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Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

pipeline programs

Ou S, Su W, Liao Y, Chougule K.
GSID: Hdtgurt8_KAJ
S Ou, W Su, Y Liao, K Chougule… - Genome …, 2019 - genomebiology.biomedcentral.com

… We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long … Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA)...

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Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J. R., Hellinga, A. J., ... & Hufford, M. B. (2019). Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome biology, 20(1), 1-18.
Ou, Shujun, et al. "Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline." Genome biology 20.1 (2019): 1-18.
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Hyperglycemia in critically ill children.

Indian journal of critical care medicine : peer-reviewed, official publication of Indian Society of Critical Care Medicine

Patki VK, Chougule SB.
PMID: 24550607
Indian J Crit Care Med. 2014 Jan;18(1):8-13. doi: 10.4103/0972-5229.125427.

OBJECTIVES: To determine the incidence and study association of hyperglycemia with outcome of critically ill children.SETTING AND DESIGN: This was a prospective observational study conducted in eight bedded pediatric intensive care unit (PICU) of a tertiary care hospital.MATERIALS AND...

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Patki VK, Chougule SB. Hyperglycemia in critically ill children. Indian J Crit Care Med. 2014;18(1):8-13doi: 10.4103/0972-5229.125427.
Patki, V. K., & Chougule, S. B. (2014). Hyperglycemia in critically ill children. Indian journal of critical care medicine : peer-reviewed, official publication of Indian Society of Critical Care Medicine, 18(1), 8-13. https://doi.org/10.4103/0972-5229.125427
Patki, Vinayak Krishnarao, and Chougule, Swati Balasaheb. "Hyperglycemia in critically ill children." Indian journal of critical care medicine : peer-reviewed, official publication of Indian Society of Critical Care Medicine vol. 18,1 (2014): 8-13. doi: https://doi.org/10.4103/0972-5229.125427
Patki VK, Chougule SB. Hyperglycemia in critically ill children. Indian J Crit Care Med. 2014 Jan;18(1):8-13. doi: 10.4103/0972-5229.125427. PMID: 24550607; PMCID: PMC3912677.
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Audit of Injuries in a Premiership Football Squad over a Five-Year Period.

Journal of sports science & medicine

Chougle A, Batty PD, Hodgkinson JP.
PMID: 24431979
J Sports Sci Med. 2005 Jun 01;4(2):211-3. eCollection 2005 Jun 01.

No abstract available.

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Chougle A, Batty PD, Hodgkinson JP. Audit of Injuries in a Premiership Football Squad over a Five-Year Period. J Sports Sci Med. 2005;4(2):211-3
Chougle, A., Batty, P. D., & Hodgkinson, J. P. (2005). Audit of Injuries in a Premiership Football Squad over a Five-Year Period. Journal of sports science & medicine, 4(2), 211-3.
Chougle, Aslam, et al. "Audit of Injuries in a Premiership Football Squad over a Five-Year Period." Journal of sports science & medicine vol. 4,2 (2005): 211-3.
Chougle A, Batty PD, Hodgkinson JP. Audit of Injuries in a Premiership Football Squad over a Five-Year Period. J Sports Sci Med. 2005 Jun 01;4(2):211-3. eCollection 2005 Jun 01. PMID: 24431979; PMCID: PMC3880890.
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Differential erythrocyte agglutination pattern in normal and cancer patients with Synadenium grantii root (Hook f) lectin.

Indian journal of clinical biochemistry : IJCB

Durgawale PP, Shukla PS, Sontakke SD, Chougule PG.
PMID: 23105302
Indian J Clin Biochem. 2001 Jan;16(1):110-2. doi: 10.1007/BF02867578.

In the present study the property of lectin agglutination in blood on normal and different cancer patients has been observed. The purifiedSynadenium grantii root lectin was non blood group specific and its utility as a diagnostic tool in malignancy...

