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A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies

pipeline programs

Guttman DS.
GSID: YjblIjWX58sJ
S Thakur, DS Guttman - BMC bioinformatics, 2016 - Springer

… Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is …

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Thakur, S., & Guttman, D. S. (2016). A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. BMC bioinformatics, 17(1), 1-18.
Thakur, Shalabh, and David S. Guttman. "A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies." BMC bioinformatics 17.1 (2016): 1-18.
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Community‐based rapid HIV testing in homeless and marginally housed adults in San Francisco

community settings

Guzman D.
GSID: DLHDhCP2szQJ
JB Bucher, KM Thomas, D Guzman, E Riley… - HIV …, 2007 - Wiley Online Library

Background Standard two‐step HIV testing is limited by poor return‐for‐results rates and misses high‐risk individuals who do not access conventional testing facilities. Methods We …

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Bucher, J. B., Thomas, K. M., Guzman, D., Riley, E., Dela Cruz, N., & Bangsberg, D. R. (2007). Community‐based rapid HIV testing in homeless and marginally housed adults in San Francisco. HIV medicine, 8(1), 28-31.
Bucher, J. B., et al. "Community‐based rapid HIV testing in homeless and marginally housed adults in San Francisco." HIV medicine 8.1 (2007): 28-31.
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Mycotic Keratitis in a Khaki Campbell Duck ( Anas platyrhynchos domesticus).

Journal of avian medicine and surgery

Sadar MJ, Guzman DS, Burton AG, Byrne BA, Wiggans KT, Hollingsworth SR.
PMID: 25843471
J Avian Med Surg. 2014 Dec;28(4):322-9. doi: 10.1647/2013-050.

A 1.5-year-old, intact female khaki Campbell duck (Anas platyrhynchos domesticus) was evaluated for lethargy and a swollen left eye (OS). Mucoid discharge, chemosis, and conjunctival hyperemia with trace aqueous flare, indicating anterior uveitis, in the anterior chamber were evident...

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Sadar MJ, Guzman DS, Burton AG, et al. Mycotic Keratitis in a Khaki Campbell Duck ( Anas platyrhynchos domesticus). J Avian Med Surg. 2014;28(4):322-9doi: 10.1647/2013-050.
Sadar, M. J., Guzman, D. S., Burton, A. G., Byrne, B. A., Wiggans, K. T., & Hollingsworth, S. R. (2014). Mycotic Keratitis in a Khaki Campbell Duck ( Anas platyrhynchos domesticus). Journal of avian medicine and surgery, 28(4), 322-9. https://doi.org/10.1647/2013-050
Sadar, Miranda J, et al. "Mycotic Keratitis in a Khaki Campbell Duck ( Anas platyrhynchos domesticus)." Journal of avian medicine and surgery vol. 28,4 (2014): 322-9. doi: https://doi.org/10.1647/2013-050
Sadar MJ, Guzman DS, Burton AG, Byrne BA, Wiggans KT, Hollingsworth SR. Mycotic Keratitis in a Khaki Campbell Duck ( Anas platyrhynchos domesticus). J Avian Med Surg. 2014 Dec;28(4):322-9. doi: 10.1647/2013-050. PMID: 25843471.
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Multiple periodicity in a nanoparticle-based single-electron transistor.

Nature communications

Bitton O, Gutman DB, Berkovits R, Frydman A.
PMID: 28864825
Nat Commun. 2017 Sep 01;8(1):402. doi: 10.1038/s41467-017-00442-6.

A single-electron transistor is a nano-device with large potential for low-power applications that can be used as logic elements in integrated circuits. In this device, the conductance oscillates with a well-defined period due to the Coulomb blockade effect. By...

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Bitton O, Gutman DB, Berkovits R, et al. Multiple periodicity in a nanoparticle-based single-electron transistor. Nat Commun. 2017;8(1):402doi: 10.1038/s41467-017-00442-6.
Bitton, O., Gutman, D. B., Berkovits, R., & Frydman, A. (2017). Multiple periodicity in a nanoparticle-based single-electron transistor. Nature communications, 8(1), 402. https://doi.org/10.1038/s41467-017-00442-6
Bitton, O, et al. "Multiple periodicity in a nanoparticle-based single-electron transistor." Nature communications vol. 8,1 (2017): 402. doi: https://doi.org/10.1038/s41467-017-00442-6
Bitton O, Gutman DB, Berkovits R, Frydman A. Multiple periodicity in a nanoparticle-based single-electron transistor. Nat Commun. 2017 Sep 01;8(1):402. doi: 10.1038/s41467-017-00442-6. PMID: 28864825; PMCID: PMC5581334.
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The 30-year mental health legacy of the Chernobyl disaster.

