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tmBioC: improving interoperability of text-mining tools with BioC.

Database : the journal of biological databases and curation

Khare R, Wei CH, Mao Y, Leaman R, Lu Z.
PMID: 25062914
Database (Oxford). 2014 Jul 25;2014. doi: 10.1093/database/bau073. Print 2014.

The lack of interoperability among biomedical text-mining tools is a major bottleneck in creating more complex applications. Despite the availability of numerous methods and techniques for various text-mining tasks, combining different tools requires substantial efforts and time owing to...

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Khare R, Wei CH, Mao Y, et al. tmBioC: improving interoperability of text-mining tools with BioC. Database (Oxford). 2014;2014doi: 10.1093/database/bau073.
Khare, R., Wei, C. H., Mao, Y., Leaman, R., & Lu, Z. (2014). tmBioC: improving interoperability of text-mining tools with BioC. Database : the journal of biological databases and curation, 2014. https://doi.org/10.1093/database/bau073
Khare, Ritu, et al. "tmBioC: improving interoperability of text-mining tools with BioC." Database : the journal of biological databases and curation vol. 2014 (2014). doi: https://doi.org/10.1093/database/bau073
Khare R, Wei CH, Mao Y, Leaman R, Lu Z. tmBioC: improving interoperability of text-mining tools with BioC. Database (Oxford). 2014 Jul 25;2014. doi: 10.1093/database/bau073. Print 2014. PMID: 25062914; PMCID: PMC4110697.
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NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data.

BMC genomics

Kim NK, Jayatillake RV, Spouge JL.
PMID: 23706083
BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349.

BACKGROUND: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.RESULTS: We propose a rigorous...

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Kim NK, Jayatillake RV, Spouge JL. NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics. 2013;14:349doi: 10.1186/1471-2164-14-349.
Kim, N. K., Jayatillake, R. V., & Spouge, J. L. (2013). NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC genomics, 14349. https://doi.org/10.1186/1471-2164-14-349
Kim, Nak-Kyeong, et al. "NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data." BMC genomics vol. 14 (2013): 349. doi: https://doi.org/10.1186/1471-2164-14-349
Kim NK, Jayatillake RV, Spouge JL. NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349. PMID: 23706083; PMCID: PMC3672025.
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The Challenges of Creating a Gold Standard for De-identification Research.

AMIA ... Annual Symposium proceedings. AMIA Symposium

Browne AC, Kayaalp M, Dodd ZA, Sagan P, McDonald CJ.
PMID: 25954338
AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014.

We created a Gold Standard corpus comprised over 20,000 records of annotated narrative clinical reports for use in the training and evaluation of NLM Scrubber, a de-identification software system for medical records. Our experience with designing the corpus demonstrated...

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Browne AC, Kayaalp M, Dodd ZA, et al. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014;2014:353-8
Browne, A. C., Kayaalp, M., Dodd, Z. A., Sagan, P., & McDonald, C. J. (2014). The Challenges of Creating a Gold Standard for De-identification Research. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2014353-8.
Browne, Allen C, et al. "The Challenges of Creating a Gold Standard for De-identification Research." AMIA ... Annual Symposium proceedings. AMIA Symposium vol. 2014 (2014): 353-8.
Browne AC, Kayaalp M, Dodd ZA, Sagan P, McDonald CJ. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014. PMID: 25954338; PMCID: PMC4420002.
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Lyme Neuroborreliosis.

Continuum (Minneapolis, Minn.)

Marques AR.
PMID: 26633786
Continuum (Minneap Minn). 2015 Dec;21(6):1729-44. doi: 10.1212/CON.0000000000000252.

PURPOSE OF REVIEW: Lyme disease, caused by the spirochete Borrelia burgdorferi, is the most common tick-borne illness in the United States and Europe. Lyme disease usually begins with the characteristic skin lesion, erythema migrans, at the site of the...