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Durgawale PP, Shukla PS, Sontakke SD, et al. Differential erythrocyte agglutination pattern in normal and cancer patients with Synadenium grantii root (Hook f) lectin. Indian J Clin Biochem. 2001;16(1):110-2doi: 10.1007/BF02867578.
Durgawale, P. P., Shukla, P. S., Sontakke, S. D., & Chougule, P. G. (2001). Differential erythrocyte agglutination pattern in normal and cancer patients with Synadenium grantii root (Hook f) lectin. Indian journal of clinical biochemistry : IJCB, 16(1), 110-2. https://doi.org/10.1007/BF02867578
Durgawale, P P, et al. "Differential erythrocyte agglutination pattern in normal and cancer patients with Synadenium grantii root (Hook f) lectin." Indian journal of clinical biochemistry : IJCB vol. 16,1 (2001): 110-2. doi: https://doi.org/10.1007/BF02867578
Durgawale PP, Shukla PS, Sontakke SD, Chougule PG. Differential erythrocyte agglutination pattern in normal and cancer patients with Synadenium grantii root (Hook f) lectin. Indian J Clin Biochem. 2001 Jan;16(1):110-2. doi: 10.1007/BF02867578. PMID: 23105302; PMCID: PMC3453605.
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Correction to "Factorial Design Based Multivariate Modeling and Optimization of Tunable Bioresponsive Arginine Grafted Poly(cystaminebis(acrylamide)-diaminohexane) Polymeric Matrix Based Nanocarriers".

Molecular pharmaceutics

Yang R, Nam K, Kim SW, Turkson J, Zou Y, Zuo YY, Haware RV, Chougule MB.
PMID: 29470076
Mol Pharm. 2018 Mar 05;15(3):1377. doi: 10.1021/acs.molpharmaceut.8b00130. Epub 2018 Feb 22.

No abstract available.

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Yang R, Nam K, Kim SW, et al. Correction to "Factorial Design Based Multivariate Modeling and Optimization of Tunable Bioresponsive Arginine Grafted Poly(cystaminebis(acrylamide)-diaminohexane) Polymeric Matrix Based Nanocarriers". Mol Pharm. 2018;15(3):1377doi: 10.1021/acs.molpharmaceut.8b00130.
Yang, R., Nam, K., Kim, S. W., Turkson, J., Zou, Y., Zuo, Y. Y., Haware, R. V., & Chougule, M. B. (2018). Correction to "Factorial Design Based Multivariate Modeling and Optimization of Tunable Bioresponsive Arginine Grafted Poly(cystaminebis(acrylamide)-diaminohexane) Polymeric Matrix Based Nanocarriers". Molecular pharmaceutics, 15(3), 1377. https://doi.org/10.1021/acs.molpharmaceut.8b00130
Yang, Rongbing, et al. "Correction to "Factorial Design Based Multivariate Modeling and Optimization of Tunable Bioresponsive Arginine Grafted Poly(cystaminebis(acrylamide)-diaminohexane) Polymeric Matrix Based Nanocarriers"." Molecular pharmaceutics vol. 15,3 (2018): 1377. doi: https://doi.org/10.1021/acs.molpharmaceut.8b00130
Yang R, Nam K, Kim SW, Turkson J, Zou Y, Zuo YY, Haware RV, Chougule MB. Correction to "Factorial Design Based Multivariate Modeling and Optimization of Tunable Bioresponsive Arginine Grafted Poly(cystaminebis(acrylamide)-diaminohexane) Polymeric Matrix Based Nanocarriers". Mol Pharm. 2018 Mar 05;15(3):1377. doi: 10.1021/acs.molpharmaceut.8b00130. Epub 2018 Feb 22. PMID: 29470076.
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TiO.

Nano convergence

Dongale TD, Patil PJ, Desai NK, Chougule PP, Kumbhar SM, Waifalkar PP, Patil PB, Vhatkar RS, Takale MV, Gaikwad PK, Kamat RK.
PMID: 28191426
Nano Converg. 2016;3(1):16. doi: 10.1186/s40580-016-0076-8. Epub 2016 Jul 18.

We report simulation of nanostructured memristor device using piecewise linear and nonlinear window functions for RRAM and neuromorphic applications. The linear drift model of memristor has been exploited for the simulation purpose with the linear and non-linear window function...

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Dongale TD, Patil PJ, Desai NK, et al. TiO. Nano Converg. 2016;3(1):16doi: 10.1186/s40580-016-0076-8.
Dongale, T. D., Patil, P. J., Desai, N. K., Chougule, P. P., Kumbhar, S. M., Waifalkar, P. P., Patil, P. B., Vhatkar, R. S., Takale, M. V., Gaikwad, P. K., & Kamat, R. K. (2016). TiO. Nano convergence, 3(1), 16. https://doi.org/10.1186/s40580-016-0076-8
Dongale, T D, et al. "TiO." Nano convergence vol. 3,1 (2016): 16. doi: https://doi.org/10.1186/s40580-016-0076-8
Dongale TD, Patil PJ, Desai NK, Chougule PP, Kumbhar SM, Waifalkar PP, Patil PB, Vhatkar RS, Takale MV, Gaikwad PK, Kamat RK. TiO. Nano Converg. 2016;3(1):16. doi: 10.1186/s40580-016-0076-8. Epub 2016 Jul 18. PMID: 28191426; PMCID: PMC5271148.
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Multicentric Metaplastic Breast Carcinoma with Squamous Differentiation.

