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Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains.

Frontiers in aging neuroscience

Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ.
PMID: 27536236
Front Aging Neurosci. 2016 Aug 03;8:183. doi: 10.3389/fnagi.2016.00183. eCollection 2016.

Human aging is associated with cognitive decline and an increased risk of neurodegenerative disease. Our objective for this study was to evaluate potential relationships between age and variation in gene expression across different regions of the brain. We analyzed...

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Brinkmeyer-Langford CL, Guan J, Ji G, et al. Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Front Aging Neurosci. 2016;8:183doi: 10.3389/fnagi.2016.00183.
Brinkmeyer-Langford, C. L., Guan, J., Ji, G., & Cai, J. J. (2016). Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Frontiers in aging neuroscience, 8183. https://doi.org/10.3389/fnagi.2016.00183
Brinkmeyer-Langford, Candice L, et al. "Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains." Frontiers in aging neuroscience vol. 8 (2016): 183. doi: https://doi.org/10.3389/fnagi.2016.00183
Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ. Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Front Aging Neurosci. 2016 Aug 03;8:183. doi: 10.3389/fnagi.2016.00183. eCollection 2016. PMID: 27536236; PMCID: PMC4971101.
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Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine.

Open forum infectious diseases

Chamcha V, Kannanganat S, Gangadhara S, Nabi R, Kozlowski PA, Montefiori DC, LaBranche CC, Wrammert J, Keele BF, Balachandran H, Sahu S, Lifton M, Santra S, Basu R, Moss B, Robinson HL, Amara RR.
PMID: 27006959
Open Forum Infect Dis. 2016 Feb 11;3(1):ofw034. doi: 10.1093/ofid/ofw034. eCollection 2016 Jan.

Background.  In this study, we analyzed the protective efficacy of a simian immunodeficiency virus (SIV) macaque 239 (SIVmac239) analogue of the clinically tested GOVX-B11 deoxyribonucleic acid (DNA)/modified vaccinia Ankara (MVA) human immunodeficiency virus vaccine. Methods.  The tested vaccine used...

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Chamcha V, Kannanganat S, Gangadhara S, et al. Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine. Open Forum Infect Dis. 2016;3(1):ofw034doi: 10.1093/ofid/ofw034.
Chamcha, V., Kannanganat, S., Gangadhara, S., Nabi, R., Kozlowski, P. A., Montefiori, D. C., LaBranche, C. C., Wrammert, J., Keele, B. F., Balachandran, H., Sahu, S., Lifton, M., Santra, S., Basu, R., Moss, B., Robinson, H. L., & Amara, R. R. (2016). Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine. Open forum infectious diseases, 3(1), ofw034. https://doi.org/10.1093/ofid/ofw034
Chamcha, Venkateswarlu, et al. "Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine." Open forum infectious diseases vol. 3,1 (2016): ofw034. doi: https://doi.org/10.1093/ofid/ofw034
Chamcha V, Kannanganat S, Gangadhara S, Nabi R, Kozlowski PA, Montefiori DC, LaBranche CC, Wrammert J, Keele BF, Balachandran H, Sahu S, Lifton M, Santra S, Basu R, Moss B, Robinson HL, Amara RR. Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine. Open Forum Infect Dis. 2016 Feb 11;3(1):ofw034. doi: 10.1093/ofid/ofw034. eCollection 2016 Jan. PMID: 27006959; PMCID: PMC4800464.
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Developing training for Data Safety Monitoring Board members: A National Institute of Allergy and Infectious Diseases case study.

Clinical trials (London, England)

Zuckerman J, van der Schalie B, Cahill K.
PMID: 26152835
Clin Trials. 2015 Dec;12(6):688-91. doi: 10.1177/1740774515591498. Epub 2015 Jul 07.

BACKGROUND: Data Safety Monitoring Boards primarily review accumulating data on clinical trials and provide recommendations to sponsors on whether a protocol should continue as planned, be modified, or be terminated. Data Safety Monitoring Boards often provide their recommendations based...

