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PolyMarker: a fast polyploid primer design pipeline

pipeline programs

Ramirez-Gonzalez RH, Uauy C, Caccamo M.
GSID: vIxSlNCbbboJ
RH Ramirez-Gonzalez, C Uauy, M Caccamo - Bioinformatics, 2015 - academic.oup.com

… Summary: The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops … PolyMarker is a pipeline that generates SNP markers by selecting candidate primers for a specified genome using local...

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Ramirez-Gonzalez, R. H., Uauy, C., & Caccamo, M. (2015). PolyMarker: a fast polyploid primer design pipeline. Bioinformatics, 31(12), 2038-2039.
Ramirez-Gonzalez, Ricardo H., Cristobal Uauy, and Mario Caccamo. "PolyMarker: a fast polyploid primer design pipeline." Bioinformatics 31.12 (2015): 2038-2039.
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PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers

pipeline programs

Nato AQ.
GSID: IDbnxjthlRIJ
AQ Nato Jr, NH Chapman, HK Sohi, HD Nguyen… - …, 2015 - academic.oup.com

… Programs attempting to select markers for linkage panels exist but lack flexibility. Results: We developed a pedigree-based analysis pipeline (PBAP) suite of programs … Here, we introduce PBAP, a pipeline of programs that automatically selects ideal subpanel(s) of...

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Nato Jr, A. Q., Chapman, N. H., Sohi, H. K., Nguyen, H. D., Brkanac, Z., & Wijsman, E. M. (2015). PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers. Bioinformatics, 31(23), 3790-3798.
Nato Jr, Alejandro Q., et al. "PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers." Bioinformatics 31.23 (2015): 3790-3798.
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RNA‐S eq bulked segregant analysis enables the identification of high‐resolution genetic markers for breeding in hexaploid wheat

pipeline programs

Ramirez‐Gonzalez RH.
GSID: WKub9mazGbsJ
RH Ramirez‐Gonzalez, V Segovia… - Plant biotechnology …, 2015 - Wiley Online Library

The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major …

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Ramirez‐Gonzalez, R. H., Segovia, V., Bird, N., Fenwick, P., Holdgate, S., Berry, S., ... & Uauy, C. (2015). RNA‐S eq bulked segregant analysis enables the identification of high‐resolution genetic markers for breeding in hexaploid wheat. Plant biotechnology journal, 13(5), 613-624.
Ramirez‐Gonzalez, Ricardo H., et al. "RNA‐S eq bulked segregant analysis enables the identification of high‐resolution genetic markers for breeding in hexaploid wheat." Plant biotechnology journal 13.5 (2015): 613-624.
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The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease.

Canine genetics and epidemiology

Pedersen NC, Brucker L, Tessier NG, Liu H, Penedo MC, Hughes S, Oberbauer A, Sacks B.
PMID: 26401342
Canine Genet Epidemiol. 2015 Aug 27;2:14. doi: 10.1186/s40575-015-0026-5. eCollection 2015.

BACKGROUND: Sebaceous adenitis (SA) and Addison's disease (AD) increased rapidly in incidence among Standard Poodles after the mid-twentieth century. Previous attempts to identify specific genetic causes using genome wide association studies and interrogation of the dog leukocyte antigen (DLA)...

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Pedersen NC, Brucker L, Tessier NG, et al. The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease. Canine Genet Epidemiol. 2015;2:14doi: 10.1186/s40575-015-0026-5.
Pedersen, N. C., Brucker, L., Tessier, N. G., Liu, H., Penedo, M. C., Hughes, S., Oberbauer, A., & Sacks, B. (2015). The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease. Canine genetics and epidemiology, 214. https://doi.org/10.1186/s40575-015-0026-5
Pedersen, Niels C, et al. "The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease." Canine genetics and epidemiology vol. 2 (2015): 14. doi: https://doi.org/10.1186/s40575-015-0026-5
Pedersen NC, Brucker L, Tessier NG, Liu H, Penedo MC, Hughes S, Oberbauer A, Sacks B. The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease. Canine Genet Epidemiol. 2015 Aug 27;2:14. doi: 10.1186/s40575-015-0026-5. eCollection 2015. PMID: 26401342; PMCID: PMC4579369.
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Interactive Effects of Immunoglobulin Gamma and Human Leucocyte Antigen Genotypes on Response to Interferon Based Therapy of Hepatitis C Virus.

Open access Macedonian journal of medical sciences

Gomaa HE, Mahmoud M, Saad NE, Hussein AS, Ismail S, Thabet EH, Farouk H, Kandil D, Heiba A, Hafez W.
PMID: 27275229
Open Access Maced J Med Sci. 2015 Jun 15;3(2):245-9. doi: 10.3889/oamjms.2015.046. Epub 2015 Apr 29.

