Overview This position is open until filled with an initial application review to take place after January 17, 2023.
Under supervision of an SDSU Faculty member, this position is intended to provided mentored advanced training to enhance professional skills and research independence in the Post Doc's academic discipline.
Examples of Post Doc responsibilities include: assisting in data collection, management, analysis and dissemination; conducting highly specialized and advanced experiments; designing research protocols; summarizing research findings; mentoring undergraduate/graduate students; preparing manuscripts, attending conferences and presenting at conferences; Work may be performed in the field or in a laboratory setting.
Tuberculosis (TB) kills 1.5 million annually, highest among infectious diseases, now having surpassed COVID19. The Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence (LPCDRP) (http://tuberculosis.sdsu.edu/) studies the genetic and epigenetic basis of antibiotic resistance, persistence, and virulence towards identification of novel drug and vaccine targets to combat the global TB pandemic. LPCDRP is housed within the Biomedical Informatics Research Center (BMIRC) and is funded by grants from the National Institute for Allergy and Infectious diseases. LPCDRP houses a BSL2 (with limited access to BSL3) for all wet-lab experiments and a dry-lab (houses its own high-performance computing infrastructure) for all in silico analyses. The laboratory collaborates with, and receives clinical samples from, a variety of hospitals in India, the Philippines, Sweden, Belgium, Belarus, Georgia, and South Africa. These sites serve as clinical and/or microbiological sites for our projects. New international collaborations are actively sought and initiated each year. The laboratory houses projects in various aspects of TB infection with the ultimate goal of translating basic scientific advances into new diagnostic, therapeutic and vaccine candidates, clinical decision support tools, and public health policy.
The laboratory houses projects on various aspects of TB infection: automated drug and vaccine target identification, role of microbiome in host-pathogen interaction, direct sequencing from the disease context, TB genomic and epigenetic (e.g. DNA methylation) analyses for identification of mechanisms of antibiotics resistance and persistence, de novo genome assembly and annotation, genome-scale Metabolic and Expression modeling (ME modeling), Phylogenomics of small variations and rearrangements (genomic structural variations), mutagenesis experiments for the confirmation of the role of mutations and methylation anomalies in phenotypic change, condition-specific culturing and phenotyping, high-fidelity long-read sequencing, high molecular weight DNA and RNA sequencing, low-input sequencing, animal model experiments (Zebrafish and mouse in collaboration with other laboratories), spatial studies of pulmonary TB, and more.
In total, our laboratory is looking to fill two postdoctoral fellowship positions, and four PhD positions. Postdoctoral positions are for one year (renewable for up to five years upon good performance). PhD positions are renewable for up to four years upon good performance.
Through this announcement, we are looking to fill a postdoctoral fellowship position. The successful candidates will join a multidisciplinary team ranging from bioinformaticians and data scientists to clinicians, microbiologists, epidemiologists, and diagnostic laboratory staff. Depending on the qualifications and preference of the successful candidates, the position could be housed entirely in our wet-lab, dry-lab, or have hybrid responsibilities.
Conducting original scientific research and develop projects investigating drug resistance in Mycobacterium tuberculosis clinical isolates using genomics, epigenetic, transcriptomic and other high-throughput data.
Design and implement new research plans
Write manuscripts and assist with grant proposal preparation
Prepare reports and presentations about status of current research
Troubleshooting and solving experimental and technical problems
Training graduate students and working closely with the labs project scientists and collaborators
Other duties as assigned
Qualifications Minimum Education
A doctoral degree in an appropriate field
0-5 years of relevant experience
Deep understanding of molecular biology, genetics, and biochemistry
Proven track record of publications as first author for postdoctoral positions
Experience in standard BSL2 laboratory protocols and safety procedures (not required for dry-lab positions)
Proficiency in Linux command line usage and one or more scripting languages (R, Python, Perl) (not required for wet lab positions, but preferable)
Ability to work independently with minimal supervision and complete projects efficiently
Ability to 'think outside the box' and design projects and experiments
Ability to think critically and have strong problem-solving skills
Experience with mutagenesis, especially on tuberculosis
Experience in culturing and DNA/RNA extraction from tuberculosis
Experience with library preparation for WGS, especially Pacific Biosciences or Nanopore sequencing
Experience with high throughput diagnostics using PCR or LAMPore.
Experience with grant writing
Experience with high-performance computing
Experience in infectious disease or pathogen genomics research
Experience in Epigenetics, phylogenomics, or metabolic modeling
Experience processing high-throughput sequencing data using popular software (e.g. VarScan2, GATK, BWA, samtools, minimap2, canu)
ADDITIONAL APPLICANT INFORMATION:
The COVID-19 vaccine is required by the CSU for all SDSU Research Foundation employees as a condition of employment. Should you be offered a position, you will be required to provide proof of vaccination status. Individuals who obtain an approved medical or religious exemption on file will be required to complete regular COVID-19 testing
A background check (including a criminal records check) must be completed satisfactorily before any candidate can be offered a position with SDSU Research Foundation
San Diego State University Research Foundation is an EEO/AA/Disability/Vets Employer
Founded in 1897, San Diego State University is a public institution of higher education located in southern California. SDSU is the oldest and largest university in San Diego and the third largest in the state. SDSU continues to gain recognition as a leader in higher education.Join SDSU and make a difference through meaningful work that contributes to knowledge and provides rich opportunities for students. The dynamic synergy between SDSU and the San Diego region furthers SDSU's excellence and global impact. Every member of our team can proudly proclaim, "I Am SDSU."In addition to SDSU, three not-for-profit auxiliary employers operate to provide services for the University. The SDSU Research Foundation furthers the educational, research and community service mission of SDSU. Aztec Shops provides a diverse portfolio of products and services including operation of the SDSU Bookstore, SDSU Dining, and management of commercial and real estate properties surrounding the campus. Associated Students of SDSU is a student-directed organization that manages programs and facilities enjoyed by students, faculty, staff, and the community-at-large.