World psychiatry : official journal of the World Psychiatric Association (WPA)

Havenaar JM, Bromet EJ, Gluzman S.
PMID: 27265712
World Psychiatry. 2016 Jun;15(2):181-2. doi: 10.1002/wps.20335.

No abstract available.

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Havenaar JM, Bromet EJ, Gluzman S. The 30-year mental health legacy of the Chernobyl disaster. World Psychiatry. 2016;15(2):181-2doi: 10.1002/wps.20335.
Havenaar, J. M., Bromet, E. J., & Gluzman, S. (2016). The 30-year mental health legacy of the Chernobyl disaster. World psychiatry : official journal of the World Psychiatric Association (WPA), 15(2), 181-2. https://doi.org/10.1002/wps.20335
Havenaar, Johan M, et al. "The 30-year mental health legacy of the Chernobyl disaster." World psychiatry : official journal of the World Psychiatric Association (WPA) vol. 15,2 (2016): 181-2. doi: https://doi.org/10.1002/wps.20335
Havenaar JM, Bromet EJ, Gluzman S. The 30-year mental health legacy of the Chernobyl disaster. World Psychiatry. 2016 Jun;15(2):181-2. doi: 10.1002/wps.20335. PMID: 27265712; PMCID: PMC4911770.
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Generation of HLA-Universal iPSC-Derived Megakaryocytes and Platelets for Survival Under Refractoriness Conditions.

Molecular medicine (Cambridge, Mass.)

Börger AK, Eicke D, Wolf C, Gras C, Aufderbeck S, Schulze K, Engels L, Eiz-Vesper B, Schambach A, Guzman CA, Lachmann N, Moritz T, Martin U, Blasczyk R, Figueiredo C.
PMID: 27262025
Mol Med. 2016 Sep;22:274-285. doi: 10.2119/molmed.2015.00235. Epub 2016 May 16.

Platelet (PLT) transfusion is indispensable to maintain homeostasis in thrombocytopenic patients. However, PLT transfusion refractoriness is a common life-threatening condition observed in multitransfused patients. The most frequent immune cause for PLT transfusion refractoriness is the presence of alloantibodies specific...

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Börger AK, Eicke D, Wolf C, et al. Generation of HLA-Universal iPSC-Derived Megakaryocytes and Platelets for Survival Under Refractoriness Conditions. Mol Med. 2016;22:274-285doi: 10.2119/molmed.2015.00235.
Börger, A. K., Eicke, D., Wolf, C., Gras, C., Aufderbeck, S., Schulze, K., Engels, L., Eiz-Vesper, B., Schambach, A., Guzman, C. A., Lachmann, N., Moritz, T., Martin, U., Blasczyk, R., & Figueiredo, C. (2016). Generation of HLA-Universal iPSC-Derived Megakaryocytes and Platelets for Survival Under Refractoriness Conditions. Molecular medicine (Cambridge, Mass.), 22274-285. https://doi.org/10.2119/molmed.2015.00235
Börger, Ann-Kathrin, et al. "Generation of HLA-Universal iPSC-Derived Megakaryocytes and Platelets for Survival Under Refractoriness Conditions." Molecular medicine (Cambridge, Mass.) vol. 22 (2016): 274-285. doi: https://doi.org/10.2119/molmed.2015.00235
Börger AK, Eicke D, Wolf C, Gras C, Aufderbeck S, Schulze K, Engels L, Eiz-Vesper B, Schambach A, Guzman CA, Lachmann N, Moritz T, Martin U, Blasczyk R, Figueiredo C. Generation of HLA-Universal iPSC-Derived Megakaryocytes and Platelets for Survival Under Refractoriness Conditions. Mol Med. 2016 Sep;22:274-285. doi: 10.2119/molmed.2015.00235. Epub 2016 May 16. PMID: 27262025; PMCID: PMC5023513.
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Elevated Temperature Differentially Influences Effector-Triggered Immunity Outputs in Arabidopsis.

Frontiers in plant science

Menna A, Nguyen D, Guttman DS, Desveaux D.
PMID: 26617631
Front Plant Sci. 2015 Nov 09;6:995. doi: 10.3389/fpls.2015.00995. eCollection 2015.