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Marques AR. Lyme Neuroborreliosis. Continuum (Minneap Minn). 2015;21(6):1729-44doi: 10.1212/CON.0000000000000252.
Marques, A. R. (2015). Lyme Neuroborreliosis. Continuum (Minneapolis, Minn.), 21(6), 1729-44. https://doi.org/10.1212/CON.0000000000000252
Marques, Adriana R. "Lyme Neuroborreliosis." Continuum (Minneapolis, Minn.) vol. 21,6 (2015): 1729-44. doi: https://doi.org/10.1212/CON.0000000000000252
Marques AR. Lyme Neuroborreliosis. Continuum (Minneap Minn). 2015 Dec;21(6):1729-44. doi: 10.1212/CON.0000000000000252. PMID: 26633786.
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PI3K and NADPH oxidase: a class act.

Blood

Kennedy AD, DeLeo FR.
PMID: 19064736
Blood. 2008 Dec 15;112(13):4788-9. doi: 10.1182/blood-2008-09-179135.

No abstract available.

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Kennedy AD, DeLeo FR. PI3K and NADPH oxidase: a class act. Blood. 2008;112(13):4788-9doi: 10.1182/blood-2008-09-179135.
Kennedy, A. D., & DeLeo, F. R. (2008). PI3K and NADPH oxidase: a class act. Blood, 112(13), 4788-9. https://doi.org/10.1182/blood-2008-09-179135
Kennedy, Adam D, and DeLeo, Frank R. "PI3K and NADPH oxidase: a class act." Blood vol. 112,13 (2008): 4788-9. doi: https://doi.org/10.1182/blood-2008-09-179135
Kennedy AD, DeLeo FR. PI3K and NADPH oxidase: a class act. Blood. 2008 Dec 15;112(13):4788-9. doi: 10.1182/blood-2008-09-179135. PMID: 19064736.
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Reprint of "Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)" [J. Struct. Biol. 160 (2007) 35-48].

Journal of structural biology

Aronova MA, Kim YC, Harmon R, Sousa AA, Zhang G, Leapman RD.
PMID: 18342742
J Struct Biol. 2008 Mar;161(3):322-35. doi: 10.1016/S1047-8477(08)00062-2.

We describe the development of quantitative electron spectroscopic tomography (QuEST), which provides 3-D distributions of elements on a nanometer scale. Specifically, it is shown that QuEST can be applied to map the distribution of phosphorus in unstained sections of...

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Aronova MA, Kim YC, Harmon R, et al. Reprint of "Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)" [J. Struct. Biol. 160 (2007) 35-48]. J Struct Biol. 2008;161(3):322-35doi: 10.1016/S1047-8477(08)00062-2.
Aronova, M. A., Kim, Y. C., Harmon, R., Sousa, A. A., Zhang, G., & Leapman, R. D. (2008). Reprint of "Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)" [J. Struct. Biol. 160 (2007) 35-48]. Journal of structural biology, 161(3), 322-35. https://doi.org/10.1016/S1047-8477(08)00062-2
Aronova, M A, et al. "Reprint of "Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)" [J. Struct. Biol. 160 (2007) 35-48]." Journal of structural biology vol. 161,3 (2008): 322-35. doi: https://doi.org/10.1016/S1047-8477(08)00062-2
Aronova MA, Kim YC, Harmon R, Sousa AA, Zhang G, Leapman RD. Reprint of "Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)" [J. Struct. Biol. 160 (2007) 35-48]. J Struct Biol. 2008 Mar;161(3):322-35. doi: 10.1016/S1047-8477(08)00062-2. PMID: 18342742.
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Reprint of "On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography" [J. Struct. Biol. 159 (2007) 507-522].

Journal of structural biology

Sousa AA, Aronova MA, Kim YC, Dorward LM, Zhang G, Leapman RD.
PMID: 18342743
J Struct Biol. 2008 Mar;161(3):336-51. doi: 10.1016/S1047-8477(08)00063-4.

