC …, 2016 - bmcgenomics.biomedcentral.com

DNA methylation is an important epigenetic modification involved in many biological processes. Reduced representation bisulfite sequencing (RRBS) is a cost-effective method …

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Baheti, S., Kanwar, R., Goelzenleuchter, M., Kocher, J. P. A., Beutler, A. S., & Sun, Z. (2016). Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data. BMC genomics, 17(1), 1-8.
Baheti, Saurabh, et al. "Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data." BMC genomics 17.1 (2016): 1-8.
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Active teaching strategies and student engagement: A comparison of traditional and non-traditional business students

non-traditional student

Arjomandi A, Seufert JH, Anwar S.
GSID: TJWhPotJL1wJ
A Arjomandi, JH Seufert, MJ O'Brien, S Anwar - 2018 - ro.uow.edu.au

… as" non-traditional". The analysis presented in this paper is based on Kahu's framework for student … An important contribution of this research is to show that non-traditional students …

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Arjomandi, A., Seufert, J. H., O'Brien, M. J., & Anwar, S. (2018). Active teaching strategies and student engagement: A comparison of traditional and non-traditional business students.
Arjomandi, Amir, et al. "Active teaching strategies and student engagement: A comparison of traditional and non-traditional business students." (2018): 120.
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SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing

pipeline programs

Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y.
GSID: 7X6GWoKIRfsJ
Z Sun, S Baheti, S Middha, R Kanwar, Y Zhang… - …, 2012 - academic.oup.com

… BSMAP version 2.43 is integrated into the pipeline as the default aligner. For RRBS, -D C-CGG option is turned on for RRBSMAP … We have compared RRBSMAP with three other alignment programs using simulated and real data, and...

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Sun, Z., Baheti, S., Middha, S., Kanwar, R., Zhang, Y., Li, X., ... & Kocher, J. P. A. (2012). SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics, 28(16), 2180-2181.
Sun, Zhifu, et al. "SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing." Bioinformatics 28.16 (2012): 2180-2181.
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Histopathological differences utilizing the nonalcoholic fatty liver disease activity score criteria in diabetic (type 2 diabetes mellitus) and non-diabetic patients with nonalcoholic fatty liver disease.

World journal of hepatology

Puchakayala BK, Verma S, Kanwar P, Hart J, Sanivarapu RR, Mohanty SR.
PMID: 26557954
World J Hepatol. 2015 Nov 08;7(25):2610-8. doi: 10.4254/wjh.v7.i25.2610.

AIM: To study clinical and histopathological features of nonalcoholic fatty liver disease (NAFLD) in patients with and without type 2 diabetes mellitus (T2DM) using updated nonalcoholic steatohepatitis clinical research network (NASH-CRN) grading system.METHODS: We retrospectively analyzed data of 235...

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Puchakayala BK, Verma S, Kanwar P, et al. Histopathological differences utilizing the nonalcoholic fatty liver disease activity score criteria in diabetic (type 2 diabetes mellitus) and non-diabetic patients with nonalcoholic fatty liver disease. World J Hepatol. 2015;7(25):2610-8doi: 10.4254/wjh.v7.i25.2610.
Puchakayala, B. K., Verma, S., Kanwar, P., Hart, J., Sanivarapu, R. R., & Mohanty, S. R. (2015). Histopathological differences utilizing the nonalcoholic fatty liver disease activity score criteria in diabetic (type 2 diabetes mellitus) and non-diabetic patients with nonalcoholic fatty liver disease. World journal of hepatology, 7(25), 2610-8. https://doi.org/10.4254/wjh.v7.i25.2610
Puchakayala, Bharat K, et al. "Histopathological differences utilizing the nonalcoholic fatty liver disease activity score criteria in diabetic (type 2 diabetes mellitus) and non-diabetic patients with nonalcoholic fatty liver disease." World journal of hepatology vol. 7,25 (2015): 2610-8. doi: https://doi.org/10.4254/wjh.v7.i25.2610
Puchakayala BK, Verma S, Kanwar P, Hart J, Sanivarapu RR, Mohanty SR. Histopathological differences utilizing the nonalcoholic fatty liver disease activity score criteria in diabetic (type 2 diabetes mellitus) and non-diabetic patients with nonalcoholic fatty liver disease. World J Hepatol. 2015 Nov 08;7(25):2610-8. doi: 10.4254/wjh.v7.i25.2610. PMID: 26557954; PMCID: PMC4635147.
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Grain iron and zinc density in pearl millet: combining ability, heterosis and association with grain yield and grain size.

