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oncinfo [2019/05/08 05:33]
admin [Open positions]
oncinfo [2020/04/21 18:08] (current)
admin [Current and former lab members]
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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]]
 +  - [[:​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 =====
  
-{{:​wiki:​public:​cave2017.jpg?direct&600|cave2017.jpg}}[[:​cave_2017|Cave 2017]]+{{:​wiki:​public:​20191113_115359-cut.jpg?nolink&2072x1901|20191113_115359-cut.jpg}} 
 + 
 +Photos: [[:​lost_maple_2019|Lost Maples 2019]], ​[[:​cave_2017|Cave 2017]]
  
-  - [[http://​uthscsa.edu/​csa/​faculty/​Zare.asp|Dr. Habil Zare]] (the PI, {{:​wiki:​public:​cv_habil_zare.pdf|CV}}, lab [[:​habils_lab_notebook|notebook]])+  - [[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]])
   - [[:​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)
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   - [[:​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
-  - [[:Meghan_Short|Meghan Short]] (Guest postdoc)+  - Dr. [[:meghan_short|Meghan Short]] (Postdoc Associate since 2019) 
 +  - [[:​shiva_kazempour|Shiva Kazempour]] (Visiting Scientist since 2019). 
 +  - Dr. [[:​raheleh_roudi|Raheleh Roudi]] (Visiting Scientist since 2020). 
 + 
 +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 =====
  
-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. There are also some opportunities to apply for postdoctoral fellowship [[:​postdoctorial_fellowship_awards|awards]]. Taking an [[:r_test|R test]] is essential in the interview process.+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]]. Taking an [[:r_test|R test]] is essential in the interview process.
  
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 ===== Computational resources ===== ===== Computational resources =====
  
-To run our //in silico// experiments,​ we use 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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 ===== Educational services ===== ===== Educational services =====
  
-The "​[[:​bioinformatics_for_biologist_workshop|Bioinformatics for biologist workshop]]"​ is a practical introduction to some basic bioinformatics tools for audience with little computational skills. Slides are available from the workshop page. Additional resources are listed at "How to begin [[:​how_to|learning]] bioinformatics?"​ 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.\\ +The "​[[:​bioinformatics_for_biologist_workshop|Bioinformatics for biologist workshop]]"​ is a practical introduction to some basic bioinformatics tools for audience with little computational skills. Slides are available from the workshop page. Additional resources are listed at "How to begin [[:​how_to|learning]] bioinformatics?"​ 
-\\ + 
-[[:​for_members|For members]]+- The [[https://​docs.google.com/​presentation/​d/​1El0rxBw8lRBCf0nhqLqaXBOTWE20o1G7k4huXX150Wo/​edit#​slide=id.g63f2c216dd_0_0|Slides]] for Habil'​s hands-on workshop in the 2019 Neurepiomics [[https://​biggsinstitute.org/​events/​neurepiomics/​|Course]]. 
 + 
 + 
 +==== How to ==== 
 + 
 +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]]
  
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