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oncinfo [2019/11/14 00:45] – [Current and former lab members] admin | oncinfo [2020/07/21 17:19] – [Current and former lab members] admin |
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- [[:clonal_decomposition|Clonal decomposition]] | - [[:clonal_decomposition|Clonal decomposition]] |
- [[:hepatocellular_carcinoma|Hepatocellular carcinoma]] | - [[:hepatocellular_carcinoma|Hepatocellular carcinoma]] |
- [[:molecular_mechanisms_ofalzheimers_disease|Molecular mechanisms of Alzheimer's disease]] | - [[:molecular_mechanisms_ofalzheimers_disease|Molecular mechanisms of Alzheimer's disease]] |
| - [[:somatic_insertions_of_transposons_in_tauopathies|Somatic insertions of transposons in tauopathies]] |
- [[:genome_evolution|Genome evolution]] | - [[:genome_evolution|Genome evolution]] |
- [[:multiomics_analysis_for_dementia|Multiomics analysis for dementia]] | - [[:multiomics_analysis_for_dementia|Multiomics analysis for dementia]] |
- [[:Rapamycin|Rapamycin effects on aging-associated pathologies]] | - [[:serum_biomarkers_for_neurodegeneration|Serum biomarkers for neurodegeneration ]] |
| - [[:rapamycin|Rapamycin effects on aging-associated pathologies]] |
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===== Current and former lab members ===== | ===== Current and former lab members ===== |
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{{:wiki:public:cave2017.jpg?direct&600|cave2017.jpg}}[[:lost_maple_2019|Lost Maple 2019]], [[:cave_2017|Cave 2017]] | {{:wiki:public:20191113_115359-cut.jpg?nolink&2072x1901|20191113_115359-cut.jpg}} |
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- [[https://www.uthscsa.edu/academics/biomedical-sciences/faculty/profile/65296/Zare,-Habil|Dr. Habil Zare]] (the PI, {{:wiki:public:cv_habil_zare_1.pdf|CV}}, lab [[:habils_lab_notebook|notebook]]) | Photos: [[:lost_maple_2019|Lost Maples 2019]], [[:cave_2017|Cave 2017]] |
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| - [[https://www.uthscsa.edu/academics/biomedical-sciences/faculty/profile/65296/Zare,-Habil|Dr. Habil Zare]] (the PI, {{:wiki:public:cv_habil_zare.pdf|CV}}, lab [[:habils_lab_notebook|notebook]]) |
- [[:shuvabrata_saha|Shuvabrata Saha]] (graduate student, left in 2014) | - [[:shuvabrata_saha|Shuvabrata Saha]] (graduate student, left in 2014) |
- [[:rupesh_agrahari|Rupesh Agrahari]] (graduate student, graduated in 2016, Update: Software Developer at Crossvale Inc in Dallas) | - [[:rupesh_agrahari|Rupesh Agrahari]] (graduate student, graduated in 2016, Update: Software Developer at Crossvale Inc in Dallas) |
- [[:amir_foroushani|Amir Foroushani]] (Postdoctoral Associate until 2016, Update: Computer Scientist at [[http://www.niaid.nih.gov/labsandresources/labs/aboutlabs/li/iiu/pages/default.aspx?wt.ac=bcIiu|Laboratory of Immunology]], NIAID, NIH) | - Dr. [[:amir_foroushani|Amir Foroushani]] (Postdoctoral Associate until 2016, Update: Computer Scientist at [[http://www.niaid.nih.gov/labsandresources/labs/aboutlabs/li/iiu/pages/default.aspx?wt.ac=bcIiu|Laboratory of Immunology]], NIAID, NIH) |
- Vignesh Kuppa (volunteer graduate student, left in 2015) | - Vignesh Kuppa (volunteer graduate student, left in 2015) |
- [[:jessica_zavadil|Jessica Zavadil]] (MD/PhD student in Dr. Christi Walter's lab at UTHSCSA, graduated in 2016) | - [[:jessica_zavadil|Jessica Zavadil]] (MD/PhD student in Dr. Christi Walter's lab at UTHSCSA, graduated in 2016) |
- [[:aamirzainulabadeen|Aamir ]][[:aamirzainulabadeen|Zainulabadeen]] (Visiting undergraduate student in summers 2016 and 2017 from Princeton University) | - [[:aamirzainulabadeen|Aamir ]][[:aamirzainulabadeen|Zainulabadeen]] (Visiting undergraduate student in summers 2016 and 2017 from Princeton University) |