Journal of clinical and diagnostic research : JCDR

Jagtap SV, Bhosale SJ, Chougule PG, Dhawan SD, Shukla D.
PMID: 26393137
J Clin Diagn Res. 2015 Jul;9(7):ED09-10. doi: 10.7860/JCDR/2015/12794.6218. Epub 2015 Jul 01.

Metaplastic breast carcinoma is a rare primary breast malignancy. A 45-year-old female patient presented with multicentric lumps in left breast of 6 months duration and history of axillary lymphadenopathy of 2 months duration. Mammography revealed two high density masses...

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Jagtap SV, Bhosale SJ, Chougule PG, et al. Multicentric Metaplastic Breast Carcinoma with Squamous Differentiation. J Clin Diagn Res. 2015;9(7):ED09-10doi: 10.7860/JCDR/2015/12794.6218.
Jagtap, S. V., Bhosale, S. J., Chougule, P. G., Dhawan, S. D., & Shukla, D. (2015). Multicentric Metaplastic Breast Carcinoma with Squamous Differentiation. Journal of clinical and diagnostic research : JCDR, 9(7), ED09-10. https://doi.org/10.7860/JCDR/2015/12794.6218
Jagtap, Sunil Vitthalrao, et al. "Multicentric Metaplastic Breast Carcinoma with Squamous Differentiation." Journal of clinical and diagnostic research : JCDR vol. 9,7 (2015): ED09-10. doi: https://doi.org/10.7860/JCDR/2015/12794.6218
Jagtap SV, Bhosale SJ, Chougule PG, Dhawan SD, Shukla D. Multicentric Metaplastic Breast Carcinoma with Squamous Differentiation. J Clin Diagn Res. 2015 Jul;9(7):ED09-10. doi: 10.7860/JCDR/2015/12794.6218. Epub 2015 Jul 01. PMID: 26393137; PMCID: PMC4572969.
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Cement-in-cement revision with the Exeter Short Revision Stem: A review of 50 consecutive hips.

Journal of clinical orthopaedics and trauma

Berg AJ, Hoyle A, Yates E, Chougle A, Mohan R.
PMID: 32001984
J Clin Orthop Trauma. 2020 Jan-Feb;11(1):47-55. doi: 10.1016/j.jcot.2019.04.002. Epub 2019 Apr 09.

Revision of a well-fixed cemented femoral stem is technically challenging. The Exeter Short Revision Stem (SRS) was developed to facilitate cement-in-cement revision mitigating some of these challenges. We present the short to mid-term results of 50 cement-in-cement revisions performed...

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Berg AJ, Hoyle A, Yates E, et al. Cement-in-cement revision with the Exeter Short Revision Stem: A review of 50 consecutive hips. J Clin Orthop Trauma. 2019;11(1):47-55doi: 10.1016/j.jcot.2019.04.002.
Berg, A. J., Hoyle, A., Yates, E., Chougle, A., & Mohan, R. (2020). Cement-in-cement revision with the Exeter Short Revision Stem: A review of 50 consecutive hips. Journal of clinical orthopaedics and trauma, 11(1), 47-55. https://doi.org/10.1016/j.jcot.2019.04.002
Berg, Andrew J, et al. "Cement-in-cement revision with the Exeter Short Revision Stem: A review of 50 consecutive hips." Journal of clinical orthopaedics and trauma vol. 11,1 (2020): 47-55. doi: https://doi.org/10.1016/j.jcot.2019.04.002
Berg AJ, Hoyle A, Yates E, Chougle A, Mohan R. Cement-in-cement revision with the Exeter Short Revision Stem: A review of 50 consecutive hips. J Clin Orthop Trauma. 2020 Jan-Feb;11(1):47-55. doi: 10.1016/j.jcot.2019.04.002. Epub 2019 Apr 09. PMID: 32001984; PMCID: PMC6985006.
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SorghumBase: a web-based portal for sorghum genetic information and community advancement.

Planta

Gladman N, Olson A, Wei S, Chougule K, Lu Z, Tello-Ruiz M, Meijs I, Van Buren P, Jiao Y, Wang B, Kumar V, Kumari S, Zhang L, Burke J, Chen J, Burow G, Hayes C, Emendack Y, Xin Z, Ware D.
PMID: 35015132
Planta. 2022 Jan 11;255(2):35. doi: 10.1007/s00425-022-03821-6.