Labeling with heavy atom clusters attached to antibody fragments is an attractive technique for determining the 3D distribution of specific proteins in cells using electron tomography. However, the small size of the labels makes them very difficult to detect...

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Sousa AA, Aronova MA, Kim YC, et al. Reprint of "On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography" [J. Struct. Biol. 159 (2007) 507-522]. J Struct Biol. 2008;161(3):336-51doi: 10.1016/S1047-8477(08)00063-4.
Sousa, A. A., Aronova, M. A., Kim, Y. C., Dorward, L. M., Zhang, G., & Leapman, R. D. (2008). Reprint of "On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography" [J. Struct. Biol. 159 (2007) 507-522]. Journal of structural biology, 161(3), 336-51. https://doi.org/10.1016/S1047-8477(08)00063-4
Sousa, A A, et al. "Reprint of "On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography" [J. Struct. Biol. 159 (2007) 507-522]." Journal of structural biology vol. 161,3 (2008): 336-51. doi: https://doi.org/10.1016/S1047-8477(08)00063-4
Sousa AA, Aronova MA, Kim YC, Dorward LM, Zhang G, Leapman RD. Reprint of "On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography" [J. Struct. Biol. 159 (2007) 507-522]. J Struct Biol. 2008 Mar;161(3):336-51. doi: 10.1016/S1047-8477(08)00063-4. PMID: 18342743.
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Access and ability to pay: the ethics of a tiered health care system.

Archives of internal medicine

Krohmal BJ, Emanuel EJ.
PMID: 17353489
Arch Intern Med. 2007 Mar 12;167(5):433-7. doi: 10.1001/archinte.167.5.433.

No abstract available.

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Krohmal BJ, Emanuel EJ. Access and ability to pay: the ethics of a tiered health care system. Arch Intern Med. 2007;167(5):433-7doi: 10.1001/archinte.167.5.433.
Krohmal, B. J., & Emanuel, E. J. (2007). Access and ability to pay: the ethics of a tiered health care system. Archives of internal medicine, 167(5), 433-7. https://doi.org/10.1001/archinte.167.5.433
Krohmal, Benjamin J, and Emanuel, Ezekiel J. "Access and ability to pay: the ethics of a tiered health care system." Archives of internal medicine vol. 167,5 (2007): 433-7. doi: https://doi.org/10.1001/archinte.167.5.433
Krohmal BJ, Emanuel EJ. Access and ability to pay: the ethics of a tiered health care system. Arch Intern Med. 2007 Mar 12;167(5):433-7. doi: 10.1001/archinte.167.5.433. PMID: 17353489.
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Does early growth hormone therapy prevent glucocorticoid-associated growth retardation in children with JIA?.

Nature clinical practice. Rheumatology

Rider LG, Leschek EW.
PMID: 18607398
Nat Clin Pract Rheumatol. 2008 Aug;4(8):394-5. doi: 10.1038/ncprheum0845. Epub 2008 Jul 08.

No abstract available.

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Rider LG, Leschek EW. Does early growth hormone therapy prevent glucocorticoid-associated growth retardation in children with JIA?. Nat Clin Pract Rheumatol. 2008;4(8):394-5doi: 10.1038/ncprheum0845.
Rider, L. G., & Leschek, E. W. (2008). Does early growth hormone therapy prevent glucocorticoid-associated growth retardation in children with JIA?. Nature clinical practice. Rheumatology, 4(8), 394-5. https://doi.org/10.1038/ncprheum0845
Rider, Lisa G, and Leschek, Ellen W. "Does early growth hormone therapy prevent glucocorticoid-associated growth retardation in children with JIA?." Nature clinical practice. Rheumatology vol. 4,8 (2008): 394-5. doi: https://doi.org/10.1038/ncprheum0845
Rider LG, Leschek EW. Does early growth hormone therapy prevent glucocorticoid-associated growth retardation in children with JIA?. Nat Clin Pract Rheumatol. 2008 Aug;4(8):394-5. doi: 10.1038/ncprheum0845. Epub 2008 Jul 08. PMID: 18607398.
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Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world.