AIM: We examined the role that immunoglobulin GM 23 and KM allotypes-genetic markers of γ and κ chains, respectively-play in response to treatment of hepatitis C virus (HCV) infection in Egyptian patients.MATERIAL AND METHODS: A total of 120 persons...

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Gomaa HE, Mahmoud M, Saad NE, et al. Interactive Effects of Immunoglobulin Gamma and Human Leucocyte Antigen Genotypes on Response to Interferon Based Therapy of Hepatitis C Virus. Open Access Maced J Med Sci. 2015;3(2):245-9doi: 10.3889/oamjms.2015.046.
Gomaa, H. E., Mahmoud, M., Saad, N. E., Hussein, A. S., Ismail, S., Thabet, E. H., Farouk, H., Kandil, D., Heiba, A., & Hafez, W. (2015). Interactive Effects of Immunoglobulin Gamma and Human Leucocyte Antigen Genotypes on Response to Interferon Based Therapy of Hepatitis C Virus. Open access Macedonian journal of medical sciences, 3(2), 245-9. https://doi.org/10.3889/oamjms.2015.046
Gomaa, Howayda E, et al. "Interactive Effects of Immunoglobulin Gamma and Human Leucocyte Antigen Genotypes on Response to Interferon Based Therapy of Hepatitis C Virus." Open access Macedonian journal of medical sciences vol. 3,2 (2015): 245-9. doi: https://doi.org/10.3889/oamjms.2015.046
Gomaa HE, Mahmoud M, Saad NE, Hussein AS, Ismail S, Thabet EH, Farouk H, Kandil D, Heiba A, Hafez W. Interactive Effects of Immunoglobulin Gamma and Human Leucocyte Antigen Genotypes on Response to Interferon Based Therapy of Hepatitis C Virus. Open Access Maced J Med Sci. 2015 Jun 15;3(2):245-9. doi: 10.3889/oamjms.2015.046. Epub 2015 Apr 29. PMID: 27275229; PMCID: PMC4877861.
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TNFRSF10C copy number variation is associated with metastatic colorectal cancer.

Journal of gastrointestinal oncology

Tanenbaum DG, Hall WA, Colbert LE, Bastien AJ, Brat DJ, Kong J, Kim S, Dwivedi B, Kowalski J, Landry JC, Yu DS.
PMID: 27284460
J Gastrointest Oncol. 2016 Jun;7(3):306-14. doi: 10.21037/jgo.2015.11.04.

BACKGROUND: Genetic markers for distant metastatic disease in patients with colorectal cancer (CRC) are not well defined. Identification of genetic alterations associated with metastatic CRC could help to guide systemic and local treatment strategies. We evaluated the association of...

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Tanenbaum DG, Hall WA, Colbert LE, et al. TNFRSF10C copy number variation is associated with metastatic colorectal cancer. J Gastrointest Oncol. 2016;7(3):306-14doi: 10.21037/jgo.2015.11.04.
Tanenbaum, D. G., Hall, W. A., Colbert, L. E., Bastien, A. J., Brat, D. J., Kong, J., Kim, S., Dwivedi, B., Kowalski, J., Landry, J. C., & Yu, D. S. (2016). TNFRSF10C copy number variation is associated with metastatic colorectal cancer. Journal of gastrointestinal oncology, 7(3), 306-14. https://doi.org/10.21037/jgo.2015.11.04
Tanenbaum, Daniel G, et al. "TNFRSF10C copy number variation is associated with metastatic colorectal cancer." Journal of gastrointestinal oncology vol. 7,3 (2016): 306-14. doi: https://doi.org/10.21037/jgo.2015.11.04
Tanenbaum DG, Hall WA, Colbert LE, Bastien AJ, Brat DJ, Kong J, Kim S, Dwivedi B, Kowalski J, Landry JC, Yu DS. TNFRSF10C copy number variation is associated with metastatic colorectal cancer. J Gastrointest Oncol. 2016 Jun;7(3):306-14. doi: 10.21037/jgo.2015.11.04. PMID: 27284460; PMCID: PMC4880759.
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De novo transcriptome assembly of two different Prunus mume cultivars.

Genomics data

Jo Y, Lian S, Cho JK, Choi H, Chu H, Cho WK.
PMID: 26697396
Genom Data. 2015 Oct 19;6:273-4. doi: 10.1016/j.gdata.2015.10.011. eCollection 2015 Dec.

