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Opening for Postdoctoral Research Fellow

January 10, 2018

The Position

The Wall Lab in the Department of Pediatrics, Division of Systems Medicine, and Department of Biomedical Data Science at Stanford University seeks a talented, highly motivated researcher with a background in computational genomics. The main project of the Lab is to identify genetic risk factors in Autism Spectrum Disorder with whole genome sequencing (WGS) data sets and associated phenotypes. Our data set is one of the largest of its kind providing a unique opportunity to analyze large-scale whole genome data sets in the cloud, to disentangle the genotype-to-phenotype roadmap for this complex polygenic disorder, and to work closely with groups of exciting collaborators.

Responsibilities include:

  • To lead in the development of computational tools and resources/databases to analyze whole genome data sets, especially for non-coding region analysis.
  • To provide bioinformatics resources to the members of the Lab.
  • To monitor and evaluate analytical aspects of new and emerging technologies.
  • To architect, implement, optimize and maintain a local data warehousing architecture capable of managing and providing efficient access to terabytes of research data.

The candidate will be called upon to present work at national and international research conferences.

Qualifications:

Required:

  • Ph.D. in computational biology/genomics or related discipline.
  • Proven understanding and experience in WGS pipelines, analyses, and databases.
  • Experience with WGS analysis tools: BWA, GATK, etc.
  • Experience with Linux/Unix/HPC environment.
  • Programming skills with proficiency in Python, Java, and/or R.

Desired:

  • Experience with cloud development ecosystems – Google or AWS.
  • Experience with statistical analysis is strongly preferred.
  • Capability of working independently as well as part of a team.
  • Ability to present/visualize outputs to multidisciplinary audience.

Interested candidates should send an email to Dennis Wall at dpwall@stanford.edu.


Stanford Researchers Explore Link Between Microbiome and Autism

October 04, 2017

The Wall Lab has launched the second phase of their Microbiome Project, now entitled M3: Microbiome, Metabolites, and the Mind! Check out this amazing press release on SF Chronicle about their project and share with others! They are actively recruiting families. Please see the study site for eligibility requirements and study procedures (all completed at home!).

Researchers explore link between gut bacteria and autism


It's Autism Awareness Month!

April 05, 2017

It’s that time of year to bring awareness to our community about autism, and what better way to do it than by attending Stanford’s events or participating in our studies! Here are some things you can do to bring awareness to your community:

2017 Dance-a-thon for Autism to benefit several autism-serving nonprofits, April 15
Join the “Bay Area Kind” team or make a donation to benefit autism-serving nonprofits in the bay area!

2017 Autism at Work Summit, April 12-14
Attend this conference at Stanford University to learn about careers for individuals with autism!

Our Studies:

Spread the word about GapMap!
We just launched our GapMap website and are looking for families affected by autism to add themselves to the map. Check it out and spread the word to help us gain a better understanding on the prevalence of autism and availability of resources!

Help us finish our Autism Glass RCT!
We are only 14 families away from completing our Autism Glass Study, so if you know any children ages 6-12 who may be interested in taking home a pair of autism glass for 6 weeks, send them over to our online screening questionnaire!


Opening for Postdoctoral Research Fellow

March 27, 2017

The Position

The Wall lab in the Division of Systems Medicine, Department of Pediatrics, has an immediate opening for a postdoctoral position. As a key member of the iHART (Hartwell Autism Informatics Research and Technology Initiative), the candidate will conduct bioinformatics and statistical analysis of whole-genome next generation sequencing data from over 5000 samples. This is an excellent opportunity for a successful candidate to perform novel research and publish results. Possible research projects include but are not limited to the development of machine learning/deep learning algorithms to study phenotype-genotype associations, applying statistical methods to identify risk genes, performing gene network analysis, and investigating the role of structural and copy number variants in the etiology of ASD and their association with the overall severity of ASD presentation.

Qualifications:

  • PhD degree in Computer Science, Bioinformatics, Computational Biology, Genomics, Molecular Biology, or related field
  • A track-record of publication in the top journals or conferences
  • Experience with one or more programming languages including Python, R, Perl, C++, Java
  • Experience in using standard bioinformatics toolkits and programs
  • Strong background in one or more of the following areas: data analysis, big data analytics, and machine learning
  • Team oriented with excellent written and verbal communication skills
  • Highly motivated, willing to learn, and capable of working independently with minimal supervision

Interested candidates should send an email to Dennis Wall at dpwall@stanford.edu.


Updates from the past few months

March 08, 2017

As always, the Wall Lab has been very busy these past few months! Here are some exciting updates:

Two new papers have been accepted for publication. First, the iHart team recently published a paper to the Pacific Symposium on Biocomputing entitled “De Novo Mutations in Autism Implicate the Synaptic Elimination Network,” which points to deregulation in synaptic elimination as a potential pathogenic mechanism for ASD. In addition, look out for another recently accepted paper that will be published soon in Translational Psychiatry! This paper, entitled “Crowdsourced validation of a machine learning classification system for autism and ADHD,” validates a screening tool with >96% accuracy to distinguish ASD from ADHD. Congratulations to the authors of these papers!

We also have some upcoming conferences and presentations that our lab will be attending. The Wall Lab is giving a table presentation at the 10th Annual Autism Spectrum Disorders Update at Stanford University on March 25th, 2017, which focuses on new research and services for individuals with autism and their parents, educators, and care providers. We will be giving a demonstration of two of our projects, Autism Glass and GapMap.

From May 10-13 in San Francisco, The International Meeting for Autism Research is taking place, and the Autism Glass team is attending! This is an annual scientific meeting to exchange scientific progress in ASD research from around the globe. The Autism Glass team will have a poster presentation along with an Autism Glass demonstration.

In addition to the above conferences and papers, here are some quick updates from several of our projects:

The Autism Glass team has been very busy. In addition to being nominated as a Katerva Award finalist and their newly redone website, they have three papers in review for preliminary studies that finished up last year, and their randomized control trial is currently underway. The study is halfway through their participant recruitment goal - If you’re interested in participating, be sure to fill out our screening questionnaire!

Likewise, GapMap is almost ready to go live to start collecting data for a more accurate estimate of autism prevalence in the US! We are very excited to launch in the next coming months. Please check back on the website for our launch!

Our Bangladesh Study, aiming to identify and diagnose every child with autism in Bangladesh before the age of 4 by analyzing mobile home videos and a short caregiver-directed questionnaire via machine learning, was recently awarded two grants: one from the Bill & Melinda Gates foundation and the other from Stanford Predictives and Diagnostics Accelerator! We are incredibly excited to be collaborating with Drs. Gary Darmstadt of Stanford University and Nalia Khan of Dhaka Shishu Children’s Hospital on this project.

Additionally, the Microbiome Project has recently finished up sending back its participants’ sequenced results and a paper is currently underway! Check out this press article from KQED published last October to learn more about the project.

And lastly, we are starting up another small study to examine how well parents with children with ASD can distinguish ASD in comparison to people without a child with ASD. We expect this to help us validate our participants’ ASD diagnoses in an accurate yet efficient way.

Check back soon for more exciting updates!