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Zuckerman J, van der Schalie B, Cahill K. Developing training for Data Safety Monitoring Board members: A National Institute of Allergy and Infectious Diseases case study. Clin Trials. 2015;12(6):688-91doi: 10.1177/1740774515591498.
Zuckerman, J., van der Schalie, B., & Cahill, K. (2015). Developing training for Data Safety Monitoring Board members: A National Institute of Allergy and Infectious Diseases case study. Clinical trials (London, England), 12(6), 688-91. https://doi.org/10.1177/1740774515591498
Zuckerman, Judith, et al. "Developing training for Data Safety Monitoring Board members: A National Institute of Allergy and Infectious Diseases case study." Clinical trials (London, England) vol. 12,6 (2015): 688-91. doi: https://doi.org/10.1177/1740774515591498
Zuckerman J, van der Schalie B, Cahill K. Developing training for Data Safety Monitoring Board members: A National Institute of Allergy and Infectious Diseases case study. Clin Trials. 2015 Dec;12(6):688-91. doi: 10.1177/1740774515591498. Epub 2015 Jul 07. PMID: 26152835; PMCID: PMC4643382.
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Stellettapeptins A and B, HIV-inhibitory cyclic depsipeptides from the marine sponge .

Tetrahedron letters

Shin HJ, Rashid MA, Cartner LK, Bokesch HR, Wilson JA, McMahon JB, Gustafson KR.
PMID: 26139946
Tetrahedron Lett. 2015 Jul 08;56(28):4215-4219. doi: 10.1016/j.tetlet.2015.05.058.

Two new HIV-inhibitory depsipeptides, stellettapeptins A (

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Shin HJ, Rashid MA, Cartner LK, et al. Stellettapeptins A and B, HIV-inhibitory cyclic depsipeptides from the marine sponge . Tetrahedron Lett. 2015;56(28):4215-4219doi: 10.1016/j.tetlet.2015.05.058.
Shin, H. J., Rashid, M. A., Cartner, L. K., Bokesch, H. R., Wilson, J. A., McMahon, J. B., & Gustafson, K. R. (2015). Stellettapeptins A and B, HIV-inhibitory cyclic depsipeptides from the marine sponge . Tetrahedron letters, 56(28), 4215-4219. https://doi.org/10.1016/j.tetlet.2015.05.058
Shin, Hee Jae, et al. "Stellettapeptins A and B, HIV-inhibitory cyclic depsipeptides from the marine sponge ." Tetrahedron letters vol. 56,28 (2015): 4215-4219. doi: https://doi.org/10.1016/j.tetlet.2015.05.058
Shin HJ, Rashid MA, Cartner LK, Bokesch HR, Wilson JA, McMahon JB, Gustafson KR. Stellettapeptins A and B, HIV-inhibitory cyclic depsipeptides from the marine sponge . Tetrahedron Lett. 2015 Jul 08;56(28):4215-4219. doi: 10.1016/j.tetlet.2015.05.058. PMID: 26139946; PMCID: PMC4484873.
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Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads.

BioData mining

Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X, Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang DW.
PMID: 27051465
BioData Min. 2016 Apr 05;9:13. doi: 10.1186/s13040-016-0090-8. eCollection 2016.

BACKGROUND: Gene isoforms are commonly found in both prokaryotes and eukaryotes. Since each isoform may perform a specific function in response to changing environmental conditions, studying the dynamics of gene isoforms is important in understanding biological processes and disease...

