Colleagues to Visit

Long-term Weekly goals

  1. Baranzini Lab
  2. Witte Lab
  3. Jimmy Ye : Aviv Regev (Broad)
  4. Zaitlen Lab : Eliza Eskin (UCLA), Alkac Price, Peter Kraft (Harvard)  
  5. MAGMA is another useful pathway analysis tool for GWAS that employs a principal component analysis-based regression framework. It is fast and features good power. 
  6. ALIGATOR is a widely used pathway analysis tool developed for GWAS. With well-controlled type I error, it takes into account common genomic confounding factors. 
  7. WGCNA is a gene-expression data analysis tool that can find clusters of highly correlated genes. It summarizes the identified clusters using module eigengenes or intramodular hub genes, and look for enriched biology or functions.
  8. DAVID is one of the most widely used pathway analysis tool for high-throughput gene-based data (i.e., mRNA gene expression, proteomics data). It includes various functions, though be aware not to use this tool for genome data analysis!
  9. DAPPLE looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature. 
  10. DEPICT is an integrative GWAS analysis method that uses both established biological annotations and gene expression data. Given associated loci, It systematically prioritizes most likely causal genes by highlighting enriched pathways and relevant tissue/cell types.
  11. ​CytoScape is a useful visualization tool for network and pathway findings. 
  1. ASD Whole Genome Sequencing Regulatory: 
  2. Asian Neuroimaging 


Short-term Research Goals

  • In the google doc , everyone research students including me has
  1. Set weekly research goals
  2. Assess your progress in relation to the goals you set
  3. Write hours that you spent for research 
  • During a weekly meeting, go over those goals and progresses in front of everyone and talk about how everyone is doing
  • This helps
    1. I as a PI keep track on students' progresses
    2. Students learn to manage their time
    3. Most importantly, I try my best to achieve my weekly goals (treat yourself in the same manner as everyone else gets treated as I am also one of the lab members)

Target Grants

  • Alfred P. Sloan Foundation
  • $55K/year for 2 years
  • Deadline: Sep/15/2015
  • Fellows are selected on the basis of their independent research accomplishments, creativity, and potential to become leaders in the scientific community through their contributions to their field.
  • Connecting the DOTS - Effectively communicating science to non-scientists
  • The David Lucile Packard Foundation
  • Nomiated by institutions
  • 18 fellows each year, $875K for 5 years
  • Within the first three years of their faculty careers
  • Nominations are due to the Foundation by Mar/15/2016; April/20/2016 all application submitted; Oct/17/2016 announcement
  • Microsoft New Faculty Fellowship Program
  • Nominated by institutions --> Stanford, Sep/01 to school, Sep/30 to foundation
  • $200K
  • Within three years of first tenure track 
  • Computing research areas and innovative application of computing 
  • Emphasis should be on advancing computing research in novel directions 
  • No collaborative project 
  • Brain Research Foundation
  • Institution nomination --> need to check internal deadlines
  • 10 awards, each $80K for 2 years
  • assistant or associate professors working in the studies of brain function
  • Research project not funded by other sources
  • Rita Allen Foundation 
  • Nomiated by institutions --> need to check internal deadlines
  • $110K/year up to 5 years
  • The Smith Family Awards Program for Excellence in Biomedical Research 
  • Open to faculties in MA, Brown, or Yale
  • Within 2.5 years of assistant professors
  • Nominated by schools --> need to check internal deadlines
  • Up to 5 awards, $300K for 3 years
  • Searle Scholars Program
    • Recently begun their appointment at the assistant professor level
    • Submission material available Sep/01/2015; deadline Sep/30/2015; only the ones begun assistant faculty on or after July/01/2014; awards will be activated on July/01/2016
    • 158 participating institutions
    • 15 receipients each year
    • $300K for 3 years
  • Pew Biomedical Scholars
    • $240K for 4 years
    • One nomination from each institutions
    • Only assistant professors less than three years 

Useful Research Materials 

  • Persistence, confidence, flexibility, working smart  
  • METAL is a widely used meta analysis tool for whole genome data analysis. 
  • LocusZoom is a good plotting tool for regional GWAS association results. 
  • MQFAM is a multivariate association analysis tool that uses canonical correlation. 

Faculty Resources

  • PLINK/SEQ is an open-source C/C++ library designed for large-scale sequencing data analysis. 
  • The VEP (Variant Effect Predictor) determines the functional effect of variants, including SNPs, insertions, deletions, CNVs or structural variants on genes, transcripts, and protein sequence, as well as regulatory regions. 
  • RV-Test is a stand-alone rare variant testing package that can analyze both population-based and related samples.

Useful Job Application Materials

  • Cover letter
    • Tailor the letter to the department
    • Intrigues me: something impressive and makes the reader want to know the full story
    • Waht makes you stand out from the other candidates applying for this job?
    • Keep the letter short and to-the-point - can scan five seconds
    • Make sure that the person's career objectives do not match the job that I am recruiting for - see whether your background aligned with the listed requirements
  • Before start job applications
    • Know about yourself
      •  How flexible you can move?
  • The BrainSpan Atlas is a foundational resource for studying transcriptional mechanisms involved in human brain development.
  • The BrainCloud is a stand-alone GUI tool for exploring the temporal dynamics and genetic control of transcription in the human prefrontal cortex across the lifespan. 
  • The PsychENCODE project aims to generate a public resource of genomic, regulatory, epigenomic, transcriptomic, and proteomic data in healthy and diseased developing and adult human brains.

Neuroimaging Genomics Resources

  • The ENIGMA Consortium is the largest international efforts in neuroimaging genomics to study brain structure, function and disease. 
  • BRAINnet is an innovative research initiative that shares a collection of neuroimaging, cognitive, clinical, and genomic data for accelerating brain research.