- [[:philip_yao|Philip Yao]] (Visiting undergraduate student in summer 2016 from the University of Michigan) | - [[:philip_yao|Philip Yao]] (Visiting undergraduate student in summer 2016 from the University of Michigan, software engineer at Amazon) |
- [[:hanie_samimi|Hanie Samimi]] (graduate student, graduated in 2018. Update: PhD student at Texas State University) | - [[:hanie_samimi|Hanie Samimi]] (graduate student, graduated in 2018. Update: PhD student at Texas State University) |
- [[:bryan_shaw|Bryan Shaw]] (graduate student, left in 2017) | - [[:bryan_shaw|Bryan Shaw]] (graduate student, left in 2017) |
- [[:angela_zhang|Angela Zhang]] (2017 Summer Camp high school student) | - [[:angela_zhang|Angela Zhang]] (2017 Summer Camp high school student) |
- [[:shilpita_mitra-behura|Shilpita Mitra-Behura]] (2017 Summer Camp high school student) | - [[:shilpita_mitra-behura|Shilpita Mitra-Behura]] (2017 Summer Camp high school student) |
- [[:ghazal_ebrahimi|Ghazal Ebrahimi ]](Volunteer undergraduate student from Sharif University) | - [[:ghazal_ebrahimi|Ghazal Ebrahimi ]](Volunteer undergraduate student from Sharif University since 2018) |
- [[:isha_mehta|Isha Mehta]] (Postdoctoral Associate) | - Dr. [[:isha_mehta|Isha Mehta]] (Postdoctoral Associate, since 2019){{ :wiki:public:skype-20200721-085353.jpeg?direct&170x184|skype-20200721-085353.jpeg}} |
- [[:meghan_short|Meghan Short]] (Guest postdoc) | - Dr. [[:meghan_short|Meghan Short]] (Postdoc Associate since 2019) |
- [[:shiva_kazempour|Shiva Kazempour]] (Visiting Scientist since 2019). | - [[:shiva_kazempour|Shiva Kazempour]] (Visiting Scientist since 2019) |
| - Dr. [[:raheleh_roudi|Raheleh Roudi]] (Visiting Scientist since 2020) |
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| To help [[https://www.livescience.com/coronavirus-flatten-the-curve.html|flatten]] the COVID-19 curve, we have been working from home since mid March 2020. [[https://docs.google.com/document/d/1iCLinpkdAGRsRW_1u_QrPKbcc77_1Kl0CgdGP5UfKjI/edit#|This]] is the full list of the things we do to increase efficiency and to maintain mental health when working from home. |
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===== Computational resources ===== | ===== Computational resources ===== |
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To run our //in silico// experiments, we use several [[https://docs.google.com/document/d/1vP0MSHRQ9oMjnv02eiqrOY0cs0WaVxp5dyLjiWtSzrQ/edit|resources]] provided by The Texas Advanced Computing Center ([[https://www.tacc.utexas.edu/|TACC]]) e.g., [[https://www.tacc.utexas.edu/systems/lonestar|Lonestar]] , which is a computing system with over 30,00 cores, and [[https://www.tacc.utexas.edu/systems/stampede|Stampede]], which is one of the 10 top supercomputers in the world with 10 petaFLOPS dedicated to scientific research. We have also access to NSF-supported [[https://portal.xsede.org|XSEDE]] recourses including [[https://portal.xsede.org/jetstream|Jetstream]]. | To run our //in silico// experiments, we use several [[https://docs.google.com/document/d/1vP0MSHRQ9oMjnv02eiqrOY0cs0WaVxp5dyLjiWtSzrQ/edit|resources]] provided by The Texas Advanced Computing Center ([[https://www.tacc.utexas.edu/|TACC]]) e.g., [[https://www.tacc.utexas.edu/systems/lonestar|Lonestar]] , which is a computing system with over 30,00 cores, and [[https://www.tacc.utexas.edu/systems/stampede|Stampede]], which is one of the 10 top supercomputers in the world with 10 petaFLOPS dedicated to scientific research. Secure HEPA compliant resources at TACC include [[https://www.tacc.utexas.edu/systems/hikari|Hikari]], which has 10K cores and is connected to [[https://www.tacc.utexas.edu/systems/corral|Corral]] with a capacity of 15 PBs. We have also access to NSF-supported [[https://portal.xsede.org|XSEDE]] recourses including [[https://portal.xsede.org/jetstream|Jetstream]]. |
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