SpringerPlus

Kanatti A, Rai KN, Radhika K, Govindaraj M, Sahrawat KL, Rao AS.
PMID: 25674488
Springerplus. 2014 Dec 26;3:763. doi: 10.1186/2193-1801-3-763. eCollection 2014.

Genetics of micronutrients and their relationships with grain yield and other traits have a direct bearing on devising effective strategies for breeding biofortified crop cultivars. A line × tester study of 196 hybrids and their 28 parental lines of...

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Kanatti A, Rai KN, Radhika K, et al. Grain iron and zinc density in pearl millet: combining ability, heterosis and association with grain yield and grain size. Springerplus. 2014;3:763doi: 10.1186/2193-1801-3-763.
Kanatti, A., Rai, K. N., Radhika, K., Govindaraj, M., Sahrawat, K. L., & Rao, A. S. (2014). Grain iron and zinc density in pearl millet: combining ability, heterosis and association with grain yield and grain size. SpringerPlus, 3763. https://doi.org/10.1186/2193-1801-3-763
Kanatti, Anand, et al. "Grain iron and zinc density in pearl millet: combining ability, heterosis and association with grain yield and grain size." SpringerPlus vol. 3 (2014): 763. doi: https://doi.org/10.1186/2193-1801-3-763
Kanatti A, Rai KN, Radhika K, Govindaraj M, Sahrawat KL, Rao AS. Grain iron and zinc density in pearl millet: combining ability, heterosis and association with grain yield and grain size. Springerplus. 2014 Dec 26;3:763. doi: 10.1186/2193-1801-3-763. eCollection 2014. PMID: 25674488; PMCID: PMC4320223.
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Evolutionary journey of the Gc protein (vitamin D-binding protein) across vertebrates.

Intrinsically disordered proteins

Anwar S, Iqbal MP, Zarina S, Bhutta ZA.
PMID: 28516027
Intrinsically Disord Proteins. 2014 Jan 01;1(1):e27450. doi: 10.4161/idp.27450. eCollection 2013.

With so many diverse functions such as transporter of vitamin D metabolites and fatty acids, actin scavenger and macrophage activating factor, Gc must have been one of the most conserved proteins in animal kingdom. Our objective was to investigate...

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Anwar S, Iqbal MP, Zarina S, et al. Evolutionary journey of the Gc protein (vitamin D-binding protein) across vertebrates. Intrinsically Disord Proteins. 2014;1(1):e27450doi: 10.4161/idp.27450.
Anwar, S., Iqbal, M. P., Zarina, S., & Bhutta, Z. A. (2013). Evolutionary journey of the Gc protein (vitamin D-binding protein) across vertebrates. Intrinsically disordered proteins, 1(1), e27450. https://doi.org/10.4161/idp.27450
Anwar, Shaheena, et al. "Evolutionary journey of the Gc protein (vitamin D-binding protein) across vertebrates." Intrinsically disordered proteins vol. 1,1 (2013): e27450. doi: https://doi.org/10.4161/idp.27450
Anwar S, Iqbal MP, Zarina S, Bhutta ZA. Evolutionary journey of the Gc protein (vitamin D-binding protein) across vertebrates. Intrinsically Disord Proteins. 2014 Jan 01;1(1):e27450. doi: 10.4161/idp.27450. eCollection 2013. PMID: 28516027; PMCID: PMC5424798.
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Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression.

PeerJ

Saeed MT, Ahmad J, Kanwal S, Holowatyj AN, Sheikh IA, Zafar Paracha R, Shafi A, Siddiqa A, Bibi Z, Khan M, Ali A.
PMID: 27703839
PeerJ. 2016 Sep 27;4:e2348. doi: 10.7717/peerj.2348. eCollection 2016.

The alteration of glucose metabolism, through increased uptake of glucose and glutamine addiction, is essential to cancer cell growth and invasion. Increased flux of glucose through the Hexosamine Biosynthetic Pathway (HBP) drives increased cellular O-GlcNAcylation (hyper-O-GlcNAcylation) and contributes to...