Prunus mume, belonging to the Prunus genus, is an Asian tree, and its common names are Chinese plum and Japanese plum. P. mume are cultivated for fruit production as well as ornamental purposes. In this study, we conducted de...

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Jo Y, Lian S, Cho JK, et al. De novo transcriptome assembly of two different Prunus mume cultivars. Genom Data. 2015;6:273-4doi: 10.1016/j.gdata.2015.10.011.
Jo, Y., Lian, S., Cho, J. K., Choi, H., Chu, H., & Cho, W. K. (2015). De novo transcriptome assembly of two different Prunus mume cultivars. Genomics data, 6273-4. https://doi.org/10.1016/j.gdata.2015.10.011
Jo, Yeonhwa, et al. "De novo transcriptome assembly of two different Prunus mume cultivars." Genomics data vol. 6 (2015): 273-4. doi: https://doi.org/10.1016/j.gdata.2015.10.011
Jo Y, Lian S, Cho JK, Choi H, Chu H, Cho WK. De novo transcriptome assembly of two different Prunus mume cultivars. Genom Data. 2015 Oct 19;6:273-4. doi: 10.1016/j.gdata.2015.10.011. eCollection 2015 Dec. PMID: 26697396; PMCID: PMC4664763.
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High quality SNPs/Indels mining and characterization in ginger from ESTs data base.

Bioinformation

Gaur M, Das A, Subudhi E.
PMID: 25848168
Bioinformation. 2015 Feb 28;11(2):85-9. doi: 10.6026/97320630011085. eCollection 2015.

Ginger (Zingiber officinale Rosc.) is an important herb of the family Zingiberaceae. It is accepted as a universal cure for a multitude of diseases in Indian systems of medicine and its rhizomes are equally popular as a spice ingredient...

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Gaur M, Das A, Subudhi E. High quality SNPs/Indels mining and characterization in ginger from ESTs data base. Bioinformation. 2015;11(2):85-9doi: 10.6026/97320630011085.
Gaur, M., Das, A., & Subudhi, E. (2015). High quality SNPs/Indels mining and characterization in ginger from ESTs data base. Bioinformation, 11(2), 85-9. https://doi.org/10.6026/97320630011085
Gaur, Mahendra, et al. "High quality SNPs/Indels mining and characterization in ginger from ESTs data base." Bioinformation vol. 11,2 (2015): 85-9. doi: https://doi.org/10.6026/97320630011085
Gaur M, Das A, Subudhi E. High quality SNPs/Indels mining and characterization in ginger from ESTs data base. Bioinformation. 2015 Feb 28;11(2):85-9. doi: 10.6026/97320630011085. eCollection 2015. PMID: 25848168; PMCID: PMC4369683.
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Association of the histone-lysine N-methyltransferase MLL5 gene with coronary artery disease in Chinese Han people.

Meta gene

Yuan Q, Xie X, Fu Z, Ma X, Yang Y, Huang D, Liu F, Dai C, Ma Y.
PMID: 25606435
Meta Gene. 2014 Jul 31;2:514-24. doi: 10.1016/j.mgene.2014.06.001. eCollection 2014 Dec.

BACKGROUND: MLL5, a member of the histone-lysine N-methyltransferase family, has been implicated in the control of the cell cycle progression and survival. The aim of this study was to explore the relationship between the interaction of histone-lysine N-methyltransferase MLL5...

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Yuan Q, Xie X, Fu Z, et al. Association of the histone-lysine N-methyltransferase MLL5 gene with coronary artery disease in Chinese Han people. Meta Gene. 2014;2:514-24doi: 10.1016/j.mgene.2014.06.001.
Yuan, Q., Xie, X., Fu, Z., Ma, X., Yang, Y., Huang, D., Liu, F., Dai, C., & Ma, Y. (2014). Association of the histone-lysine N-methyltransferase MLL5 gene with coronary artery disease in Chinese Han people. Meta gene, 2514-24. https://doi.org/10.1016/j.mgene.2014.06.001
Yuan, Qinghua, et al. "Association of the histone-lysine N-methyltransferase MLL5 gene with coronary artery disease in Chinese Han people." Meta gene vol. 2 (2014): 514-24. doi: https://doi.org/10.1016/j.mgene.2014.06.001
Yuan Q, Xie X, Fu Z, Ma X, Yang Y, Huang D, Liu F, Dai C, Ma Y. Association of the histone-lysine N-methyltransferase MLL5 gene with coronary artery disease in Chinese Han people. Meta Gene. 2014 Jul 31;2:514-24. doi: 10.1016/j.mgene.2014.06.001. eCollection 2014 Dec. PMID: 25606435; PMCID: PMC4287819.
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Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling.