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Liang M, Raley C, Zheng X, et al. Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData Min. 2016;9:13doi: 10.1186/s13040-016-0090-8.
Liang, M., Raley, C., Zheng, X., Kutty, G., Gogineni, E., Sherman, B. T., Sun, Q., Chen, X., Skelly, T., Jones, K., Stephens, R., Zhou, B., Lau, W., Johnson, C., Imamichi, T., Jiang, M., Dewar, R., Lempicki, R. A., Tran, B., Kovacs, J. A., & Huang, D. W. (2016). Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData mining, 913. https://doi.org/10.1186/s13040-016-0090-8
Liang, Ma, et al. "Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads." BioData mining vol. 9 (2016): 13. doi: https://doi.org/10.1186/s13040-016-0090-8
Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X, Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang DW. Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData Min. 2016 Apr 05;9:13. doi: 10.1186/s13040-016-0090-8. eCollection 2016. PMID: 27051465; PMCID: PMC4820869.
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Enabling Ontology Based Semantic Queries in Biomedical Database Systems.

International journal of semantic computing

Zheng S, Wang F, Lu J.
PMID: 25541585
Int J Semant Comput. 2014 Mar;8(1):67-83. doi: 10.1142/S1793351X14500032.

There is a lack of tools to ease the integration and ontology based semantic queries in biomedical databases, which are often annotated with ontology concepts. We aim to provide a middle layer between ontology repositories and semantically annotated databases...

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Zheng S, Wang F, Lu J. Enabling Ontology Based Semantic Queries in Biomedical Database Systems. Int J Semant Comput. 2014;8(1):67-83doi: 10.1142/S1793351X14500032.
Zheng, S., Wang, F., & Lu, J. (2014). Enabling Ontology Based Semantic Queries in Biomedical Database Systems. International journal of semantic computing, 8(1), 67-83. https://doi.org/10.1142/S1793351X14500032
Zheng, Shuai, et al. "Enabling Ontology Based Semantic Queries in Biomedical Database Systems." International journal of semantic computing vol. 8,1 (2014): 67-83. doi: https://doi.org/10.1142/S1793351X14500032
Zheng S, Wang F, Lu J. Enabling Ontology Based Semantic Queries in Biomedical Database Systems. Int J Semant Comput. 2014 Mar;8(1):67-83. doi: 10.1142/S1793351X14500032. PMID: 25541585; PMCID: PMC4275106.
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Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data.

PloS one

Mudunuri US, Khouja M, Repetski S, Venkataraman G, Che A, Luke BT, Girard FP, Stephens RM.
PMID: 24312478
PLoS One. 2013 Dec 02;8(12):e80503. doi: 10.1371/journal.pone.0080503. eCollection 2013.

As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not...

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Mudunuri US, Khouja M, Repetski S, et al. Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data. PLoS One. 2013;8(12):e80503doi: 10.1371/journal.pone.0080503.
Mudunuri, U. S., Khouja, M., Repetski, S., Venkataraman, G., Che, A., Luke, B. T., Girard, F. P., & Stephens, R. M. (2013). Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data. PloS one, 8(12), e80503. https://doi.org/10.1371/journal.pone.0080503
Mudunuri, Uma S, et al. "Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data." PloS one vol. 8,12 (2013): e80503. doi: https://doi.org/10.1371/journal.pone.0080503
Mudunuri US, Khouja M, Repetski S, Venkataraman G, Che A, Luke BT, Girard FP, Stephens RM. Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data. PLoS One. 2013 Dec 02;8(12):e80503. doi: 10.1371/journal.pone.0080503. eCollection 2013. PMID: 24312478; PMCID: PMC3846626.
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An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer.

Breast cancer : basic and clinical research

Danforth DN, Warner AC, Wangsa D, Ried T, Duelli D, Filie AC, Prindiville SA.
PMID: 26078587
Breast Cancer (Auckl). 2015 Jun 08;9:31-40. doi: 10.4137/BCBCR.S23577. eCollection 2015.

BACKGROUND: There is a strong need to define the molecular changes in normal at-risk breast epithelium to identify biomarkers and new targets for breast cancer prevention and to develop a molecular signature for risk assessment. Improved methods of breast...