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Saeed MT, Ahmad J, Kanwal S, et al. Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression. PeerJ. 2016;4:e2348doi: 10.7717/peerj.2348.
Saeed, M. T., Ahmad, J., Kanwal, S., Holowatyj, A. N., Sheikh, I. A., Zafar Paracha, R., Shafi, A., Siddiqa, A., Bibi, Z., Khan, M., & Ali, A. (2016). Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression. PeerJ, 4e2348. https://doi.org/10.7717/peerj.2348
Saeed, Muhammad Tariq, et al. "Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression." PeerJ vol. 4 (2016): e2348. doi: https://doi.org/10.7717/peerj.2348
Saeed MT, Ahmad J, Kanwal S, Holowatyj AN, Sheikh IA, Zafar Paracha R, Shafi A, Siddiqa A, Bibi Z, Khan M, Ali A. Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression. PeerJ. 2016 Sep 27;4:e2348. doi: 10.7717/peerj.2348. eCollection 2016. PMID: 27703839; PMCID: PMC5047222.
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Synthesis and Characterization of Nanocrystalline Doped-ZnO Powder for Advanced Varistor Application.

Journal of nanoscience and nanotechnology

Anwar MS, Ahmed F, Koo BH.
PMID: 26726501
J Nanosci Nanotechnol. 2015 Oct;15(10):8271-4. doi: 10.1166/jnn.2015.11284.

The nanocrystalline doped ZnO powder has been synthesized by solution combustion method using sucrose as fuel and zinc acetate as oxidant. The as-prepared nanopowders were characterized by XRD, showing particle size approximately 39 and 48 nm for fuel to...

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Anwar MS, Ahmed F, Koo BH. Synthesis and Characterization of Nanocrystalline Doped-ZnO Powder for Advanced Varistor Application. J Nanosci Nanotechnol. 2015;15(10):8271-4doi: 10.1166/jnn.2015.11284.
Anwar, M. S., Ahmed, F., & Koo, B. H. (2015). Synthesis and Characterization of Nanocrystalline Doped-ZnO Powder for Advanced Varistor Application. Journal of nanoscience and nanotechnology, 15(10), 8271-4. https://doi.org/10.1166/jnn.2015.11284
Anwar, M S, et al. "Synthesis and Characterization of Nanocrystalline Doped-ZnO Powder for Advanced Varistor Application." Journal of nanoscience and nanotechnology vol. 15,10 (2015): 8271-4. doi: https://doi.org/10.1166/jnn.2015.11284
Anwar MS, Ahmed F, Koo BH. Synthesis and Characterization of Nanocrystalline Doped-ZnO Powder for Advanced Varistor Application. J Nanosci Nanotechnol. 2015 Oct;15(10):8271-4. doi: 10.1166/jnn.2015.11284. PMID: 26726501.
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Costs of integrating demand-based reproductive health commodity model into the Government and NGO service delivery systems in Bangladesh: a supply side perspective.

SpringerPlus

Islam Z, Sarker AR, Anwar S, Kabir H, Gazi R.
PMID: 26722628
Springerplus. 2015 Dec 23;4:808. doi: 10.1186/s40064-015-1610-6. eCollection 2015.

To estimate additional total cost and average cost of integrating the demand-based reproductive health commodity model into the existing Government and NGO facilities in Bangladesh. Activity based cost analysis was conducted during 2006-2008 in two low performing rural sub-districts...

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Islam Z, Sarker AR, Anwar S, et al. Costs of integrating demand-based reproductive health commodity model into the Government and NGO service delivery systems in Bangladesh: a supply side perspective. Springerplus. 2015;4:808doi: 10.1186/s40064-015-1610-6.
Islam, Z., Sarker, A. R., Anwar, S., Kabir, H., & Gazi, R. (2015). Costs of integrating demand-based reproductive health commodity model into the Government and NGO service delivery systems in Bangladesh: a supply side perspective. SpringerPlus, 4808. https://doi.org/10.1186/s40064-015-1610-6
Islam, Ziaul, et al. "Costs of integrating demand-based reproductive health commodity model into the Government and NGO service delivery systems in Bangladesh: a supply side perspective." SpringerPlus vol. 4 (2015): 808. doi: https://doi.org/10.1186/s40064-015-1610-6
Islam Z, Sarker AR, Anwar S, Kabir H, Gazi R. Costs of integrating demand-based reproductive health commodity model into the Government and NGO service delivery systems in Bangladesh: a supply side perspective. Springerplus. 2015 Dec 23;4:808. doi: 10.1186/s40064-015-1610-6. eCollection 2015. PMID: 26722628; PMCID: PMC4689723.
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Parastomal Hernia, Risky Zone & Prophilactic Mesh.