MAIN CONCLUSION: SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular...

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Gladman N, Olson A, Wei S, et al. SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta. 2022;255(2):35doi: 10.1007/s00425-022-03821-6.
Gladman, N., Olson, A., Wei, S., Chougule, K., Lu, Z., Tello-Ruiz, M., Meijs, I., Van Buren, P., Jiao, Y., Wang, B., Kumar, V., Kumari, S., Zhang, L., Burke, J., Chen, J., Burow, G., Hayes, C., Emendack, Y., Xin, Z., & Ware, D. (2022). SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta, 255(2), 35. https://doi.org/10.1007/s00425-022-03821-6
Gladman, Nicholas, et al. "SorghumBase: a web-based portal for sorghum genetic information and community advancement." Planta vol. 255,2 (2022): 35. doi: https://doi.org/10.1007/s00425-022-03821-6
Gladman N, Olson A, Wei S, Chougule K, Lu Z, Tello-Ruiz M, Meijs I, Van Buren P, Jiao Y, Wang B, Kumar V, Kumari S, Zhang L, Burke J, Chen J, Burow G, Hayes C, Emendack Y, Xin Z, Ware D. SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta. 2022 Jan 11;255(2):35. doi: 10.1007/s00425-022-03821-6. PMID: 35015132.
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Formulation development of itraconazole PEGylated nano-lipid carriers for pulmonary aspergillosis using hot-melt extrusion technology.

International journal of pharmaceutics: X

Shadambikar G, Marathe S, Ji N, Almutairi M, Bandari S, Zhang F, Chougule M, Repka M.
PMID: 33748741
Int J Pharm X. 2021 Mar 03;3:100074. doi: 10.1016/j.ijpx.2021.100074. eCollection 2021 Dec.

Pulmonary delivery is a promising alternative for the oral treatment of pulmonary aspergillosis. This study aimed to develop continuous and scalable itraconazole PEGylated nano-lipid carriers (ITZ-PEG-NLC) for inhalation delivery. The feasibility of preparing NLCs utilizing hot-melt extrusion (HME) coupled...

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Shadambikar G, Marathe S, Ji N, et al. Formulation development of itraconazole PEGylated nano-lipid carriers for pulmonary aspergillosis using hot-melt extrusion technology. Int J Pharm X. 2021;3:100074doi: 10.1016/j.ijpx.2021.100074.
Shadambikar, G., Marathe, S., Ji, N., Almutairi, M., Bandari, S., Zhang, F., Chougule, M., & Repka, M. (2021). Formulation development of itraconazole PEGylated nano-lipid carriers for pulmonary aspergillosis using hot-melt extrusion technology. International journal of pharmaceutics: X, 3100074. https://doi.org/10.1016/j.ijpx.2021.100074
Shadambikar, Gauri, et al. "Formulation development of itraconazole PEGylated nano-lipid carriers for pulmonary aspergillosis using hot-melt extrusion technology." International journal of pharmaceutics: X vol. 3 (2021): 100074. doi: https://doi.org/10.1016/j.ijpx.2021.100074
Shadambikar G, Marathe S, Ji N, Almutairi M, Bandari S, Zhang F, Chougule M, Repka M. Formulation development of itraconazole PEGylated nano-lipid carriers for pulmonary aspergillosis using hot-melt extrusion technology. Int J Pharm X. 2021 Mar 03;3:100074. doi: 10.1016/j.ijpx.2021.100074. eCollection 2021 Dec. PMID: 33748741; PMCID: PMC7973123.
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Self-Assembling PCL-PAMAM Linear Dendritic Block Copolymers (LDBCs) for Bioimaging and Phototherapeutic Applications.

ACS applied bio materials

Chandrasiri I, Abebe DG, Loku Yaddehige M, Williams JSD, Zia MF, Dorris A, Barker A, Simms BL, Parker A, Vinjamuri BP, Le N, Gayton JN, Chougule MB, Hammer NI, Flynt A, Delcamp JH, Watkins DL.
PMID: 35021798
ACS Appl Bio Mater. 2020 Sep 21;3(9):5664-5677. doi: 10.1021/acsabm.0c00432. Epub 2020 Aug 10.

This study represents a successful approach toward employing polycaprolactone-polyamidoamine (PCL-PAMAM) linear dendritic block copolymer (LDBC) nanoparticles as small-molecule carriers in NIR imaging and photothermal therapy. A feasible and robust synthetic strategy was used to synthesize a library of amphiphilic...

