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oncinfo [2021/10/25 14:44] – [Open positions] admin | oncinfo [2024/02/01 21:13] – habil |
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===== List of projects ===== | ===== List of projects ===== |
- [[:multiomics_analysis_for_dementia|Multiomics analysis for dementia]] | - [[:multiomics_analysis_for_dementia|Multiomics analysis for dementia]] |
- [[:serum_biomarkers_for_neurodegeneration|Serum biomarkers for neurodegeneration ]] | - [[:serum_biomarkers_for_neurodegeneration|Serum biomarkers for neurodegeneration ]] |
| - [[:the_effect_of_cellular_senescence_in_neurodegeneration|The effect of cellular senescence in neurodegeneration ]] |
- [[:rapamycin|Rapamycin effects on aging-associated pathologies]] | - [[:rapamycin|Rapamycin effects on aging-associated pathologies]] |
| - [[:obesity|Epitranscriptomics of obesity]] |
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===== Current and former lab members ===== | ===== Current and former lab members ===== |
{{:wiki:public:20191113_115359-cut.jpg?nolink&2072x1901|20191113_115359-cut.jpg}} | {{:wiki:public:20191113_115359-cut.jpg?nolink&2072x1901|20191113_115359-cut.jpg}} |
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Photos: {{:wiki:public:rahelehl.jpg?linkonly|Raheleh's}} goodbye lunch 2021, [[:lost_maple_2019|Lost Maples 2019]], [[:cave_2017|Cave 2017]] | Photos: Habil and [[https://uthealthsanantonio.zenfolio.com/p206362730|Shiva]] 2022, {{:wiki:public:rahelehl.jpg?linkonly|Raheleh's}} good bye lunch 2021, [[: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, {{:cv_habil_zare.pdf|CV}}, lab [[:habils_lab_notebook|notebook]]) | - [[https://www.uthscsa.edu/academics/biomedical-sciences/profile/zare|Dr. Habil Zare]] (the PI, [[https://www.dropbox.com/scl/fi/x490hnsowipfu1u6v5zwc/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, 2014-2016, Update: Software Developer at Crossvale Inc in Dallas) | - [[:rupesh_agrahari|Rupesh Agrahari]] (graduate student, 2014-2016, Update: Software Developer at Crossvale Inc in Dallas) |
- [[: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, 2018-2020) | - [[:ghazal_ebrahimi|Ghazal Ebrahimi ]](Volunteer undergraduate student from Sharif University, 2018-2020) |
- Dr. [[:isha_mehta|Isha Mehta]] (Postdoctoral Associate, since 2019){{ :wiki:public:skype-20200721-085353.jpeg?direct&170x184|skype-20200721-085353.jpeg}} | - Dr. [[:isha_mehta|Isha Mehta]] (Postdoctoral Associate, 2019-2022, Update: Research Scientist at the University of Pittsburgh School of Medicine){{ :wiki:public:skype-20200721-085353.jpeg?direct&170x184|skype-20200721-085353.jpeg}} |
- Dr. [[:meghan_short|Meghan Short]] (Postdoc Associate 2019-2020, Update: Postdoctoral Associate in [[https://huttenhower.sph.harvard.edu/|Huttenhower]] Lab at the Broad Institute) | - Dr. [[:meghan_short|Meghan Short]] (Postdoc Associate 2019-2020, Update: Postdoctoral Associate in [[https://huttenhower.sph.harvard.edu/|Huttenhower]] Lab at the Broad Institute, Update: [[https://www.tuftsctsi.org/people/meghan-short/|Statistician]] at Tufts Medical Center) |
- [[:shiva_kazempour|Shiva Kazempour]] (Visiting Scientist since 2019) | - [[:shiva_kazempour|Shiva Kazempour]] (Visiting Scientist 2019-2021 and PhD student since 2022) |
- Dr. [[:raheleh_roudi|Raheleh Roudi]] (Visiting Scientist 2020, Update: Postdoctoral Associate in [[https://med.umn.edu/bio/dom-a-z/guisheng-song|Song]] Lab at University of Minnesota Twin Cities) | - Dr. [[:raheleh_roudi|Raheleh Roudi]] (Visiting Scientist 2020-2021, Postdoctoral Associate in [[https://med.umn.edu/bio/dom-a-z/guisheng-song|Song]] Lab at University of Minnesota Twin Cities, Update [[https://profiles.stanford.edu/raheleh-roudi|2022]]: Research Scientist in the Department of Radiology at Stanford University) |
| - Dr. [[:mohsen_sharifitabar|Mohsen Sharifi Tabar]] (Senior Research Scientist since 2022) |
| - Mehdi Manshadi (Guest PhD student 2020, [[https://oncinfo.org/_media/wiki:public:mehdi-manshadi-thesis_20230909.pdf|Thesis]]) |
| - Alan Shaji & Mia Wallace (High school students in the 2022 Northside summer [[https://pipettegazette.uthscsa.edu/2017/08/11/a-window-into-science-northside-isd-summer-mentorship-program/|program]]) |
| - Dr. [[:sogand_sajedi|Sogand Sajedi]] (Postdoc Associate 2022, Update: Postdoctoral Associate at the MD Amderson) |