Hernia : the journal of hernias and abdominal wall surgery

De Keersmacker G, Beckers R, Heindryckx E, Kyle-Leinhase I, Pletinckx P, Claeys D, Muysoms F, Hernando LB, Ureña MA, Monclús JL, Del Valle AR, Montes DM, Pavón CC, Ceinos CJ, Cidoncha AC, Quindós PL, Franklin M, Hernandez M, Glover M, Glass J, Adedeiji A, Molina E, De La Paz O, Lalan J, Arias L, Tamayo Y, Mykytiuk S, Vlasov V, Mykytiuk O, Vlasova K, Köhler G, Pallwein-Prettner L, Luketina RR, Koch OO, Emmanuel K, Fang ZX, Ren F, Zhou JP, Liu DC, Tian J, Tu C, Winder J, Juza R, Pauli E, Chukwumah C, Meehan L, Bilkhu A, Anwar S, Bertoglio C, Magistro C, De Martini P, Lo Conte D, Di Lernia S, Ferrari G, Pugliese R, Köckerling F, Bellomo MP, Bona A, Borasi A, Borreca D, Filippa C, Manfredi S, De Paolis P, Lysenko R, Zuvela M, Galun D.
PMID: 26518816
Hernia. 2015 Apr;19:S25-31. doi: 10.1007/BF03355322.

No abstract available.

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De Keersmacker G, Beckers R, Heindryckx E, et al. Parastomal Hernia, Risky Zone & Prophilactic Mesh. Hernia. 2015;19:S25-31doi: 10.1007/BF03355322.
De Keersmacker, G., Beckers, R., Heindryckx, E., Kyle-Leinhase, I., Pletinckx, P., Claeys, D., Muysoms, F., Hernando, L. B., Ureña, M. A., Monclús, J. L., Del Valle, A. R., Montes, D. M., Pavón, C. C., Ceinos, C. J., Cidoncha, A. C., Quindós, P. L., Franklin, M., Hernandez, M., Glover, M., Glass, J., Adedeiji, A., Molina, E., De La Paz, O., Lalan, J., Arias, L., Tamayo, Y., Mykytiuk, S., Vlasov, V., Mykytiuk, O., Vlasova, K., Köhler, G., Pallwein-Prettner, L., Luketina, R. R., Koch, O. O., Emmanuel, K., Fang, Z. X., Ren, F., Zhou, J. P., Liu, D. C., Tian, J., Tu, C., Winder, J., Juza, R., Pauli, E., Chukwumah, C., Meehan, L., Bilkhu, A., Anwar, S., Bertoglio, C., Magistro, C., De Martini, P., Lo Conte, D., Di Lernia, S., Ferrari, G., Pugliese, R., Köckerling, F., Bellomo, M. P., Bona, A., Borasi, A., Borreca, D., Filippa, C., Manfredi, S., De Paolis, P., Lysenko, R., Zuvela, M., & Galun, D. (2015). Parastomal Hernia, Risky Zone & Prophilactic Mesh. Hernia : the journal of hernias and abdominal wall surgery, 19S25-31. https://doi.org/10.1007/BF03355322
De Keersmacker, G, et al. "Parastomal Hernia, Risky Zone & Prophilactic Mesh." Hernia : the journal of hernias and abdominal wall surgery vol. 19 (2015): S25-31. doi: https://doi.org/10.1007/BF03355322
De Keersmacker G, Beckers R, Heindryckx E, Kyle-Leinhase I, Pletinckx P, Claeys D, Muysoms F, Hernando LB, Ureña MA, Monclús JL, Del Valle AR, Montes DM, Pavón CC, Ceinos CJ, Cidoncha AC, Quindós PL, Franklin M, Hernandez M, Glover M, Glass J, Adedeiji A, Molina E, De La Paz O, Lalan J, Arias L, Tamayo Y, Mykytiuk S, Vlasov V, Mykytiuk O, Vlasova K, Köhler G, Pallwein-Prettner L, Luketina RR, Koch OO, Emmanuel K, Fang ZX, Ren F, Zhou JP, Liu DC, Tian J, Tu C, Winder J, Juza R, Pauli E, Chukwumah C, Meehan L, Bilkhu A, Anwar S, Bertoglio C, Magistro C, De Martini P, Lo Conte D, Di Lernia S, Ferrari G, Pugliese R, Köckerling F, Bellomo MP, Bona A, Borasi A, Borreca D, Filippa C, Manfredi S, De Paolis P, Lysenko R, Zuvela M, Galun D. Parastomal Hernia, Risky Zone & Prophilactic Mesh. Hernia. 2015 Apr;19:S25-31. doi: 10.1007/BF03355322. PMID: 26518816.
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Surgical Outcome of Spontaneous Supra Tentorial Intracerebral Hemorrhage.