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Chandrasiri I, Abebe DG, Loku Yaddehige M, et al. Self-Assembling PCL-PAMAM Linear Dendritic Block Copolymers (LDBCs) for Bioimaging and Phototherapeutic Applications. ACS Appl Bio Mater. 2020;3(9):5664-5677doi: 10.1021/acsabm.0c00432.
Chandrasiri, I., Abebe, D. G., Loku Yaddehige, M., Williams, J. S. D., Zia, M. F., Dorris, A., Barker, A., Simms, B. L., Parker, A., Vinjamuri, B. P., Le, N., Gayton, J. N., Chougule, M. B., Hammer, N. I., Flynt, A., Delcamp, J. H., & Watkins, D. L. (2020). Self-Assembling PCL-PAMAM Linear Dendritic Block Copolymers (LDBCs) for Bioimaging and Phototherapeutic Applications. ACS applied bio materials, 3(9), 5664-5677. https://doi.org/10.1021/acsabm.0c00432
Chandrasiri, Indika, et al. "Self-Assembling PCL-PAMAM Linear Dendritic Block Copolymers (LDBCs) for Bioimaging and Phototherapeutic Applications." ACS applied bio materials vol. 3,9 (2020): 5664-5677. doi: https://doi.org/10.1021/acsabm.0c00432
Chandrasiri I, Abebe DG, Loku Yaddehige M, Williams JSD, Zia MF, Dorris A, Barker A, Simms BL, Parker A, Vinjamuri BP, Le N, Gayton JN, Chougule MB, Hammer NI, Flynt A, Delcamp JH, Watkins DL. Self-Assembling PCL-PAMAM Linear Dendritic Block Copolymers (LDBCs) for Bioimaging and Phototherapeutic Applications. ACS Appl Bio Mater. 2020 Sep 21;3(9):5664-5677. doi: 10.1021/acsabm.0c00432. Epub 2020 Aug 10. PMID: 35021798.
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Sedation Usage in COVID-19 Acute Respiratory Distress Syndrome: A Multicenter Study.

The Annals of pharmacotherapy

Tapaskar N, Colon Hidalgo D, Koo G, Shingada K, Rao S, Rodriguez R, Alcantar D, Espinoza Barrera D, Lee R, Rameshkumar N, Amine M, Rodrigues S, Giron F, Chaugule A, Rech MA.
PMID: 34075807
Ann Pharmacother. 2021 Jun 02;10600280211021925. doi: 10.1177/10600280211021925. Epub 2021 Jun 02.

BACKGROUND: Patients with COVID-19 acute respiratory distress syndrome (ARDS) have been shown to have high sedation requirements.OBJECTIVE: The purpose of this study was to compare sedative use between patients with COVID-19 ARDS and non-COVID-19 ARDS.METHODS: This was a retrospective...

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Tapaskar N, Colon Hidalgo D, Koo G, et al. Sedation Usage in COVID-19 Acute Respiratory Distress Syndrome: A Multicenter Study. Ann Pharmacother. 2021;10600280211021925doi: 10.1177/10600280211021925.
Tapaskar, N., Colon Hidalgo, D., Koo, G., Shingada, K., Rao, S., Rodriguez, R., Alcantar, D., Espinoza Barrera, D., Lee, R., Rameshkumar, N., Amine, M., Rodrigues, S., Giron, F., Chaugule, A., & Rech, M. A. (2021). Sedation Usage in COVID-19 Acute Respiratory Distress Syndrome: A Multicenter Study. The Annals of pharmacotherapy, 10600280211021925. https://doi.org/10.1177/10600280211021925
Tapaskar, Natalie, et al. "Sedation Usage in COVID-19 Acute Respiratory Distress Syndrome: A Multicenter Study." The Annals of pharmacotherapy vol. (2021): 10600280211021925. doi: https://doi.org/10.1177/10600280211021925
Tapaskar N, Colon Hidalgo D, Koo G, Shingada K, Rao S, Rodriguez R, Alcantar D, Espinoza Barrera D, Lee R, Rameshkumar N, Amine M, Rodrigues S, Giron F, Chaugule A, Rech MA. Sedation Usage in COVID-19 Acute Respiratory Distress Syndrome: A Multicenter Study. Ann Pharmacother. 2021 Jun 02;10600280211021925. doi: 10.1177/10600280211021925. Epub 2021 Jun 02. PMID: 34075807.
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Showing 1 to 12 of 127 entries