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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. | 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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===== Open positions ===== | ===== Open positions ===== |
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Research assistantship and postdoctoral opportunities are available in the Oncinfo Lab. See the [[https://jobs.sciencecareers.org/job/486328/research-positions-in-computational-biology-at-all-levels-postdoctoral-phd-and-ms-students/?TrackID=148656|2018]] [{{:wiki:public:recruit_oncinfo_2018.pdf|pdf]}} and [[https://jobs.sciencecareers.org/job/498929/computational-biologist-interested-in-neurodegenerative-disorders-and-cancer-research/?TrackID=9|2019]] [{{:wiki:public:approved.pdf|pdf}} ] advertisements for more details on the postdoctoral position, and also if you are interested in joining the lab as a graduate student. PhD applicants must be strong in machine learning and knowledgeable in molecular biology to be successful in multidisciplinary research as illustrated in our exemplar[[:machine_learning_and_molecular_biology_requirements| papers]]. Even if the application deadline is passed, strong applicants with a masters degree may start //immediately// as a visiting scientist with possibility of joining the PhD program within a year. There are also some opportunities to apply for postdoctoral fellowship [[:postdoctorial_fellowship_awards|awards]]. Experienced postdocs can be promoted to an Instructor and then a Research Assistant Professor position. Taking an [[:r_test|R test]] is essential in the interview process. Also, be prepared to play [[https://www.google.com/search?q=minesweeper&oq=min&aqs=chrome.0.69i59j69i57j69i59j69i60l2j69i61j69i65l2.874j0j7&sourceid=chrome&ie=UTF-8|Minesweeper]] during the interview. | Research assistantship and postdoctoral opportunities are available in the Oncinfo Lab. See the [[https://jobs.sciencecareers.org/job/486328/research-positions-in-computational-biology-at-all-levels-postdoctoral-phd-and-ms-students/?TrackID=148656|2018]] [{{:wiki:public:recruit_oncinfo_2018.pdf|pdf]}} and [[https://jobs.sciencecareers.org/job/498929/computational-biologist-interested-in-neurodegenerative-disorders-and-cancer-research/?TrackID=9|2019]] [{{:wiki:public:approved.pdf|pdf}} ] advertisements for more details on the postdoctoral position, and also if you are interested in joining the lab as a graduate student. PhD applicants must be strong in machine learning and knowledgeable in molecular biology to be successful in multidisciplinary research as illustrated in our exemplar[[:machine_learning_and_molecular_biology_requirements| papers]]. Even if the application deadline is passed, strong applicants with a masters degree may start //immediately// as a visiting scientist with possibility of joining the PhD program within a year. There are also some opportunities to apply for postdoctoral fellowship [[:postdoctorial_fellowship_awards|awards]]. Experienced postdocs can be promoted to an Instructor and then a Research Assistant Professor position. Taking an [[:r_test|R test]] is essential in the interview process. Also, be prepared to play [[https://www.google.com/search?q=minesweeper&oq=min&aqs=chrome.0.69i59j69i57j69i59j69i60l2j69i61j69i65l2.874j0j7&sourceid=chrome&ie=UTF-8|Minesweeper]] during the interview. |
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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. 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]]. | 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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==== How to ==== | ==== How to ==== |
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Please feel free to use and contribute to our [[:how_to|How to]] page, which is a list of miscellaneous solutions for data analysis and other challenges in computational biology. \\ \\ [[:for_members|For members]] | Please feel free to use and contribute to our [[:how_to|How to]] page, which is a list of miscellaneous solutions for data analysis and other challenges in computational biology. \\ |
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| [[:for_members|For members]] |
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Views: | ===== Location: ===== |
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| 2.030V, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229 |
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