Pakistan journal of medical sciences

Rehman WA, Anwar MS.
PMID: 29067043
Pak J Med Sci. 2017 Jul-Aug;33(4):804-807. doi: 10.12669/pjms.334.12172.

OBJECTIVE: To assess the risks and benefits of surgical treatment (Open Craniotomy) of Intra-cerebral hematoma (ICH).METHODS: Twenty seven patients of ICH who underwent surgical treatment at Neurosurgical department of Sheikh Zayed Hospital, Rahim Yar Khan, from 1RESULTS: Mean age...

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Rehman WA, Anwar MS. Surgical Outcome of Spontaneous Supra Tentorial Intracerebral Hemorrhage. Pak J Med Sci. 2017;33(4):804-807doi: 10.12669/pjms.334.12172.
Rehman, W. A., & Anwar, M. S. (2017). Surgical Outcome of Spontaneous Supra Tentorial Intracerebral Hemorrhage. Pakistan journal of medical sciences, 33(4), 804-807. https://doi.org/10.12669/pjms.334.12172
Rehman, Waqar Aziz, and Anwar, Muhammad Sohaib. "Surgical Outcome of Spontaneous Supra Tentorial Intracerebral Hemorrhage." Pakistan journal of medical sciences vol. 33,4 (2017): 804-807. doi: https://doi.org/10.12669/pjms.334.12172
Rehman WA, Anwar MS. Surgical Outcome of Spontaneous Supra Tentorial Intracerebral Hemorrhage. Pak J Med Sci. 2017 Jul-Aug;33(4):804-807. doi: 10.12669/pjms.334.12172. PMID: 29067043; PMCID: PMC5648942.
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Quantitative .

Frontiers in medicine

Shatil AS, Uddin MN, Matsuda KM, Figley CR.
PMID: 29515998
Front Med (Lausanne). 2018 Feb 20;5:31. doi: 10.3389/fmed.2018.00031. eCollection 2018.

PURPOSE: Postmortem MRI can be used to reveal important pathologies and establish radiology-pathology correlations. However, quantitative MRI values are altered by tissue fixation. Therefore, the purpose of this study was to investigate time-dependent effects of formalin fixation on MRI...

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Shatil AS, Uddin MN, Matsuda KM, et al. Quantitative . Front Med (Lausanne). 2018;5:31doi: 10.3389/fmed.2018.00031.
Shatil, A. S., Uddin, M. N., Matsuda, K. M., & Figley, C. R. (2018). Quantitative . Frontiers in medicine, 531. https://doi.org/10.3389/fmed.2018.00031
Shatil, Anwar S, et al. "Quantitative ." Frontiers in medicine vol. 5 (2018): 31. doi: https://doi.org/10.3389/fmed.2018.00031
Shatil AS, Uddin MN, Matsuda KM, Figley CR. Quantitative . Front Med (Lausanne). 2018 Feb 20;5:31. doi: 10.3389/fmed.2018.00031. eCollection 2018. PMID: 29515998; PMCID: PMC5826187.
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