Journal of clinical oncology : official journal of the American Society of Clinical Oncology

Kamangar F, Dores GM, Anderson WF.
PMID: 16682732
J Clin Oncol. 2006 May 10;24(14):2137-50. doi: 10.1200/JCO.2005.05.2308.

Efforts to reduce global cancer disparities begin with an understanding of geographic patterns in cancer incidence, mortality, and prevalence. Using the GLOBOCAN (2002) and Cancer Incidence in Five Continents databases, we describe overall cancer incidence, mortality, and prevalence, age-adjusted...

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Kamangar F, Dores GM, Anderson WF. Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world. J Clin Oncol. 2006;24(14):2137-50doi: 10.1200/JCO.2005.05.2308.
Kamangar, F., Dores, G. M., & Anderson, W. F. (2006). Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 24(14), 2137-50. https://doi.org/10.1200/JCO.2005.05.2308
Kamangar, Farin, et al. "Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world." Journal of clinical oncology : official journal of the American Society of Clinical Oncology vol. 24,14 (2006): 2137-50. doi: https://doi.org/10.1200/JCO.2005.05.2308
Kamangar F, Dores GM, Anderson WF. Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world. J Clin Oncol. 2006 May 10;24(14):2137-50. doi: 10.1200/JCO.2005.05.2308. PMID: 16682732.
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High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays.

BMC genomics

Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang WY, Hayes RB, Chanock SJ, Jones RC, Ramakrishnan R.
PMID: 19943955
BMC Genomics. 2009 Nov 28;10:561. doi: 10.1186/1471-2164-10-561.

BACKGROUND: Single nucleotide polymorphisms (SNPs) have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution in the human genomes. There is a need...

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Wang J, Lin M, Crenshaw A, et al. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics. 2009;10:561doi: 10.1186/1471-2164-10-561.
Wang, J., Lin, M., Crenshaw, A., Hutchinson, A., Hicks, B., Yeager, M., Berndt, S., Huang, W. Y., Hayes, R. B., Chanock, S. J., Jones, R. C., & Ramakrishnan, R. (2009). High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC genomics, 10561. https://doi.org/10.1186/1471-2164-10-561
Wang, Jun, et al. "High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays." BMC genomics vol. 10 (2009): 561. doi: https://doi.org/10.1186/1471-2164-10-561
Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang WY, Hayes RB, Chanock SJ, Jones RC, Ramakrishnan R. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics. 2009 Nov 28;10:561. doi: 10.1186/1471-2164-10-561. PMID: 19943955; PMCID: PMC2789104.
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DOMINE: a comprehensive collection of known and predicted domain-domain interactions.

Nucleic acids research

Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R.
PMID: 21113022
Nucleic Acids Res. 2011 Jan;39:D730-5. doi: 10.1093/nar/gkq1229. Epub 2010 Nov 27.

DOMINE is a comprehensive collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated DOMINE includes 2285 new domain-domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by...

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Yellaboina S, Tasneem A, Zaykin DV, et al. DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res. 2010;39:D730-5doi: 10.1093/nar/gkq1229.
Yellaboina, S., Tasneem, A., Zaykin, D. V., Raghavachari, B., & Jothi, R. (2011). DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic acids research, 39D730-5. https://doi.org/10.1093/nar/gkq1229
Yellaboina, Sailu, et al. "DOMINE: a comprehensive collection of known and predicted domain-domain interactions." Nucleic acids research vol. 39 (2011): D730-5. doi: https://doi.org/10.1093/nar/gkq1229
Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R. DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res. 2011 Jan;39:D730-5. doi: 10.1093/nar/gkq1229. Epub 2010 Nov 27. PMID: 21113022; PMCID: PMC3013741.
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Showing 1 to 12 of 64 entries