Pseudomonas syringae is a Gram-negative bacterium that infects multiple plant species by manipulating cellular processes via injection of type three secreted effectors (T3SEs) into host cells. Nucleotide-binding leucine-rich repeat (NLR) resistance (R) proteins recognize specific T3SEs and trigger a...

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Menna A, Nguyen D, Guttman DS, et al. Elevated Temperature Differentially Influences Effector-Triggered Immunity Outputs in Arabidopsis. Front Plant Sci. 2015;6:995doi: 10.3389/fpls.2015.00995.
Menna, A., Nguyen, D., Guttman, D. S., & Desveaux, D. (2015). Elevated Temperature Differentially Influences Effector-Triggered Immunity Outputs in Arabidopsis. Frontiers in plant science, 6995. https://doi.org/10.3389/fpls.2015.00995
Menna, Alexandra, et al. "Elevated Temperature Differentially Influences Effector-Triggered Immunity Outputs in Arabidopsis." Frontiers in plant science vol. 6 (2015): 995. doi: https://doi.org/10.3389/fpls.2015.00995
Menna A, Nguyen D, Guttman DS, Desveaux D. Elevated Temperature Differentially Influences Effector-Triggered Immunity Outputs in Arabidopsis. Front Plant Sci. 2015 Nov 09;6:995. doi: 10.3389/fpls.2015.00995. eCollection 2015. PMID: 26617631; PMCID: PMC4637416.
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Helen Ollendorff Curth: A dermatologist's lasting legacy.

International journal of women's dermatology

Guzman AK, James WD.
PMID: 28492044
Int J Womens Dermatol. 2017 Feb 16;3(1):S70-S74. doi: 10.1016/j.ijwd.2017.02.015. eCollection 2017 Mar.

No abstract available.

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Guzman AK, James WD. Helen Ollendorff Curth: A dermatologist's lasting legacy. Int J Womens Dermatol. 2017;3(1):S70-S74doi: 10.1016/j.ijwd.2017.02.015.
Guzman, A. K., & James, W. D. (2017). Helen Ollendorff Curth: A dermatologist's lasting legacy. International journal of women's dermatology, 3(1), S70-S74. https://doi.org/10.1016/j.ijwd.2017.02.015
Guzman, Anthony K, and James, William D. "Helen Ollendorff Curth: A dermatologist's lasting legacy." International journal of women's dermatology vol. 3,1 (2017): S70-S74. doi: https://doi.org/10.1016/j.ijwd.2017.02.015
Guzman AK, James WD. Helen Ollendorff Curth: A dermatologist's lasting legacy. Int J Womens Dermatol. 2017 Feb 16;3(1):S70-S74. doi: 10.1016/j.ijwd.2017.02.015. eCollection 2017 Mar. PMID: 28492044; PMCID: PMC5419040.
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Log-periodic route to fractal functions.

Physical review. E, Statistical, nonlinear, and soft matter physics

Gluzman S, Sornette D.
PMID: 11909200
Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3):036142. doi: 10.1103/PhysRevE.65.036142. Epub 2002 Mar 07.

Log-periodic oscillations have been found to decorate the usual power-law behavior found to describe the approach to a critical point, when the continuous scale-invariance symmetry is partially broken into a discrete-scale invariance symmetry. For Ising or Potts spins with...

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Gluzman S, Sornette D. Log-periodic route to fractal functions. Phys Rev E Stat Nonlin Soft Matter Phys. 2002;65(3):036142doi: 10.1103/PhysRevE.65.036142.
Gluzman, S., & Sornette, D. (2002). Log-periodic route to fractal functions. Physical review. E, Statistical, nonlinear, and soft matter physics, 65(3), 036142. https://doi.org/10.1103/PhysRevE.65.036142
Gluzman, S, and Sornette, D. "Log-periodic route to fractal functions." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 65,3 (2002): 036142. doi: https://doi.org/10.1103/PhysRevE.65.036142
Gluzman S, Sornette D. Log-periodic route to fractal functions. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3):036142. doi: 10.1103/PhysRevE.65.036142. Epub 2002 Mar 07. PMID: 11909200.
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Self-consistent theory of rupture by progressive diffuse damage.