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Danforth DN, Warner AC, Wangsa D, et al. An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer. Breast Cancer (Auckl). 2015;9:31-40doi: 10.4137/BCBCR.S23577.
Danforth, D. N., Warner, A. C., Wangsa, D., Ried, T., Duelli, D., Filie, A. C., & Prindiville, S. A. (2015). An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer. Breast cancer : basic and clinical research, 931-40. https://doi.org/10.4137/BCBCR.S23577
Danforth, David N, et al. "An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer." Breast cancer : basic and clinical research vol. 9 (2015): 31-40. doi: https://doi.org/10.4137/BCBCR.S23577
Danforth DN, Warner AC, Wangsa D, Ried T, Duelli D, Filie AC, Prindiville SA. An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer. Breast Cancer (Auckl). 2015 Jun 08;9:31-40. doi: 10.4137/BCBCR.S23577. eCollection 2015. PMID: 26078587; PMCID: PMC4462519.
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Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies.

Chemical science

Baloban M, Shcherbakova DM, Pletnev S, Pletnev VZ, Lagarias JC, Verkhusha VV.
PMID: 28936332
Chem Sci. 2017 Jun 01;8(6):4546-4557. doi: 10.1039/c7sc00855d. Epub 2017 May 04.

Brighter near-infrared (NIR) fluorescent proteins (FPs) are required for multicolor microscopy and deep-tissue imaging. Here, we present structural and biochemical analyses of three monomeric, spectrally distinct phytochrome-based NIR FPs, termed miRFPs. The miRFPs are closely related and differ by...

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Baloban M, Shcherbakova DM, Pletnev S, et al. Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Chem Sci. 2017;8(6):4546-4557doi: 10.1039/c7sc00855d.
Baloban, M., Shcherbakova, D. M., Pletnev, S., Pletnev, V. Z., Lagarias, J. C., & Verkhusha, V. V. (2017). Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Chemical science, 8(6), 4546-4557. https://doi.org/10.1039/c7sc00855d
Baloban, Mikhail, et al. "Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies." Chemical science vol. 8,6 (2017): 4546-4557. doi: https://doi.org/10.1039/c7sc00855d
Baloban M, Shcherbakova DM, Pletnev S, Pletnev VZ, Lagarias JC, Verkhusha VV. Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Chem Sci. 2017 Jun 01;8(6):4546-4557. doi: 10.1039/c7sc00855d. Epub 2017 May 04. PMID: 28936332; PMCID: PMC5590093.
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LUNGx Challenge for computerized lung nodule classification: reflections and lessons learned.

Journal of medical imaging (Bellingham, Wash.)

Armato SG, Hadjiiski L, Tourassi GD, Drukker K, Giger ML, Li F, Redmond G, Farahani K, Kirby JS, Clarke LP.
PMID: 26158094
J Med Imaging (Bellingham). 2015 Apr;2(2):020103. doi: 10.1117/1.JMI.2.2.020103.

No abstract available.

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Armato SG, Hadjiiski L, Tourassi GD, et al. LUNGx Challenge for computerized lung nodule classification: reflections and lessons learned. J Med Imaging (Bellingham). 2015;2(2):020103doi: 10.1117/1.JMI.2.2.020103.
Armato, S. G., Hadjiiski, L., Tourassi, G. D., Drukker, K., Giger, M. L., Li, F., Redmond, G., Farahani, K., Kirby, J. S., & Clarke, L. P. (2015). LUNGx Challenge for computerized lung nodule classification: reflections and lessons learned. Journal of medical imaging (Bellingham, Wash.), 2(2), 020103. https://doi.org/10.1117/1.JMI.2.2.020103
Armato, Samuel G, et al. "LUNGx Challenge for computerized lung nodule classification: reflections and lessons learned." Journal of medical imaging (Bellingham, Wash.) vol. 2,2 (2015): 020103. doi: https://doi.org/10.1117/1.JMI.2.2.020103
Armato SG, Hadjiiski L, Tourassi GD, Drukker K, Giger ML, Li F, Redmond G, Farahani K, Kirby JS, Clarke LP. LUNGx Challenge for computerized lung nodule classification: reflections and lessons learned. J Med Imaging (Bellingham). 2015 Apr;2(2):020103. doi: 10.1117/1.JMI.2.2.020103. PMID: 26158094; PMCID: PMC4489507.
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Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

