Bioinformatics Scientists in Lung Cancer and Melanoma Studies (multiple positions), Integrative Tumor Epidemiology Branch

The Integrative Tumor Epidemiology Branch (ITEB) of the NCI Division of Cancer Epidemiology & Genetics (DCEG) is seeking bioinformatics scientists for doctorate-level contractor and postdoctoral fellowship positions. The ITEB mission is to conduct large-scale, international epidemiological research on cancer etiology and progression through integrative analyses of risk factors and tissue profiling to inform prevention and clinical strategies. Learn more about the ITEB program of research.

Position Description

The bioinformatics scientists will work closely with Maria Teresa Landi, M.D., Ph.D., senior investigator, ITEB and senior advisor for genomic epidemiology, Trans-Divisional Research Program (TDRP), and in collaboration with other principal investigators, senior bioinformaticians and epidemiologists within ITEB, across other branches in DCEG, and external leaders in cancer genomics. Dr. Landi's research focuses on understanding tumor etiology and evolution for potential translational applications. She leads large-scale multidisciplinary research projects primarily on genetic and environmental determinants of lung cancer and melanoma. Dr. Landi pioneers cutting-edge analyses of genomic, transcriptomic, and epigenomic data, and integrates molecular data with histological and radiological imaging and clinical and epidemiological data.

Successful candidates have the possibility to work on several exciting lung cancer and melanoma studies:

1. EAGLE, a study designed to investigate the genetic and environmental determinants of lung cancer in smokers by integrating molecular, environmental, clinical and behavioral data from 2,100 lung cancer cases and 2,120 population-based controls; and
2. Sherlock-Lung, which aims to characterize the genomic and evolutionary landscape of lung cancers in never smokers (LCINS) and to develop an integrated molecular, histological, and radiological classification of these tumors. The target sample size is 2,000 multi-ethnic and geographically diverse LCINS.
3. Mapping LCINS incidence rates in the U.S., integrating information on social features and environmental exposures to uncover LCINS hotspots and possible causes.
4. Melanoma studies that aim to uncover genetic susceptibilities to melanoma using familial lineage tracing from thousands of individuals, as well as worldwide melanoma GWAS data including understudied populations.

Currently, as part of Sherlock-Lung we are analyzing deep whole-genome sequencing (WGS) data from >1,400 tumor/normal samples and RNA-seq and methylation tumor/normal data from >1,800 samples in collaboration with genomics leaders worldwide. To further characterize LCINS tumor evolution and cell-of-origin, we are also conducting long-read PacBio HiFi DNA sequencing and single-cell sequencing (for both DNA and RNA) from a subset of normal and tumor samples. By integrating this data with bulk RNA-Seq and WGS data, we aim to characterize LCINS genome and transcriptome at the cellular level, and to investigate evolutionary trajectories by incorporating single-cell approaches. We plan to extend genomics analyses to tumor-adjacent normal lung tissues to shed light on when/how malignant clones are formed and evolve. We are also developing genomic analysis algorithms, pipelines and web-based interactive tools for genomics analyses and data visualization to be shared with the research community.

The bioinformatics scientists will be responsible for performing both standard and complex integrative analyses of large-scale multi-omics data. Related tasks include, but are not limited to, data manipulation, algorithmic implementation, statistical programming, genetic/genomic data analyses, data visualization, manuscript drafting, and presentation of results to the scientific community within and beyond DCEG. This position will also require investigation of publicly available cancer genomic databases and bioinformatics pipelines for different data types, including DNA sequencing, and transcriptome, methylation, and microbiome profiling across a range of tissues and cancer types. In addition, this position includes providing support and expertise in installing, troubleshooting, and running analytical pipelines using open-source scientific software on local high-performance computers as well as Cloud-based platforms.

Qualifications

Doctorate Level Qualifications (Postdoctoral and Contractor positions available)

Required

1. Doctorate degree in bioinformatics, computational biology, computer science, biostatistics, applied mathematics or a related field, with a minimum of 3 years of working experience in bioinformatics.
2. Extensive experience in programming using different languages (including bash and R), high performance computing clusters, and job submission Engine (e.g., SLURM).
3. Team-oriented with excellent written, presentation and verbal communication skills, with demonstrated ability to learn and adopt bioinformatics techniques and resources.
4. Extensive experience in data processing and visualization, and strong familiarity with statistical analyses for biological data.
5. Familiarity with cancer genomics related data analysis or experience of performing studies related to cancer genomics.
6. Strong publication record.

Preferred

1. Strong experience in NGS bioinformatics analysis for different types of omics data.
2. Expert knowledge of relevant bioinformatics tools for NGS data and genetic databases for processing, analysis and visualization.
3. Familiarity and working knowledge of tools to explore and investigate cancer genomics with publicly available data sources (such as dbGaP, TCGA, ENCODE, 1000 Genomes, GTEX, gnomAD, cBioPortal, ICGC, UKBB).
4. Experience in performing statistical analysis of large datasets by running open source and custom developed analysis pipelines in R.
5. Experience in developing R shiny app and complex data visualization based on popular R packages (e.g., ggplot2).
6. Experience in preparing manuscripts based on original research to be published in peer-reviewed journals.

Additional Details

The NCI is an exciting place to work, and the position provides excellent learning opportunities from world leaders in the field and possibilities for professional advancement. Pay is commensurate with qualifications and includes a comprehensive benefit package. These are positions at a government agency in Rockville, Maryland.

To Apply

Please send a resume and cover letter addressing your qualifications for the position to Dr. Phuc Hoang, with “Bioinformatics Scientist Application” in the subject line. The application will be open until the positions are filled.