Physical review. E, Statistical, nonlinear, and soft matter physics

Gluzman S, Sornette D.
PMID: 11415195
Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jun;63(6):066129. doi: 10.1103/PhysRevE.63.066129. Epub 2001 May 25.

We analyze a self-consistent theory of crack growth controlled by a cumulative damage variable d(t) dependent on stress history, in the quasistatic regime where the sound wave velocity is taken as infinite. Depending upon the damage exponent m, which...

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Gluzman S, Sornette D. Self-consistent theory of rupture by progressive diffuse damage. Phys Rev E Stat Nonlin Soft Matter Phys. 2001;63(6):066129doi: 10.1103/PhysRevE.63.066129.
Gluzman, S., & Sornette, D. (2001). Self-consistent theory of rupture by progressive diffuse damage. Physical review. E, Statistical, nonlinear, and soft matter physics, 63(6), 066129. https://doi.org/10.1103/PhysRevE.63.066129
Gluzman, S, and Sornette, D. "Self-consistent theory of rupture by progressive diffuse damage." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 63,6 (2001): 066129. doi: https://doi.org/10.1103/PhysRevE.63.066129
Gluzman S, Sornette D. Self-consistent theory of rupture by progressive diffuse damage. Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jun;63(6):066129. doi: 10.1103/PhysRevE.63.066129. Epub 2001 May 25. PMID: 11415195.
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Recombination and clonality in natural populations of Escherichia coli.

Trends in ecology & evolution

Guttman DS.
PMID: 21237956
Trends Ecol Evol. 1997 Jan;12(1):16-22. doi: 10.1016/s0169-5347(96)10057-4.

Bacteria such as Escherichia coli have been commonly viewed as being primarily clonal organisms. As such, the genetic variation within clones was thought to be almost exclusively the result of the mutational process. This conclusion has recently been challenged...

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Guttman DS. Recombination and clonality in natural populations of Escherichia coli. Trends Ecol Evol. 1997;12(1):16-22doi: 10.1016/s0169-5347(96)10057-4.
Guttman, D. S. (1997). Recombination and clonality in natural populations of Escherichia coli. Trends in ecology & evolution, 12(1), 16-22. https://doi.org/10.1016/s0169-5347(96)10057-4
Guttman, D S. "Recombination and clonality in natural populations of Escherichia coli." Trends in ecology & evolution vol. 12,1 (1997): 16-22. doi: https://doi.org/10.1016/s0169-5347(96)10057-4
Guttman DS. Recombination and clonality in natural populations of Escherichia coli. Trends Ecol Evol. 1997 Jan;12(1):16-22. doi: 10.1016/s0169-5347(96)10057-4. PMID: 21237956.
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The toll-like receptor 2/6 ligand MALP-2 reduces the viability of Mycobacterium tuberculosis in murine macrophages.

The open microbiology journal

Palma C, Iona E, Ebensen T, Guzman CA, Cassone A.
PMID: 19471610
Open Microbiol J. 2009 Apr 03;3:47-52. doi: 10.2174/1874285800903010047.

Toll-like receptors (TLRs) sense conserved structures of pathogens and influence macrophage functions. Here we investigated the impact of TLR signaling on the modulation of macrophage defense mechanisms against infection of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis. We...

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Palma C, Iona E, Ebensen T, et al. The toll-like receptor 2/6 ligand MALP-2 reduces the viability of Mycobacterium tuberculosis in murine macrophages. Open Microbiol J. 2009;3:47-52doi: 10.2174/1874285800903010047.
Palma, C., Iona, E., Ebensen, T., Guzman, C. A., & Cassone, A. (2009). The toll-like receptor 2/6 ligand MALP-2 reduces the viability of Mycobacterium tuberculosis in murine macrophages. The open microbiology journal, 347-52. https://doi.org/10.2174/1874285800903010047
Palma, Carla, et al. "The toll-like receptor 2/6 ligand MALP-2 reduces the viability of Mycobacterium tuberculosis in murine macrophages." The open microbiology journal vol. 3 (2009): 47-52. doi: https://doi.org/10.2174/1874285800903010047
Palma C, Iona E, Ebensen T, Guzman CA, Cassone A. The toll-like receptor 2/6 ligand MALP-2 reduces the viability of Mycobacterium tuberculosis in murine macrophages. Open Microbiol J. 2009 Apr 03;3:47-52. doi: 10.2174/1874285800903010047. PMID: 19471610; PMCID: PMC2685717.
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Showing 1 to 12 of 188 entries