"Postdoctoral Scholar - Computational Biology"

A postdoctoral position is available at the University of California, Irvine under the leadership of Dr. Stanley Ng. The successful candidate will explore the relationship between multiple molecular layers from epigenome to phenome at clonal resolution in various tissues. Studies will involve the analysis of multiple data modalities from human and mouse tissues, including spatially-resolved somatic DNA mutations, gene and protein expression, cryogenic electron tomography (cryoET) images, among other data layers. Bioinformatic integration of distinct data types and subsequent statistical and machine learning analyses will be performed to elucidate how alterations to various molecular layers in individual clones can lead to their respective contributions to disease development/progression, malignant transformation, and treatment-specific resistance. For cryoET data, computer vision based deep learning models will be developed to identify abnormal biomolecular structures in diseased cells at nanoscale resolution. These studies will facilitate the identification of novel risk markers and therapeutic targets that will be validated in independent biological specimens and datasets.

Applicants should hold a PhD or MD/PhD degree and have extensive experience in at least 1 programming language and machine learning models. Ideally, candidates will also have some familiarity with basic biology, next-generation sequencing data, and statistical modelling of high-dimensional datasets, as reflected in published research articles. Postdocs are expected to work independently, while collaborating with bioinformaticians, biologists, clinicians, scientists, and otherwise obtain the necessary tools and knowledge as appropriate to achieve scientific aims.

Our lab employs bleeding-edge computational modelling approaches and state-of-the-art technologies. UC Irvine is a world-class research university with highly ranked graduate programs in biomedical sciences. Our Southern California location is home to one of the largest academic research and biotechnology hubs in the US. Lab members enjoy direct access to this outstanding community of clinicians and scientists, as well as the wide range of recreational activities available in our region. Successful candidates will join an interdisciplinary and highly collaborative team working to develop the next generation of tools and technologies to advance precision diagnostics and therapeutics.

Essential Skills

• A PhD or MD/PhD degree with a focus on Epigenetics, Genetics, Genomics, Biology, Bioinformatics, Machine Learning, or a related field
• Extensive experience in a research environment and at least 1 first-author publication in a reputable scientific journal
• Proficiency in R, Python, and/or other programming languages, and familiarity with working in a Linux-based high-performance computing environment
• Ability to work independently to drive projects forward
• Ability to communicate effectively and collaborate as part of a multidisciplinary team
• Ability to compose and deliver comprehensive presentations at scientific meetings and prepare research articles for peer-reviewed publications

Ideal Skills

• Expertise in statistical model development and the analysis of high-dimensional data, including next generation sequencing datasets
• Experience with sectioning, fixing, and staining tissues for histology imaging, laser capture microdissection, and sample prep for (single-cell) sequencing
• Expertise with ATAC-Seq, methylation profiling, genome/exome/targeted sequencing, mutation calling, single-cell analysis, RNA-Seq, proteomics, spatial technologies from 10X, NanoString or similar, cryoET or cryoEM analysis
• Expertise in machine learning and mathematical/statistical inference (e.g., image classification/segmentation using deep neural networks, reinforcement learning, regularized regression and classification models, clustering, optimization)
• Experience in developing computational analysis pipelines
• Expertise with multi-core/multi-threaded parallelization using GPU-based hardware acceleration or similar
• Experience with building highly distributable software (e.g., R packages, Python modules, Linux-based command-line tools, C programs, MATLAB applications, GitHub)

A doctoral degree (e.g., Ph.D., M.D.) or the foreign equivalent is required. The applicant can either have their PhD at the time of the application, or could be working towards the PhD. Department: https://biochem.uci.edu Lab: https://ngbiomedresearch.softr.app/