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We currently have openings for graduate students and postdoctoral fellows in computational systems biology. In particular, we are looking for researchers interested in studying human disease and drug development using systems biology and genomic techniques. Specific positions are listed below. If you are interested, please email us at natelewis3 at gmail or n4lewis ucsd edu

Development of gene networks for Autism clinical presentation and progression

Autism is a prenatal disorder due to dysregulation of multiple biological processes from proliferation and neurogenesis to synaptic development and neural network assembly. Through multimodality analyses of regulatory and brain-specific risk genes, networks, and signaling pathways, our recent work has developed a mechanistic model of how many different ASD risk genes may converge on similar molecular pathways to disrupt complex prenatal spatiotemporal developmental programs that lead to ASD. Identified hyperactivation of specific signaling pathways are correlated with early-age social symptom severity in ASD toddlers. Current work aims to define genomic dysregulations that account for early-age functional and neuroanatomical maldevelopment as well as predict clinical outcome. We are now seeking exceptional candidates interested in analyzing transcriptomic in the context of large multimodality genetic risk load, fMRI, MRI, eye tracking  and clinical datasets of more than a thousand children.  We aim to develop genomic network-level as well as multimodel biomarkers for autism diagnosis and prognosis. The researcher in this position will work with a dynamic team of outstanding graduate students, postdocs, and other researchers in the Lewis and Courchesne labs at UCSD. She or he will be expected to take the lead in preparing manuscripts, presentations, and patents. This work will leverage experience in bioinformatics, genomics, transcriptomics, systems biology, and machine learning. Necessary skills include an ability to operate in Linux-based systems and experience in programming languages such as MATLAB and/or Python. Interested candidates are encouraged to contact Nathan Lewis at n4lewis ucsd edu.

Systems Glycobiology at UC San Diego

We have an opening for a postdoctoral researcher to join our group, and are seeking one who is skilled in gene regulatory network analysis, interpretation of pooled CRISPR screens, or metabolic network analysis. In our lab, over the past few years, we have been developing novel systems biology approaches to address fundamental questions in the glycobiology community. This field is of prime importance since glycans are found on more than half of the proteins synthesized by mammalian cells and these glycans play an essential role in diverse range of processes including cell adhesion and migration, cell-cell communication, host-pathogen interactions, and protein folding. The complexity of these carbohydrate moieties and their synthesis has made them very difficult to study, despite their importance. However, here we have been taking a number of computational and experimental approaches to unravel their biosynthetic pathways, identify the regulators of their biosynthesis, and elucidate their biological importance. The postdoctoral fellow that we’re looking for would aid in the discovery of regulators through the analysis of pooled genome-wide CRISPR screens we have conducted and other types of genomic data (e.g., ENCODE, etc.). Optionally, the fellow could also contribute to our work in which we are developing methods, adapted from metabolic modeling and machine-learning approaches, to model the synthesis and regulation of glycans. As part of this position, the fellow will take part in a few courses to learn all about glycobiology and be part of the Glycobiology Research and Training Center at UCSD. Finally, this position is part of an NIH funded program that requires that the candidate be a US citizen or permanent resident. If you are interested in joining us through this, please contact me asap, along with sharing your CV.