Journal of chemical theory and computation

Khavrutskii IV, Wallqvist A.
PMID: 21151738
J Chem Theory Comput. 2010 Nov 09;6(11):3427-3441. doi: 10.1021/ct1003302.

This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference...

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Khavrutskii IV, Wallqvist A. Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. J Chem Theory Comput. 2010;6(11):3427-3441doi: 10.1021/ct1003302.
Khavrutskii, I. V., & Wallqvist, A. (2010). Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. Journal of chemical theory and computation, 6(11), 3427-3441. https://doi.org/10.1021/ct1003302
Khavrutskii, Ilja V, and Wallqvist, Anders. "Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange." Journal of chemical theory and computation vol. 6,11 (2010): 3427-3441. doi: https://doi.org/10.1021/ct1003302
Khavrutskii IV, Wallqvist A. Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. J Chem Theory Comput. 2010 Nov 09;6(11):3427-3441. doi: 10.1021/ct1003302. PMID: 21151738; PMCID: PMC2998072.
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Analysis of Botulinum Neurotoxin Serotype A Metalloprotease Inhibitors: Analogs of a Chemotype for Therapeutic Development in the Context of a Three-Zone Pharmacophore.

Open access bioinformatics

Burnett JC, Li B, Pai R, Cardinale SC, Butler MM, Peet NP, Moir D, Bavari S, Bowlin T.
PMID: 21103387
Open Access Bioinformatics. 2010 Apr 01;2010(2):11-18. doi: 10.2147/OAB.S7251.

Botulinum neurotoxins (BoNTs), and in particular serotype A, are the most poisonous of known biological substances, and are responsible for the flaccid paralysis of the disease state botulism. Because of the extreme toxicity of these enzymes, BoNTs are considered...

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Burnett JC, Li B, Pai R, et al. Analysis of Botulinum Neurotoxin Serotype A Metalloprotease Inhibitors: Analogs of a Chemotype for Therapeutic Development in the Context of a Three-Zone Pharmacophore. Open Access Bioinformatics. 2010;2010(2):11-18doi: 10.2147/OAB.S7251.
Burnett, J. C., Li, B., Pai, R., Cardinale, S. C., Butler, M. M., Peet, N. P., Moir, D., Bavari, S., & Bowlin, T. (2010). Analysis of Botulinum Neurotoxin Serotype A Metalloprotease Inhibitors: Analogs of a Chemotype for Therapeutic Development in the Context of a Three-Zone Pharmacophore. Open access bioinformatics, 2010(2), 11-18. https://doi.org/10.2147/OAB.S7251
Burnett, James C, et al. "Analysis of Botulinum Neurotoxin Serotype A Metalloprotease Inhibitors: Analogs of a Chemotype for Therapeutic Development in the Context of a Three-Zone Pharmacophore." Open access bioinformatics vol. 2010,2 (2010): 11-18. doi: https://doi.org/10.2147/OAB.S7251
Burnett JC, Li B, Pai R, Cardinale SC, Butler MM, Peet NP, Moir D, Bavari S, Bowlin T. Analysis of Botulinum Neurotoxin Serotype A Metalloprotease Inhibitors: Analogs of a Chemotype for Therapeutic Development in the Context of a Three-Zone Pharmacophore. Open Access Bioinformatics. 2010 Apr 01;2010(2):11-18. doi: 10.2147/OAB.S7251. PMID: 21103387; PMCID: PMC2983112.
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