Bioinformatics Programmer I - Spatial Cancer
Baylor College of Medicine
Texas Medical Center, TX
Job posting number: #7243242 (Ref:19220-en_US)
Posted: May 9, 2024
Job Description
Summary
We are hiring a bioinformatics programmer in the Lester and Sue Smith Breast Center at Baylor College of Medicine. The Breast Center is a collaborative environment dedicated to breast health and disease research, as well as prevention, diagnosis, and treatment of different forms of breast cancer. We are looking for an individual to work in the area of computational cancer biology and who would work well in a collaborative environment.
The candidate will be working in a computational laboratory funded by the Cancer Prevention & Research Institute of Texas (CPRIT). The laboratory is interested in integrating various modalities of single-cell sequencing data and spatial genomics data to better understand the contribution of spatial multi-cellular environments during invasive transitions of breast cancer, such as metastasis, cancer progression, and local invasion.
For more information, please visit the following link: https://www.bcm.edu/people-search/qian-zhu-119781
Job Duties
- Basic sequencing-based analysis tools for processing of FASTQ files, particularly single cell sequencing data (RNA, DNA, and chromatin accessibility). The candidate should be familiar with quality control steps, alignment, trimming, and duplicate detection, and alignment filtering. Examples of such tools are Bowtie, Trimmomatic, CutAdapt, HISAT, etc. Familiarity with a pipeline language such as Snakemake is desirable.
- Single-cell RNA-sequencing, chromatin accessibility, and CUT&RUN/CUT&Tag analysis tools. Examples include Seurat, MACS2, Monocle, SnapATAC.
- Spatial transcriptomics and/or proteomic analysis tools, including Giotto, SquidPy, HistoCAT. Experiences working with 10X Visium, spatial imaging mass cytometry (IMC), and single cell Xenium/CosMx/Merscope data are particularly desirable.
- Summarize research findings using sound statistics and informative plots/figures.
- Present results in lab meetings and to collaborators.
- Collaborate with investigators in the breast center and beyond.
- Work together with other bioinformatic tools developers in the laboratory in implementing algorithms and software packages
- Download data from repositories (GEO) for public data integration, interrogation, and hypothesis generation.
Minimum Qualifications
- Bachelor's degree in Computer Science, Biological Science, or a related field.
- No experience required.
Preferred Qualifications
- Master’s degree in a related field.
- Website building.
- Web programming using JavaScript, HTML, CSS.
- Front-end programming using responsive frameworks such as Bootstrap, JQuery.
- C++/C programming.
- Knows how to use Google, StackOverFlow, ChatGPT for troubleshooting bugs/increasing coding efficiency.
Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer.
19220
Baylor College of Medicine fosters diversity among its students, trainees, faculty and staff as a prerequisite to accomplishing our institutional mission, and setting standards for excellence in training healthcare providers and biomedical scientists, promoting scientific innovation, and providing patient-centered care. - Diversity, respect, and inclusiveness create an environment that is conducive to academic excellence, and strengthens our institution by increasing talent, encouraging creativity, and ensuring a broader perspective. - Diversity helps position Baylor to reduce disparities in health and healthcare access and to better address the needs of the community we serve. - Baylor is committed to recruiting and retaining outstanding students, trainees, faculty and staff from diverse backgrounds by providing a welcoming, supportive learning environment for all members of the Baylor community.