Frontiers in cardiovascular medicine

McGarrity S, Halldórsson H, Palsson S, Johansson PI, Rolfsson Ó.
PMID: 27148541
Front Cardiovasc Med. 2016 Apr 18;3:10. doi: 10.3389/fcvm.2016.00010. eCollection 2016.

High-throughput biochemical profiling has led to a requirement for advanced data interpretation techniques capable of integrating the analysis of gene, protein, and metabolic profiles to shed light on genotype-phenotype relationships. Herein, we consider the current state of knowledge of...

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McGarrity S, Halldórsson H, Palsson S, et al. Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling. Front Cardiovasc Med. 2016;3:10doi: 10.3389/fcvm.2016.00010.
McGarrity, S., Halldórsson, H., Palsson, S., Johansson, P. I., & Rolfsson, �. �. (2016). Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling. Frontiers in cardiovascular medicine, 310. https://doi.org/10.3389/fcvm.2016.00010
McGarrity, Sarah, et al. "Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling." Frontiers in cardiovascular medicine vol. 3 (2016): 10. doi: https://doi.org/10.3389/fcvm.2016.00010
McGarrity S, Halldórsson H, Palsson S, Johansson PI, Rolfsson Ó. Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling. Front Cardiovasc Med. 2016 Apr 18;3:10. doi: 10.3389/fcvm.2016.00010. eCollection 2016. PMID: 27148541; PMCID: PMC4834436.
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A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data.

Advances in bioinformatics

Galli M, Zoppis I, De Sio G, Chinello C, Pagni F, Magni F, Mauri G.
PMID: 27293431
Adv Bioinformatics. 2016;2016:3791214. doi: 10.1155/2016/3791214. Epub 2016 May 17.

Biomarkers able to characterise and predict multifactorial diseases are still one of the most important targets for all the "omics" investigations. In this context, Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry Imaging (MALDI-MSI) has gained considerable attention in recent years, but it...

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Galli M, Zoppis I, De Sio G, et al. A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data. Adv Bioinformatics. 2016;2016:3791214doi: 10.1155/2016/3791214.
Galli, M., Zoppis, I., De Sio, G., Chinello, C., Pagni, F., Magni, F., & Mauri, G. (2016). A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data. Advances in bioinformatics, 20163791214. https://doi.org/10.1155/2016/3791214
Galli, Manuel, et al. "A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data." Advances in bioinformatics vol. 2016 (2016): 3791214. doi: https://doi.org/10.1155/2016/3791214
Galli M, Zoppis I, De Sio G, Chinello C, Pagni F, Magni F, Mauri G. A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data. Adv Bioinformatics. 2016;2016:3791214. doi: 10.1155/2016/3791214. Epub 2016 May 17. PMID: 27293431; PMCID: PMC4886047.
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Association of blaOXA-23 and bap with the persistence of Acinetobacter baumannii within a major healthcare system.

Frontiers in microbiology

Luo TL, Rickard AH, Srinivasan U, Kaye KS, Foxman B.
PMID: 25814985
Front Microbiol. 2015 Mar 12;6:182. doi: 10.3389/fmicb.2015.00182. eCollection 2015.

OBJECTIVES: Acinetobacter baumannii is an emerging opportunistic nosocomial pathogen. Two factors that may enhance persistence in healthcare settings are antimicrobial resistance and biofilm-forming ability. The aim of this work was to determine whether A. baumannii isolates that persist in...

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Luo TL, Rickard AH, Srinivasan U, et al. Association of blaOXA-23 and bap with the persistence of Acinetobacter baumannii within a major healthcare system. Front Microbiol. 2015;6:182doi: 10.3389/fmicb.2015.00182.
Luo, T. L., Rickard, A. H., Srinivasan, U., Kaye, K. S., & Foxman, B. (2015). Association of blaOXA-23 and bap with the persistence of Acinetobacter baumannii within a major healthcare system. Frontiers in microbiology, 6182. https://doi.org/10.3389/fmicb.2015.00182
Luo, Ting L, et al. "Association of blaOXA-23 and bap with the persistence of Acinetobacter baumannii within a major healthcare system." Frontiers in microbiology vol. 6 (2015): 182. doi: https://doi.org/10.3389/fmicb.2015.00182
Luo TL, Rickard AH, Srinivasan U, Kaye KS, Foxman B. Association of blaOXA-23 and bap with the persistence of Acinetobacter baumannii within a major healthcare system. Front Microbiol. 2015 Mar 12;6:182. doi: 10.3389/fmicb.2015.00182. eCollection 2015. PMID: 25814985; PMCID: PMC4357298.
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Showing 1 to 12 of 1851 entries